The role of histidine residues in low-pH-mediated viral membrane fusion

A central event in the invasion of a host cell by an enveloped virus is the fusion of viral and cell membranes. For many viruses, membrane fusion is driven by specific viral surface proteins that undergo large-scale conformational rearrangements, triggered by exposure to low pH in the endosome upon internalization. Here, we present evidence suggesting that in both class I (helical hairpin proteins) and class 11 (beta-structure-rich proteins) pH-dependent fusion proteins the protonation of specific histidine residues triggers fusion via an analogous molecular mechanism. These histidines are located in the vicinity of positively charged residues in the prefusion conformation, and they subsequently form salt bridges with negatively charged residues in the postfusion conformation. The molecular surfaces involved in the corresponding structural rearrangements leading to fusion are highly conserved and thus might provide a suitable common target for the design of antivirals, which could be active against a diverse range of pathogenic viruses.

A study of field emission from semiconductors

In an attempt to clarify the behaviour of semi-conductor field emitters the properties of a narrow band gap material were investigated. A retarding potential analyser was built and tested using a tungsten emitter. The energy distribution of electrons emitted from single crystals of lead telluride (band gap 0.3 eV) and gallium phosphide (band gap 2.26 eV) were measured. The halfwidths of the distributions are discussed with respect to the relevant parameters for the materials. Methods of tip preparation had to be developed. The halfwidth of the energy distribution of electrons field emitted from carbon fibres was measured to be 0.21 ± 0.01 eV. A mechanism explaining the long lifetime of the emitters in poor vacuua is proposed.

An investigation of reading ability and visual function with eccentric visual field

This study investigated the detrimental effect of central field loss (CFL) on reading ability and general visual function. The aim was to improve the understanding of reading with eccentric retina in order that reading performances of individuals with CFL may be maximised. To improve visual ability of individuals with CFL, it is important to be able to accurately measure the outcome of any intervention. Various methods for determining visual function were therefore compared with perceived visual performance (as measured with a quality of life questionnaire) before and after surgical removal of choroidal new vessels (CNV) in macular disease patients. The results highlight the importance of low contrast measures (low contrast visual acuity and contrast sensitivity) when investigating perceived reading performance. Reading speed was found to be important for reflecting changes in general visual quality of life. Potential causes for reduced peripheral reading ability were investigated using both normally sighted and CFL subjects. For normally sighted subjects reading eccentrically with rapid serial visual presentation (RSVP) text, the inferior visual field was a better position (in terms of reading speed) for the presentation of the text. The size of the visual span was found to reduce with increasing eccentricity of fixation, providing a potential reason for reduced peripheral reading performances. The investigation of the ability to use context when reading with peripheral retina resulted in conflicting results. Studies in this thesis found both a reduction and no reduction in the ability of the peripheral retina to utilise context compared to the fovea. Individuals with long-term CFL showed no improvement in peripheral reading ability over that found for normally sighted subjects reading at the same eccentricity.

Non-standard techniques for the investigation of the visual field

The study investigated the potential applications and the limitations of non-standard techniques of visual field investigation utilizing automated perimetry. Normal subjects exhibited a greater sensitivity to kinetic stimuli than to static stimuli of identical size. The magnitude of physiological SKD was found to be largely independent of age, stimulus size, meridian and eccentricity. The absence of a dependency on stimulus size indicated that successive lateral spatial summation could not totally account for the underlying mechanism of physiological SKD. The visual field indices MD and LV exhibited a progressive deterioration during the time course of a conventional central visual field examination both for normal subjects and for ocular hypertensive patients. The fatigue effect was more pronounced in the latter stages and for the second eye tested. The confidence limits for the definition of abnormality should reflect the greater effect of fatigue on the second eye. A 330 cdm-2 yellow background was employed for blue-on-yellow perimetry. Instrument measurement range was preserved by positioning a concave mirror behind the stimulus bulb to increase the light output by 60% . The mean magnitude of SWS pathway isolation was approximately 1.4 log units relative to a 460nm stimulus filter. The absorption spectra of the ocular media exhibited an exponential increase with increase in age, whilst that of the macular pigment showed no systematic trend. The magnitude of ocular media absorption was demonstrated to reduce with increase in wavelength. Ocular media absorption was significantly greater in diabetic patients than in normal subjects. Five diabetic patients with either normal or borderline achromatic sensitivity exhibited an abnormal blue-on-yellow sensitivity; two of these patients showed no signs of retinopathy. A greater vulnerability of the SWS pathway to the diabetic disease process was hypothesized.

Full-field electronic dispersion compensation of a 10 Gbit/s OOK signal over 4 x 124 km field-installed single-mode fibre

We experimentally demonstrate the use of full-field electronic dispersion compensation (EDC) to achieve a bit error rate of 5 x 10(-5) at 22.3 dB optical signal-to-noise ratio for single-channel 10 Gbit/s on-off keyed signal after transmission over 496 km field-installed single-mode fibre with an amplifier spacing of 124 km. This performance is achieved by designing the EDC so as to avoid electronic amplification of the noise content of the signal during full-field reconstruction. We also investigate the tolerance of the system to key signal processing parameters, and numerically demonstrate that single-channel 2160 km single mode fibre transmission without in-line optical dispersion compensation can be achieved using this technique with 80 km amplifier spacing and optimized system parameters.

The benefit of combining standard automated perimetry and multifocal visual evoked potential hemifield intersector analysis in suspecious glaucomatous visual field defects

Several analysis protocols have been tested to identify early visual field losses in glaucoma patients using the mfVEP technique, some were successful in detection of field defects, which were comparable to the standard SAP visual field assessment, and others were not very informative and needed more adjustment and research work. In this study we implemented a novel analysis approach and evaluated its validity and whether it could be used effectively for early detection of visual field defects in glaucoma. The purpose of this study is to examine the benefit of adding mfVEP hemifield Intersector analysis protocol to the standard HFA test when there is suspicious glaucomatous visual field loss. 3 groups were tested in this study; normal controls (38 eyes), glaucoma patients (36 eyes) and glaucoma suspect patients (38 eyes). All subjects had a two standard Humphrey visual field HFA test 24-2, optical coherence tomography of the optic nerve head, and a single mfVEP test undertaken in one session. Analysis of the mfVEP results was done using the new analysis protocol; the Hemifield Sector Analysis HSA protocol. The retinal nerve fibre (RNFL) thickness was recorded to identify subjects with suspicious RNFL loss. The hemifield Intersector analysis of mfVEP results showed that signal to noise ratio (SNR) difference between superior and inferior hemifields was statistically significant between the 3 groups (ANOVA p<0.001 with a 95% CI). The difference between superior and inferior hemispheres in all subjects were all statistically significant in the glaucoma patient group 11/11 sectors (t-test p<0.001), partially significant 5/11 in glaucoma suspect group (t-test p<0.01) and no statistical difference between most sectors in normal group (only 1/11 was significant) (t-test p<0.9). Sensitivity and specificity of the HSA protocol in detecting glaucoma was 97% and 86% respectively, while for glaucoma suspect were 89% and 79%. The use of SAP and mfVEP results in subjects with suspicious glaucomatous visual field defects, identified by low RNFL thickness, is beneficial in confirming early visual field defects. The new HSA protocol used in the mfVEP testing can be used to detect glaucomatous visual field defects in both glaucoma and glaucoma suspect patient. Using this protocol in addition to SAP analysis can provide information about focal visual field differences across the horizontal midline, and confirm suspicious field defects. Sensitivity and specificity of the mfVEP test showed very promising results and correlated with other anatomical changes in glaucoma field loss. The Intersector analysis protocol can detect early field changes not detected by standard HFA test.

Branching Populations of Cells Bearing a Continuous Label

2000 Mathematics Subject Classification: 60J80.

The gauge invariant currents of the Maxwellian field

We show that a conserved current for the Maxwellian field, which is invariant under the gauge group of that field, is the sum of two currents Ф+T, where Ф corresponds to a Poincare symmetry of the field, and T is a topological form that is conserved under every dynamics.

Using overlay test to evaluate fracture properties of field-aged asphalt concrete

Field material testing provides firsthand information on pavement conditions which are most helpful in evaluating performance and identifying preventive maintenance or overlay strategies. High variability of field asphalt concrete due to construction raises the demand for accuracy of the test. Accordingly, the objective of this study is to propose a reliable and repeatable methodology to evaluate the fracture properties of field-aged asphalt concrete using the overlay test (OT). The OT is selected because of its efficiency and feasibility for asphalt field cores with diverse dimensions. The fracture properties refer to the Paris’ law parameters based on the pseudo J-integral (A and n) because of the sound physical significance of the pseudo J-integral with respect to characterizing the cracking process. In order to determine A and n, a two-step OT protocol is designed to characterize the undamaged and damaged behaviors of asphalt field cores. To ensure the accuracy of determined undamaged and fracture properties, a new analysis method is then developed for data processing, which combines the finite element simulations and mechanical analysis of viscoelastic force equilibrium and evolution of pseudo displacement work in the OT specimen. Finally, theoretical equations are derived to calculate A and n directly from the OT test data. The accuracy of the determined fracture properties is verified. The proposed methodology is applied to a total of 27 asphalt field cores obtained from a field project in Texas, including the control Hot Mix Asphalt (HMA) and two types of warm mix asphalt (WMA). The results demonstrate a high linear correlation between n and −log A for all the tested field cores. Investigations of the effect of field aging on the fracture properties confirm that n is a good indicator to quantify the cracking resistance of asphalt concrete. It is also indicated that summer climatic condition clearly accelerates the rate of aging. The impact of the WMA technologies on fracture properties of asphalt concrete is visualized by comparing the n-values. It shows that the Evotherm WMA technology slightly improves the cracking resistance, while the foaming WMA technology provides the comparable fracture properties with the HMA. After 15 months aging in the field, the cracking resistance does not exhibit significant difference between HMA and WMAs, which is confirmed by the observations of field distresses.

Annotated record of the detailed examination of Mn deposits from R/V Moana Wave Cruise Mn-74-01 stations

Cruise MN-74-01 of the R/V Moana Wave was the first part of the field work of the NSF-IDOE Inter-University Ferromanganese Research Program in 1974. This program was designed to investigate the origin, growth, and distribution of copper/nickel-rich manganese nodules in the Pacific Ocean. The field effort was designed to satisfy sample requirements of the 15 principal investigators, while increasing general knowledge of the copper/nickel-rich nodule deposits of the equatorial Pacific. This report is the first of a series of cruise reports designed to assist sample requests for documented nodules, sediment, and water samples so the laboratory results can be realistically compared and related to the environment of nodule growth.

Magnetostratigraphy of ODP Leg 178 holes

We present revised magnetostratigraphic interpretations for Ocean Drilling Program Sites 1095, 1096, and 1101, cored in sediment drifts located off the Pacific margin of the Antarctic Peninsula. The revised interpretations incorporate a variety of observations and results obtained since the end of Leg 178, of which the most significant are new paleomagnetic measurements from U-channel samples, composite depth scales that allow stratigraphic correlation between multiple holes cored at a site, and revised biostratigraphic interpretations. The U-channel data, which include more than 102,000 paleomagnetic observations from more than 13,400 intervals along U-channel samples, are included as electronic files. The magnetostratigraphic records at all three sites are consistent with sedimentation being continuous over the intervals cored, although the data resolution does not preclude short hiatuses less than a few hundred thousand years in duration. The magnetostratigraphic records start at the termination of Subchron C4Ar.2n (9.580 Ma) at ~515 meters composite depth (mcd) for Site 1095, at the onset of Subchron C3n.2n (4.620 Ma) at ~489.68 mcd for Site 1096, and at the onset of Subchron C2An.1n (3.040 Ma) at 209.38 meters below seafloor for Site 1101. All three sites provide paleomagnetic records that extend upward through the Brunhes Chron.

Calcium Channel Blocker Use and Risk of Prostate Cancer by TMPRSS2:ERG Gene Fusion Status

BACKGROUND: Calcium channel blockers (CCBs) may affect prostate cancer (PCa) growth by various mechanisms including those related to androgens. The fusion of the androgen-regulated gene TMPRSS2 and the oncogene ERG (TMPRSS2:ERG or T2E) is common in PCa, and prostate tumors that harbor the gene fusion are believed to represent a distinct disease subtype. We studied the association of CCB use with the risk of PCa, and molecular subtypes of PCa defined by T2E status.

METHODS: Participants were residents of King County, Washington, recruited for population-based case-control studies (1993-1996 or 2002-2005). Tumor T2E status was determined by fluorescence in situ hybridization using tumor tissue specimens from radical prostatectomy. Detailed information on use of CCBs and other variables was obtained through in-person interviews. Binomial and polytomous logistic regression were used to generate odds ratios (ORs) and 95% confidence intervals (CIs).

RESULTS: The study included 1,747 PCa patients and 1,635 age-matched controls. A subset of 563 patients treated with radical prostatectomy had T2E status determined, of which 295 were T2E positive (52%). Use of CCBs (ever vs. never) was not associated with overall PCa risk. However, among European-American men, users had a reduced risk of higher-grade PCa (Gleason scores ≥7: adjusted OR = 0.64; 95% CI: 0.44-0.95). Further, use of CCBs was associated with a reduced risk of T2E positive PCa (adjusted OR = 0.38; 95% CI: 0.19-0.78), but was not associated with T2E negative PCa.

CONCLUSIONS: This study found suggestive evidence that use of CCBs is associated with reduced relative risks for higher Gleason score and T2E positive PCa. Future studies of PCa etiology should consider etiologic heterogeneity as PCa subtypes may develop through different causal pathways. 

Studies of turbulent flows in continuous casting of steel with and without magnetic field

This thesis develops and tests various transient and steady-state computational models such as direct numerical simulation (DNS), large eddy simulation (LES), filtered unsteady Reynolds-averaged Navier-Stokes (URANS) and steady Reynolds-averaged Navier-Stokes (RANS) with and without magnetic field to investigate turbulent flows in canonical as well as in the nozzle and mold geometries of the continuous casting process. The direct numerical simulations are first performed in channel, square and 2:1 aspect rectangular ducts to investigate the effect of magnetic field on turbulent flows. The rectangular duct is a more practical geometry for continuous casting nozzle and mold and has the option of applying magnetic field either perpendicular to broader side or shorter side. This work forms the part of a graphic processing unit (GPU) based CFD code (CU-FLOW) development for magnetohydrodynamic (MHD) turbulent flows. The DNS results revealed interesting effects of the magnetic field and its orientation on primary, secondary flows (instantaneous and mean), Reynolds stresses, turbulent kinetic energy (TKE) budgets, momentum budgets and frictional losses, besides providing DNS database for two-wall bounded square and rectangular duct MHD turbulent flows. Further, the low- and high-Reynolds number RANS models (k-ε and Reynolds stress models) are developed and tested with DNS databases for channel and square duct flows with and without magnetic field. The MHD sink terms in k- and ε-equations are implemented as proposed by Kenjereš and Hanjalić using a user defined function (UDF) in FLUENT. This work revealed varying accuracies of different RANS models at different levels. This work is useful for industry to understand the accuracies of these models, including continuous casting. After realizing the accuracy and computational cost of RANS models, the steady-state k-ε model is then combined with the particle image velocimetry (PIV) and impeller probe velocity measurements in a 1/3rd scale water model to study the flow quality coming out of the well- and mountain-bottom nozzles and the effect of stopper-rod misalignment on fluid flow. The mountain-bottom nozzle was found more prone to the longtime asymmetries and higher surface velocities. The left misalignment of stopper gave higher surface velocity on the right leading to significantly large number of vortices forming behind the nozzle on the left. Later, the transient and steady-state models such as LES, filtered URANS and steady RANS models are combined with ultrasonic Doppler velocimetry (UDV) measurements in a GaInSn model of typical continuous casting process. LES-CU-LOW is the fastest and the most accurate model owing to much finer mesh and a smaller timestep. This work provided a good understanding on the performance of these models. The behavior of instantaneous flows, Reynolds stresses and proper orthogonal decomposition (POD) analysis quantified the nozzle bottom swirl and its importance on the turbulent flow in the mold. Afterwards, the aforementioned work in GaInSn model is extended with electromagnetic braking (EMBr) to help optimize a ruler-type brake and its location for the continuous casting process. The magnetic field suppressed turbulence and promoted vortical structures with their axis aligned with the magnetic field suggesting tendency towards 2-d turbulence. The stronger magnetic field at the nozzle well and around the jet region created large scale and lower frequency flow behavior by suppressing nozzle bottom swirl and its front-back alternation. Based on this work, it is advised to avoid stronger magnetic field around jet and nozzle bottom to get more stable and less defect prone flow.

STORM - a novel information fusion and cluster interpretation technique

Analysis of data without labels is commonly subject to scrutiny by unsupervised machine learning techniques. Such techniques provide more meaningful representations, useful for better understanding of a problem at hand, than by looking only at the data itself. Although abundant expert knowledge exists in many areas where unlabelled data is examined, such knowledge is rarely incorporated into automatic analysis. Incorporation of expert knowledge is frequently a matter of combining multiple data sources from disparate hypothetical spaces. In cases where such spaces belong to different data types, this task becomes even more challenging. In this paper we present a novel immune-inspired method that enables the fusion of such disparate types of data for a specific set of problems. We show that our method provides a better visual understanding of one hypothetical space with the help of data from another hypothetical space. We believe that our model has implications for the field of exploratory data analysis and knowledge discovery.

Design and characterization of automated agricultural vehicle systems

Nowadays, technological advancements have brought industry and research towards the automation of various processes. Automation brings a reduction in costs and an improvement in product quality. For this reason, companies are pushing research to investigate new technologies. The agriculture industry has always looked towards automating various processes, from product processing to storage. In the last years, the automation of harvest and cultivation phases also has become attractive, pushed by the advancement of autonomous driving. Nevertheless, ADAS systems are not enough. Merging different technologies will be the solution to obtain total automation of agriculture processes. For example, sensors that estimate products' physical and chemical properties can be used to evaluate the maturation level of fruit. Therefore, the fusion of these technologies has a key role in industrial process automation. In this dissertation, ADAS systems and sensors for precision agriculture will be both treated. Several measurement procedures for characterizing commercial 3D LiDARs will be proposed and tested to cope with the growing need for comparison tools. Axial errors and transversal errors have been investigated. Moreover, a measurement method and setup for evaluating the fog effect on 3D LiDARs will be proposed. Each presented measurement procedure has been tested. The obtained results highlight the versatility and the goodness of the proposed approaches. Regarding the precision agriculture sensors, a measurement approach for the Moisture Content and density estimation of crop directly on the field is presented. The approach regards the employment of a Near Infrared spectrometer jointly with Partial Least Square statistical analysis. The approach and the model will be described together with a first laboratory prototype used to evaluate the NIRS approach. Finally, a prototype for on the field analysis is realized and tested. The test results are promising, evidencing that the proposed approach is suitable for Moisture Content and density estimation.