Shape predicates allow unbounded verification of linearizability using canonical abstraction

Canonical abstraction is a static analysis technique that represents states as 3-valued logical structures, and is able to construct finite representations of systems with infinite statespaces for verification. The granularity of the abstraction can be altered by the definition of instrumentation predicates, which derive their meaning from other predicates. We introduce shape predicates for preserving certain structures of the state during abstraction. We show that shape predicates allow linearizability to be verified for concurrent data structures using canonical abstraction alone, and use the approach to verify a stack and two queue algorithms. This contrasts with previous efforts to verify linearizability with canonical abstraction, which have had to employ other techniques as well

Analysing Scientific Collaborations of New Zealand Institutions using Scopus Bibliometric Data

Scientific collaborations are among the main enablers of development in small national science systems. Although analysing scientific collaborations is a well-established subject in scientometrics, evaluations of scientific collaborations within a country remain speculative with studies based on a limited number of fields or using data too inadequate to be representative of collaborations at a national level. This study represents a unique view on the collaborative aspect of scientific activities in New Zealand. We perform a quantitative study based on all Scopus publications in all subjects for more than 1500 New Zealand institutions over a period of 6 years to generate an extensive mapping of scientific collaboration at a national level. The comparative results reveal the level of collaboration between New Zealand institutions and business enterprises, government institutions, higher education providers, and private not for profit organisations in 2010-2015. Constructing a collaboration network of institutions, we observe a power-law distribution indicating that a small number of New Zealand institutions account for a large proportion of national collaborations. Network centrality concepts are deployed to identify the most central institutions of the country in terms of collaboration. We also provide comparative results on 15 universities and Crown research institutes based on 27 subject classifications.Comment: 10 pages, 15 figures, accepted author copy with link to research data, Analysing Scientific Collaborations of New Zealand Institutions using Scopus Bibliometric Data. In Proceedings of ACSW 2018: Australasian Computer Science Week 2018, January 29-February 2, 2018, Brisbane, QLD, Australi

A modal proof theory for final polynomial coalgebras

AbstractAn infinitary proof theory is developed for modal logics whose models are coalgebras of polynomial functors on the category of sets. The canonical model method from modal logic is adapted to construct a final coalgebra for any polynomial functor. The states of this final coalgebra are certain “maximal” sets of formulas that have natural syntactic closure properties.The syntax of these logics extends that of previously developed modal languages for polynomial coalgebras by adding formulas that express the “termination” of certain functions induced by transition paths. A completeness theorem is proven for the logic of functors which have the Lindenbaum property that every consistent set of formulas has a maximal extension. This property is shown to hold if the deducibility relation is generated by countably many inference rules.A counter-example to completeness is also given. This is a polynomial functor that is not Lindenbaum: it has an uncountable set of formulas that is deductively consistent but has no maximal extension and is unsatisfiable, even though all of its countable subsets are satisfiable

Resistance of subarctic soil fungal and invertebrate communities to disruption of below-ground carbon supply

The supply of recent photosynthate from plants to soils is thought to be a critical mechanism regulating the activity and diversity of soil biota. In the Arctic, large-scale vegetation transitions are underway in response to warming, and there is an urgent need to understand how these changes affect soil biodiversity and function. We investigated how abundance and diversity of soil fungi and invertebrates responded to a reduction in fresh below-ground photosynthate supply in treeline birch and willow, achieved using stem girdling. We hypothesised that birch forest would support greater abundance of ectomycorrhizal (ECM) fungal species and fauna than willow shrubs, and that girdling would result in a rapid switch from ECM fungi to saprotrophs as canopy supply of C was cut, with a concomitant decline in soil fauna. Birch forest had greater fungal and faunal abundance with a large contribution of root-associated ascomycetes (ericoid mycorrhizal fungi and root endophytes) compared to willow shrub plots, which had a higher proportion of saprotrophs and, contrary to our expectations, ECM fungi. Broad-scale soil fungal and faunal functional group composition was not significantly changed by girdling, even in the third year of treatment. Within the ECM community, there were some changes, with genera that are believed to be particularly C-demanding declining in girdled plots. However, it was notable how most ECM fungi remained present after 3 years of isolation of the below-ground compartment from contemporary photosynthate supply. Synthesis. In a treeline/tundra ecosystem, distinct soil communities existed in contrasting vegetation patches within the landscape, but the structure of these communities was resistant to canopy disturbance and concomitant reduction of autotrophic C inputs

Rhizosphere allocation by canopy-forming species dominates soil CO2 efflux in a subarctic landscape

In arctic ecosystems, climate change has increased plant productivity. As arctic carbon (C) stocks are predominantly located below ground, the effects of greater plant productivity on soil C storage will significantly determine the net sink/source potential of these ecosystems, but vegetation controls on soil CO2 efflux remain poorly resolved. To identify the role of canopy‐forming species in below‐ground C dynamics, we conducted a girdling experiment with plots distributed across 1 km2 of treeline birch (Betula pubescens) forest and willow (Salix lapponum) patches in northern Sweden and quantified the contribution of canopy vegetation to soil CO2 fluxes and below‐ground productivity. Girdling birches reduced total soil CO2 efflux in the peak growing season by 53% ‐double the expected amount, given that trees contribute only half of the total leaf area in the forest. Root and mycorrhizal mycelial production also decreased substantially. At peak season, willow shrubs contributed 38% to soil CO2 efflux in their patches. Our findings indicate that C, recently fixed by trees and tall shrubs, makes a substantial contribution to soil respiration. It is critically important that these processes are taken into consideration in the context of a greening arctic since productivity and ecosystem C sequestration are not synonymous

Three Pathogens in Sympatric Populations of Pumas, Bobcats, and Domestic Cats: Implications for Infectious Disease Transmission

Anthropogenic landscape change can lead to increased opportunities for pathogen transmission between domestic and non-domestic animals. Pumas, bobcats, and domestic cats are sympatric in many areas of North America and share many of the same pathogens, some of which are zoonotic. We analyzed bobcat, puma, and feral domestic cat samples collected from targeted geographic areas. We examined exposure to three pathogens that are taxonomically diverse (bacterial, protozoal, viral), that incorporate multiple transmission strategies (vector-borne, environmental exposure/ingestion, and direct contact), and that vary in species-specificity. Bartonella spp., Feline Immunodeficiency Virus (FIV), and Toxoplasma gondii IgG were detected in all three species with mean respective prevalence as follows: puma 16%, 41% and 75%; bobcat 31%, 22% and 43%; domestic cat 45%, 10% and 1%. Bartonella spp. were highly prevalent among domestic cats in Southern California compared to other cohort groups. Feline Immunodeficiency Virus exposure was primarily associated with species and age, and was not influenced by geographic location. Pumas were more likely to be infected with FIV than bobcats, with domestic cats having the lowest infection rate. Toxoplasma gondii seroprevalence was high in both pumas and bobcats across all sites; in contrast, few domestic cats were seropositive, despite the fact that feral, free ranging domestic cats were targeted in this study. Interestingly, a directly transmitted species-specific disease (FIV) was not associated with geographic location, while exposure to indirectly transmitted diseases – vector-borne for Bartonella spp. and ingestion of oocysts via infected prey or environmental exposure for T. gondii – varied significantly by site. Pathogens transmitted by direct contact may be more dependent upon individual behaviors and intra-specific encounters. Future studies will integrate host density, as well as landscape features, to better understand the mechanisms driving disease exposure and to predict zones of cross-species pathogen transmission among wild and domestic felids

A Modal Proof Theory for Polynomial Coalgebras

The abstract mathematical structures known as coalgebras are of increas-ing interest in computer science for their use in modelling certain types of data structures and programs. Traditional algebraic methods describe objects in terms of their construction, whilst coalgebraic methods describe objects in terms of their decomposition, or observational behaviour. The latter techniques are particularly useful for modelling infinite data struc-tures and providing semantics for object-oriented programming languages, such as Java. There have been many different logics developed for reasoning about coalgebras of particular functors, most involving modal logic. We define a modal logic for coalgebras of polynomial functors, extending Rößiger’s logic [33], whose proof theory was limited to using finite constant sets, by adding an operator from Goldblatt [11]. From the semantics we de-fine a canonical coalgebra that provides a natural construction of a final coalgebra for the relevant functor. We then give an infinitary axiomatiza-tion and syntactic proof relation that is sound and complete for functors constructed from countable constant sets. Acknowledgments I am deeply indebted to my supervisor, Professor Robert Goldblatt, for pointing me in the right direction and keeping my wheels on the tracks. His mathematical advice is the best anyone could hope for. I would like to thank Ranald Clouston for many discussions on logic and life in general. This thesis (and my life in general) are the better for them. I would like to thank all the people at the Centre for Logic, Language and Computation at Victoria who have taught me through my undergrad-uate years for introducing me to the exciting world of logic. Financially, I have been supported by a scholarship from the Logic and Computation programme of the New Zealand Institute for Mathematics and its Applications. I am grateful for the hospitality of the Institute fo

On-farm estimation of energy balance in dairy cows using only frequent body weight measurements and body condition score

Precise energy balance estimates for individual cows are of great importance to monitor health, reproduction, and feed management. Energy balance is usually calculated as energy input minus output (EBinout), requiring measurements of feed intake and energy output sources (milk, maintenance, activity, growth, and pregnancy). Except for milk yield, direct measurements of the other sources are difficult to obtain in practice, and estimates contain considerable error sources, limiting on-farm use. Alternatively, energy balance can be estimated from body reserve changes (EBbody) using body weight (BW) and body condition score (BCS). Automated weighing systems exist and new technology performing semi-automated body condition scoring has emerged, so frequent automated BW and BCS measurements are feasible. We present a method to derive individual EBbody estimates from frequently measured BW and BCS and evaluate the performance of the estimated EBbody against the traditional EBinout method. From 76 Danish Holstein and Jersey cows, parity 1 or 2+, on a glycerol-rich or a whole grain-rich total mixed ration, BW was measured automatically at each milking. The BW was corrected for the weight of milk produced and for gutfill. Changes in BW and BCS were used to calculate changes in body protein, body lipid, and EBbody during the first 150 d in milk. The EBbody was compared with the traditional EBinout by isolating the term within EBinout associated with most uncertainty; that is, feed energy content (FEC); FEC = (EBbody + EMilk + EMaintenance + Eactivity)/dry matter intake, where the energy requirements are for milk produced (EMilk), maintenance (EMaintenance), and activity (EActivity). Estimated FEC agreed well with FEC values derived from tables (the mean estimate was 0.21 MJ of effective energy/kg of dry matter or 2.2% higher than the mean table value). Further, the FEC profile did not suggest systematic bias in EBbody with stage of lactation. The EBbody estimated from daily BW, adjusted for milk and meal-related gutfill and combined with frequent BCS, can provide a successful tool. This offers a pragmatic solution to on-farm calculation of energy balance with the perspective of improved precision under commercial conditions