Development of an Er:YAG laser for Range-finding

Long distance, high precision range-finding requires high energy, short duration laser pulses that exceed 1MW peak power, as specified by defence companies. However, eye safety is a particularly important consideration for a laser system that will be used outdoors. Currently, this is often achieved by frequency shifting the 1064nm output from a Q-switched Nd:YAG laser to the ‘eye-safe’ band (1.5 um to 1.8 um). A 1617 nm or 1645 nm Er:YAG laser operating on the 4I13/2 to 4I15/2 transition can satisfy this need without additional frequency shifting systems. Although this transition has long been used in a variety of erbium-doped gain media, advancements in diode pumping have made these lasers more compact and efficient. The lower level of the 1.6 um transition in erbium is within the ground state manifold, making it a quasi-three-level system, leading to re-absorption from the lower laser level. It also suffers from low gain due to Stark splitting of the upper laser level. The gain is further reduced by up-conversion that depletes ions from the upper laser level. Er:Glass and Er:YAG lasers previously constructed by our research group were useful for coherent laser radars (CLR's) and Doppler wind-field mapping. This project aimed to build an Er:YAG laser with higher pulse energy and shorter (< 10 ns) pulse duration. This was expected to be a serious challenge based on the outcomes of all previous work. Our approach was to use a Co-Planar Folded zig-zag Slab (CPFS) architecture to provide a sufficiently long path length in the gain medium to compensate for the low inherent gain. The CPFS geometry was first demonstrated using Nd:YAG in the mid 1990’s, but was never previously attempted with Er:YAG. In this thesis, I describe the design and construction of Q-switched Er:YAG lasers for this purpose, followed by a more powerful cavity-dumped Er:YAG laser. Both lasers were resonantly pumped using 1.47 um laser diode bars. To the best of our knowledge these are the first CPFS Er:YAG lasers demonstrated. Our first Q-switched laser produced 15.5 mJ pulses with FWHM duration of less than 25 ns, corresponding to a peak power of 620kW, from 60W peak pump power. The final version of the Q-switched laser used a shorter crystal and resonator to reduce the pulse duration, and produced 6 mJ pulses with pulse durations of less than 15 ns, but with a peak power of only 400kW. These are the equal shortest duration pulses from an actively Q-switched Er:YAG laser at the present time. The results from both lasers are compared with the theoretical predictions adapted from a model of the dynamics of a quasi-threelevel laser. These investigations demonstrate the difficulties in building a Q-switched Er:YAG laser capable of safely meeting the project requirements. This thesis also describes the development and characterisation of a cavity-dumped CPFS Er:YAG laser. Cavity-dumped lasers are generally capable of shorter pulse durations and can therefore produce higher peak powers. This laser produced 10 mJ pulses with 4.5 ns duration, corresponding to a peak power of over 2MW. This represents the highest peak power at 1645 nm reported at the present time.Thesis (Ph.D.) -- University of Adelaide, School of Physical Sciences, 201

Nuclear factor one transcription factors as epigenetic regulators in cancer

Tumour heterogeneity poses a distinct obstacle to therapeutic intervention. While the initiation of tumours across various physiological systems is frequently associated with signature mutations in genes that drive proliferation and bypass senescence, increasing evidence suggests that tumour progression and clonal diversity is driven at an epigenetic level. The tumour microenvironment plays a key role in driving diversity as cells adapt to demands imposed during tumour growth, and is thought to drive certain subpopulations back to a stem cell-like state. This stem cell-like phenotype primes tumour cells to react to external cues via the use of developmental pathways that facilitate changes in proliferation, migration and invasion. Because the dynamism of this stem cell-like state requires constant chromatin remodelling and rapid alterations at regulatory elements, it is of great therapeutic interest to identify the cell-intrinsic factors that confer these epigenetic changes that drive tumour progression. The nuclear factor one (NFI) family are transcription factors that play an important role in the development of many mammalian organ systems. While all four family members have been shown to act as either oncogenes or tumour suppressors across various cancer models, evidence has emerged implicating them as key epigenetic regulators during development and within tumours. Notably, NFIs have also been shown to regulate chromatin accessibility at distal regulatory elements that drive tumour cell dissemination and metastasis. Here we summarize the role of the NFIs in cancer, focusing largely on the potential mechanisms associated with chromatin remodelling and epigenetic modulation of gene expression

A morphology independent approach for identifying dividing adult neural stem cells in the mouse hippocampus

Background: Type 1 adult hippocampal neural stem cells (AH-NSCs) continue to generate neurons throughout life, albeit at a very low rate. The relative quiescence of this population of cells has led to many studies investigating factors that may increase their division. Current methods of identifying dividing AH-NSCs in vivo require the identification and tracing of radial processes back to nuclei within the subgranular zone. However, caveats to this approach include the time-intensive nature of identifying AH-NSCs with such a process, as well as the fact that this approach ignores the relatively more active population of horizontally oriented AH-NSCs that also reside in the subgranular zone. Results: Here we describe, and then verify using Hes5::GFP mice, that labeling for the cell cycle marker Ki67 and selection against the intermediate progenitor cell marker TBR2 (Ki67; TBR2 nuclei) is sufficient to identify dividing horizontally and radially oriented AH-NSCs in the adult mouse hippocampus. Conclusions: These findings provide a simple and accurate way to quantify dividing AH-NSCs in vivo using a morphology-independent approach that will facilitate studies into neurogenesis within the hippocampal stem cell niche of the adult brain. Developmental Dynamics 247:194–200, 2018

Long-term self-renewing stem cells in the adult mouse hippocampus identified by intravital imaging.

Neural stem cells (NSCs) generate neurons throughout life in the mammalian hippocampus. However, the potential for long-term self-renewal of individual NSCs within the adult brain remains unclear. We used two-photon microscopy and followed NSCs that were genetically labeled through conditional recombination driven by the regulatory elements of the stem cell-expressed genes GLI family zinc finger 1 (Gli1) or achaete-scute homolog 1 (Ascl1). Through intravital imaging of NSCs and their progeny, we identify a population of Gli1-targeted NSCs showing long-term self-renewal in the adult hippocampus. In contrast, once activated, Ascl1-targeted NSCs undergo limited proliferative activity before they become exhausted. Using single-cell RNA sequencing, we show that Gli1- and Ascl1-targeted cells have highly similar yet distinct transcriptional profiles, supporting the existence of heterogeneous NSC populations with diverse behavioral properties. Thus, we here identify long-term self-renewing NSCs that contribute to the generation of new neurons in the adult hippocampus.Wellcome Trus

Oral cancer awareness amongst hospital nursing staff: a pilot study

<p>Abstract</p> <p>Background</p> <p>Oral cancer is as prevalent as cervical and testicular cancer in the United Kingdom. Nursing staff provide the oral health care for the patient population in hospital. Admission to hospital provides a 'window of opportunity' for oral cancer 'screening' via an oral health check during nursing clerking. This study aimed to investigate whether nursing staff are aware of risk factors for oral cancer, its clinical signs, and could therefore provide a 'screening' service for oral cancer.</p> <p>Method</p> <p>Through the use of a questionnaire we assessed 121 nursing staff on oral health check behaviour and attitudes; their knowledge of risk factors for oral cancer; their understanding of common clinical signs of oral cancer; and their undergraduate and postgraduate training in oral health and oral cancer.</p> <p>Results</p> <p>Over 80% thought oral health checks were important although only 49% performed this task regularly; approximately 70% identified smoking as a risk factor but less than 30% identified alcohol. Awareness of the clinical signs of oral cancer was low with 21% identifying white patches, 15% identifying ulceration and only 2% identifying red patches despite their malignant potential. Nurses within 3 years of qualification were significantly better at recognising risk factors for oral cancer than their colleagues, identifying a need for continuing postgraduate education on oral health and oral cancer. Sixty-one percent of nursing staff received oral healthcare as an undergraduate with 34 percent receiving postgraduate training.</p> <p>Conclusion</p> <p>An oral health check upon admission to hospital provides an opportunity for nurses to 'screen' for oral diseases including oral cancer and allows nurses a greater role in total patient care. Nurses' awareness of oral cancer risk factors and clinical signs was, however, poor. This study highlights a need for improved education of nurses on oral cancer to make the oral health check on admission viable for oral cancer screening.</p

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Optimising Treatment Outcomes for Children and Adults Through Rapid Genome Sequencing of Sepsis Pathogens. A Study Protocol for a Prospective, Multi-Centre Trial (DIRECT)

BackgroundSepsis contributes significantly to morbidity and mortality globally. In Australia, 20,000 develop sepsis every year, resulting in 5,000 deaths, and more than AUD$846 million in expenditure. Prompt, appropriate antibiotic therapy is effective in improving outcomes in sepsis. Conventional culture-based methods to identify appropriate therapy have limited yield and take days to complete. Recently, nanopore technology has enabled rapid sequencing with real-time analysis of pathogen DNA. We set out to demonstrate the feasibility and diagnostic accuracy of pathogen sequencing direct from clinical samples, and estimate the impact of this approach on time to effective therapy when integrated with personalised software-guided antimicrobial dosing in children and adults on ICU with sepsis.MethodsThe DIRECT study is a pilot prospective, non-randomized multicentre trial of an integrated diagnostic and therapeutic algorithm combining rapid direct pathogen sequencing and software-guided, personalised antibiotic dosing in children and adults with sepsis on ICU.Participants and interventionsDIRECT will collect microbiological and pharmacokinetic samples from approximately 200 children and adults with sepsis admitted to one of four ICUs in Brisbane. In Phase 1, we will evaluate Oxford Nanopore Technologies MinION sequencing direct from blood in 50 blood culture-proven sepsis patients recruited from consecutive patients with suspected sepsis. In Phase 2, a further 50 consecutive patients with suspected sepsis will be recruited in whom MinION sequencing will be combined with Bayesian software-guided (ID-ODS) personalised antimicrobial dosing.Outcome measuresThe primary outcome is time to effective antimicrobial therapy, defined as trough drug concentrations above the MIC of the pathogen. Secondary outcomes are diagnostic accuracy of MinION sequencing from whole blood, time to pathogen identification and susceptibility testing using sequencing direct from whole blood and from positive blood culture broth.DiscussionRapid pathogen sequencing coupled with antimicrobial dosing software has great potential to overcome the limitations of conventional diagnostics which often result in prolonged inappropriate antimicrobial therapy. Reduced time to optimal antimicrobial therapy may reduce sepsis mortality and ICU length of stay. This pilot study will yield key feasibility data to inform further, urgently needed sepsis studies. Phase 2 of the trial protocol is registered with the ANZCTR (ACTRN12620001122943).Trial registrationRegistered with the Australia New Zealand Clinical Trials Registry Number ACTRN1262000112294