Performance comparison of hyperspectral target detection algorithms

This thesis performs a performance comparison on existing hyperspectral target detection algorithms. The algorithms chosen for this analysis include multiple adaptive matched filters and the physics based modeling invariant technique. The adaptive matched filter algorithms can be divided into either structured (geometrical) or unstructured (statistical) algorithms. The difference between these two categories is in the manner in which the background is characterized. The target detection procedure includes multiple pre-processing steps that are examined here as well. The effects of atmospheric compensation, dimensionality reduction, background characterization, and target subspace creation are all analyzed in terms of target detection performance. At each step of the process, techniques were chosen that consistently improved target detection performance. The best case scenario for each algorithm is used in the final comparison of performance. The results for multiple targets were computed and statistical matched filter algorithms were shown to outperform all others in a fair comparison. This fair comparison utilized a FLAASH atmospheric compensation for the matched filters that was equivalent to the physics based invariant process. The invariant technique was shown to outperform the geometric matched filters that it uses in its approach. Each of these techniques showed improvement over the SAM algorithm for three of the four targets analyzed. Multiple theories are proposed to explain the anomalous results for the most difficult target

Can oral infection be a risk factor for Alzheimer’s disease?

Alzheimer’s disease (AD) is a scourge of longevity that will drain enormous resources from public health budgets in the future. Currently, there is no diagnostic biomarker and/or treatment for this most common form of dementia in humans. AD can be of early familial-onset or sporadic with a late-onset. Apart from the two main hallmarks, amyloid-beta and neurofibrillary tangles, inflammation is a characteristic feature of AD neuropathology. Inflammation may be caused by a local central nervous system insult and/or by peripheral infections. Numerous microorganisms are suspected in AD brains ranging from bacteria (mainly oral and non-oral Treponema species), viruses (Herpes simplex type I) and yeasts (Candida species). A causal relationship between periodontal pathogens/non-oral Treponema species of bacteria has been proposed via the amyloid-beta and inflammatory links. Periodontitis constitutes a peripheral oral infection that can provide the brain with intact bacteria and virulence factors and inflammatory mediators due to daily, transient bacteraemias. If and when genetic risk factors meet environmental risk factors in the brain, disease is expressed, in which neurocognition may be impacted, leading to the development of dementia. To achieve the goal of finding a diagnostic biomarker and possible prophylactic treatment for AD, there is an initial need to solve the etiological puzzle contributing to its pathogenesis. This review therefore addresses oral infection as the plausible aetiology of late onset AD (LOAD)

A Study of Herpes Simplex Virus Latency in Cultured Cells

A distinctive feature of herpes simplex virus (HSV) is the ability to establish latency in the neuronal cells of the sensory ganglia. The current working model for the organization of the latent HSV type 1 (HSV-1) genome is that it persists as a circular episome associated with nucleosomes in a chromatin-like arrangement. Thus, latent HSV-1 genomes in vivo are in a physical state that differs from the characteristic unit length molecules found in virion DNA. During latency HSV-1 gene expression is restricted to a family of latency associated transcripts (LAT) detectable in the sensory ganglia of experimental animals and humans. An in vitro latency system has been utilized to investigate the molecular biology of HSV latency. The main objectives of the research were the examination of the process of reactivation, particularly the role of the HSV-1 polypeptide Vmw110 and the elucidation of the properties of mutant in1814 during latency in vitro. The HSV-1 deletion mutant dl1403 was previously shown to be unable to reactivate latent HSV type 2 (HSV-2) in the in vitro latency system. The failure of dll403 to reactivate latent HSV-2 suggested a role for Vmw110 in the reactivation process but did not exclude the possiblity of a role for LAT or that Vmw110 acted in conjunction with other immediate early (IE) polypeptides. These aspects of reactivation were investigated using a combination of hybrid adenoviruses and inframe deletion mutants of HSV-1. Superinfection of latently infected monolayers with these viruses revealed that during reactivation in vitro there was no requirement for LAT and that the only prerequisite was a functional Vmw110. Specific features intrinsic to Vmw110 that were important for the ability of Vmw110 to activate gene expression in the absence of Vmw175 in transient transfection assays were essential for reactivation. Mutant in1814 contains a 12 base pair (bp) inframe insertion in the gene encoding Vmw65 such that the polypeptide it encodes is unable to interact with cellular proteins and thereby transinduce IE gene expression. Southern hybridization analysis demonstrated that in1814 reactivates latent HSV-2, although less efficiently than wild type (wt) HSV-1 or the rescuent 1814R. Infection of human foetal lung (HFL) cells at low multiplicity (0.1 particle/cell) with in1814 resulted in the efficient establishment of latency from which the majority of input particles could be recovered by superinfection with tsK at 38.

Object Detection in High Resolution Aerial Images and Hyperspectral Remote Sensing Images

With rapid developments in satellite and sensor technologies, there has been a dramatic increase in the availability of remotely sensed images. However, the exploration of these images still involves a tremendous amount of human interventions, which are tedious, time-consuming, and inefficient. To help imaging experts gain a complete understanding of the images and locate the objects of interest in a more accurate and efficient way, there is always an urgent need for developing automatic detection algorithms. In this work, we delve into the object detection problems in remote sensing applications, exploring the detection algorithms for both hyperspectral images (HSIs) and high resolution aerial images. In the first part, we focus on the subpixel target detection problem in HSIs with low spatial resolutions, where the objects of interest are much smaller than the image pixel spatial resolution. To this end, we explore the detection frameworks that integrate image segmentation techniques in designing the matched filters (MFs). In particular, we propose a novel image segmentation algorithm to identify the spatial-spectral coherent image regions, from which the background statistics were estimated for deriving the MFs. Extensive experimental studies were carried out to demonstrate the advantages of the proposed subpixel target detection framework. Our studies show the superiority of the approach when comparing to state-of-the-art methods. The second part of the thesis explores the object based image analysis (OBIA) framework for geospatial object detection in high resolution aerial images. Specifically, we generate a tree representation of the aerial images from the output of hierarchical image segmentation algorithms and reformulate the object detection problem into a tree matching task. We then proposed two tree-matching algorithms for the object detection framework. We demonstrate the efficiency and effectiveness of the proposed tree-matching based object detection framework. In the third part, we study object detection in high resolution aerial images from a machine learning perspective. We investigate both traditional machine learning based framework and end-to-end convolutional neural network (CNN) based approach for various object detection tasks. In the traditional detection framework, we propose to apply the Gaussian process classifier (GPC) to train an object detector and demonstrate the advantages of the probabilistic classification algorithm. In the CNN based approach, we proposed a novel scale transfer module that generates enhanced feature maps for object detection. Our results show the efficiency and competitiveness of the proposed algorithms when compared to state-of-the-art counterparts

The Control of Varicella-Zoster Virus Immediate Early Gene Expression

Analysis of the cis-acting motifs and trans-acting factors responsible for regulating the expression of the varicella-zoster virus (VZV) major immediate early (IE) gene was undertaken. The control of VZV IE gene expression has relevance to the fields of eukaryotic gene regulation and herpesvirus biology. In order to analyse the control sequences of the VZV major IE gene, knowledge of the location of the 5' end of its mRNA was required. Primer extension and SI nuclease analyses concurred in defining it as being 74 base pairs (bp) upstream of the proposed translation initiation site. Analysis of DNA sequences upstream of the start site revealed a candidate for a 'TATA' motif present at -25 to -30 bp, a finding common to many genes transcribed by eukaryotic RNA polymerase II. Analysis of the activity of the control region of the VZV major IE gene was undertaken using plasmids in which sequences to -1150 were inserted upstream of the "reporter" genes encoding B-galactosidase or chloramphenicol acetyl transferase. The activities of the complete control region and of a series of deletions were then determined in a range of cell types, using short term transfection assays. A significant finding to emerge from these experiments was that the control sequences responsible for the transcription of the VZV major IE gene do not direct a high level of expression of reporter genes in any of the cell types tested. The baseline level of transcriptional activity was dependent on sequences located between nucleotides -131 and -25. Co-transfection of a plasmid which expresses the herpes simplex virus type 1 (HSV-1) protein Vmw65 resulted in a 20-50 fold stimulation of expression from the VZV IE promoter. This effect depended on the presence of regulatory sequences between -409 bp and -130 bp. A second set of co-transfection experiments investigated the effect on the VZV control sequences of a plasmid encoding the transactivating product of the adenovirus 5 ElA gene. The presence of this polypeptide resulted in stimulation of expression by 10 fold. In contrast with the effect of Vmw65, the activity of the ElA gene product depended on sequences present within the first 131 bp of the mRNA start site. Gel retardation and DNAase I protection assays were used to locate sites at which proteins bind to the control sequences. Results from these experiments reinforced and expanded the conclusions made from the functional assays. DNA fragments from the promoter region, -35 to -130, were shown to bind two proteins. Sequence analysis and competition experiments identified these proteins as belonging to two families of transcription factors known as 'CCAAT box binding' proteins and the 'ATF/CRE' family. A second protein binding region was present between -409 and -246 and was shown to consist of two binding sites for the cellular transcription factor Oct-1, which binds to the consensus ATGCAAAT. The proximal binding site could be expanded to incorporate a TAATGARAT motif known to allow Vmw65 to participate in the formation of a complex including Oct-1 and other cellular proteins, thus allowing Vmw65 mediated transactivation. Both sites were shown to bind Oct-1 and the proximal site was also shown to bind Vmw65 with high affinity, probably explaining the effect of this protein on VZV IE gene expression. In view of these results the analysis of VZV open reading frame (orf) 10 was undertaken. Sequence comparison of orf10 and Vmw65 had shown considerable homologies between the amino-terminal portions of the proteins but the absence from orf10 of a carboxy-terminal region of 78 amino acids known to be essential for transcriptional activation by Vmw65. Both the functional activity of orf10 and its ability to participate in complex formation at TAATGARAT motifs were tested. A plasmid, constructed to express the product of VZV orf10, failed to stimulate expression from plasmids containing HSV-1 or VZV IE control sequences. The product of VZV orf10 was also produced in vitro and failed to participate in the formation of DNA binding complexes when incubated with cellular proteins and the TAATGARAT motif. Two other VZV orfs were studied. The first was number 66, which encodes a protein which shows many similarities to known protein kinases. The system chosen to express this orf utilised the HSV-1 temperature sensitive mutant tsK and HSV-1 IE control sequences. At nonpermissive temperatures tsK overproduces IE polypeptides, generating quantities sufficient for biochemical characterisation of heterologous orfs expressed in this way. In order to simplify the selection of recombinant viruses containing VZV orfs the E. coli B-galactosidase enzyme, with HSV-1 IE control sequences, was inserted into the thymidine kinase gene of tsK

Involvement of the exocrine pancreas during covid-19 infection and possible pathogenetic hypothesis: a concise review

The gastrointestinal system may be affected by COVID-19 infection with an incidence variable from 3% up to 79%. Several works show that the pancreas, both in its exocrine and endocrine function, can be affected by this viral infection, although this organ has been poorly analyzed in this current epidemic context. This mini-review aims to provide a summary of available studies on exocrine pancreas involvement during COVID-19 infection. A search through MEDLINE/PubMed was conducted on the topic in hand. With regard to exocrine function, some studies highlight the presence of an associated hyperenzymemia (hyperamylasemia, hyperlipasemia), while others describe isolated and rare cases of acute pancreatitis. More attention should be paid to pancreatic impairment in subjects with COVID-19, as this may prove to be one of the elements aggravating its clinical course. Indeed, acute pancreatitis, especially when presenting in severe forms with hyperstimulation of the pro-inflammatory response, may represent a crucial factor in the progression of COVID-19, entailing both an increase in hospitalization days and in mortality rate

A Mutational Analysis of the Structure and Function of the Herpes Simplex Virus Immediate Early Protein Vmw175

Herpes simplex virus type 1 (HSV-1) expresses three main classes of genes (immediate-early [IE], early [E] and late [L]) in a temporal cascade upon infection of tissue culture cells. These three groups of genes can also be defined by the sensitivity of their expression to metabolic inhibitors of protein or DNA synthesis. IE genes are transcribed in the absence of de novo protein synthesis and their transcription is stimulated by a component of the virus particle, Vmw65. IE gene products are required for the activation of later classes of viral genes, whose expression varies in sensitivity to inhibitors of viral DNA replication. Early genes are expressed at maximal levels in the absence of DNA synthesis, whilst true late genes are critically dependent on replication for expression. The predominant transcriptional regulatory protein specified by HSV-1 is the IE protein Vmw175, whose functions are essential for virus growth. Studies of viruses with temperature sensitive lesions in this protein have shown that Vmw175 is a complex multifunctional protein required for the transcriptional activation of many HSV-1 promoters and the repression of its own transcription. Cloned Vmw175 is a promiscuous transactivator of transcription of RNA polymerase type II promoters. In addition cloned Vmw175 represses transcription from its own promoter, probably by binding to a specific target sequence at the start site for transcription. The aim of the work described in this thesis was to investigate the relationship between the structure and function of this protein, and to define which regions of the protein are involved in each of its various activities. A panel of plasmid-borne in-frame insertion and deletion mutants of the gene encoding Vmw175 were constructed and assayed for their ability to regulate transcription in transient transfection assays. Fusions of HSV promoters to the chloramphenicol acetyl transferase gene were used to assay the ability of each mutant to transactivate an HSV early promoter (that of the gene encoding glycoprotein gD) and to repress the promoter of its own gene, IE3, in transiently transfected cells. By this approach it was possible to define the regions of the Vmw175 amino acid sequence that are required for transcriptional activation and repression. Large stretches of the protein are relatively unimportant for either function, while the regions most sensitive to disruption correlate to sequences conserved between Vmw175 and VZV 140K, the corresponding transactivating protein of another alphaherpesvirus, varicella-zoster virus. The region from amino acids 275 to 495 is particularly important for both repression and transactivation; whilst that from around 840 to 1100 seems to be more important for transactivation than repression. A monoclonal antibody directed against Vmw175 was used to visualize expression and localization of Vmw175 in transfected cells by indirect immunofluorescence. This provided confirmation that each of the mutant plasmids expressed Vmw175. Each of the 39 insertion mutant proteins exhibited a pattern of nuclear localization indistinguishable from that of wild-type, but when amino acids 682-774 were deleted a signal essential for nuclear localization was lost. A strong candidate for a nuclear localization signal centres around amino acid 728 and is strongly conserved in the VZV homologue. This sequence PREGRKRKSP contains four consecutive arginine (R) and lysine (K) residues and is related to a signal in the SV40 large T antigen required for nuclear localization. Vmw175 is known to bind directly to a number of HSV-1 sequences, some of which contain the consensus sequence ATCGTC. The binding of Vmw175 to this sequence at the transcriptional start site of IE gene 3 is thought to be involved in the mechanism of autoregulation. In order to correlate the transcriptional activity of each mutant with its ability to bind to DNA, the site specific DNA binding activity of each mutant was assayed. In these experiments nuclear extracts of transfected cells were incubated with a DNA probe spanning the IE3 cap site and protein complexes detected using the gel retardation technique. The results show that a critical region of Vmw175, amino acid residues 275-495, includes structures which are essential for specific DNA binding, transactivation and repression

Donkey milk fermentation by lactococcus lactis subsp. Cremoris and lactobacillus rhamnosus affects the antiviral and antibacterial milk properties

Background: Milk is considered an important source of bioactive peptides, which can be produced by endogenous or starter bacteria, such as lactic acid bacteria, that are considered effective and safe producers of food-grade bioactive peptides. Among the various types of milk, donkey milk has been gaining more and more attention for its nutraceutical properties. Methods: Lactobacillus rhamnosus 17D10 and Lactococcus lactis subsp. cremoris 40FEL3 were selected for their ability to produce peptides from donkey milk. The endogenous peptides and those obtained after bacterial fermentation were assayed for their antioxidant, antibacterial, and antiviral activities. The peptide mixtures were characterized by means of LC-MS/MS and then analyzed in silico using the Milk Bioactive Peptide DataBase. Results: The peptides produced by the two selected bacteria enhanced the antioxidant activity and reduced E. coli growth. Only the peptides produced by L. rhamnosus 17D10 were able to reduce S. aureus growth. All the peptide mixtures were able to inhibit the replication of HSV-1 by more than 50%. Seventeen peptides were found to have 60% sequence similarity with already known bioactive peptides. Conclusions: A lactic acid bacterium fermentation process is able to enhance the value of donkey milk through bioactivities that are important for human health

Self-Optimisation of Automated Continuous Reactors

The optimisation of problematic reaction steps in the synthesis of a drug compound is crucial for pharmaceutical process development. In recent traditions, this has carried out using design of experiments (DoE), which shows the key reaction variables and provides optimum reaction conditions. The process can require a lot of experiments and be time and resource consuming. The speed of optimisation experiments can be increased by using automated platforms complete with online analysis, which carry out reactions and acquire analytical samples without any human intervention. If these experiments can be carried out in continuous reactors then they will benefit from faster kinetics, enhanced heat and mass transfer, improved safety and higher productivity over their batch counterparts. An automated self-optimising flow reactor combines a continuous reactor with online analysis and feedback loop. The feedback loop contains full computerised control and monitoring of all equipment as well as a minimising algorithm, which will use the results from the online analysis to predict new optimum conditions. The technique has been shown to optimise the synthesis of small organic compounds but has, so far, yet to be widely used in pharmaceutical process development. This thesis has improved self-optimising technologies in order to make it a useful technique in pharmaceutical process development. First, the final bond forming step in the synthesis of an active pharmaceutical ingredient was optimised for yield. Studies were primarily carried out on a model compound in order to establish the correct reactor setup before transferring to the active compound, which found an optimum yield of 89%. The work also provided mechanistic evidence for generation of impurities. Next, response surface models were successfully fitted to the data obtained from a branch and fit algorithm optimisation of a Claisen-Schmidt condensation. In depth statistical calculations show how DoE models can be generated from self-optimisation data with good fit and predictability (R2 > 0.95, Q2 > 0.90), and with the aid of commercial DoE software. Further work developed the use of direct mass spectrometry (MS) as the online analytical method. The short method times and real-time analysis of MS allowed a steady state detection function to be built, followed by a linear calibration model of all the species in the amidation of a methyl ester. The reaction was optimised for yield using branch and fit algorithm, and DoE, with excellent agreement between the two techniques in both optimum conditions and responses. Finally, changes were made to the optimisation program to reduce the amount of material required for automated optimisations. Reaction pulses of sub-reactor volumes were pumped through the reactor, dispersed in a continuous phase of miscible solvent. Residence time distribution experiments were carried out to characterise the dispersion of the reactor and calculate the minimum reactor pulse volume. Optimisations were primarily carried out using pattern search algorithm and a multi-objective evolutionary algorithm, the latter of which generated a three target function optimum, reducing the amount of waste by 81%. Overall this work has shown how self-optimisation can be a valuable tool for pharmaceutical process development. The existing technique has been improved by demonstrating its use in the synthesis of pharmaceutical compounds, combining it with existing DoE techniques, adding new forms of online analysis, and reducing the amount of material required to deliver a multi-target optimum