Cost Function Statistical Analysis in Double Random Phase Encoding

We examine the Amplitude-Encoding (AE) case of the Double Random Phase Encoding (DRPE) technique. A cost function is the function we use to evaluate an attempted decryption with our original input image. For systems with a relatively small key-space we can evaluate the output of every key to get an overall idea of the spread of these keys in key-space. However for larger systems this is not practical. Based on a normalised root mean squared cost function we wish to identify expressions for the mean and variance of the output (decrypted) intensity for a sample set of keys in a large system (256x256 pixels)

Multispectral lensless digital holographic microscope: imaging MCF-7 and MDA-MB-231 cancer cell cultures

Digital holography is the process where an object’s phase and amplitude information is retrieved from intensity images obtained using a digital camera (e.g. CCD or CMOS sensor). In-line digital holographic techniques offer full use of the recording device’s sampling bandwidth, unlike off-axis holography where object information is not modulated onto carrier fringes. Reconstructed images are obscured by the linear superposition of the unwanted, out of focus, twin images. In addition to this, speckle noise degrades overall quality of the reconstructed images. The speckle effect is a phenomenon of laser sources used in digital holographic systems. Minimizing the effects due to speckle noise, removal of the twin image and using the full sampling bandwidth of the capture device aids overall reconstructed image quality. Such improvements applied to digital holography can benefit applications such as holographic microscopy where the reconstructed images are obscured with twin image information. Overcoming such problems allows greater flexibility in current image processing techniques, which can be applied to segmenting biological cells (e.g. MCF-7 and MDA-MB- 231) to determine their overall cell density and viability. This could potentially be used to distinguish between apoptotic and necrotic cells in large scale mammalian cell processes, currently the system of choice, within the biopharmaceutical industry

Resolution limits in practical digital holographic systems

We examine some fundamental theoretical limits on the ability of practical digital holography DH systems to resolve detail in an image. Unlike conventional diffraction-limited imaging systems, where a projected image of the limiting aperture is used to define the system performance, there are at least three major effects that determine the performance of a DH system: i The spacing between adjacent pixels on the CCD, ii an averaging effect introduced by the finite size of these pixels, and iii the finite extent of the camera face itself. Using a theoretical model, we define a single expression that accounts for all these physical effects. With this model, we explore several different DH recording techniques: off-axis and inline, considering both the dc terms, as well as the real and twin images that are features of the holographic recording process. Our analysis shows that the imaging operation is shift variant and we demonstrate this using a simple example. We examine how our theoretical model can be used to optimize CCD design for lensless DH capture. We present a series of experimental results to confirm the validity of our theoretical model, demonstrating recovery of super- Nyquist frequencies for the first time

Resolution limits in practical digital holographic systems

We examine some fundamental theoretical limits on the ability of practical digital holography DH systems to resolve detail in an image. Unlike conventional diffraction-limited imaging systems, where a projected image of the limiting aperture is used to define the system performance, there are at least three major effects that determine the performance of a DH system: i The spacing between adjacent pixels on the CCD, ii an averaging effect introduced by the finite size of these pixels, and iii the finite extent of the camera face itself. Using a theoretical model, we define a single expression that accounts for all these physical effects. With this model, we explore several different DH recording techniques: off-axis and inline, considering both the dc terms, as well as the real and twin images that are features of the holographic recording process. Our analysis shows that the imaging operation is shift variant and we demonstrate this using a simple example. We examine how our theoretical model can be used to optimize CCD design for lensless DH capture. We present a series of experimental results to confirm the validity of our theoretical model, demonstrating recovery of super- Nyquist frequencies for the first time

Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung

Pseudomonas aeruginosa, the leading cause of morbidity and mortality in people with cystic fibrosis (CF), adapts for survival in the CF lung through both mutation and gene expression changes. Frequent clonal strains such as the Australian Epidemic Strain-1 (AES-1), have increased ability to establish infection in the CF lung and to superimpose and replace infrequent clonal strains. Little is known about the factors underpinning these properties. Analysis has been hampered by lack of expression array templates containing CF-strain specific genes. We sequenced the genome of an acute infection AES-1 isolate from a CF infant (AES-1R) and constructed a non-redundant micro-array (PANarray) comprising AES-1R and seven other sequenced P. aeruginosa genomes. The unclosed AES-1R genome comprised 6.254Mbp and contained 6957 putative genes, including 338 not found in the other seven genomes. The PANarray contained 12,543 gene probe spots; comprising 12,147 P. aeruginosa gene probes, 326 quality-control probes and 70 probes for non-P. aeruginosa genes, including phage and plant genes. We grew AES-1R and its isogenic pair AES-1M, taken from the same patient 10.5 years later and not eradicated in the intervening period, in our validated artificial sputum medium (ASMDM) and used the PANarray to compare gene expression of both in duplicate. 675 genes were differentially expressed between the isogenic pairs, including upregulation of alginate, biofilm, persistence genes and virulence-related genes such as dihydroorotase, uridylate kinase and cardiolipin synthase, in AES-1M. Non-PAO1 genes upregulated in AES-1M included pathogenesis-related (PAGI-5) genes present in strains PACS2 and PA7, and numerous phage genes. Elucidation of these genes' roles could lead to targeted treatment strategies for chronically infected CF patients. © 2011 Naughton et al

Systematic errors of an optical encryption system due to the discrete values of a spatial light modulator

An optical implementation of the amplitude encoded double random phase encryption/decryption technique is implemented, and both numerical and experimental results are presented. In particular, we examine the effect of quantization in the decryption process due to the discrete values and quantized levels, which a spatial light modulator (SLM) can physically display. To do this, we characterize a transmissive SLM using Jones matrices and then map a complex image to the physically achievable levels of the SLM using the pseudorandom encoding technique. We present both numerical and experimental results that quantify the performance of the system

Tree migration-rates : narrowing the gap between inferred post-glacial rates and projected rates

Faster-than-expected post-glacial migration rates of trees have puzzled ecologists for a long time. In Europe, post-glacial migration is assumed to have started from the three southern European peninsulas (southern refugia), where large areas remained free of permafrost and ice at the peak of the last glaciation. However, increasing palaeobotanical evidence for the presence of isolated tree populations in more northerly microrefugia has started to change this perception. Here we use the Northern Eurasian Plant Macrofossil Database and palaeoecological literature to show that post-glacial migration rates for trees may have been substantially lower (60–260 m yr–1) than those estimated by assuming migration from southern refugia only (115–550 m yr–1), and that early-successional trees migrated faster than mid- and late-successional trees. Post-glacial migration rates are in good agreement with those recently projected for the future with a population dynamical forest succession and dispersal model, mainly for early-successional trees and under optimal conditions. Although migration estimates presented here may be conservative because of our assumption of uniform dispersal, tree migration-rates clearly need reconsideration. We suggest that small outlier populations may be a key factor in understanding past migration rates and in predicting potential future range-shifts. The importance of outlier populations in the past may have an analogy in the future, as many tree species have been planted beyond their natural ranges, with a more beneficial microclimate than their regional surroundings. Therefore, climate-change-induced range-shifts in the future might well be influenced by such microrefugia

Toward Human-Carnivore Coexistence: Understanding Tolerance for Tigers in Bangladesh

Fostering local community tolerance for endangered carnivores, such as tigers (Panthera tigris), is a core component of many conservation strategies. Identification of antecedents of tolerance will facilitate the development of effective tolerance-building conservation action and secure local community support for, and involvement in, conservation initiatives. We use a stated preference approach for measuring tolerance, based on the ‘Wildlife Stakeholder Acceptance Capacity’ concept, to explore villagers’ tolerance levels for tigers in the Bangladesh Sundarbans, an area where, at the time of the research, human-tiger conflict was severe. We apply structural equation modeling to test an a priori defined theoretical model of tolerance and identify the experiential and psychological basis of tolerance in this community. Our results indicate that beliefs about tigers and about the perceived current tiger population trend are predictors of tolerance for tigers. Positive beliefs about tigers and a belief that the tiger population is not currently increasing are both associated with greater stated tolerance for the species. Contrary to commonly-held notions, negative experiences with tigers do not directly affect tolerance levels; instead, their effect is mediated by villagers’ beliefs about tigers and risk perceptions concerning human-tiger conflict incidents. These findings highlight a need to explore and understand the socio-psychological factors that encourage tolerance towards endangered species. Our research also demonstrates the applicability of this approach to tolerance research to a wide range of socio-economic and cultural contexts and reveals its capacity to enhance carnivore conservation efforts worldwide