Optimisation of Bioenergy Supply Chains

This thesis aims to address the optimal strategic design of bioenergy supply chains and provide insight into the future implications of these systems. Among the bioenergy supply chains, biomass-to-biofuel (as the main focus), biomass-to-bioelectricity and biomass-to-hydrogen routes are studied within the context of this thesis. To solve these problems, mathematical programming, especially mixed integer linear programming (MILP), models and solution approaches are developed. Regarding the biofuel supply chains, deterministic, spatially-explicit, static optimisation models are developed first based on single economic objective considering first and hybrid generation systems. A “neighbourhood” flow approach is also proposed for the solution of these models. This approach provides significant computational savings when compared to similar models in literature. The single objective modelling framework is then extended to a multi-objective optimisation model which considers economic and environmental objectives simultaneously. The multi-objective model can provide insight into the trade-offs between the two conflicting objectives. Finally, the single objective static model is further developed into deterministic and stochastic multi-period modelling frameworks to incorporate temporal effects such as change of demand and biomass availability with time as well as uncertainty related to different aspects such as biomass availability. Regarding the bioelectricity supply chains, a deterministic, spatially-explicit, static, multi-objective mathematical programming model is developed based on mixed integer nonlinear optimisation. This considers electricity generation through biomass enhanced carbon capture and storage (BECCS) systems. The model aims to address issues such as carbon tax levels required to incentivise decarbonisation in the power sector as well as the potential impacts of biomass availability and commodity (carbon and coal) prices. The biomass-to-hydrogen route is considered as one of the possible conversion pathways within a deterministic, spatially-explicit, multi-period model developed for the optimal strategic design of future hydrogen supply chains. A two-step hierarchical solution approach is also proposed to increase computational efficiency during the solution of the large scale problem. The model results provide insight into the optimal evolution of a hydrogen supply chain through time

Applying Deep Learning in Augmented Reality Tracking

An existing deep learning architecture has been adapted to solve the detection problem in camera-based tracking for augmented reality (AR). A known target, in this case a planar object, is rendered under various viewing conditions including varying orientation, scale, illumination and sensor noise. The resulting corpus is used to train a convolutional neural network to match given patches in an incoming image. The results show comparable or better performance compared to state of art methods. Timing performance of the detector needs improvement but when considered in conjunction with the robust pose estimation process promising results are shown. © 2016 IEEE

The importance of economies of scale, transport costs and demand patterns in optimising hydrogen fuelling infrastructure: An exploration with SHIPMod (Spatial hydrogen infrastructure planning model)

Hydrogen is widely recognised as an important option for future road transportation, but a widespread infrastructure must be developed if the potential for hydrogen is to be achieved. This paper and related appendices which can be downloaded as Supplementary material present a mixed-integer linear programming model (called SHIPMod) that optimises a hydrogen supply chains for scenarios of hydrogen fuel demand in the UK, including the spatial arrangement of carbon capture and storage infrastructure. In addition to presenting a number of improvements on past practice in the literature, the paper focuses attention on the importance of assumptions regarding hydrogen demand. The paper draws on socio-economic data to develop a spatially detailed scenario of possible hydrogen demand. The paper then shows that assumptions about the level and spatial dispersion of hydrogen demand have a significant impact on costs and on the choice of hydrogen production technologies and distribution mechanisms

Downregulation of Mcl-1 has anti-inflammatory pro-resolution effects and enhances bacterial clearance from the lung

Phagocytes not only coordinate acute inflammation and host defense at mucosal sites, but also contribute to tissue damage. Respiratory infection causes a globally significant disease burden and frequently progresses to acute respiratory distress syndrome, a devastating inflammatory condition characterized by neutrophil recruitment and accumulation of protein-rich edema fluid causing impaired lung function. We hypothesized that targeting the intracellular protein myeloid cell leukemia 1 (Mcl-1) by a cyclin-dependent kinase inhibitor (AT7519) or a flavone (wogonin) would accelerate neutrophil apoptosis and resolution of established inflammation, but without detriment to bacterial clearance. Mcl-1 loss induced human neutrophil apoptosis, but did not induce macrophage apoptosis nor impair phagocytosis of apoptotic neutrophils. Neutrophil-dominant inflammation was modelled in mice by either endotoxin or bacteria (Escherichia coli). Downregulating inflammatory cell Mcl-1 had anti-inflammatory, pro-resolution effects, shortening the resolution interval (R(i)) from 19 to 7 h and improved organ dysfunction with enhanced alveolar–capillary barrier integrity. Conversely, attenuating drug-induced Mcl-1 downregulation inhibited neutrophil apoptosis and delayed resolution of endotoxin-mediated lung inflammation. Importantly, manipulating lung inflammatory cell Mcl-1 also accelerated resolution of bacterial infection (R(i); 50 to 16 h) concurrent with enhanced bacterial clearance. Therefore, manipulating inflammatory cell Mcl-1 accelerates inflammation resolution without detriment to host defense against bacteria, and represents a target for treating infection-associated inflammation

Apoptosis Is Essential for Neutrophil Functional Shutdown and Determines Tissue Damage in Experimental Pneumococcal Meningitis

During acute bacterial infections such as meningitis, neutrophils enter the tissue where they combat the infection before they undergo apoptosis and are taken up by macrophages. Neutrophils show pro-inflammatory activity and may contribute to tissue damage. In pneumococcal meningitis, neuronal damage despite adequate chemotherapy is a frequent clinical finding. This damage may be due to excessive neutrophil activity. We here show that transgenic expression of Bcl-2 in haematopoietic cells blocks the resolution of inflammation following antibiotic therapy in a mouse model of pneumococcal meningitis. The persistence of neutrophil brain infiltrates was accompanied by high levels of IL-1β and G-CSF as well as reduced levels of anti-inflammatory TGF-β. Significantly, Bcl-2-transgenic mice developed more severe disease that was dependent on neutrophils, characterized by pronounced vasogenic edema, vasculitis, brain haemorrhages and higher clinical scores. In vitro analysis of neutrophils demonstrated that apoptosis inhibition completely preserves neutrophil effector function and prevents internalization by macrophages. The inhibitor of cyclin-dependent kinases, roscovitine induced apoptosis in neutrophils in vitro and in vivo. In wild type mice treated with antibiotics, roscovitine significantly improved the resolution of the inflammation after pneumococcal infection and accelerated recovery. These results indicate that apoptosis is essential to turn off activated neutrophils and show that inflammatory activity and disease severity in a pyogenic infection can be modulated by targeting the apoptotic pathway in neutrophils

Antioxidant Protects against Increases in Low Molecular Weight Hyaluronan and Inflammation in Asphyxiated Newborn Pigs Resuscitated with 100% Oxygen

BACKGROUND: Newborn resuscitation with 100% oxygen is associated with oxidative-nitrative stresses and inflammation. The mechanisms are unclear. Hyaluronan (HA) is fragmented to low molecular weight (LMW) by oxidative-nitrative stresses and can promote inflammation. We examined the effects of 100% oxygen resuscitation and treatment with the antioxidant, N-acetylcysteine (NAC), on lung 3-nitrotyrosine (3-NT), LMW HA, inflammation, TNFα and IL1ß in a newborn pig model of resuscitation. METHODS & PRINCIPAL FINDINGS: Newborn pigs (n = 40) were subjected to severe asphyxia, followed by 30 min ventilation with either 21% or 100% oxygen, and were observed for the subsequent 150 minutes in 21% oxygen. One 100% oxygen group was treated with NAC. Serum, bronchoalveolar lavage (BAL), lung sections, and lung tissue were obtained. Asphyxia resulted in profound hypoxia, hypercarbia and metabolic acidosis. In controls, HA staining was in airway subepithelial matrix and no 3-NT staining was seen. At the end of asphyxia, lavage HA decreased, whereas serum HA increased. At 150 minutes after resuscitation, exposure to 100% oxygen was associated with significantly higher BAL HA, increased 3NT staining, and increased fragmentation of lung HA. Lung neutrophil and macrophage contents, and serum TNFα and IL1ß were higher in animals with LMW than those with HMW HA in the lung. Treatment of 100% oxygen animals with NAC blocked nitrative stress, preserved HMW HA, and decreased inflammation. In vitro, peroxynitrite was able to fragment HA, and macrophages stimulated with LMW HA increased TNFα and IL1ß expression. CONCLUSIONS & SIGNIFICANCE: Compared to 21%, resuscitation with 100% oxygen resulted in increased peroxynitrite, fragmentation of HA, inflammation, as well as TNFα and IL1ß expression. Antioxidant treatment prevented the expression of peroxynitrite, the degradation of HA, and also blocked increases in inflammation and inflammatory cytokines. These findings provide insight into potential mechanisms by which exposure to hyperoxia results in systemic inflammation

Type-II Colloidal Quantum Wells: CdSe/CdTe Core/Crown Heteronanoplatelets

Solution-processed quantum wells, also known as colloidal nanoplatelets (NPLs), are emerging as promising materials for colloidal optoelectronics. In this work, we report the synthesis and characterization of CdSe/CdTe core/crown NPLs exhibiting a Type-II electronic structure and Type-II specific optical properties. Here, based on a core-seeded approach, the CdSe/CdTe core/crown NPLs were synthesized with well-controlled CdTe crown coatings. Uniform and epitaxial growth of CdTe crown region was verified by using structural characterization techniques including transmission electron microscopy (TEM) with quantitative EDX analysis and X-ray diffraction (XRD). Also the optical properties were systematically studied in these Type-II NPLs that reveal strongly red-shifted photoluminescence (up to similar to 150 nm) along with 2 orders of magnitude longer fluorescence lifetimes (up to 190 ns) compared to the Type-I NPLs owing to spatially indirect excitons at the Type-II interface between the CdSe core and the CdTe crown regions. Photoluminescence excitation spectroscopy confirms that this strongly red-shifted emission actually arises from the CdSe/CdTe NPLs. In addition, temperature-dependent time-resolved fluorescence spectroscopy was performed to reveal the temperature-dependent fluorescence decay kinetics of the Type-II NPLs exhibiting interesting behavior. Also, water-soluble Type-II NPLs were achieved via ligand exchange of the CdSe/CdTe core/crown NPLs by using 3-mercaptopropionic acid (MPA), which allows for enhanced charge extraction efficiency owing to their shorter chain length and enables high quality film formation by layer-by-layer (LBL) assembly. With all of these appealing properties, the CdSe/CdTe core/crown heterostructures having Type-II electronic structure presented here are highly promising for light-harvesting applications

Susceptibility of Human Lymphoid Tissue Cultured ex vivo to Xenotropic Murine Leukemia Virus-Related Virus (XMRV) Infection

BACKGROUND: Xenotropic murine leukemia virus-related virus (XMRV) was generated after a recombination event between two endogenous murine leukemia viruses during the production of a prostate cancer cell line. Although the associations of the XMRV infection with human diseases appear unlikely, the XMRV is a retrovirus of undefined pathogenic potential, able to replicate in human cells in vitro. Since recent studies using animal models for infection have yielded conflicting results, we set out an ex vivo model for XMRV infection of human tonsillar tissue to determine whether XMRV produced by 22Rv1 cells is able to replicate in human lymphoid organs. Tonsil blocks were infected and infection kinetics and its pathogenic effects were monitored RESULTS: XMRV, though restricted by APOBEC, enters and integrates into the tissue cells. The infection did not result in changes of T or B-cells, immune activation, nor inflammatory chemokines. Infectious viruses could be recovered from supernatants of infected tonsils by reinfecting DERSE XMRV indicator cell line, although these supernatants could not establish a new infection in fresh tonsil culture, indicating that in our model, the viral replication is controlled by innate antiviral restriction factors. CONCLUSIONS: Overall, the replication-competent retrovirus XMRV, present in a high number of laboratories, is able to infect human lymphoid tissue and produce infectious viruses, even though they were unable to establish a new infection in fresh tonsillar tissue. Hereby, laboratories working with cell lines producing XMRV should have knowledge and understanding of the potential biological biohazardous risks of this virus

Lgl2 Executes Its Function as a Tumor Suppressor by Regulating ErbB Signaling in the Zebrafish Epidermis

Changes in tissue homeostasis, acquisition of invasive cell characteristics, and tumor formation can often be linked to the loss of epithelial cell polarity. In carcinogenesis, the grade of neoplasia correlates with impaired cell polarity. In Drosophila, lethal giant larvae (lgl), discs large (dlg), and scribble, which are components of the epithelial apico-basal cell polarity machinery, act as tumor suppressors, and orthologs of this evolutionary conserved pathway are lost in human carcinoma with high frequency. However, a mechanistic link between neoplasia and vertebrate orthologs of these tumor-suppressor genes remains to be fully explored at the organismal level. Here, we show that the pen/lgl2 mutant phenotype shares two key cellular and molecular features of mammalian malignancy: cell autonomous epidermal neoplasia and epithelial-to-mesenchymal-transition (EMT) of basal epidermal cells including the differential expression of several regulators of EMT. Further, we found that epidermal neoplasia and EMT in pen/lgl2 mutant epidermal cells is promoted by ErbB signalling, a pathway of high significance in human carcinomas. Intriguingly, EMT in the pen/lgl2 mutant is facilitated specifically by ErbB2 mediated E-cadherin mislocalization and not via canonical snail–dependent down-regulation of E-cadherin expression. Our data reveal that pen/lgl2 functions as a tumor suppressor gene in vertebrates, establishing zebrafish pen/lgl2 mutants as a valuable cancer model