The DHR1 domain of DOCK180 binds to SNX5 and regulates cation-independent mannose 6-phosphate receptor transport

DOCK180 is the archetype of the DOCK180-family guanine nucleotide exchange factor for small GTPases Rac1 and Cdc42. DOCK180-family proteins share two conserved domains, called DOCK homology region (DHR)-1 and -2. Although the function of DHR2 is to activate Rac1, DHR1 is required for binding to phosphoinositides. To better understand the function of DHR1, we searched for its binding partners by direct nanoflow liquid chromatography/tandem mass spectrometry, and we identified sorting nexins (SNX) 1, 2, 5, and 6, which make up a multimeric protein complex mediating endosome-to-trans-Golgi-network (TGN) retrograde transport of the cation-independent mannose 6-phosphate receptor (CI-MPR). Among these SNX proteins, SNX5 was coimmunoprecipitated with DOCK180 most efficiently. In agreement with this observation, DOCK180 colocalized with SNX5 at endosomes. The RNA interference-mediated knockdowns of SNX5 and DOCK180, but not Rac1, resulted in the redistribution of CI-MPR from TGN to endosomes. Furthermore, expression of the DOCK180 DHR1 domain was sufficient to restore the perturbed CI-MPR distribution in DOCK180 knockdown cells. These data suggest that DOCK180 regulates CI-MPR trafficking via SNX5 and that this function is independent of its guanine nucleotide exchange factor activity toward Rac1.

System identification of linear vibrating structures

Methods of dynamic modelling and analysis of structures, for example the finite element method, are well developed. However, it is generally agreed that accurate modelling of complex structures is difficult and for critical applications it is necessary to validate or update the theoretical models using data measured from actual structures. The techniques of identifying the parameters of linear dynamic models using Vibration test data have attracted considerable interest recently. However, no method has received a general acceptance due to a number of difficulties. These difficulties are mainly due to (i) Incomplete number of Vibration modes that can be excited and measured, (ii) Incomplete number of coordinates that can be measured, (iii) Inaccuracy in the experimental data (iv) Inaccuracy in the model structure. This thesis reports on a new approach to update the parameters of a finite element model as well as a lumped parameter model with a diagonal mass matrix. The structure and its theoretical model are equally perturbed by adding mass or stiffness and the incomplete number of eigen-data is measured. The parameters are then identified by an iterative updating of the initial estimates, by sensitivity analysis, using eigenvalues or both eigenvalues and eigenvectors of the structure before and after perturbation. It is shown that with a suitable choice of the perturbing coordinates exact parameters can be identified if the data and the model structure are exact. The theoretical basis of the technique is presented. To cope with measurement errors and possible inaccuracies in the model structure, a well known Bayesian approach is used to minimize the least squares difference between the updated and the initial parameters. The eigen-data of the structure with added mass or stiffness is also determined using the frequency response data of the unmodified structure by a structural modification technique. Thus, mass or stiffness do not have to be added physically. The mass-stiffness addition technique is demonstrated by simulation examples and Laboratory experiments on beams and an H-frame.

A biological-inspired support frame for an artificial cornea

Bilateral corneal blindness represents a quarter of the total blind, world-wide. The artificial cornea in assorted forms, was developed to replace opaque non-functional corneas and to return sight in otherwise hopeless cases that were not amenable to corneal grafts; believed to be 2% of corneal blind. Despite technological advances in materials design and tissue engineering no artificial cornea has provided absolute, long-term success. Formidable problems exist, due to a combination of unpredictable wound healing and unmanageable pathology. To have a solid guarantee of reliable success an artificial cornea must possess three attributes: an optical window to replace the opaque cornea; a strong, long term union to surrounding ocular tissue; and the ability to induce desired host responses. A unique artificial cornea possesses all three functional attributes- the Osteo-odonto-keratoprosthesis (OOKP). The OOKP has a high success rate and can survive for up to twenty years, but it is complicated both in structure and in surgical procedure; it is expensive and not universally available. The aim of this project was to develop a synthetic substitute for the OOKP, based upon key features of the tooth and bone structure. In doing so, surgical complexity and biological complications would be reduced. Analysis of the biological effectiveness of the OOKP showed that the structure of bone was the most crucial component for implant retention. An experimental semi-rigid hydroxyapatite framework was fabricated with a complex bone-like architecture, which could be fused to the optical window. The first method for making such a framework, was pressing and sintering of hydroxyapatite powders; however, it was not possible to fabricate a void architecture with the correct sizes and uniformity of pores. Ceramers were synthesised using alternative pore forming methods, providing for improved mechanical properties and stronger attachment to the plastic optical window. Naturally occurring skeletal structures closely match the structural features of all forms of natural bone. Synthetic casts were fabricated using the replamineform process, of desirable natural artifacts, such as coral and sponges. The final method of construction by-passed ceramic fabrication in favour of pre-formed coral derivatives and focused on methods for polymer infiltration, adhesion and fabrication. Prototypes were constructed and evaluated; a fully penetrative synthetic OOKP analogue was fabricated according to the dimensions of the OOKP. Fabrication of the cornea shaped OOKP synthetic analogue was also attempted.

Contrast sensitivity for complex and random gratings

This thesis studied the effect of (i) the number of grating components and (ii) parameter randomisation on root-mean-square (r.m.s.) contrast sensitivity and spatial integration. The effectiveness of spatial integration without external spatial noise depended on the number of equally spaced orientation components in the sum of gratings. The critical area marking the saturation of spatial integration was found to decrease when the number of components increased from 1 to 5-6 but increased again at 8-16 components. The critical area behaved similarly as a function of the number of grating components when stimuli consisted of 3, 6 or 16 components with different orientations and/or phases embedded in spatial noise. Spatial integration seemed to depend on the global Fourier structure of the stimulus. Spatial integration was similar for sums of two vertical cosine or sine gratings with various Michelson contrasts in noise. The critical area for a grating sum was found to be a sum of logarithmic critical areas for the component gratings weighted by their relative Michelson contrasts. The human visual system was modelled as a simple image processor where the visual stimuli is first low-pass filtered by the optical modulation transfer function of the human eye and secondly high-pass filtered, up to the spatial cut-off frequency determined by the lowest neural sampling density, by the neural modulation transfer function of the visual pathways. The internal noise is then added before signal interpretation occurs in the brain. The detection is mediated by a local spatially windowed matched filter. The model was extended to include complex stimuli and its applicability to the data was found to be successful. The shape of spatial integration function was similar for non-randomised and randomised simple and complex gratings. However, orientation and/or phase randomised reduced r.m.s contrast sensitivity by a factor of 2. The effect of parameter randomisation on spatial integration was modelled under the assumption that human observers change the observer strategy from cross-correlation (i.e., a matched filter) to auto-correlation detection when uncertainty is introduced to the task. The model described the data accurately.

Wear of high aluminium zinc-based alloys in plain bearing applications

Two zinc-based alloys of high aluminium content, Super Cosmal alloy containing 60% Al, 6% Si, 1% Cu, 0.3% Mn and HAZCA alloy containing 60% Al, 8% Si, 2% Cu, 0.06% Mg were produced by sand casting. Foundry characteristics in particular, fluidity, mode of solidification and feeding ability were examined. Metallographic analysis of structures was carried out using optical and scanning electron microscopy and their mechanical properties were determined using standard techniques. Dry wear characteristics were determined using a pin-on-disc test, and boundary-lubricated wear was studied using full bearing tests. Results from casting experiments were evaluated and compared with the behaviour of a standard ZA-27 alloy and those from tribological tests with both ZA-27 alloy and a leaded tin-bronze (SAE660) under the same testing conditions. The presence of silicon was beneficial, reducing the temperature range of solidification, improving feeding efficiency and reducing gravity segregation of phases. Use of chills and melt degassing was found necessary to achieve soundness and enhanced mechanical properties. Dry wear tests were performed against a steel counterface for sliding speeds of 0.25, 0.5, 1.0 and 2 m/s and for a range of loads up to 15 kgf. The high aluminium alloys showed wear rates as low as those of ZA-27 at speeds of 0.25 and 0.5 m/s for the whole range of applied loads. ZA-27 performed better at higher speeds. The build up of a surface film on the wearing surface of the test pins was found to be responsible for the mild type of wear of the zinc based alloys. The constitution of the surface film was determined as a complex mixture of aluminium, zinc and iron oxides and metallic elements derived from both sliding materials. For full bearing tests, bushes were machined from sand cast bars and were tested against a steel shaft in the presence of a light spindle oil as the lubricant. Results showed that all zinc based alloys run-in more rapidly than bronze, and that wear in Super Cosmal and HAZCA alloys after prolonged running were similar to those in ZA-27 bearings and significantly smaller than those of the bronze.

Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Fiber Bragg grating structures inscribed using 800nm femtosecond laser in single- and multi-core mid-IR glass fibers with their spectral, thermal and strain properties

Single- and multi-core passive and active germanate and tellurite glass fibers represent a new class of fiber host for in-fiber photonics devices and applications in mid-IR wavelength range, which are in increasing demand. Fiber Bragg grating (FBG) structures have been proven as one of the most functional in-fiber devices and have been mass-produced in silicate fibers by UV-inscription for almost countless laser and sensor applications. However, because of the strong UV absorption in germanate and tellurite fibers, FBG structures cannot be produced by UVinscription. In recent years femtosecond (fs) lasers have been developed for laser machining and microstructuring in a variety of glass fibers and planar substrates. A number of papers have been reported on fabrication of FBGs and long-period gratings in optical fibers and also on the photosensitivity mechanism using 800nm fs lasers. In this paper, we demonstrate for the first time the fabrication of FBG structures created in passive and active single- and three-core germanate and tellurite glass fibers by using 800nm fs-inscription and phase mask technique. With a fs peak power intensity in the order of 1011W/cm2, the FBG spectra with 2nd and 3rd order resonances at 1540nm and 1033nm in a single-core germanate glass fiber and 2nd order resonances between ~1694nm and ~1677nm with strengths up to 14dB in all three cores of three-core passive and active tellurite fibers were observed. Thermal and strain properties of the FBGs made in these mid-IR glass fibers were characterized, showing an average temperature responsivity of ~20pm/°C and a strain sensitivity of 1.219±0.003pm/µe.

Optimization and characterization of femtosecond laser inscribed in-fiber microchannels for liquid sensing

In-fiber microchannels were fabricated directly in standard single mode fiber using the femtosecond laser inscribe and etch technique. This method of creating in-fiber microchannels offers great versatility since it allows complex three dimensional structures to be inscribed and then etched with hydrofluoric acid. Four in-fiber microchannel designs were experimentally investigated using this technique. Device characteristics were evaluated through monitoring the spectral change while inserting index matching oils into each microchannel - a R.I. sensitivity up to 1.55 dB/RIU was achieved. Furthermore, a simple Fabry-Pérot based refractometer with a R.I. sensitivity of 2.75 nm/RIU was also demonstrated. © 2014 SPIE.

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity:in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide−MHC binding affinity. The ISC−PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide−MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms - q2, SEP, and NC - ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).

Microwave properties of an inhomogeneous optically illuminated plasma in a microstrip gap

The optical illumination of a microstrip gap on a thick semiconductor substrate creates an inhomogeneous electron-hole plasma in the gap region. This allows the study of the propagation mechanism through the plasma region. This paper uses a multilayer plasma model to explain the origin of high losses in such structures. Measured results are shown up to 50 GHz and show good agreement with the simulated multilayer model. The model also allows the estimation of certain key parameters of the plasma, such as carrier density and diffusion length, which are difficult to measure by direct means. The detailed model validation performed here will enable the design of more complex microwave structures based on this architecture. While this paper focuses on monocrystalline silicon as the substrate, the model is easily adaptable to other semiconductor materials such as GaAs.

Optimization and characterization of femtosecond laser inscribed in-fiber microchannels for liquid sensing

In-fiber microchannels were fabricated directly in standard single mode fiber using the femtosecond laser inscribe and etch technique. This method of creating in-fiber microchannels offers great versatility, since it allows complex three-dimensional structures to be inscribed and then preferentially etched with hydrofluoric acid. In addition, inscription does not require a photosensitive fiber; the modification is induced through nonlinear processes triggered by an ultrashort laser pulse. Four in-fiber microchannel designs were experimentally investigated using this technique - microhole, microslot channel along the core, microslot channel perpendicular to the core and helical channel around the core. Each device design was evaluated through monitoring the optical spectral change while inserting a range of index matching oils into each microchannel; an R.I. sensitivity up to 1.55 dB/RIU was achieved in these initial tests. Furthermore, an all femtosecond laser inscribed Fabry-Pérot-based refractometer with an R.I. sensitivity of 2.75 nm/RIU was also demonstrated. The Fabry-Pérot refractometer was formed by positioning a microchannel between two femtosecond laser inscribed point-by-point fiber Bragg gratings.

Aerodynamic load characteristics evaluation and tri-axial performance testing on fiber reinforced polymer connections and metal fasteners to promote hurricane damage mitigation

Damages during extreme wind events highlight the weaknesses of mechanical fasteners at the roof-to-wall connections in residential timber frame buildings. The allowable capacity of the metal fasteners is based on results of unidirectional component testing that do not simulate realistic tri-axial aerodynamic loading effects. The first objective of this research was to simulate hurricane effects and study hurricane-structure interaction at full-scale, facilitating better understanding of the combined impacts of wind, rain, and debris on inter-component connections at spatial and temporal scales. The second objective was to evaluate the performance of a non-intrusive roof-to-wall connection system using fiber reinforced polymer (FRP) materials and compare its load capacity to the capacity of an existing metal fastener under simulated aerodynamic loads. ^ The Wall of Wind (WoW) testing performed using FRP connections on a one-story gable-roof timber structure instrumented with a variety of sensors, was used to create a database on aerodynamic and aero-hydrodynamic loading on roof-to-wall connections tested under several parameters: angles of attack, wind-turbulence content, internal pressure conditions, with and without effects of rain. Based on the aerodynamic loading results obtained from WoW tests, sets of three force components (tri-axial mean loads) were combined into a series of resultant mean forces, which were used to test the FRP and metal connections in the structures laboratory up to failure. A new component testing system and test protocol were developed for testing fasteners under simulated triaxial loading as opposed to uni-axial loading. The tri-axial and uni-axial test results were compared for hurricane clips. Also, comparison was made between tri-axial load capacity of FRP and metal connections. ^ The research findings demonstrate that the FRP connection is a viable option for use in timber roof-to-wall connection system. Findings also confirm that current testing methods of mechanical fasteners tend to overestimate the actual load capacities of a connector. Additionally, the research also contributes to the development a new testing protocol for fasteners using tri-axial simultaneous loads based on the aerodynamic database obtained from the WoW testing. ^

Paleoenvironments and geochemical signals from the late Barremian to the middle Aptian in a Tethyan marginal basin, northeast Spain: Implications for carbon sequestration in restricted basins

The hallmark of oceanic anoxic event 1a (OAE1a) (early Aptian ~125 Ma) corresponds to worldwide deposition of black shales with total organic carbon (TOC) content > 2% and a δ13C positive excursion up to ~5‰. OAE1a has been related to large igneous province volcanism and dissociation of methane hydrates during the Lower Cretaceous. However, the occurrence of atypical, coeval and diachronous organic-rich deposits associated with OAE1a, which are also characterized by positive spikes of the δ 13C in epicontinental to restricted marine environments of the Tethys Ocean, indicates localized responses decoupled from complex global forcing factors. ^ The present research is a high-resolution, multiproxy approach to assess the paleoenvironmental conditions that led to enhanced carbon sequestration from the late Barremian to the middle Aptian in a restricted, Tethyan marginal basin prior to and during OAE1a. I studied the lower 240 m of the El Pui section, Organyà Basin, Spanish Pyrenees. The basin developed as the result of extensional tectonism linked to the opening of the Atlantic Ocean. At the field scale the section consists of a sequence of alternating beds of cm – m-scale, medium-gray to grayish-black limestones and marlstones with TOC up to ~4%. ^ The results indicate that the lowest 85 m of the section, from latest Barremian -earliest Aptian, characterize a deepening phase of the basin concomitant with sustained riverine flux and intensified primary productivity. These changes induced a shift in the sedimentation pattern and decreased the oxygen levels in the water column through organic matter respiration and limited ventilation of the basin. ^ The upper 155 m comprising the earliest – late-early Aptian document the occurrence of OAE1a and its associated geochemical signatures (TOC up to 3% and a positive shift in δ13C of ~5‰). However, a low enrichment of redox-sensitive trace elements indicates that the basin did not achieve anoxic conditions. The results also suggest that a shallower-phase of the basin, coeval with platform progradation, may have increased ventilation of the basin at the same time that heightened sedimentation rates and additional input of organic matter from terrestrial sources increased the burial and preservation rate of TOC in the sediment.^

Aerodynamic Load Characteristics Evaluation and Tri-Axial Performance Testing on Fiber Reinforced Polymer Connections and Metal Fasteners to Promote Hurricane Damage Mitigation

Damages during extreme wind events highlight the weaknesses of mechanical fasteners at the roof-to-wall connections in residential timber frame buildings. The allowable capacity of the metal fasteners is based on results of unidirectional component testing that do not simulate realistic tri-axial aerodynamic loading effects. The first objective of this research was to simulate hurricane effects and study hurricane-structure interaction at full-scale, facilitating better understanding of the combined impacts of wind, rain, and debris on inter-component connections at spatial and temporal scales. The second objective was to evaluate the performance of a non-intrusive roof-to-wall connection system using fiber reinforced polymer (FRP) materials and compare its load capacity to the capacity of an existing metal fastener under simulated aerodynamic loads. The Wall of Wind (WoW) testing performed using FRP connections on a one-story gable-roof timber structure instrumented with a variety of sensors, was used to create a database on aerodynamic and aero-hydrodynamic loading on roof-to-wall connections tested under several parameters: angles of attack, wind-turbulence content, internal pressure conditions, with and without effects of rain. Based on the aerodynamic loading results obtained from WoW tests, sets of three force components (tri-axial mean loads) were combined into a series of resultant mean forces, which were used to test the FRP and metal connections in the structures laboratory up to failure. A new component testing system and test protocol were developed for testing fasteners under simulated tri-axial loading as opposed to uni-axial loading. The tri-axial and uni-axial test results were compared for hurricane clips. Also, comparison was made between tri-axial load capacity of FRP and metal connections. The research findings demonstrate that the FRP connection is a viable option for use in timber roof-to-wall connection system. Findings also confirm that current testing methods of mechanical fasteners tend to overestimate the actual load capacities of a connector. Additionally, the research also contributes to the development a new testing protocol for fasteners using tri-axial simultaneous loads based on the aerodynamic database obtained from the WoW testing.

Tamed and Compatible Symplectic Forms on Four-Dimensional Almost Complex Lie Algebras

We are able to give a complete description of four-dimensional Lie algebras g which satisfy the tame-compatible question of Donaldson for all almost complex structures J on g are completely described. As a consequence, examples are given of (non-unimodular) four-dimensional Lie algebras with almost complex structures which are tamed but not compatible with symplectic forms.? Note that Donaldson asked his question for compact four-manifolds. In that context, the problem is still open, but it is believed that any tamed almost complex structure is in fact compatible with a symplectic form. In this presentation, I will define the basic objects involved and will give some insights on the proof. The key for the proof is translating the problem into a Linear Algebra setting. This is a joint work with Dr. Draghici.