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Spatio-temporal variation in lesser sandeel growth and demography, causes and consequences
Get PDFIn large parts of the north-east Atlantic, the lesser sandeel (Ammodytes marinus) is an important prey for seabirds, marine mammals and fish. A. marinus shows strong spatio-temporal variation in abundance and size, including a sustained decline in size in several locations in the North Sea. The variation in size has been hypothesised to be mainly driven by variability in food conditions, but exploring this hypothesis on a larger spatial scale has so far been hampered by the lack of zooplankton data of sufficient spatio-temporal and taxonomic resolution.;Further, the extent to which the clear spatial structure in the sandeel population is reflected in the populations of their seabird predators is not clear. This thesis aims to address these gaps and contribute to the mechanistic understanding of bottom-up effects in the zooplankton-sandeel-seabird food chain. As declines in the abundance and size of sandeels as a result of changes in their zooplankton prey are thought to have played a large role in driving the dramatic declines of seabirds in large parts of north-east Atlantic, understanding drivers and bottom-up processes in this food chain is of large importance.;The thesis first addresses the lack of the kind of high-resolution zooplankton data required for exploring the role of food conditions in sandeel dynamics. For this purpose, an approach for the generation of prey fields from spatially aggregated Continuous Plankton Recorder data is developed. The generated prey fields are then used to examine spatio-temporal patterns in sandeel food conditions, focusing mainly on the North Sea and covering the time period 1975 to 2016.;In the western North Sea, there have been clear declines in both the total amount of energy available to sandeels and the abundance of small copepods, which make up a large proportion of the sandeel diet. In terms of Calanus spp., which are also an important part of the sandeel diet, there was no clear change in abundances of Calanus finmarchicus in the examined locations, while abundances of Calanus helgolandicus showed a clear increase in most of the study area around 2000. The average prey size generally increased over time in the western North Sea, whereas it instead declined in the north-east.;Further, due to the differences in the timing of the feeding seasons, it is clear that 0 group and 1+ group sandeels experienced different prey fields, with, for example, a larger abundance of smaller copepods during the 0 group feeding season.;To explore to what extent this variation in food conditions can explain spatiotemporal variation in sandeel size, a dynamic energy budget growth model is then developed. This model estimates size daily throughout the first sandeel growth season as a function of food conditions, temperature, light conditions as well as size at and timing of metamorphosis. The model is run in six locations: southern Iceland, the Faroes, Shetland and three locations further south in the North Sea, including Dogger Bank, the Firth of Forth and the East Central Grounds.;In the more southerly locations considered, model predictions agreed well with observations in terms of long-term mean lengths and spatial differences in length and the model also reproduced a previously observed decline in length in the north-western North Sea. Agreement with observations in the Faroes and Iceland was poorer. Food conditions played the main role in driving predicted variation in size, with Calanus spp. being particularly important. Timing of metamorphosis also had a substantial impact on predicted sandeel size. In contrast, the direct effect of temperature was negligible.;Finally, the thesis explores the extent to which spatial patterns in the sandeel population along the coast of the UK propagate up to their seabird predators. To do this, geographical patterns in the synchrony of breeding success in black-legged kittiwake (Rissa tridactyla) colonies are examined in areas where sandeels are an important part of the diet. The distance between colonies was a strong determinant of between colonysynchrony, with the scale of synchrony in kittiwake and sandeel populations being similar. Further, the colonies also formed clusters with synchronous breeding success with a clear spatial pattern, which generally aligned with the spatial structure of the kittiwake,' sandeel prey.;The results of the thesis thus suggest that food conditions play an important role in driving observed variation in sandeel size. This implies that past and ongoing climate change-driven changes in the sandeel prey field are likely to have a large impact on sandeel growth rates, with potential knock-on effects on demographic rates. Further ,the results suggest that processes occurring at the level of the sandeel are reflected in the structure of the local kittiwake population, indicating that the sandeels are able to mediate changes occurring at lower trophic levels up to the level of their seabird predators.In large parts of the north-east Atlantic, the lesser sandeel (Ammodytes marinus) is an important prey for seabirds, marine mammals and fish. A. marinus shows strong spatio-temporal variation in abundance and size, including a sustained decline in size in several locations in the North Sea. The variation in size has been hypothesised to be mainly driven by variability in food conditions, but exploring this hypothesis on a larger spatial scale has so far been hampered by the lack of zooplankton data of sufficient spatio-temporal and taxonomic resolution.;Further, the extent to which the clear spatial structure in the sandeel population is reflected in the populations of their seabird predators is not clear. This thesis aims to address these gaps and contribute to the mechanistic understanding of bottom-up effects in the zooplankton-sandeel-seabird food chain. As declines in the abundance and size of sandeels as a result of changes in their zooplankton prey are thought to have played a large role in driving the dramatic declines of seabirds in large parts of north-east Atlantic, understanding drivers and bottom-up processes in this food chain is of large importance.;The thesis first addresses the lack of the kind of high-resolution zooplankton data required for exploring the role of food conditions in sandeel dynamics. For this purpose, an approach for the generation of prey fields from spatially aggregated Continuous Plankton Recorder data is developed. The generated prey fields are then used to examine spatio-temporal patterns in sandeel food conditions, focusing mainly on the North Sea and covering the time period 1975 to 2016.;In the western North Sea, there have been clear declines in both the total amount of energy available to sandeels and the abundance of small copepods, which make up a large proportion of the sandeel diet. In terms of Calanus spp., which are also an important part of the sandeel diet, there was no clear change in abundances of Calanus finmarchicus in the examined locations, while abundances of Calanus helgolandicus showed a clear increase in most of the study area around 2000. The average prey size generally increased over time in the western North Sea, whereas it instead declined in the north-east.;Further, due to the differences in the timing of the feeding seasons, it is clear that 0 group and 1+ group sandeels experienced different prey fields, with, for example, a larger abundance of smaller copepods during the 0 group feeding season.;To explore to what extent this variation in food conditions can explain spatiotemporal variation in sandeel size, a dynamic energy budget growth model is then developed. This model estimates size daily throughout the first sandeel growth season as a function of food conditions, temperature, light conditions as well as size at and timing of metamorphosis. The model is run in six locations: southern Iceland, the Faroes, Shetland and three locations further south in the North Sea, including Dogger Bank, the Firth of Forth and the East Central Grounds.;In the more southerly locations considered, model predictions agreed well with observations in terms of long-term mean lengths and spatial differences in length and the model also reproduced a previously observed decline in length in the north-western North Sea. Agreement with observations in the Faroes and Iceland was poorer. Food conditions played the main role in driving predicted variation in size, with Calanus spp. being particularly important. Timing of metamorphosis also had a substantial impact on predicted sandeel size. In contrast, the direct effect of temperature was negligible.;Finally, the thesis explores the extent to which spatial patterns in the sandeel population along the coast of the UK propagate up to their seabird predators. To do this, geographical patterns in the synchrony of breeding success in black-legged kittiwake (Rissa tridactyla) colonies are examined in areas where sandeels are an important part of the diet. The distance between colonies was a strong determinant of between colonysynchrony, with the scale of synchrony in kittiwake and sandeel populations being similar. Further, the colonies also formed clusters with synchronous breeding success with a clear spatial pattern, which generally aligned with the spatial structure of the kittiwake,' sandeel prey.;The results of the thesis thus suggest that food conditions play an important role in driving observed variation in sandeel size. This implies that past and ongoing climate change-driven changes in the sandeel prey field are likely to have a large impact on sandeel growth rates, with potential knock-on effects on demographic rates. Further ,the results suggest that processes occurring at the level of the sandeel are reflected in the structure of the local kittiwake population, indicating that the sandeels are able to mediate changes occurring at lower trophic levels up to the level of their seabird predators
Human-oriented design, automatic collision avoidance by better man-machine interaction and information flow
Get PDFDespite the technological advancement and the automation of operations, yet, human involvement plays a fundamental role in ships navigation. Human is indispensable in any operation for their intellectual abilities of decision-making skills, based on available inputs and outputs. Moreover, the maritime industry has one of the most demanding operational obligations, where a single mistake can lead to catastrophic consequences that threaten lives, properties and environment. However, maritime accident statistics have revealed that more than 75% of maritime accidents are directly or indirectly linked to human errors (Chauvin, 2011). Out of all the accidents at sea; collision, contacts and grounding are estimated to be around 54.4%. It is obvious that reducing human errors will essentially enhance maritime safety and reduce the frequency of accidents at sea.The main aim of this research is to prevent these accidents by developing an Automatic Collision Avoidance System and by designing a human-oriented communication flow on the ship's navigational bridge. This will increase the situational awareness of the crew to take necessary and timely actions, including speed reduction and manoeuvring. Additionally, this will allow crew members to make objective decisions based on real and correct information, rather than wrong decisions built on a wrong interpretation of the surrounding situation.The developed automatic collision avoidance system has been inspired by the well-known safety reputation, aviation industry. In aviation, to prevent mid-air collisions, the aeroplanes are fitted with the Traffic Alert Collision Avoidance System (TCAS). This is an independent system that automatically detects collision situation, alerts the pilots about the collision risk and provide the best avoidance action to prevent mid-air collisions.The ship's bridge navigational simulator has been utilised to validate the effectiveness and operation of the automatic collision avoidance system against the classical approach. Real ships collision investigation reports, from the Maritime Accident Investigation Branch (MAIB), were utilised to create scenarios for validation experiments, which were constructed using these real collision scenarios in the simulator environment to quantify the performance of the participants (OOW).Despite the technological advancement and the automation of operations, yet, human involvement plays a fundamental role in ships navigation. Human is indispensable in any operation for their intellectual abilities of decision-making skills, based on available inputs and outputs. Moreover, the maritime industry has one of the most demanding operational obligations, where a single mistake can lead to catastrophic consequences that threaten lives, properties and environment. However, maritime accident statistics have revealed that more than 75% of maritime accidents are directly or indirectly linked to human errors (Chauvin, 2011). Out of all the accidents at sea; collision, contacts and grounding are estimated to be around 54.4%. It is obvious that reducing human errors will essentially enhance maritime safety and reduce the frequency of accidents at sea.The main aim of this research is to prevent these accidents by developing an Automatic Collision Avoidance System and by designing a human-oriented communication flow on the ship's navigational bridge. This will increase the situational awareness of the crew to take necessary and timely actions, including speed reduction and manoeuvring. Additionally, this will allow crew members to make objective decisions based on real and correct information, rather than wrong decisions built on a wrong interpretation of the surrounding situation.The developed automatic collision avoidance system has been inspired by the well-known safety reputation, aviation industry. In aviation, to prevent mid-air collisions, the aeroplanes are fitted with the Traffic Alert Collision Avoidance System (TCAS). This is an independent system that automatically detects collision situation, alerts the pilots about the collision risk and provide the best avoidance action to prevent mid-air collisions.The ship's bridge navigational simulator has been utilised to validate the effectiveness and operation of the automatic collision avoidance system against the classical approach. Real ships collision investigation reports, from the Maritime Accident Investigation Branch (MAIB), were utilised to create scenarios for validation experiments, which were constructed using these real collision scenarios in the simulator environment to quantify the performance of the participants (OOW)
Understanding crystallographic defects in hard materials, a study in ECCI and EBSD
Get PDFThis thesis investigates the crystallographic defects inherent in two hard materials, tungsten carbide embedded in a cobalt matrix (WC-Co) and diamonds. The scanning electron microscopy (SEM) techniques of electron channelling contrast imaging (ECCI), cathodoluminescence (CL) imaging and electron backscatter diffraction (EBSD) allowed for the investigation of the crystallographic defects. Initial work on WC identified the dislocations and subgrain structures in grains of known crystallographic orientation. By combining ECCI and EBSD, new insights into the microstructure of WC grains were revealed. The advantage of using these techniques over the more common TEM based techniques is that ECCI and EBSD allow for analysis over a large field of view, in this case 75 μm ×75 μm. These large scale analyses reveal the microstructure and misorientation and dislocations throughout an entire WC grain. ECCI exposed dislocations while EBSD data revealed small changes in crystallographic orientation resulting from dislocations and subgrains, thereby corroborating the ECCI data. Further investigation of dislocations in WC categorized the type of dislocations found in grains of known crystallographic orientation using ECCI and EBSD. Dislocations and their Burgers vectors are described. The type of dislocations found in a particular grain are discussed in relation to their orientation with respect to neighbouring grains. Using ECCI and EBSD to categorize dislocations in the basal and prismatic planes helps explain how WC grains deform plastically. Plastic deformation is studied by indenting WC grains and studying the damage with ECCI and EBSD analysis. Misorientation surrounding the indent is investigated by EBSD for two different indenter tips. Using ECCI to reveal slip bands around indents in grains exposes different defects and deformation depending on the crystallographic orientation of grains. This novel ECCI work agrees with previous TEM data on slip systems in indented WC grains. Using ECCI presents an advantage over TEM in this case in that damage in grains can be imaged over a wider field of view with simpler sample preparation. The characterization of twinned gem-quality diamonds, also known as macles, using ECCI, EBSD and CL reveals that twinned diamonds are all composed of two sibling twins with around 180° between the siblings. CL is helpful in understanding the initial twin nucleation and distinct periods of crystallization in the diamond's history while EBSD is used to corroborate CL. This study shows that the twinning plane is not linear, but jagged, corroborating previous research indicating that these are not true contact twins, rather they contain some intergrowths. EBSD confirms that these are undeniable twins as the plane separating the two siblings is a twin Coincident Site Lattices (CSL) grain boundary. CL and EBSD together are powerful tools for characterizing the twinning plane and growth mechanism in diamonds and this work describes the novel use of these techniques to understand diamond crystallization.This thesis investigates the crystallographic defects inherent in two hard materials, tungsten carbide embedded in a cobalt matrix (WC-Co) and diamonds. The scanning electron microscopy (SEM) techniques of electron channelling contrast imaging (ECCI), cathodoluminescence (CL) imaging and electron backscatter diffraction (EBSD) allowed for the investigation of the crystallographic defects. Initial work on WC identified the dislocations and subgrain structures in grains of known crystallographic orientation. By combining ECCI and EBSD, new insights into the microstructure of WC grains were revealed. The advantage of using these techniques over the more common TEM based techniques is that ECCI and EBSD allow for analysis over a large field of view, in this case 75 μm ×75 μm. These large scale analyses reveal the microstructure and misorientation and dislocations throughout an entire WC grain. ECCI exposed dislocations while EBSD data revealed small changes in crystallographic orientation resulting from dislocations and subgrains, thereby corroborating the ECCI data. Further investigation of dislocations in WC categorized the type of dislocations found in grains of known crystallographic orientation using ECCI and EBSD. Dislocations and their Burgers vectors are described. The type of dislocations found in a particular grain are discussed in relation to their orientation with respect to neighbouring grains. Using ECCI and EBSD to categorize dislocations in the basal and prismatic planes helps explain how WC grains deform plastically. Plastic deformation is studied by indenting WC grains and studying the damage with ECCI and EBSD analysis. Misorientation surrounding the indent is investigated by EBSD for two different indenter tips. Using ECCI to reveal slip bands around indents in grains exposes different defects and deformation depending on the crystallographic orientation of grains. This novel ECCI work agrees with previous TEM data on slip systems in indented WC grains. Using ECCI presents an advantage over TEM in this case in that damage in grains can be imaged over a wider field of view with simpler sample preparation. The characterization of twinned gem-quality diamonds, also known as macles, using ECCI, EBSD and CL reveals that twinned diamonds are all composed of two sibling twins with around 180° between the siblings. CL is helpful in understanding the initial twin nucleation and distinct periods of crystallization in the diamond's history while EBSD is used to corroborate CL. This study shows that the twinning plane is not linear, but jagged, corroborating previous research indicating that these are not true contact twins, rather they contain some intergrowths. EBSD confirms that these are undeniable twins as the plane separating the two siblings is a twin Coincident Site Lattices (CSL) grain boundary. CL and EBSD together are powerful tools for characterizing the twinning plane and growth mechanism in diamonds and this work describes the novel use of these techniques to understand diamond crystallization
A study of the metabolic immune responses produced by some natural products
Get PDFMacrophages play a crucial role in inflammatory conditions by producing a range of pro-inflammatory molecules, including cytokines, nitric oxide and reactive oxygen species (ROS). Several studies have demonstrated the physiological and inflammatory responses of macrophages to different stimuli, such as lipopolysaccharide (LPS), the Gram-negative-derived bacterial cell wall component. However, research is lacking on the metabolic responses of macrophages to these stimuli.;Recently, the involvement of metabolic pathways in the regulation of LPS signalling and macrophage activation has become a focus of research in inflammation. The aim of the present study was to assess and characterise cytokine production and the metabolic profiles of THP-1 monocyte-derived macrophage cells following stimulation with LPS, alone or in combination with different natural products.;Some of these natural products, such as melittin and eicosanoids, were considered to act as vaccine adjuvants and to enhance the LPS-stimulated release of cytokines and inflammatory metabolite signalling, while others, such as propolis and gypenoside (Gyp), were suggested to antagonise LPS action, thereby modulating immune responses. Macrophages were therefore viewed as having the potential to undergo different reprogrammed pathways once activated by LPS.;In this study, THP-1 cells were differentiated using phorbol 12-myristate 13-acetate (PMA) for 48 hours and then rested for 24 hours by replacing the PMA-containing culture medium with normal medium. The cells were then treated with LPS alone, a natural product alone or a combination of the natural product and LPS for another 24 hours.;The THP-1 macrophages were then evaluated for the release of tumour necrosis factor-α (TNF-α) and the cytokines interleukin-1β (IL-1β), IL-6 and IL-10 using enzyme-linked immunosorbent assay (ELISA) methods. The cells were extracted and their metabolites were characterised by liquid chromatography-mass spectrometry (LC-MS).;LPS treatment of THP-1 cells mainly increased glycolysis and the pentose phosphate pathway and decreased the TCA cycle activity. Several biomarker metabolites were altered significantly by LPS, including NADPH, glutathione, oxidised glutathione, L-citrulline, L-arginine, L-ornithine, hypoxanthine, xanthine and urate. The addition of melittin enhanced the LPS effects on the cellular metabolome and cytokine secretion. Several fatty acids, including arachidonic acid, were substantially affected by melittin. Similar responses were found for eicosenoid compounds, which were able to stimulate the immune response and enhance the LPS inflammatory activities.;By contrast, propolis (samples obtained from different geographic regions) and Gyp were able to trigger anti-inflammatory actions and inhibit the LPS-induced cytokine release, while also antagonising LPS effects on the cellular metabolome.;These findings point to a need to evaluate the possible anti-inflammatory actions of some reported natural products as a strategy for identifying new therapies and confirming the targeted pathways and/or metabolites affected by inflammatory conditions. Understanding the metabolic pathways in reprogrammed macrophages is critical for planning further investigations of immune adjuvants for vaccines. The immunomodulatory effects observed in THP-1 cells highlight the potential use of natural products in clinical therapies.Macrophages play a crucial role in inflammatory conditions by producing a range of pro-inflammatory molecules, including cytokines, nitric oxide and reactive oxygen species (ROS). Several studies have demonstrated the physiological and inflammatory responses of macrophages to different stimuli, such as lipopolysaccharide (LPS), the Gram-negative-derived bacterial cell wall component. However, research is lacking on the metabolic responses of macrophages to these stimuli.;Recently, the involvement of metabolic pathways in the regulation of LPS signalling and macrophage activation has become a focus of research in inflammation. The aim of the present study was to assess and characterise cytokine production and the metabolic profiles of THP-1 monocyte-derived macrophage cells following stimulation with LPS, alone or in combination with different natural products.;Some of these natural products, such as melittin and eicosanoids, were considered to act as vaccine adjuvants and to enhance the LPS-stimulated release of cytokines and inflammatory metabolite signalling, while others, such as propolis and gypenoside (Gyp), were suggested to antagonise LPS action, thereby modulating immune responses. Macrophages were therefore viewed as having the potential to undergo different reprogrammed pathways once activated by LPS.;In this study, THP-1 cells were differentiated using phorbol 12-myristate 13-acetate (PMA) for 48 hours and then rested for 24 hours by replacing the PMA-containing culture medium with normal medium. The cells were then treated with LPS alone, a natural product alone or a combination of the natural product and LPS for another 24 hours.;The THP-1 macrophages were then evaluated for the release of tumour necrosis factor-α (TNF-α) and the cytokines interleukin-1β (IL-1β), IL-6 and IL-10 using enzyme-linked immunosorbent assay (ELISA) methods. The cells were extracted and their metabolites were characterised by liquid chromatography-mass spectrometry (LC-MS).;LPS treatment of THP-1 cells mainly increased glycolysis and the pentose phosphate pathway and decreased the TCA cycle activity. Several biomarker metabolites were altered significantly by LPS, including NADPH, glutathione, oxidised glutathione, L-citrulline, L-arginine, L-ornithine, hypoxanthine, xanthine and urate. The addition of melittin enhanced the LPS effects on the cellular metabolome and cytokine secretion. Several fatty acids, including arachidonic acid, were substantially affected by melittin. Similar responses were found for eicosenoid compounds, which were able to stimulate the immune response and enhance the LPS inflammatory activities.;By contrast, propolis (samples obtained from different geographic regions) and Gyp were able to trigger anti-inflammatory actions and inhibit the LPS-induced cytokine release, while also antagonising LPS effects on the cellular metabolome.;These findings point to a need to evaluate the possible anti-inflammatory actions of some reported natural products as a strategy for identifying new therapies and confirming the targeted pathways and/or metabolites affected by inflammatory conditions. Understanding the metabolic pathways in reprogrammed macrophages is critical for planning further investigations of immune adjuvants for vaccines. The immunomodulatory effects observed in THP-1 cells highlight the potential use of natural products in clinical therapies
Antisolvent crystallisation in oscillatory baffled platforms
No full textContinuous manufacturing finds application in a variety of disciplines. It demonstrates a number of advantages, such as more controllable processes and allows particle attributes to be attained that would otherwise be unattainable. Antisolvent crystallisation is a widely used method of crystallisation in both academia and industry. It is employed to crystallise compounds that are not amenable to other techniques such as cooling crystallisation and can be utilised to produce crystal products with unique properties.;Oscillatory baffled crystallisers (OBCs) are platforms that generate intense mixing by the oscillatory motion of fluid through periodic constrictions, referred to as baffles. The oscillatory motion generates eddy currents through these baffles and induce highly turbulent and efficient mixing. By the superimposition of a net flow, the process can operate at near plug-flow conditions and is the principle of the continuous oscillatory baffled crystalliser (COBC). OBCs have been extensively studied for cooling crystallisations, but their application in antisolvent crystallisation has been limited.;The continuous antisolvent crystallisation of anthranilic acid in a COBC has been investigated for the first time as a function of antisolvent volume fraction and flow conditions, demonstrating the effects of a number of process variables on product outcomes. Metastable form II polymorph of anthranilic acid was consistently produced in a continuous unseeded antisolvent crystallisation from an ethanol and water solvent system.;The incorporation of process analytical technology (PAT) allowed for monitoring of various process conditions in real time, giving insight into the evolution of the antisolvent crystallisation process in continuous flow. Local mixing effects were deemed to be significant in the COBC at the point of contact of solution and antisolvent, such that variable flow rates at fixed antisolvent compositions resulted in different product sizes whilst resulting in the same final solution concentration.;Polymorph control in a moving baffle oscillatory baffled crystalliser (MBOBC) was demonstrated for the anthranilic acid system. By variation of seeding conditions and startup strategy, the continuous production of either stable form I or metastable form II polymorph could be controlled. This demonstrated a novel continuous nucleation platform for an antisolvent crystallisation process that could potentially be coupled with a COBC or other platform for reliable continuous production of a specified polymorph with targeted crystal attributes.;Growth and secondary nucleation kinetic parameters were determined by means of isothermal seeded batch experiments in a batch moving fluid oscillatory baffled crystalliser (MFOBC). Models were developed from these determined parameters, and further refined by the incorporation of a solvent factor that improved the fit of the model predictions to the experimentally measured attributes. The determined parameters were applied to the optimisation of a 30 m DN15 COBC with multiple antisolvent addition points and demonstrates the first such strategy utilising experimentally determined kinetic parameters.;This work has demonstrated novel approaches for the development of antisolvent crystallisation processes in continuous flow in oscillatory baffled crystallisers, detailing a number of control strategies and advancing the knowledge and understanding of such processes for future implementation.Continuous manufacturing finds application in a variety of disciplines. It demonstrates a number of advantages, such as more controllable processes and allows particle attributes to be attained that would otherwise be unattainable. Antisolvent crystallisation is a widely used method of crystallisation in both academia and industry. It is employed to crystallise compounds that are not amenable to other techniques such as cooling crystallisation and can be utilised to produce crystal products with unique properties.;Oscillatory baffled crystallisers (OBCs) are platforms that generate intense mixing by the oscillatory motion of fluid through periodic constrictions, referred to as baffles. The oscillatory motion generates eddy currents through these baffles and induce highly turbulent and efficient mixing. By the superimposition of a net flow, the process can operate at near plug-flow conditions and is the principle of the continuous oscillatory baffled crystalliser (COBC). OBCs have been extensively studied for cooling crystallisations, but their application in antisolvent crystallisation has been limited.;The continuous antisolvent crystallisation of anthranilic acid in a COBC has been investigated for the first time as a function of antisolvent volume fraction and flow conditions, demonstrating the effects of a number of process variables on product outcomes. Metastable form II polymorph of anthranilic acid was consistently produced in a continuous unseeded antisolvent crystallisation from an ethanol and water solvent system.;The incorporation of process analytical technology (PAT) allowed for monitoring of various process conditions in real time, giving insight into the evolution of the antisolvent crystallisation process in continuous flow. Local mixing effects were deemed to be significant in the COBC at the point of contact of solution and antisolvent, such that variable flow rates at fixed antisolvent compositions resulted in different product sizes whilst resulting in the same final solution concentration.;Polymorph control in a moving baffle oscillatory baffled crystalliser (MBOBC) was demonstrated for the anthranilic acid system. By variation of seeding conditions and startup strategy, the continuous production of either stable form I or metastable form II polymorph could be controlled. This demonstrated a novel continuous nucleation platform for an antisolvent crystallisation process that could potentially be coupled with a COBC or other platform for reliable continuous production of a specified polymorph with targeted crystal attributes.;Growth and secondary nucleation kinetic parameters were determined by means of isothermal seeded batch experiments in a batch moving fluid oscillatory baffled crystalliser (MFOBC). Models were developed from these determined parameters, and further refined by the incorporation of a solvent factor that improved the fit of the model predictions to the experimentally measured attributes. The determined parameters were applied to the optimisation of a 30 m DN15 COBC with multiple antisolvent addition points and demonstrates the first such strategy utilising experimentally determined kinetic parameters.;This work has demonstrated novel approaches for the development of antisolvent crystallisation processes in continuous flow in oscillatory baffled crystallisers, detailing a number of control strategies and advancing the knowledge and understanding of such processes for future implementation
Investigating the different mechanisms involved in a silane-alkoxide system
Get PDFRecent publications by Grubbs and Stoltz have focussed on the combination of triethylsilane with potassium tert-butoxide to afford a system which is capable of carrying out a number of synthetically useful transformations. This includes i) the reductive cleavage of C-O bonds in ethers, ii) the reductive cleavage of C-S bonds in thioethers, and iii) the regioselective silylation of arenes and heteroarenes. A number of mechanistic studies have been carried out, but so far no conclusive mechanism is known for these transformations.;Recent work in the Murphy group has focussed on the combination of small molecules with potassium tert-butoxide to form in situ electron donors. This thesis will focus on mechanistic studies on the combination of triethylsilane with potassium tert-butoxide, which is capable of carrying out the reductive debenzylation of N-benzylindoles (Scheme 1). Experimental and computational studies show that it is likely that this transformation proceeds via single electron transfer.;Scheme 1 - Debenzylation of N-Benzylindoles Mediated by Et3SiH/KOtBu [includes graphic];N-arylindoles were shown to undergo ring-opening and subsequent ring-closure to afford 9,10-dihydroacridines (Scheme 2). Mechanistic studies suggest that this transformation may either proceed via single electron transfer or via hydrogen atom transfer.;Scheme 2 - Conversion of N-Arylindoles to 9,10-Dihydroacridines Mediated by Et3SiH/KOtBu [includes graphic];Finally, the reduction and subsequent cyclisation of nitriles was shown to proceed via hydride transfer from the Et3SiH/KOtBu system, with the displacement of the methoxide group occurring via a concerted nucleophilic aromatic substitution (i.e. without the formation of a Meisenheimer intermediate, Scheme 3).;Scheme 3 - Concerted Nucleophilic Aromatic Substitution to Afford Indolines [includes graphic]Recent publications by Grubbs and Stoltz have focussed on the combination of triethylsilane with potassium tert-butoxide to afford a system which is capable of carrying out a number of synthetically useful transformations. This includes i) the reductive cleavage of C-O bonds in ethers, ii) the reductive cleavage of C-S bonds in thioethers, and iii) the regioselective silylation of arenes and heteroarenes. A number of mechanistic studies have been carried out, but so far no conclusive mechanism is known for these transformations.;Recent work in the Murphy group has focussed on the combination of small molecules with potassium tert-butoxide to form in situ electron donors. This thesis will focus on mechanistic studies on the combination of triethylsilane with potassium tert-butoxide, which is capable of carrying out the reductive debenzylation of N-benzylindoles (Scheme 1). Experimental and computational studies show that it is likely that this transformation proceeds via single electron transfer.;Scheme 1 - Debenzylation of N-Benzylindoles Mediated by Et3SiH/KOtBu [includes graphic];N-arylindoles were shown to undergo ring-opening and subsequent ring-closure to afford 9,10-dihydroacridines (Scheme 2). Mechanistic studies suggest that this transformation may either proceed via single electron transfer or via hydrogen atom transfer.;Scheme 2 - Conversion of N-Arylindoles to 9,10-Dihydroacridines Mediated by Et3SiH/KOtBu [includes graphic];Finally, the reduction and subsequent cyclisation of nitriles was shown to proceed via hydride transfer from the Et3SiH/KOtBu system, with the displacement of the methoxide group occurring via a concerted nucleophilic aromatic substitution (i.e. without the formation of a Meisenheimer intermediate, Scheme 3).;Scheme 3 - Concerted Nucleophilic Aromatic Substitution to Afford Indolines [includes graphic
Emotion recognition in video using deep learning method with subtract pre-processing
Get PDFThe main purpose of this paper is to distinguished human expression using a deep learning method. This paper present a new preprocessing method to extract the features of human expression from videos, and then uses deep learning methods to analysis the human emotions. A facial expression is usually regarded as a fixed moment of human disposition. However, recently, researchers have realized the importance of time information for expression recognition.;At the same time, the ability of feature extraction in deep learning has also received attention. The method used in this paper uses time information to distinguish expressions. The paper is divided into several chapters to describe the background technology of expression analysis. Relevant information mentioned includes: picture and video information;Basic knowledge of convolution neural network; The basic principle of recurrent neural network; Background technology of face features and traditional classification methods; Application of depth learning method in video; Related technologies of object detection and the amount of classical deep learning models. With this background knowledge, a complete video facial expression analysis scheme can be formed.;Chapter 1 is the overall planning of the thesis. Chapter 2 systematically introduces the relevant knowledge of deep learning, including the composition of deep convolution network, the composition of deep loop network, the use of activation function, classical classification network and target detection network. Pretreatment is also needed in facial expression recognition, including face detection, face correction, etc.;Chapter 2 introduces face processing algorithms, such as Viola&Jones face detection model and multi-person face detection model. At the same time, the knowledge of actual model training and the analysis experience of experimental results are introduced. At the end of the chapter 2, the classical data sets used in learning are listed. In chapter 3, a new pre-processing method for video temporal feature extraction is proposed.;The whole expression recognition process includes face recognition, face alignment and the training of depth learning classifiers. RAVDESS video data set is used in training the depth learning model. After reasonable training, the model was tested in video and real-time video and achieved acceptable results. Chapter 4 summarizes and assesses practical work and discusses future work direction, combining the experience from this work with the problems encountered.The main purpose of this paper is to distinguished human expression using a deep learning method. This paper present a new preprocessing method to extract the features of human expression from videos, and then uses deep learning methods to analysis the human emotions. A facial expression is usually regarded as a fixed moment of human disposition. However, recently, researchers have realized the importance of time information for expression recognition.;At the same time, the ability of feature extraction in deep learning has also received attention. The method used in this paper uses time information to distinguish expressions. The paper is divided into several chapters to describe the background technology of expression analysis. Relevant information mentioned includes: picture and video information;Basic knowledge of convolution neural network; The basic principle of recurrent neural network; Background technology of face features and traditional classification methods; Application of depth learning method in video; Related technologies of object detection and the amount of classical deep learning models. With this background knowledge, a complete video facial expression analysis scheme can be formed.;Chapter 1 is the overall planning of the thesis. Chapter 2 systematically introduces the relevant knowledge of deep learning, including the composition of deep convolution network, the composition of deep loop network, the use of activation function, classical classification network and target detection network. Pretreatment is also needed in facial expression recognition, including face detection, face correction, etc.;Chapter 2 introduces face processing algorithms, such as Viola&Jones face detection model and multi-person face detection model. At the same time, the knowledge of actual model training and the analysis experience of experimental results are introduced. At the end of the chapter 2, the classical data sets used in learning are listed. In chapter 3, a new pre-processing method for video temporal feature extraction is proposed.;The whole expression recognition process includes face recognition, face alignment and the training of depth learning classifiers. RAVDESS video data set is used in training the depth learning model. After reasonable training, the model was tested in video and real-time video and achieved acceptable results. Chapter 4 summarizes and assesses practical work and discusses future work direction, combining the experience from this work with the problems encountered
The effect of viral plasticity on the coexistence and eco-evolutionary dynamics of host-phage systems
Get PDFViruses infect host cells to hijack the host machinery for viral reproduction, which can lead to host mortality for unicellular organisms. In marine environments, viruses are recognized as an important factor altering phytoplankton and bacterioplankton growth and dynamics. However, it is still unclear the exact role that viruses play in the regulation of their host populations. As a consequence, generalizing viral-mediated processes is still a big challenge in ecology as well as in other fields (e.g. medical or commercial, where viruses are suggested as an alternative to antibiotics for humans, plants, or animals).;Lab experiments reveal that viral performance (represented by infection time and offspring number) varies with physiological changes in their hosts, effectively the virus' environment. These variations are referred as viral phenotypic plasticity, as the viral traits vary when environmental conditions change. In the past, models studying viral plasticity focused on intracellular dynamics. However, these latter are too detailed to be included in models that study host-virus population-level interactions in the long term, which hinders our understanding of systems that range from pathogens infecting gut bacteria to marine phage shaping the ocean communities;Here, we compiled experimental data to represent lytic viral plasticity through functional forms that are biologically meaningful, and which we included in a standard host-virus model to understand the effect of viral plasticity on (i) the evolutionary response of the viral traits as well as population dynamics, (ii) the persistence of the host-virus systems, and (iii) the coevolution between host and virus. We show that the plasticity of the viral offspring number mostly drives the phage ecological and evolutionary dynamics. Moreover, plasticity can invert predictions on the short-term population dynamics of the viral-host system made by classic models that neglect viral plasticity.;Considering viral plasticity leads to a dynamic viral control of the host population, and enables coexistence in region where classic (nonplastic) models predict the collapse of the population. Finally, the coevolution of host-phage populations shows beneficial mutualistic interactions where the presence of virus, instead of having a negative effect, increases the fitness of the host.Viruses infect host cells to hijack the host machinery for viral reproduction, which can lead to host mortality for unicellular organisms. In marine environments, viruses are recognized as an important factor altering phytoplankton and bacterioplankton growth and dynamics. However, it is still unclear the exact role that viruses play in the regulation of their host populations. As a consequence, generalizing viral-mediated processes is still a big challenge in ecology as well as in other fields (e.g. medical or commercial, where viruses are suggested as an alternative to antibiotics for humans, plants, or animals).;Lab experiments reveal that viral performance (represented by infection time and offspring number) varies with physiological changes in their hosts, effectively the virus' environment. These variations are referred as viral phenotypic plasticity, as the viral traits vary when environmental conditions change. In the past, models studying viral plasticity focused on intracellular dynamics. However, these latter are too detailed to be included in models that study host-virus population-level interactions in the long term, which hinders our understanding of systems that range from pathogens infecting gut bacteria to marine phage shaping the ocean communities;Here, we compiled experimental data to represent lytic viral plasticity through functional forms that are biologically meaningful, and which we included in a standard host-virus model to understand the effect of viral plasticity on (i) the evolutionary response of the viral traits as well as population dynamics, (ii) the persistence of the host-virus systems, and (iii) the coevolution between host and virus. We show that the plasticity of the viral offspring number mostly drives the phage ecological and evolutionary dynamics. Moreover, plasticity can invert predictions on the short-term population dynamics of the viral-host system made by classic models that neglect viral plasticity.;Considering viral plasticity leads to a dynamic viral control of the host population, and enables coexistence in region where classic (nonplastic) models predict the collapse of the population. Finally, the coevolution of host-phage populations shows beneficial mutualistic interactions where the presence of virus, instead of having a negative effect, increases the fitness of the host
Economic integration of the East African community
Get PDFThis thesis contributes to the debate of the consequences of preferential liberalization through assessment of the trade and welfare effects of a Preferential Trade Agreement(PTA) on its member countries. In particular, it examines the potential and actual impacts of the East African Community (EAC), which is hailed as one of the most successful PTAs in Africa (Koami et al. 2016). The aim of this thesis is to understand how formation of the EAC affected the economies of its member countries and whether it is the best trade liberalization strategy for them. The thesis undertakes both theoretical and empirical analyses to examine the trade and welfare effects of the EAC. It is comprised of five main chapters. Chapter 1 surveys the academic literature on the welfare effects of PTAs and presents the aims and objectives of this thesis. The main goal is to provide a background for subsequent analyses. It gives a brief overview of the evolution of PTAs, examines the theoretical literature on static and dynamic effects of PTAs and reviews the ex-ante and ex-post models for evaluation of the welfare effects of PTAs. Chapter 2 gives a background to the EAC and underscores the need for research on its trade and welfare effects on member countries. It undertakes a political economy analysis of the challenges facing the implementation of the EAC Treaty. It also investigates how far the lessons learnt from previous attempts at integration among the EAC countries have shaped the current progress.;Chapter 3 theoretically analyses the welfare effects from the formation of a PTA using a stylized three-country model of international trade under oligopoly. It compares the differences in welfare implications between a Free Trade Agreement (FTA)and a Customs Union (CU) on the member countries who differ in their market sizes. The findings show that both are welfare improving for the member countries provided that the difference in market sizes is not too large. Comparing the FTA and CU, the smaller partner in the trade agreement will prefer an FTA over a CU. This is because the profits gains for the firm from protection of the regional market due to higher tariffs in an FTA outweighs the forgone gains in consumer surplus and tariff revenue due to lower tariffs in a CU. On the other hand, the larger partner will prefer a CU over an FTA since its population size will lead to higher consumer surplus and tariff revenue that will outweigh forgone gains from firm's profits. The findings of this chapter sheds light on some of the reasons why the EAC is facing challenges in its implementation. Chapter 4 empirically assesses whether the EAC countries economically benefited from trade liberalization. It quantifies the trade creation, trade diversion and the welfare effects of trade liberalization on the EAC countries using an estimation and general equilibrium simulation procedure by Anderson et al. (2015) built around the structural micro-foundations of the gravity equation. The results show that the EAC integration generated large trade creation effects for all member countries that superseded the trade diversion effects. Kenya, which is the most industrialized country in the EAC, was the only country that did not have a trade diversion effect. On the other hand, the welfare analysis indicate that the EAC led to economic gains for its member countries of between 0.01 - 0.9 percent of real GDP with Kenya enjoying the highest gains. The welfare gains for Kenya were due to producer surpluses while the welfare gains for all other EAC countries stemmed from consumer surpluses. These finding suggest that the EAC has achieved its objective of generating welfare gains for its member countries. Second, the findings also show that the benefits of trade liberalization among developing countries will be inclined to the most industrialized countries. Chapter 5 empirically investigates the effects of the East African Community (EAC) in lowering trade costs for the agricultural, manufacturing and mining sectors.;The first part of the chapter calculates comprehensive trade costs, using an approach by Novy (2013), and decomposes it into tariffs and non-tariff trade costs. The second part of the chapter, uses these measures of trade costs in a gravity model to estimate the effects of the EAC on tariffs and Non-Tariff Measures (NTMs). The results indicate that the EAC is associated with the reduction of overall trade costs across all sectors. When the trade costs are further broken down into tariffs and NTMs, the impact of the EAC is seen to have been more successful in reduction of tariffs than NTMs across all sectors. This indicates that as EAC countries reduced tariffs, they adopted NTMs to protect their domestic industries from regional competition. The only sector with a significant reduction in NTMs is the manufacturing sector and this can be attributed to the weak industrial capacities in most EAC countries. Gains from lower domestic prices will outweigh the firm's profits if their domestic market were protected.This thesis contributes to the debate of the consequences of preferential liberalization through assessment of the trade and welfare effects of a Preferential Trade Agreement(PTA) on its member countries. In particular, it examines the potential and actual impacts of the East African Community (EAC), which is hailed as one of the most successful PTAs in Africa (Koami et al. 2016). The aim of this thesis is to understand how formation of the EAC affected the economies of its member countries and whether it is the best trade liberalization strategy for them. The thesis undertakes both theoretical and empirical analyses to examine the trade and welfare effects of the EAC. It is comprised of five main chapters. Chapter 1 surveys the academic literature on the welfare effects of PTAs and presents the aims and objectives of this thesis. The main goal is to provide a background for subsequent analyses. It gives a brief overview of the evolution of PTAs, examines the theoretical literature on static and dynamic effects of PTAs and reviews the ex-ante and ex-post models for evaluation of the welfare effects of PTAs. Chapter 2 gives a background to the EAC and underscores the need for research on its trade and welfare effects on member countries. It undertakes a political economy analysis of the challenges facing the implementation of the EAC Treaty. It also investigates how far the lessons learnt from previous attempts at integration among the EAC countries have shaped the current progress.;Chapter 3 theoretically analyses the welfare effects from the formation of a PTA using a stylized three-country model of international trade under oligopoly. It compares the differences in welfare implications between a Free Trade Agreement (FTA)and a Customs Union (CU) on the member countries who differ in their market sizes. The findings show that both are welfare improving for the member countries provided that the difference in market sizes is not too large. Comparing the FTA and CU, the smaller partner in the trade agreement will prefer an FTA over a CU. This is because the profits gains for the firm from protection of the regional market due to higher tariffs in an FTA outweighs the forgone gains in consumer surplus and tariff revenue due to lower tariffs in a CU. On the other hand, the larger partner will prefer a CU over an FTA since its population size will lead to higher consumer surplus and tariff revenue that will outweigh forgone gains from firm's profits. The findings of this chapter sheds light on some of the reasons why the EAC is facing challenges in its implementation. Chapter 4 empirically assesses whether the EAC countries economically benefited from trade liberalization. It quantifies the trade creation, trade diversion and the welfare effects of trade liberalization on the EAC countries using an estimation and general equilibrium simulation procedure by Anderson et al. (2015) built around the structural micro-foundations of the gravity equation. The results show that the EAC integration generated large trade creation effects for all member countries that superseded the trade diversion effects. Kenya, which is the most industrialized country in the EAC, was the only country that did not have a trade diversion effect. On the other hand, the welfare analysis indicate that the EAC led to economic gains for its member countries of between 0.01 - 0.9 percent of real GDP with Kenya enjoying the highest gains. The welfare gains for Kenya were due to producer surpluses while the welfare gains for all other EAC countries stemmed from consumer surpluses. These finding suggest that the EAC has achieved its objective of generating welfare gains for its member countries. Second, the findings also show that the benefits of trade liberalization among developing countries will be inclined to the most industrialized countries. Chapter 5 empirically investigates the effects of the East African Community (EAC) in lowering trade costs for the agricultural, manufacturing and mining sectors.;The first part of the chapter calculates comprehensive trade costs, using an approach by Novy (2013), and decomposes it into tariffs and non-tariff trade costs. The second part of the chapter, uses these measures of trade costs in a gravity model to estimate the effects of the EAC on tariffs and Non-Tariff Measures (NTMs). The results indicate that the EAC is associated with the reduction of overall trade costs across all sectors. When the trade costs are further broken down into tariffs and NTMs, the impact of the EAC is seen to have been more successful in reduction of tariffs than NTMs across all sectors. This indicates that as EAC countries reduced tariffs, they adopted NTMs to protect their domestic industries from regional competition. The only sector with a significant reduction in NTMs is the manufacturing sector and this can be attributed to the weak industrial capacities in most EAC countries. Gains from lower domestic prices will outweigh the firm's profits if their domestic market were protected
The use of silyl enol ethers as alkene equivalents in the Pauson-Khand Reaction
Get PDFOver the past two decades, work within our laboratories has focused on the development of the Pauson-Khand reaction to deliver novel methodologies for the construction of flexible cyclopentenone scaffolds. To date, the Pauson-Khand reaction has been widely used to synthesise cyclopentenone motifs in natural product synthesis and beyond. However, there is a distinct lack of examples which use functionalised reacting partners to form diverse cyclopentenones.;To address this notable deficiency, we employed, for the first time, silyl enol ethers as alkene equivalents for the intramolecular Pauson-Khand reaction to generate oxygenated cyclopentenones. Using this method, 17 novel cyclopentenones have been synthesised, which feature oxygenation on the cyclopentenone ring. Furthermore, two oxygenated cyclopentenones were readily converted into their fluorinated analogues in one step.;In addition to the methodology development, we sought to employ this novel Pauson-Khand reaction in the arena of total synthesis of natural products. In this regard, we selected Xeromphalinone C, a natural product isolated in 2010, which is part of a family of natural products featuring oxygenated cyclopentenone motifs. A novel synthetic sequence to Xeromphalinone C was established, which used our novel Pauson-Khand reaction methodology as a key step, completing the first total synthesis of Xeromphalinone C in 1.6% yield over 16 steps. This highlighted the utility of our novel methodology as a useful step for the synthesis of complex, functionalised cyclopentenone molecules.Over the past two decades, work within our laboratories has focused on the development of the Pauson-Khand reaction to deliver novel methodologies for the construction of flexible cyclopentenone scaffolds. To date, the Pauson-Khand reaction has been widely used to synthesise cyclopentenone motifs in natural product synthesis and beyond. However, there is a distinct lack of examples which use functionalised reacting partners to form diverse cyclopentenones.;To address this notable deficiency, we employed, for the first time, silyl enol ethers as alkene equivalents for the intramolecular Pauson-Khand reaction to generate oxygenated cyclopentenones. Using this method, 17 novel cyclopentenones have been synthesised, which feature oxygenation on the cyclopentenone ring. Furthermore, two oxygenated cyclopentenones were readily converted into their fluorinated analogues in one step.;In addition to the methodology development, we sought to employ this novel Pauson-Khand reaction in the arena of total synthesis of natural products. In this regard, we selected Xeromphalinone C, a natural product isolated in 2010, which is part of a family of natural products featuring oxygenated cyclopentenone motifs. A novel synthetic sequence to Xeromphalinone C was established, which used our novel Pauson-Khand reaction methodology as a key step, completing the first total synthesis of Xeromphalinone C in 1.6% yield over 16 steps. This highlighted the utility of our novel methodology as a useful step for the synthesis of complex, functionalised cyclopentenone molecules
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