no / This research report was commissioned to assess and evaluate the criminal justice and business case for the Officer Next Door (OND) program. Since its establishment in 1998, the OND program has sought to provide Housing Tasmania residents with a reassurance policing approach based on early intervention in criminal and anti-social behaviour on Housing Tasmania broadacre estates.

Next Generation Networks (NGNs) aim to provide a unified network infrastructure to offer multimedia data and telecommunication services through IP convergence. NGNs utilize multiple broadband, QoS-enabled transport technologies, creating a converged packet-switched network infrastructure, where service-related functions are separated from the transport functions. This requires significant changes in the way how networks are managed to handle the complexity and heterogeneity of NGNs. This thesis proposes a Service Oriented Architecture (SOA) based management framework that integrates heterogeneous management systems in a loose coupling manner. The key benefit of the proposed management architecture is the reduction of the complexity through service and data integration. A network management middleware layer that merges low level management functionality with higher level management operations to resolve the problem of heterogeneity was proposed. A prototype was implemented using Web Services and a testbed was developed using trouble ticket systems as the management application to demonstrate the functionality of the proposed framework. Test results show the correcting functioning of the system. It also concludes that the proposed framework fulfils the principles behind the SOA philosophy.

With the rapid progress of next-generation sequencing (NGS) technologies, new tools and methods have emerged to investigate the transcriptomics of various organisms. RNA sequencing (RNA-seq) employs NGS to evaluate the presence and abundance of RNA transcripts in biological samples. This technique offers a comprehensive snapshot of the RNA dynamics within cells. With the ability to profile the entire transcriptome of organisms rapidly and accurately, RNA-seq has become the state-of-the-art method for transcriptome profiling, surpassing the traditional microarray approach. Single-cell RNA sequencing (scRNA-seq) was introduced in 2009 to profile the single-cell gene expression in highly heterogeneous samples such as brain tissue and tumors. The advancement of scRNA-seq technologies enables the in-depth transcriptomic study in each cell subtype. When selecting an scRNA-seq method, researchers must weigh the trade-off between profiling more single cells versus obtaining more comprehensive transcripts per cell, while considering the overall costs. The throughput of full-length scRNA-seq methods is usually lower, as each single cell needs to be processed separately to produce scRNA-seq libraries. However, full-length methods enable the researchers to investigate the splicing variants and allele-specific expression. Non-full-length methods only capture the 3' or 5' ends of transcripts, which limits their application in isoform detection, but as cells are pooled after barcoding for cDNA synthesis, the throughput is 2–3 orders of magnitude higher than full-length methods. We developed a droplet-based platform for full-length single-cell RNA-seq, which enabled the efficient recovery of full-length mRNA from individual cells in a high-throughput manner. The developed platform can process ~8,000 single cells within 2 days and detect ~20% more genes compared to Drop-seq. Besides scRNA-seq technology development, we also applied a low-input RNA-seq method to study the transcriptomics in different biological samples. When handling precious biological samples, a low-input method is necessary to profile the transcriptome of homogeneous cell populations. We first studied the epigenomic and transcriptomic regulations in colorectal cancer (CRC) using MOWChIP-seq, a low-input high-throughput method, in conjunction with our low-input RNA-seq approach. Fusobacterium nucleatum (Fnn) is closely related to the progression of cancers like CRC and pancreatic cancer. However, the molecular mechanisms of how Fnn adjusts the tumor microenvironment (TME) and leads to poor clinical outcomes are still unclear. In this in-vitro study, we characterized how hypoxia, an important TME ignored by previous research, facilitates Fnn infection of CRC and corresponding alterations of global epigenome and transcriptome. We infer that hypoxia has similar effects as Fnn infection alone on the CRC cells. The Fnn infection under hypoxia further boosts the proliferation and progression of CRC. We then applied our low-input RNA-seq method to study brain neuroscience and immunology. Psychedelics like DOI show promising clinical efficacy in patients with psychiatric conditions. Although psychedelics exhibit rapid antidepression action and long-lasting effectiveness compared to conventional treatment, their acute psychotic symptoms and potential for drug abuse discourage their application in clinical practice. In this case, it is important to comprehend the molecular mechanisms responsible for psychedelics' clinical efficacy. This understanding can pave the way for the development of improved treatments that do not rely on psychedelics. After profiling the transcriptome of mouse brain samples exposed to psychedelics with different post-exposure times, we concluded that the psychedelic-induced transcriptomic variations are more transient than epigenomic changes. In the second brain neuroscience project, we first applied 3-color FACS sorting to differentiate four neuron and non-neuron subtypes in human postmortem prefrontal cortex tissues. Then we profiled the gene expression of the four subtypes and validated the FACS sorting by examining the expression of marker genes. Differentially expressed genes between each subtype and the others were extracted and proceeded to gene ontology analysis. We identified unique altered biological pathways related to each subtype. The immunology research focuses on revealing the difference between low-grade inflammation and monocyte exhaustion, as well as the unique biological pathways they regulate. Therefore, we profiled the transcriptome of bone marrow-derived monocytes stimulated by PBS control, a low- or high-dose LPS. In addition to wild-type mice, we also included TRAM-deficient and IRAK-M-deficient mice. We concluded that low-dose LPS specifically regulates the TRAM-dependent pathway of TLR4 signaling, and high-dose LPS exclusively upregulates exhaustion markers by impacting metabolic and proliferative pathways. / Doctor of Philosophy / Transcriptomics is the comprehensive study of RNA transcripts derived from an organism's genome. RNA plays a vital role in maintaining the fundamental functions of cells and organisms. In eukaryotes, the genetic information stored in the DNA of cells is transferred to messenger RNA (mRNA) molecules through a process called transcription. These mRNA molecules serve as a bridge between DNA and proteins, as they carry the instructions encoded in genes to ribosomes for protein synthesis. Studying mRNA transcripts reveals various cellular mechanisms and their impact on overall organism function, gene regulation, and disease pathways. With the aid of next-generation sequencing, various RNA-seq approaches have been developed to study mRNA transcripts quantitatively in the past decades. To better understand the gene expression regulations in biological samples, we first applied bulk RNA-seq to profile the transcriptome of various samples under different conditions. Our in-house bulk RNA-seq protocol has been proven to be both high-performance and cost-effective compared to commercial kits. To better understand cellular diversity and uncover rare cell types in heterogeneous biological samples, we developed a droplet-based scRNA-seq platform that can recover full-length mRNA transcripts in a high throughput manner. It can profile the transcriptome of thousands of single cells within two days. It combines the advantages of the droplet-based scRNA-seq method (high throughput) and the well plate-based scRNA-seq method (full-length mRNA recovery).

For over thirty years, Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) has been a major contributor to morbidity and mortality in the commercial swine industry across the globe. This highly mutagenic RNA virus causes significant economic losses wherever it is prevalent, leading to $664 million in annual losses in the United States. Unfortunately, the current prevention and diagnostic techniques available have proven to be insufficient in controlling the spread of this disease. We describe an alternative diagnostic method exploiting the rapid turnaround time and long-read capacity of Oxford Nanopore Technology's MinION next-generation sequencer. We have developed a novel primer set designed to span Open Reading Frames 3 through 7 of the PRRSV genome, which has allowed for multiplexing of samples, thus reducing individual cost of testing, while yielding significantly more information than previously available. This novel primer pair and sequencing technique have distinguished mixed infections within individual animals and may be used to determine vaccination status. This new approach will help producers and veterinarians make better-informed decisions about co-mingling of animals and vaccination strategies, thus reducing the emergence of new, pathogenic strains of PRRSV. / Master of Science / Porcine reproductive and respiratory syndrome virus (PRRSV) is a common, economically important pathogen in commercial swine production. The virus was first identified in the late 1980's during outbreaks in the United States and Europe. In female pigs, the disease is characterized by abortion storms, and the delivery of mummified fetuses or very weak, ill piglets. Neonates often display signs of pneumonia, respiratory distress, and many die from hypoxia. Surviving piglets are highly susceptible to other diseases and are poor growers compared to other, unaffected piglets. Boars may show signs of respiratory disease and can also have decreased libido and reproductive success for months at a time. The virus is prone to mutating once a pig is infected, preventing herds from mounting sufficient immunity to protect against new, mutant strains. Identifying infected pigs early and accurately is crucial to managing PRRSV outbreaks. Currently available diagnostic tests for PRRSV have many limitations, thus we have developed a new diagnostic test using next-generation sequencing technology. Oxford Nanopore Technology provides a commercially available nanopore sequencer, the MinION, that can read long DNA strands in real-time. With this technology we have expanded the area of the PRRSV genome that can be sequenced, which allows us to better identify and distinguish strains of PRRSV in infected, and vaccinated pigs. This new testing method will allow veterinarians and practitioners across the country to better identify and predict outbreaks in their herds, helping them develop better management strategies against PRRSV.

As zoos and aquariums have become increasingly focused on conservation education, their menageries of unique and diverse learning opportunities have been underutilized. Through a new postsecondary-level animal behavior laboratory experience at an aquarium (“ZooU”), this study demonstrates that active learning pedagogy aligned with the Next Generation Science Standards (NGSS) could facilitate expansion of education at zoos and aquariums beyond their conservation education niche. Generally, students indicated that ZooU provided new opportunities for them to explore their own interests, demonstrate their learning, and augment their previous laboratory and aquarium experiences. Following both self- and researcher assessments of the students’ work, integrated analyses revealed that students who engaged in more active learning activities at the aquarium demonstrated a greater increase in skills aligned with the NGSS. Additionally, a novel intra-individual analysis was utilized to embrace the variation between learners that typically confounds the results of education studies with repeated measures design. Common challenges for education at zoos and aquariums are discussed through the context of ZooU as a foundation for future investigations. A practical NGSS-aligned guide to field trips at zoos and aquariums—written specifically for science teachers—is also included to support broader utilization of zoos and aquariums as educational resources.

The maritime industry is growing more and more for every year that passes. As the industry grows it also becomes a more attractive target for cyber criminals. The amount ofcyberattacks in the industry are few, but it is growing at an alarming rate. This literaturestudy identifies the most common datacom systems and infrastructure in the maritimeindustry and their vulnerabilities. This paper also identifies possible solutions and improvements that can be made to existing datacom systems to make them less susceptible tocyber attacks. The results show that there are many solutions that could be implementedthat would increase the cyber security in the industry, but many of them require international cooperation to implement. Therefore standards are suggested to be implemented inorder to push organisations to update their systems. Additionally, this paper delves intothe aviation industry to examine how the datacom infrastructure utilized in the maritimeindustry could be adopted to enhance both efficiency and security

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24241号 / 農博第2520号 / 新制||農||1094(附属図書館) / 学位論文||R4||N5412(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 宮川 恒, 教授 三芳 秀人, 教授 森 直樹 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

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