title: A refinement theory for μ∼Charts

authors: Reeve, Greg

abstract: The language μ-Charts is one of many Statechart-like languages, a family of visual languages that are used for designing reactive systems. We introduce a logic for reasoning about and constructing refinements for μ-Charts. The logic itself is interesting and important because it allows reasoning about μ-charts in terms of partial relations rather than the more traditional traces approach. The method of derivation of the logic is also worthy of report. AZ-based model for the language μ-Charts is constructed and the existing logic and refinement calculus of Z is used as the basis for the logic of μ-Charts. As well as describing the logic we introduce some of the ways such a logic can be used to reason about properties of μ-Charts and the refinement of abstract specifications into concrete realisations of reactive systems.
A refinement theory for Statechart-like languages is an important contribution because it allows us to formally investigate and reason about properties of the object language μ-Charts. In particular, we can conjecture and prove general properties required of the object language. This allows us to contrast possible language design decisions and comment on their consequences with respect to the design of Statechart-like languages. 
This thesis gives a comprehensive description of the μ-Charts language and details the development of a partial relations based logic and refinement calculus for the language. The logic and refinement calculus are presented as natural deduction style proof rules that allow us to give formal proofs of language properties and provide the basis for a formal program development framework. The notion of refinement that is encoded by the refinement rules is also extensively investigated.

text: A refinement theory for μ∼Charts The language μ-Charts is one of many Statechart-like languages, a family of visual languages that are used for designing reactive systems. We introduce a logic for reasoning about and constructing refinements for μ-Charts. The logic itself is interesting and important because it allows reasoning about μ-charts in terms of partial relations rather than the more traditional traces approach. The method of derivation of the logic is also worthy of report. AZ-based model for the language μ-Charts is constructed and the existing logic and refinement calculus of Z is used as the basis for the logic of μ-Charts. As well as describing the logic we introduce some of the ways such a logic can be used to reason about properties of μ-Charts and the refinement of abstract specifications into concrete realisations of reactive systems.
A refinement theory for Statechart-like languages is an important contribution because it allows us to formally investigate and reason about properties of the object language μ-Charts. In particular, we can conjecture and prove general properties required of the object language. This allows us to contrast possible language design decisions and comment on their consequences with respect to the design of Statechart-like languages. 
This thesis gives a comprehensive description of the μ-Charts language and details the development of a partial relations based logic and refinement calculus for the language. The logic and refinement calculus are presented as natural deduction style proof rules that allow us to give formal proofs of language properties and provide the basis for a formal program development framework. The notion of refinement that is encoded by the refinement rules is also extensively investigated.

year: 2005

title: Assessing the use of molecular techniques to determine terrestrial invertebrate diversity in New Zealand mangroves and detection of blue ducks in New Zealand streams

authors: Doyle, Erin Jane

subjects: DNA barcoding

abstract: Biodiversity monitoring requires reliable methods for species detection and identification. Here, I examine the use of molecular approaches, including mitochondrial DNA sequencing (barcoding) and environmental DNA (eDNA) analyses in two New Zealand-based case studies. In the first study, I used DNA barcoding to assess the diversity of arthropods collected from the mangroves within RAMSAR protected wetland area in the Firth of Thames, New Zealand. Over one year, a total of 9829 individuals were collected and of these 251 were sequenced. COI sequences were largely congruent with morpho-species designations. The sequences formed 101 putative species, 39% of which contained specimens from outside of New Zealand. 44% of the putative species found at the Thames sites had not been previously found in an inland habitat.  I conclude that the terrestrial arthropod community of the mangrove forest in the Firth of Thames is distinctly different from other New Zealand habitats, and may include species not found elsewhere. In the second study, I examined the use environmental DNA (eDNA) as a tool for detecting the presence of New Zealand’s endemic blue duck, or whio, (Hymenolaimus malacorhynchos) in rivers, through water sampling. Species specific primers were designed to target a section of the mitochondrial control region. Water samples were collected from running water within artificial blue duck habitats using an in situ filtration system, eDNA was then extracted from the filter. Any blue duck DNA present in the sample was selectively amplified using the species specific primers. This allowed for blue ducks to be detected through sequencing of the PCR product. In 66% of these cases, it was possible to detect blue duck DNA from the filtered water samples. On this basis, I conclude that there is sufficient “proof of concept” to warrant further investigation into the methods developed here, specifically, the testing of samples from natural environments, in which the presence of H. malacorhynchos has been confirmed by traditional methods.

text: Assessing the use of molecular techniques to determine terrestrial invertebrate diversity in New Zealand mangroves and detection of blue ducks in New Zealand streams Biodiversity monitoring requires reliable methods for species detection and identification. Here, I examine the use of molecular approaches, including mitochondrial DNA sequencing (barcoding) and environmental DNA (eDNA) analyses in two New Zealand-based case studies. In the first study, I used DNA barcoding to assess the diversity of arthropods collected from the mangroves within RAMSAR protected wetland area in the Firth of Thames, New Zealand. Over one year, a total of 9829 individuals were collected and of these 251 were sequenced. COI sequences were largely congruent with morpho-species designations. The sequences formed 101 putative species, 39% of which contained specimens from outside of New Zealand. 44% of the putative species found at the Thames sites had not been previously found in an inland habitat.  I conclude that the terrestrial arthropod community of the mangrove forest in the Firth of Thames is distinctly different from other New Zealand habitats, and may include species not found elsewhere. In the second study, I examined the use environmental DNA (eDNA) as a tool for detecting the presence of New Zealand’s endemic blue duck, or whio, (Hymenolaimus malacorhynchos) in rivers, through water sampling. Species specific primers were designed to target a section of the mitochondrial control region. Water samples were collected from running water within artificial blue duck habitats using an in situ filtration system, eDNA was then extracted from the filter. Any blue duck DNA present in the sample was selectively amplified using the species specific primers. This allowed for blue ducks to be detected through sequencing of the PCR product. In 66% of these cases, it was possible to detect blue duck DNA from the filtered water samples. On this basis, I conclude that there is sufficient “proof of concept” to warrant further investigation into the methods developed here, specifically, the testing of samples from natural environments, in which the presence of H. malacorhynchos has been confirmed by traditional methods.

year: 2015

title: Evidence for late polynesian colonization of New Zealand: University of Waikato radiocarbon measurements

authors: Hogg, Alan G.

subjects: radiocarbon

abstract: We present radiocarbon determinations for 271 New Zealand archaeological samples measured at the University of Waikato Radiocarbon Dating Laboratory between 1975 and 1995. A discard protocol is applied to the series and the list culled to winnow the acceptable dates from those that may incorporate error. None of the 221 acceptable ¹⁴C determinations older than 600 BP (in the case of terrestrial samples) or 930 BP (in the case of marine and estuarine shell) extends beyond cal AD 1250. This conclusion supports the short chronology model of New Zealand prehistory presented by Anderson (1991).

text: Evidence for late polynesian colonization of New Zealand: University of Waikato radiocarbon measurements We present radiocarbon determinations for 271 New Zealand archaeological samples measured at the University of Waikato Radiocarbon Dating Laboratory between 1975 and 1995. A discard protocol is applied to the series and the list culled to winnow the acceptable dates from those that may incorporate error. None of the 221 acceptable ¹⁴C determinations older than 600 BP (in the case of terrestrial samples) or 930 BP (in the case of marine and estuarine shell) extends beyond cal AD 1250. This conclusion supports the short chronology model of New Zealand prehistory presented by Anderson (1991).

year: 1997