Through the Glass: A Glimpse into the Management of Visible Labs

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

Mollusca Non-Grata: The influence of top-down control and residence time on the abundance, distribution, and behavior of non-native marine snails in Washington State

Thesis (Ph.D.)--University of Washington, 2016-06

Evocations of Nature in the Piano Music of Franz Liszt and the Seeds of Impressionism

Thesis (D.M.A.)--University of Washington, 2016-06

Functional analysis of neurotransmission at β2-laminin deficient terminals

beta2-Laminin is important for the formation of neuromuscular junctions in vertebrates. Previously, we have inactivated the gene that encodes for beta2-laminin in mice and observed predominantly prejunctional structural defects. In this study, we have used both intra- and extracellular recording methods to investigate evoked neurotransmission in beta2-laminin-deficient mice, from postnatal day 8 (P8) through to day 18(P18). Our results confirmed that there was a decrease in the frequency of spontaneous release, but no change in the postjunctional response to such release. Analysis of evoked neurotransmission showed an increase in the frequency of stimuli that failed to elicit an evoked postjunctional response in the mutants compared to litter mate controls, resulting in a 50% reduction in mean quantal content at mutant terminals. Compared to littermate controls, beta2-laminin-deficient terminals showed greater synaptic depression when subjected to high frequency stimulation. Furthermore, the paired pulse ratio of the first two stimuli was significantly lower in beta2-laminin mutant terminals. Statistical analysis of the binomial parameters of release showed that the decrease in quantal content was due to a decrease in the number of release sites without any significant change in the average probability of release. This suggestion was supported by the observation of fewer synaptic vesicle protein 2 (SV2)-positive varicosities in beta2-laminin-deficient terminals and by ultrastructural observations showing smaller terminal profiles and increased Schwann cell invasion in beta2-laminin mutants; the differences between beta2-laminin mutants and wild-type mice were the same at both P8 and P18. From these results we conclude that beta2-laminin plays a role in the early structural development of the neuromuscular junction. We also suggest that transmitter release activity may act as a deterrent to Schwarm cell invasion in the absence of beta2-laminin.

A common oscillator for perceptual rivalries?

Perceptual rivalry is an oscillation of conscious experience that takes place despite univarying, if ambiguous, sensory input. Much current interest is focused on the controversy over the neural site of binocular rivalry, a variety of perceptual rivalry for which a number of different cortical regions have been implicated. Debate continues over the relative role of higher levels of processing compared with primary visual cortex and the suggestion that different forms of rivalry involve different cortical areas. Here we show that the temporal pattern of disappearance and reappearance in motion-induced blindness (MIB) (Bonneh et al, 2001 Nature 411 798-801) is highly correlated with the pattern of oscillation reported during binocular rivalry in the same individual. This correlation holds over a wide range of inter-individual variation. Temporal similarity in the two phenomena was strikingly confirmed by the effects of the hallucinogen LSD, which produced the same, extraordinary, pattern of increased rhythmicity in both kinds of perceptual oscillation. Furthermore, MIB demonstrates the two properties previously considered characteristic of binocular rivalry. Namely the distribution of dominance periods can be approximated by a gamma distribution and, in line with Levelt's second proposition of binocular rivalry, predominance of one perceptual phase can be increased through a reduction in the predominance time of the opposing phase. We conclude that (i) MIB is a form of perceptual rivalry, and (ii) there may be a common oscillator responsible for timing aspects of all forms of perceptual rivalry.

Options for guaranteeing the effective management of the world's protected areas

A rapid increase in the number and size of protected areas has prompted interest in their effectiveness and calls for guarantees that they are providing a good return on investment by maintaining their values. Research reviewed here suggests that many remain under threat and a significant number are already suffering deterioration. One suggestion for encouraging good management is to develop a protected-area certification system: however this idea remains controversial and has created intense debate. We list a typology of options for guaranteeing good protected-area management, and give examples, including: danger lists; self-reporting systems against individual or standardised criteria; and independent assessment including standardised third-party reporting, use of existing certification systems such as those for forestry and farming and certification tailored specifically to protected areas. We review the arguments for and against certification and identify some options, such as: development of an accreditation scheme to ensure that assessment systems meet minimum standards; building up experience from projects that are experimenting with certification in protected areas; and initiating certification schemes for specific users such as private protected areas or institutions like the World Heritage Convention.

The status of hollow-bearing trees required for the conservation of arboreal marsupials in the dry sclerophyll forests of south-east Queensland, Australia

At 38 sites in the dry sclerophyll forests of south-east Queensland, Australia, hollow-bearing trees were studied to determine the effects of past forestry practices on their density, size and spatial distribution. The density of hollow-bearing trees was reduced at sites that had been altered by poisoning and ringbarking of unmerchantable trees. This was especially the case for living hollow-bearing trees that were now at densities too low to support the full range of arboreal marsupials. Although there are presently enough hollow-bearing stags (i.e., dead hollow-bearing trees) to provide additional denning and nesting opportunities, the standing life of these hollow-bearing stags is lower than the living counterparts which means denning and nesting sites may be limited in the near future. The mean diameter at breast height (DBH) of hollow-bearing stags was significantly less than that of living hollow-bearing trees. This indicated that many large hollow-bearing stags may have a shorter standing life than smaller hollow-bearing stags. Hollow-bearing trees appear to be randomly distributed throughout the forest in both silviculturally treated and untreated areas. This finding is at odds with the suggestion by some forest managers that hollow-bearing trees should have a clumped distribution in dry sclerophyll forests of south-east Queensland.

Does birth weight predict childhood diet in the Avon longitudinal study of parents and children?

Study objective: Low birth weight predicts cardiovascular disease in adulthood, and one possible explanation is that children with lower birth weight consume more fat than those born heavier. Therefore, the objective of this study was to investigate associations between birth weight and childhood diet, and in particular, to test the hypothesis that birth weight is inversely related to total and saturated fat intake. Design: Prospective cohort study. Setting: South west England. Participants: A subgroup of children enrolled in the Avon longitudinal study of parents and children, with data on birth weight and also diet at ages 8, 18, 43 months, and 7 years ( 1152, 998, 848, and 771 children respectively). Main results: Associations between birth weight and diet increased in strength from age 8 to 43 months, but had diminished by age 7 years. Fat, saturated fat, and protein intakes were inversely, and carbohydrate intake was positively associated with birth weight at 43 months of age, after adjusting for age, sex, and energy intake. After adjustment for other confounders, all associations were weakened, although there was still a suggestion of a relation with saturated fat ( -0.48 (95% CI -0.97, 0.02) g/day per 500 g increase in birth weight. Similar patterns were seen in boys and girls separately, and when the sample was restricted to those with complete data at all ages. Conclusions: A small inverse association was found between birth weight and saturated fat intake in children at 43 months of age but this was not present at 7 years of age. This study therefore provides little evidence that birth weight modifies subsequent childhood diet.

The identification and characterisation of alleles of sucrose phosphate synthase gene family III in sugarcane

Little is known about the extent of allelic diversity of genes in the complex polyploid, sugarcane. Using sucrose phosphate synthase (SPS) Gene (SPS) Family III as an example, we have amplified and sequenced a 400 nt region from this gene from two sugarcane lines that are parents of a mapping population. Ten single nucleotide polymorphisms (SNPs) were identified within the 400 nt region of which seven were present in both lines. In the elite commercial cultivar Q165(A), 10 sequence haplotypes were identified, with four haplotypes recovered at 9% or greater frequency. Based on SNP presence, two clusters of haplotypes were observed. In IJ76-514, a Saccharum officinarum accession, 8 haplotypes were identified with 4 haplotypes recovered at 13% or greater frequency. Again, two clusters of haplotypes were observed. The results suggest that there may be two SPS Gene Family III genes per genome in sugarcane, each with different numbers of different alleles. This suggestion is supported by sequencing results in an elite parental sorghum line, 403463-2-1, in which 4 haplotypes, corresponding to two broad types, were also identified. Primers were designed to the sugarcane SNPs and screened over bulked DNA from high and low Sucrose-containing progeny from a cross between Q165(A) and IJ76-514. The SNP frequency did not vary in the two bulked DNA samples, suggesting that these SNPs from this SPS gene family are not associated with variation in sucrose content. Using an ecotilling approach, two of the SPS Gene Family III haplotypes were mapped to two different linkage groups in homology group 1 in Q165(A). Both haplotypes mapped near QTLs for increased sucrose content but were not themselves associated with any sugar-related trait.

The relationship between media reporting of suicide and actual suicide in Australia

This study aimed to determine whether media items about suicide were associated with differential increases in actual suicides. Data were available on 4635 suicide-related items appearing in Australian newspapers and on radio and television news and current affairs shows between March 2000 and February 2001. These data were combined with national data on completed suicides occurring during the same period, by a process that involved identifying the date and geographical reach of the media items and determining the number of suicides occurring in the same location in selected weeks pre- and post-item. Regression analyses were conducted to determine whether the likelihood of an increase in post-item suicides could be explained by particular item characteristics. We found that 39% of media items were followed by an increase in mate suicides, and 31% by an increase in female suicides. Media items were more likely to be associated with increases in both male and female suicides if they occurred in the context of multiple other reports on suicide (versus occurring in isolation), if they were broadcast on television (versus other media), and if they were about completed suicide (versus attempted suicide or suicidal ideation). Different item content appeared to be influential for males and females, with an increase in male suicides being associated with items about an individual's experience of suicide and opinion pieces, and an increase in female suicides being associated with items about mass- or murder-suicide. Item prominence and quality were not differentially associated with increases in male or female suicides. Further research on this topic is required, but in the meantime there is a need to remain vigilant about how suicide news is reported. Mental health professionals and suicide experts should collaborate with media professionals to try to balance 'public interest' against the risk of harm. (c) 2005 Published by Elsevier Ltd.

Trends for in situ and invasive melanoma in Queensland, Australia, 1982-2002

Objectives Queensland, the north-eastern state of Australia, has the highest incidence of melanoma in the world. Control measures started earlier here than probably anywhere else in the world; early detection programmes started in the 1960s and primary prevention in the 1980s. Data from the population-based Queensland Cancer Registry therefore provide an internationally unique data source with which to assess trends for in situ and invasive melanomas and to consider the implications for early detection and primary prevention. Methods We used Poisson regression to estimate the annual percentage change in rates across 21 years of incidence data for in situ and invasive lesions, stratified by age and sex. Joinpoint analyses were used to assess whether there had been a statistically significant change in the trends. Results In situ melanomas increased by 10.4% (95% CI: 10.1%, 11.1%) per year among males and 8.4% (7.9%, 8.9%) per year among females. The incidence of invasive lesions also increased, but not as quickly; males 2.6% (2.4%, 2.8%), females 1.2% (0.9%, 1.5%). Valid data on thickness was only available for 1991 to 2002 and for this period thin-invasive lesions were increasing faster than thick-invasive lesions (for example, among males: thin 3.8%, thick 2.0%). We found some suggestive evidence of lower proportionate increase for the most recent years for both in-situ and invasive lesions, but this did not achieve statistical significance. Among people younger than 35 years, the incidence of invasive melanoma was stable and there was a suggestion of a birth cohort effect from about 1958. Mortality rates were stable across all ages, and there was a suggestion of decreasing rates among young women, although this did not achieve statistical significance. Conclusion Age-standardised incidence is continuing to increase and this, in combination with a shift to proportionately more in situ lesions, suggests that the stabilisation of mortality rates is due, in large part, to earlier detection. For primary prevention, after a substantial period of sustained effort in Queensland, there is some suggestive, but not definitive, evidence that progress is being made. Incidence rates are stabilising in those younger than 35 years and the proportionate increase for both in situ and invasive lesions appears to be lower for the most recent period compared with previous periods. However, even taking the most favourable view of these trends, primary prevention is unlikely to lead to decreases in the overall incidence rate of melanoma for at least another 20 years. Consequently, the challenge for primary prevention programmes will be to maintain momentum over the long term. If this can be achieved, the eventual public-health benefits are likely to be substantial.

Type X pottery, Morobe Province, Papua New Guinea: Petrography and possible Micronesian relationships

Type X is one of four Post-Lapita pottery styles reported from Huon Peninsula and the Siassi Islands of Papua New Guinea. Previous petrographic work was inconclusive about its likely area of origin but indicated a possible Huon Peninsula source. Renewed analysis of a larger sample supports this conclusion and confirms the use of grog temper. This kind of temper is otherwise not recorded in the New Guinea region, and its use in the production of Type X was probably culturally driven. Comparisons between Type X and grog-tempered pottery from Palau, Yap, and Pohnpei in Micronesia lead to the suggestion that Type X probably derived from an otherwise unrecorded contact between Huon Peninsula and Palau about 1000 years ago. The article reviews other evidence for interaction between the New Guinea-Bismarck Archipelago region and various parts of Micronesia and concludes that the proposed Type X connection with Palau is but one of several prehistoric contacts between different parts of the regions. Recognition of such contacts, which could have been unintentional and on a small scale, may contribute to explaining the complex ethnolinguistic situation of Huon Peninsula.

Isolates of 'Candidatus Nostocoida limicola' Blackall et al. 2000 should be described as three novel species of the genus Tetrasphaera, as Tetrasphaera jenkinsii sp nov., Tetrasphaera vanveenii sp nov and Tetrasphaera veronensis sp nov.

Despite differences in their morphologies, comparative analyses of 16S rRNA gene sequences revealed high levels of similarity (> 94 %) between strains of the filamentous bacterium 'Candidatus Nostocoida limicola' and the cocci Tetrasphaera australiensis and Tetrasphaera japonica and the rod Tetrasphaera elongata, all isolated from activated sludge. These sequence data and their chemotaxonomic characters, including cell wall, menaquinone and lipid compositions and fingerprints of their 16S-23S rRNA intergenic regions, support the proposition that these isolates should be combined into a single genus containing six species, in the family Intrasporangiaceae in the Actinobacteria. This suggestion receives additional support from DNA-DNA hybridization data and when partial sequences of the rpoC1 gene are compared between these strains. Even though few phenotypic characterization data were obtained for these slowly growing isolates, it is proposed, on the basis of the extensive chemotaxonomic and molecular evidence presented here, that 'Candidatus N. limicola' strains Ben 17, Ben 18, Ben 67, Ben 68 and Ben 74 all be placed into the species Tetrasphaera jenkinsii sp. nov. (type strain Ben 74(T) = DSM 17519(T) = NCIMB 14128(T)), 'Candidatus N. limicola' strain Ben 70 into Tetrasphaera vanveenii sp. nov. (type strain Ben 70(T) = DSM 17518(T) = NCIMB 14127(T)) and 'Candidatus N. limicola' strains Ver 1 and Ver 2 into Tetrasphaera veronensis sp. nov. (type strain Ver 1(T) = DSM 17520(T) = NCIMB 14129(T)).

The role of Temporal Context in the Tritone Paradox

The Tritone Paradox refers to a sequence of two specially synthesised "Shepard" tones which may sound ascending to one listener, and descending to another. The present study examines a recent suggestion that people's responses on this task may be determined by neural processes which are sensitive to temporal variations in pitch - so-called spectral motion detectors. Twelve listeners with normal hearing were presented with pairs of Shepard tones in each of two conditions - first in the traditional sequential manner, and then simultaneously, with one tone presented to each ear. Results indicated that respondents were able to judge consistent relationships between the tones even when presented simultaneously, and a high degree of similarity was observed between responses in each condition. The implications of these results for current theories of the Tritone Paradox are discussed.

Diagnosis of diabetes mellitus: case of different cutoff values: A data mining approach

Objective: An estimation of cut-off points for the diagnosis of diabetes mellitus (DM) based on individual risk factors. Methods: A subset of the 1991 Oman National Diabetes Survey is used, including all patients with a 2h post glucose load >= 200 mg/dl (278 subjects) and a control group of 286 subjects. All subjects previously diagnosed as diabetic and all subjects with missing data values were excluded. The data set was analyzed by use of the SPSS Clementine data mining system. Decision Tree Learners (C5 and CART) and a method for mining association rules (the GRI algorithm) are used. The fasting plasma glucose (FPG), age, sex, family history of diabetes and body mass index (BMI) are input risk factors (independent variables), while diabetes onset (the 2h post glucose load >= 200 mg/dl) is the output (dependent variable). All three techniques used were tested by use of crossvalidation (89.8%). Results: Rules produced for diabetes diagnosis are: A- GRI algorithm (1) FPG>=108.9 mg/dl, (2) FPG>=107.1 and age>39.5 years. B- CART decision trees: FPG >=110.7 mg/dl. C- The C5 decision tree learner: (1) FPG>=95.5 and 54, (2) FPG>=106 and 25.2 kg/m2. (3) FPG>=106 and =133 mg/dl. The three techniques produced rules which cover a significant number of cases (82%), with confidence between 74 and 100%. Conclusion: Our approach supports the suggestion that the present cut-off value of fasting plasma glucose (126 mg/dl) for the diagnosis of diabetes mellitus needs revision, and the individual risk factors such as age and BMI should be considered in defining the new cut-off value.