Design, expression, and processing of epitomized hepatitis C virus-encoded CTL epitopes

Hepatitis C virus (HCV) vaccine efficacy may crucially depend on immunogen length and coverage of viral sequence diversity. However, covering a considerable proportion of the circulating viral sequence variants would likely require long immunogens, which for the conserved portions of the viral genome, would contain unnecessarily redundant sequence information. In this study, we present the design and in vitro performance analysis of a novel "epitome" approach that compresses frequent immune targets of the cellular immune response against HCV into a shorter immunogen sequence. Compression of immunological information is achieved by partial overlapping shared sequence motifs between individual epitopes. At the same time, sequence diversity coverage is provided by taking advantage of emerging cross-reactivity patterns among epitope variants so that epitope variants associated with the broadest variant cross-recognition are preferentially included. The processing and presentation analysis of specific epitopes included in such a compressed, in vitro-expressed HCV epitome indicated effective processing of a majority of tested epitopes, although re-presentation of some epitopes may require refined sequence design. Together, the present study establishes the epitome approach as a potential powerful tool for vaccine immunogen design, especially suitable for the induction of cellular immune responses against highly variable pathogens.

COMPRESSION BEHAVIOR AT HIGH STRAIN RATE FOR AN ULTRA HIGH PERFORMANCE CONCRETE

The need for a stronger and more durable building material is becoming more important as the structural engineering field expands and challenges the behavioral limits of current materials. One of the demands for stronger material is rooted in the effects that dynamic loading has on a structure. High strain rates on the order of 101 s-1 to 103 s-1, though a small part of the overall types of loading that occur anywhere between 10-8 s-1 to 104 s-1 and at any point in a structures life, have very important effects when considering dynamic loading on a structure. High strain rates such as these can cause the material and structure to behave differently than at slower strain rates, which necessitates the need for the testing of materials under such loading to understand its behavior. Ultra high performance concrete (UHPC), a relatively new material in the U.S. construction industry, exhibits many enhanced strength and durability properties compared to the standard normal strength concrete. However, the use of this material for high strain rate applications requires an understanding of UHPC’s dynamic properties under corresponding loads. One such dynamic property is the increase in compressive strength under high strain rate load conditions, quantified as the dynamic increase factor (DIF). This factor allows a designer to relate the dynamic compressive strength back to the static compressive strength, which generally is a well-established property. Previous research establishes the relationships for the concept of DIF in design. The generally accepted methodology for obtaining high strain rates to study the enhanced behavior of compressive material strength is the split Hopkinson pressure bar (SHPB). In this research, 83 Cor-Tuf UHPC specimens were tested in dynamic compression using a SHPB at Michigan Technological University. The specimens were separated into two categories: ambient cured and thermally treated, with aspect ratios of 0.5:1, 1:1, and 2:1 within each category. There was statistically no significant difference in mean DIF for the aspect ratios and cure regimes that were considered in this study. DIF’s ranged from 1.85 to 2.09. Failure modes were observed to be mostly Type 2, Type 4, or combinations thereof for all specimen aspect ratios when classified according to ASTM C39 fracture pattern guidelines. The Comite Euro-International du Beton (CEB) model for DIF versus strain rate does not accurately predict the DIF for UHPC data gathered in this study. Additionally, a measurement system analysis was conducted to observe variance within the measurement system and a general linear model analysis was performed to examine the interaction and main effects that aspect ratio, cannon pressure, and cure method have on the maximum dynamic stress.

Chondrocyte mechanotransduction: effects of compression on deformation of intracellular organelles and relevance to cellular biosynthesis

OBJECTIVE: The effects of mechanical deformation of intact cartilage tissue on chondrocyte biosynthesis in situ have been well documented, but the mechanotransduction pathways that regulate such phenomena have not been elucidated completely. The goal of this study was to examine the effects of tissue deformation on the morphology of a range of intracellular organelles which play a major role in cell biosynthesis and metabolism. DESIGN: Using chemical fixation, high pressure freezing, and electron microscopy, we imaged chondrocytes within mechanically compressed cartilage explants at high magnification and quantitatively and qualitatively assessed changes in organelle volume and shape caused by graded levels of loading. RESULTS: Compression of the tissue caused a concomitant reduction in the volume of the extracellular matrix (ECM), chondrocyte, nucleus, rough endoplasmic reticulum, and mitochondria. Interestingly, however, the Golgi apparatus was able to resist loss of intraorganelle water and retain a portion of its volume relative to the remainder of the cell. These combined results suggest that a balance between intracellular mechanical and osmotic gradients govern the changes in shape and volume of the organelles as the tissue is compressed. CONCLUSIONS: Our results lead to the interpretive hypothesis that organelle volume changes appear to be driven mainly by osmotic interactions while shape changes are mediated by structural factors, such as cytoskeletal interactions that may be linked to extracellular matrix deformations. The observed volume and shape changes of the chondrocyte organelles and the differential behavior between organelles during tissue compression provide evidence for an important mechanotransduction pathway linking translational and post-translational events (e.g., elongation and sulfation of glycosaminoglycans (GAGs) in the Golgi) to cell deformation.

Ultrastructural quantification of cell death after injurious compression of bovine calf articular cartilage

OBJECTIVE: It has been suggested that chondrocyte death by apoptosis may play a role in the pathogenesis of cartilage destruction in osteoarthritis, but the results of in-vivo and in-vitro investigations have been conflicting. To investigate further the cell death in our in-vitro model for traumatic joint injury, we performed a quantitative analysis by electron microscopy (EM) of cell morphology after injurious compression. For comparison, the TUNEL assay was also performed. DESIGN: Articular cartilage explant disks were harvested from newborn calf femoropatellar groove. The disks were subjected to injurious compression (50% strain at a strain rate of 100%/s), incubated for 3 days, and then fixed for quantitative morphological analysis. RESULTS: By TUNEL, the cell apoptosis rate increased from 7 +/- 2% in unloaded controls to 33 +/- 6% after injury (P=0.01; N=8 animals). By EM, the apoptosis rate increased from 5 +/- 1% in unloaded controls to 62 +/- 10% in injured cartilage (P=0.02, N=5 animals). Analysis by EM also identified that of the dead cells in injured disks, 97% were apoptotic by morphology. CONCLUSIONS: These results confirm a significant increase in cell death after injurious compression and suggest that most cell death observed here was by an apoptotic process.

Magnetic resonance imaging findings in dogs with traumatic intervertebral disk extrusion with or without spinal cord compression: 31 cases (2006-2010)

OBJECTIVE To determine the prevalence of spinal cord compression subsequent to traumatic intervertebral disk (IVD) extrusion in dogs, characterize factors associated with spinal cord compression in dogs with traumatic IVD extrusion, and evaluate the outcomes of dogs with traumatic IVD extrusion with or without spinal cord compression. DESIGN Retrospective case series. ANIMALS 31 dogs with traumatic IVD extrusion. PROCEDURES Medical records and MRI findings were reviewed for dogs with a history of trauma to the spinal region. Dogs were included in the study if a neurologic examination and MRI were performed and there was a description of clinical signs and MRI findings including identification of the spinal cord segment affected by IVD extrusion, presence or absence of spinal cord compression, treatment, and outcome available for review. RESULTS 31 of 50 (62%) dogs had traumatic IVD extrusions without any other detectable vertebral lesions; 9 (29%) and 22 (71%) of those 31 dogs did and did not have spinal cord compression, respectively. Dogs with spinal cord compression were significantly older and more likely to be chondrodystrophic and have evidence of generalized IVD degeneration, compared with dogs without spinal cord compression. The outcome for dogs with spinal cord compression was similar to that for dogs without spinal cord compression. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated traumatic IVD extrusion was common and should be considered as a differential diagnosis for dogs with trauma to the spinal region, and spinal cord compression should be evaluated, especially in older or chondrodystrophic dogs.

Influence of Loudness Compression on Hearing with Bone Anchored Hearing Implants

Bone Anchored Hearing Implants (BAHI) are routinely used in patients with conductive or mixed hearing loss, e.g. if conventional air conduction hearing aids cannot be used. New sound processors and new fitting software now allow the adjustment of parameters such as loudness compression ratios or maximum power output separately. Today it is unclear, how the choice of these parameters influences aided speech understanding in BAHI users. In this prospective experimental study, the effect of varying the compression ratio and lowering the maximum power output in a BAHI were investigated. Twelve experienced adult subjects with a mixed hearing loss participated in this study. Four different compression ratios (1.0; 1.3; 1.6; 2.0) were tested along with two different maximum power output settings, resulting in a total of eight different programs. Each participant tested each program during two weeks. A blinded Latin square design was used to minimize bias. For each of the eight programs, speech understanding in quiet and in noise was assessed. For speech in quiet, the Freiburg number test and the Freiburg monosyllabic word test at 50, 65, and 80 dB SPL were used. For speech in noise, the Oldenburg sentence test was administered. Speech understanding in quiet and in noise was improved significantly in the aided condition in any program, when compared to the unaided condition. However, no significant differences were found between any of the eight programs. In contrast, on a subjective level there was a significant preference for medium compression ratios of 1.3 to 1.6 and higher maximum power output.

Real-life results of balloon kyphoplasty for vertebral compression fractures from the SWISSspine registry

BACKGROUND CONTEXT The Swiss Federal Office of Public Health mandated a nationwide health technology assessment-registry for balloon kyphoplasty (BKP) for decision making on reimbursement of these interventions. The early results of the registry led to a permanent coverage of BKP by basic health insurance. The documentation was continued for further evidence generation. PURPOSE This analysis reports on the 1 year results of patients after BKP treatment. STUDY DESIGN Prospective multicenter observational case series. PATIENT SAMPLE The data on 625 cases with 819 treated vertebrae were documented from March 2005 to May 2012. OUTCOME MEASURES Surgeon-administered outcome instruments were primary intervention form for BKP and the follow-up form; patient self-reported measures were EuroQol-5D questionnaire, North American Spine Society outcome instrument /Core Outcome Measures Index (including visual analog scale), and a comorbidity questionnaire. Outcome measures were back pain, medication, quality of life (QoL), cement extrusions, and new fractures within the first postoperative year. METHODS Data were recorded preoperatively and at 3 to 6-month and 1-year follow-ups. Wilcoxon signed-rank test was used for comparison of pre- with postoperative measurements. Multivariate logistic regression was used to identify factors with a significant influence on the outcome. RESULTS Seventy percent of patients were women with mean age of 71 years (range, 18-91 years); mean age of men was 65 years (range, 15-93 years). Significant and clinically relevant reduction of back pain, improvement of QoL, and reduction of pain killer consumption was seen within the first postoperative year. Preoperative back pain decreased from 69.3 to 29.0 at 3 to 6-month and remained unchanged at 1-year follow-ups. Consequently, QoL improved from 0.23 to 0.71 and 0.75 at the same follow-up intervals. The overall vertebra-based cement extrusion rates with and without extrusions into intervertebral discs were 22.1% and 15.3%, respectively. Symptomatic cement extrusions with radiculopathy were five (0.8%). A new vertebral fracture within a year from the BKP surgery was observed in 18.4% of the patients. CONCLUSIONS The results of the largest observational study for BKP so far are consistent with published randomized trials and systematic reviews. In this routine health care setting, BKP is safe and effective in reducing pain, improving QoL, and lowering pain_killer consumption and has an acceptable rate of cement extrusions. Postoperative outcome results show clear and significant clinical improvement at early follow-up that remain stable during the first postoperative year.

The influence of different osteosynthesis configurations with locking compression plates (LCP) on stability and fracture healing after an oblique 45° angle osteotomy

Background Locking compression plates are used in various configurations with lack of detailed information on consequent bone healing. Study design In this in vivo study in sheep 5 different applications of locking compression plate (LCP) were tested using a 45° oblique osteotomy simulating simple fracture pattern. 60 Swiss Alpine sheep where assigned to 5 different groups with 12 sheep each (Group 1: interfragmentary lag screw and an LCP fixed with standard cortex screws as neutralisation plate; Group 2: interfragmentary lag screw and LCP with locking head screws; Group 3: compression plate technique (hybrid construct); Group 4: internal fixator without fracture gap; Group 5: internal fixator with 3 mm gap at the osteotomy site). One half of each group (6 sheep) was monitored for 6 weeks, and the other half (6 sheep) where followed for 12 weeks. Methods X-rays at 3, 6, 9 and 12 weeks were performed to monitor the healing process. After sacrifice operated tibiae were tested biomechanically for nondestructive torsion and compared to the tibia of the healthy opposite side. After testing specimens were processed for microradiography, histology, histomorphometry and assessment of calcium deposition by fluorescence microscopy. Results In all groups bone healing occurred without complications. Stiffness in biomechanical testing showed a tendency for higher values in G2 but results were not statistically significant. Values for G5 were significantly lower after 6 weeks, but after 12 weeks values had improved to comparable results. For all groups, except G3, stiffness values improved between 6 and 12 weeks. Histomorphometrical data demonstrate endosteal callus to be more marked in G2 at 6 weeks. Discussion and conclusion All five configurations resulted in undisturbed bone healing and are considered safe for clinical application.

Bio-inspired FPGA Architecture for Self-Calibration of an Image Compression Core based on Wavelet Transforms in Embedded Systems

A generic bio-inspired adaptive architecture for image compression suitable to be implemented in embedded systems is presented. The architecture allows the system to be tuned during its calibration phase. An evolutionary algorithm is responsible of making the system evolve towards the required performance. A prototype has been implemented in a Xilinx Virtex-5 FPGA featuring an adaptive wavelet transform core directed at improving image compression for specific types of images. An Evolution Strategy has been chosen as the search algorithm and its typical genetic operators adapted to allow for a hardware friendly implementation. HW/SW partitioning issues are also considered after a high level description of the algorithm is profiled which validates the proposed resource allocation in the device fabric. To check the robustness of the system and its adaptation capabilities, different types of images have been selected as validation patterns. A direct application of such a system is its deployment in an unknown environment during design time, letting the calibration phase adjust the system parameters so that it performs efcient image compression. Also, this prototype implementation may serve as an accelerator for the automatic design of evolved transform coefficients which are later on synthesized and implemented in a non-adaptive system in the final implementation device, whether it is a HW or SW based computing device. The architecture has been built in a modular way so that it can be easily extended to adapt other types of image processing cores. Details on this pluggable component point of view are also given in the paper.

The design of an agent to bend DNA.

An artificial DNA bending agent has been designed to assess helix flexibility over regions as small as a protein binding site. Bending was obtained by linking a pair of 15-base-long triple helix forming oligonucleotides (TFOs) by an adjustable polymeric linker. By design, DNA bending was introduced into the double helix within a 10-bp spacer region positioned between the two sites of 15-base triple helix formation. The existence of this bend has been confirmed by circular permutation and phase-sensitive electrophoresis, and the directionality of the bend has been determined as a compression of the minor helix groove. The magnitude of the resulting duplex bend was found to be dependent on the length of the polymeric linker in a fashion consistent with a simple geometric model. Data suggested that a 50-70 degrees bend was achieved by binding of the TFO chimera with the shortest linker span (18 rotatable bonds). Equilibrium analysis showed that, relative to a chimera which did not bend the duplex, the stability of the triple helix possessing a 50-70 degrees bend was reduced by less than 1 kcal/mol of that of the unbent complex. Based upon this similarity, it is proposed that duplex DNA may be much more flexible with respect to minor groove compression than previously assumed. It is shown that this unusual flexibility is consistent with recent quantitation of protein-induced minor groove bending.

Geometric 3D point cloud compression

The use of 3D data in mobile robotics applications provides valuable information about the robot’s environment but usually the huge amount of 3D information is unmanageable by the robot storage and computing capabilities. A data compression is necessary to store and manage this information but preserving as much information as possible. In this paper, we propose a 3D lossy compression system based on plane extraction which represent the points of each scene plane as a Delaunay triangulation and a set of points/area information. The compression system can be customized to achieve different data compression or accuracy ratios. It also supports a color segmentation stage to preserve original scene color information and provides a realistic scene reconstruction. The design of the method provides a fast scene reconstruction useful for further visualization or processing tasks.

Parametric Optimization of Inductively Driven Liner Compression Driver System

Thesis (Master's)--University of Washington, 2016-06

Data transmission by pulse compression

Pulse compression techniques originated in radar.The present work is concerned with the utilization of these techniques in general, and the linear FM (LFM) technique in particular, for comnunications. It introduces these techniques from an optimum communications viewpoint and outlines their capabilities.It also considers the candidacy of the class of LFM signals for digital data transmission and the LFM spectrum. Work related to the utilization of LFM signals for digital data transmission has been mostly experimental and mainly concerned with employing two rectangular LFM pulses (or chirps) with reversed slopes to convey the bits 1 and 0 in an incoherent node.No systematic theory for LFM signal design and system performance has been available. Accordingly, the present work establishes such a theory taking into account coherent and noncoherent single-link and multiplex signalling modes. Some new results concerning the slope-reversal chirp pair are obtained. The LFM technique combines the typical capabilities of pulse compression with a relative ease of implementation. However, these merits are often hampered by the difficulty of handling the LFM spectrum which cannot generally be expressed closed-form. The common practice is to obtain a plot of this spectrum with a digital computer for every single set of LFM pulse parameters.Moreover, reported work has been Justly confined to the spectrum of an ideally rectangular chirp pulse with no rise or fall times.Accordingly, the present work comprises a systerratic study of the LFM spectrum which takes the rise and fall time of the chirp pulse into account and can accommodate any LFM pulse with any parameters.It· formulates rather simple and accurate prediction criteria concerning the behaviour of this spectrum in the different frequency regions. These criteria would facilitate the handling of the LFM technique in theory and practice.

The application of knowledge based expert systems to mechanical engineering design

Investigation of the different approaches used by Expert Systems researchers to solve problems in the domain of Mechanical Design and Expert Systems was carried out. The techniques used for conventional formal logic programming were compared with those used when applying Expert Systems concepts. A literature survey of design processes was also conducted with a view to adopting a suitable model of the design process. A model, comprising a variation on two established ones, was developed and applied to a problem within what are described as class 3 design tasks. The research explored the application of these concepts to Mechanical Engineering Design problems and their implementation on a microcomputer using an Expert System building tool. It was necessary to explore the use of Expert Systems in this manner so as to bridge the gap between their use as a control structure and for detailed analytical design. The former application is well researched into and this thesis discusses the latter. Some Expert System building tools available to the author at the beginning of his work were evaluated specifically for their suitability for Mechanical Engineering design problems. Microsynics was found to be the most suitable on which to implement a design problem because of its simple but powerful Semantic Net Knowledge Representation structure and the ability to use other types of representation schemes. Two major implementations were carried out. The first involved a design program for a Helical compression spring and the second a gearpair system design. Two concepts were proposed in the thesis for the modelling and implementation of design systems involving many equations. The method proposed enables equation manipulation and analysis using a combination of frames, semantic nets and production rules. The use of semantic nets for purposes other than for psychology and natural language interpretation, is quite new and represents one of the major contributions to knowledge by the author. The development of a purpose built shell program for this type of design problems was recommended as an extension of the research. Microsynics may usefully be used as a platform for this development.

New fiber laser architecture with transform-limited nonlinear spectral compression

We numerically demonstrate a new fiber laser architecture supporting spectral compression of negatively chirped pulses in passive normally dispersive fiber. Such a process is beneficial for improving the energy efficiency of the cavity as it prevents narrow spectral filtering from being highly dissipative. The proposed laser design provides an elegant way of generating transform-limited picosecond pulses. © 2012 IEEE.