Alley cropping of willows and grassland for bioenergy provision: productivity, tree-crop interactions and energy balance

The demand for biomass for bioenergy has increased rapidly in industrialized countries in the recent years. Biogenic energy carriers are known to reduce CO2 emissions. However, the resource-inefficient production of biomass often caused negative impacts on the environment, e.g. biodiversity losses, nitrate leaching, and erosion. The detrimental effects evolved mainly from annual crops. Therefore, the aim of modern bioenergy cropping systems is to combine yield stability and environmental benefits by the establishment of mixed-cropping systems. A particular emphasis is on perennial crops which are perceived as environmentally superior to annual crops. Agroforestry systems represent such mixed perennial cropping systems and consist of a mix of trees and arable crops or grassland within the same area of land. Agroforestry practices vary across the globe and alley cropping is a type of agroforestry system which is well adapted to the temperate zone, with a high degree of mechanization. Trees are planted in rows and crops are planted in the alleyways, which facilitates their management by machinery. This study was conducted to examine a young alley cropping system of willows and two grassland mixtures for bioenergy provision under temperate climate conditions. The first part of the thesis identified possible competition effects between willows and the two grassland mixtures. Since light seemed to be the factor most affecting the yield performance of the understory in temperate agroforestry systems, a biennial in situ artificial shade experiment was established over a separate clover-grass stand to quantify the effects of shade. Data to possible below- and aboveground interactions among willows and the two grassland mixtures and their effects on productivity, sward composition, and quality were monitored along a tree-grassland interface within the alleys. In the second part, productivity of the alley cropping system was examined on a triennial time frame and compared to separate grassland and willow stands as controls. Three different conversion technologies (combustion of hay, integrated generation of solid fuel and biogas from biomass, whole crop digestion) were applied to grassland biomass as feedstock and analyzed for its energetic potential. The energetic potential of willow wood chips was calculated by applying combustion as conversion technique. Net energy balances of separate grassland stands, agroforestry and pure willow stands evaluated their energy efficiency. Results of the biennial artificial shade experiment showed that severe shade (80 % light reduction) halved grassland productivity on average compared to a non-shaded control. White clover as heliophilous plant responded sensitively to limited radiation and its dry matter contribution in the sward decreased with increasing shade, whereas non-leguminous forbs (mainly segetal species) benefited. Changes in nutritive quality could not be confirmed by this experiment. Through the study on interactions within the alleys of the young agroforestry system it was possible to outline changes of incident light, soil temperature and sward composition of clover-grass along the tree-grassland interface. Nearly no effects of trees on precipitation, soil moisture and understory productivity occurred along the interface during the biennial experiment. Considering the results of the productivity and the net energy yield alley cropping system had lower than pure grassland stands, irrespective of the grassland seed mixture or fertilization, but was higher than that for pure willow stands. The comparison of three different energetic conversion techniques for the grassland biomass showed highest net energy yields for hay combustion, whereas the integrated generation of solid fuel and biogas from biomass (IFBB) and whole crop digestion performed similarly. However, due to the low fuel quality of hay, its direct combustion cannot be recommended as a viable conversion technique, whereas IFBB fuels were of a similar quality to wood chip from willow.

Development of mechanical methods for cell-tray propagation and field transplanting of dwarf napiergrass (Pennisetum purpureum Schumach.)

Since dwarf napiergrass (Pennisetum purpureum Schumach.) must be propagated vegetatively due to lack of viable seeds, root splitting and stem cuttings are generally used to obtain true-to-type plant populations. These ordinary methods are laborious and costly, and are the greatest barriers for expanding the cultivation area of this crop. The objectives of this research were to develop nursery production of dwarf napiergrass in cell trays and to compare the efficiency of mechanical versus manual methods for cell-tray propagation and field transplanting. After defoliation of herbage either by a sickle (manually) or hand-mowing machine, every potential aerial tiller bud was cut to a single one for transplanting into cell trays as stem cuttings and placed in a glasshouse over winter. The following June, nursery plants were trimmed to a 25–cm length and transplanted in an experimental field (sandy soil) with 20,000 plants ha^(−1) either by shovel (manually) or Welsh onion planter. Labour time was recorded for each process. The manual defoliation of plants required 44% more labour time for preparing the stem cuttings (0.73 person-min. stemcutting^(−1)) compared to using hand-mowing machinery (0.51 person-min. stem-cutting^(−1)). In contrast, labour time for transplanting required an extra 0.30 person-min. m^(−2) (14%) using the machinery compared to manual transplanting, possibly due to the limited plot size for machinery operation. The transplanting method had no significant effect on plant establishment or plant growth, except for herbage yield 110 days after planting. Defoliation of herbage by machinery, production using a cell-tray nursery and mechanical transplanting reduced the labour intensity of dwarf napiergrass propagation.

The Control of Human Arm Movement Models and Mechanical Constraints

A serial-link manipulator may form a mobile closed kinematic chain when interacting with the environment, if it is redundant with respect to the task degrees of freedom (DOFs) at the endpoint. If the mobile closed chain assumes a number of configurations, then loop consistency equations permit the manipulator and task kinematics to be calibrated simultaneously using only the joint angle readings; endpoint sensing is not required. Example tasks include a fixed endpoint (0 DOF task), the opening of a door (1 DOF task), and point contact (3 DOF task). Identifiability conditions are derived for these various tasks.

Trajectory and Force Control of a Direct Drive Arm

Using the MIT Serial Link Direct Drive Arm as the main experimental device, various issues in trajectory and force control of manipulators were studied in this thesis. Since accurate modeling is important for any controller, issues of estimating the dynamic model of a manipulator and its load were addressed first. Practical and effective algorithms were developed fro the Newton-Euler equations to estimate the inertial parameters of manipulator rigid-body loads and links. Load estimation was implemented both on PUMA 600 robot and on the MIT Serial Link Direct Drive Arm. With the link estimation algorithm, the inertial parameters of the direct drive arm were obtained. For both load and link estimation results, the estimated parameters are good models of the actual system for control purposes since torques and forces can be predicted accurately from these estimated parameters. The estimated model of the direct drive arm was them used to evaluate trajectory following performance by feedforward and computed torque control algorithms. The experimental evaluations showed that the dynamic compensation can greatly improve trajectory following accuracy. Various stability issues of force control were studied next. It was determined that there are two types of instability in force control. Dynamic instability, present in all of the previous force control algorithms discussed in this thesis, is caused by the interaction of a manipulator with a stiff environment. Kinematics instability is present only in the hybrid control algorithm of Raibert and Craig, and is caused by the interaction of the inertia matrix with the Jacobian inverse coordinate transformation in the feedback path. Several methods were suggested and demonstrated experimentally to solve these stability problems. The result of the stability analyses were then incorporated in implementing a stable force/position controller on the direct drive arm by the modified resolved acceleration method using both joint torque and wrist force sensor feedbacks.

An Application of Augmented Reality (AR) in the Teaching of an Arc Welding Robot

Augmented Reality (AR) is an emerging technology that utilizes computer vision methods to overlay virtual objects onto the real world scene so as to make them appear to co-exist with the real objects. Its main objective is to enhance the user’s interaction with the real world by providing the right information needed to perform a certain task. Applications of this technology in manufacturing include maintenance, assembly and telerobotics. In this paper, we explore the potential of teaching a robot to perform an arc welding task in an AR environment. We present the motivation, features of a system using the popular ARToolkit package, and a discussion on the issues and implications of our research.

The Inertio-Elastic Planar Entry Flow of Low-Viscosity Elastic Fluids in Micro-fabricated Geometries

The non-Newtonian flow of dilute aqueous polyethylene oxide (PEO) solutions through microfabricated planar abrupt contraction-expansions is investigated. The contraction geometries are fabricated from a high-resolution chrome mask and cross-linked PDMS gels using the tools of soft-lithography. The small length scales and high deformation rates in the contraction throat lead to significant extensional flow effects even with dilute polymer solutions having time constants on the order of milliseconds. The dimensionless extra pressure drop across the contraction increases by more than 200% and is accompanied by significant upstream vortex growth. Streak photography and videomicroscopy using epifluorescent particles shows that the flow ultimately becomes unstable and three-dimensional. The moderate Reynolds numbers (0.03 ≤ Re ≤ 44) associated with these high Deborah number (0 ≤ De ≤ 600) microfluidic flows results in the exploration of new regions of the Re-De parameter space in which the effects of both elasticity and inertia can be observed. Understanding such interactions will be increasingly important in microfluidic applications involving complex fluids and can best be interpreted in terms of the elasticity number, El = De/Re, which is independent of the flow kinematics and depends only on the fluid rheology and the characteristic size of the device.

Pressure-jump-induced kinetics reveals a hydration dependent folding/unfolding mechanism of ribonuclease A

Pressure-jump (p-jump)-induced relaxation kinetics was used to explore the energy landscape of protein folding/unfolding of Y115W, a fluorescent variant of ribonuclease A. Pressure-jumps of 40MPa amplitude (5ms dead-time) were conducted both to higher (unfolding) and to lower (folding) pressure, in the range from 100 to 500MPa, between 30 and 50°C. Significant deviations from the expected symmetrical protein relaxation kinetics were observed. Whereas downward p-jumps resulted always in single exponential kinetics, the kinetics induced by upward p-jumps were biphasic in the low pressure range and monophasic at higher pressures. The relative amplitude of the slow phase decreased as a function of both pressure and temperature. At 50°C, only the fast phase remained. These results can be interpreted within the framework of a two-dimensional energy surface containing a pressure- and temperature-dependent barrier between two unfolded states differing in the isomeric state of the Asn-113–Pro-114 bond. Analysis of the activation volume of the fast kinetic phase revealed a temperature-dependent shift of the unfolding transition state to a larger volume. The observed compensation of this effect by glycerol offers an explanation for its protein stabilizing effect

Evaluation of the model representation of the evolution of convective systems using satellite observations of outgoing longwave radiation

We introduce a technique for assessing the diurnal development of convective storm systems based on outgoing longwave radiation fields. Using the size distribution of the storms measured from a series of images, we generate an array in the lengthscale-time domain based on the standard score statistic. It demonstrates succinctly the size evolution of storms as well as the dissipation kinematics. It also provides evidence related to the temperature evolution of the cloud tops. We apply this approach to a test case comparing observations made by the Geostationary Earth Radiation Budget instrument to output from the Met Office Unified Model run at two resolutions. The 12km resolution model produces peak convective activity on all lengthscales significantly earlier in the day than shown by the observations and no evidence for storms growing in size. The 4km resolution model shows realistic timing and growth evolution although the dissipation mechanism still differs from the observed data.

Proteornics analysis unravels the functional repertoire of coronavirus nonstructural protein 3

Severe acute respiratory syndrome (SARS) coronavirus infection and growth are dependent on initiating signaling and enzyme actions upon viral entry into the host cell. Proteins packaged during virus assembly may subsequently form the first line of attack and host manipulation upon infection. A complete characterization of virion components is therefore important to understanding the dynamics of early stages of infection. Mass spectrometry and kinase profiling techniques identified nearly 200 incorporated host and viral proteins. We used published interaction data to identify hubs of connectivity with potential significance for virion formation. Surprisingly, the hub with the most potential connections was not the viral M protein but the nonstructurall protein 3 (nsp3), which is one of the novel virion components identified by mass spectrometry. Based on new experimental data and a bioinformatics analysis across the Coronaviridae, we propose a higher-resolution functional domain architecture for nsp3 that determines the interaction capacity of this protein. Using recombinant protein domains expressed in Escherichia coli, we identified two additional RNA-binding domains of nsp3. One of these domains is located within the previously described SARS-unique domain, and there is a nucleic acid chaperone-like domain located immediately downstream of the papain-like proteinase domain. We also identified a novel cysteine-coordinated metal ion-binding domain. Analyses of interdomain interactions and provisional functional annotation of the remaining, so-far-uncharacterized domains are presented. Overall, the ensemble of data surveyed here paint a more complete picture of nsp3 as a conserved component of the viral protein processing machinery, which is intimately associated with viral RNA in its role as a virion component.

Characterisation and regulation of E2F-6 and E2F-6b in the rat heart: a potential target for myocardial regeneration?

The E2F transcription factors are instrumental in regulating cell cycle progression and growth, including that in cardiomyocytes, which exit the cell cycle shortly after birth. E2F-6 has been demonstrated to act as a transcriptional repressor; however, its potential role in normal cardiomyocyte proliferation and hypertrophy has not previously been investigated. Here we report the isolation and characterisation of E2F-6 and E2F-6b in rat cardiomyocytes and consider its potential as a target for myocardial regeneration following injury. At the mRNA level, both rat E2F-6 and the alternatively spliced variant, E2F-6b, were expressed in E18 myocytes and levels were maintained throughout development into adulthood. Interestingly, E2F-6 protein expression was down-regulated during myocyte development suggesting that it is regulated post-transcriptionally in these cells. During myocyte hypertrophy, the mRNA expressions of E2F-6 and E2F-6b were not regulated whereas E2F-6 protein was up-regulated significantly. Indeed, E2F-6 protein expression levels closely parallel the developmental withdrawal of myocytes from the cell cycle and the subsequent reactivation of their cell cycle machinery during hypertrophic growth. Furthermore, depletion of E2F-6, using anti-sense technology, results in death of cultured neonatal myocytes. Taken together, abrogation of E2F-6 expression in neonatal cardiomyocytes leads to a significant decrease in their viability, consistent with the notion that E2F-6 might be required for maintaining normal myocyte growth.

Inhibition of E2F abrogates the development of cardiac myocyte hypertrophy

Growth of the post- natal mammalian heart occurs primarily by cardiac myocyte hypertrophy. Previously, we and others have shown that a partial re- activation of the cell cycle machinery occurs in myocytes undergoing hypertrophy such that cells progress through the G(1)/ S transition. In this study, we have examined the regulation of the E2F family of transcription factors that are crucial for the G(1)/ S phase transition during normal cardiac development and the development of myocyte hypertrophy in the rat. Thus, mRNA and protein levels of E2F- 1, 3, and 4 and DP- 1 and DP- 2 were down- regulated during development to undetectable levels in adult myocytes. Interestingly, E2F- 5 protein levels were substantially up- regulated during development. In contrast, an induction of E2F- 1, 3, and 4 and the DP- 1 protein was observed during the development of myocyte hypertrophy in neonatal myocytes treated with serum or phenylephrine, whereas the protein levels of E2F- 5 were decreased with serum stimulation. E2F activity, as measured by a cyclin E promoter luciferase assay and E2F- DNA binding activity, increased significantly during the development of hypertrophy with serum and phenylephrine compared with non- stimulated cells. Inhibiting E2F activity with a specific peptide that blocks E2F- DP heterodimerization prevented the induction of hypertrophic markers ( atrial natriuretic factor and brain natriuretic peptide) in response to serum and phenylephrine, reduced the increase in myocyte size, and inhibited protein synthesis in stimulated cells. Thus, we have shown that the inhibition of E2F function prevents the development of hypertrophy. Targeting E2F function might be a useful approach for treating diseases that cause pathophysiological hypertrophic growth.

Slicing of soft, flexible solids with industrial applications

Thin slices of soft flexible solids have negligible bending resistance and hence store negligible elastic strain energy; furthermore such offcuts are rarely permanently deformed after slicing. Cutting forces thus depend only on work of separation (toughness work) and friction. These simplifying assumptions are not as restrictive as it might seem, and the mechanics are found to apply to a wide variety of foodstuffs and biological materials. The fracture toughness of such materials may be determined from cutting experiments: the use of scissors instrumented for load and displacement is a popular method where toughness is obtained from the work areas beneath load–displacement plots. Surprisingly, there is no analysis for the variation of forces with scissor blade opening and this paper provides the theory. Comparison is made with experimental results in cutting with scissors. The analysis is generalised to cutting with blades of variable curvature and applied to a commercial food cutting device having a rotating spiral plan form blade. The strong influence of the ‘slice/push ratio’ (blade tangential speed to blade edge normal speed) on the cutting forces is revealed. Small cutting forces are important in food cutting machinery as damage to slices is minimised. How high slice/push ratios may be achieved by choice of blade profile is discussed.

Activation of pro-survival Akt and ERK1/2 signalling pathways underlie the anti-apoptotic effects of flavanones in cortical neurons

There is growing interest in the potential beneficial effects of flavonoids in the aging and diseased brain. We have investigated the potential of the flavanone hesperetin and two of its metabolites, hesperetin-7-O-beta-D-glucuronide and 5-nitro-hesperetin, to inhibit oxidative stress-induced neuronal apoptosis. Exposure of cortical neurons to hydrogen peroxide led to the activation of apoptosis signal-regulating kinase 1 via its de-phosphorylation at Ser963, the phosphorylation of c-jun N-terminal kinase and c-Jun (Ser73) and the activation of caspase 3 and caspase 9. Whilst hesperetin glucuronide failed to exert protection, both hesperetin and 5-nitro-hesperetin were effective at preventing neuronal apoptosis via a mechanism involving the activation/phosphorylation of both Akt/protein kinase B and extracellular signal-regulated kinase 1 and 2 (ERK1/2). Protection against oxidative injury and the activation of Akt and ERK1/2 followed a bell-shaped response and was most apparent at 100 nmol/L concentrations. The activation of ERK1/2 and Akt by flavanones led to the inhibition of the pro-apoptotic proteins, apoptosis signal-regulating kinase 1, by phosphorylation at Ser83 and Bad, by phosphorylation at both Ser136 and Ser112 and to the inhibition of peroxide-induced caspase 9 and caspase 3 activation. Thus, flavanones may protect neurons against oxidative insults via the modulation of neuronal apoptotic machinery.

Reprogramming the cell cycle machinery to treat cardiovascular disease

Coronary artery disease is one of the most common heart pathologies. Restriction of blood flow to the heart by atherosclerotic lesions, leading to angina pectoris and myocardial infarction, damages the heart, resulting in impaired cardiac function. Damaged myocardium is replaced by scar tissue since surviving cardiomyocytes are unable to proliferate to replace lost heart tissue. Although narrowing of the coronary arteries can be treated successfully using coronary revascularisation procedures, re-occlusion of the treated vessels remains a significant clinical problem. Cell cycle control mechanisms are key in both the impaired cardiac repair by surviving cardiomyocytes and re-narrowing of treated vessels by maladaptive proliferation of vascular smooth muscle cells. Strategies targeting the cell cycle machinery in the heart and vasculature offer promise both for the improvement of cardiac repair following MI and the prevention of restenosis and bypass graft failure following revascularisation procedures.

Design and development of a dextrous manipulator

This paper develops a novel method of actuation for robotic hands. The solution employs Bowden cable routed to each joint as the means by which the finger is actuated. The use of Bowden cable is shown to be feasible for this purpose, even with the changing frictional forces associated with it's use. This method greatly simplifies the control of the hand by removing the coupling between joints, and allows for direct and accurate translation between the joints and the motors driving the Bowden wires. The design also allows for two degrees of freedom (with the same centre of rotation) to be realised in the largest knuckle of each finger, meaning biological finger kinematics are more accurately emulated.