A Process-Oriented Architecture for Complex System Modelling

A fine-grained massively-parallel process-oriented model of platelets (potentially artificial) within a blood vessel is presented. This is a CSP inspired design, expressed and implemented using the occam-pi language. It is part of the TUNA pilot study on nanite assemblers at the universities of York, Surrey and Kent. The aim for this model is to engineer emergent behaviour from the platelets, such that they respond to a wound in the blood vessel wall in a way similar to that found in the human body -- i.e. the formation of clots to stem blood flow from the wound and facilitate healing. An architecture for a three dimensional model (relying strongly on the dynamic and mobile capabilities of occam-pi) is given, along with mechanisms for visualisation and interaction. The biological accuracy of the current model is very approximate. However, its process-oriented nature enables simple refinement (through the addition of processes modelling different stimulants/inhibitors of the clotting reaction, different platelet types and other participating organelles) to greater and greater realism. Even with the current system, simple experiments are possible and have scientific interest (e.g. the effect of platelet density on the success of the clotting mechanism in stemming blood flow: too high or too low and the process fails). General principles for the design of large and complex system models are drawn. The described case study runs to millions of processes engaged in ever-changing communication topologies. It is free from deadlock, livelock, race hazards and starvation em by design, employing a small set of synchronisation patterns for which we have proven safety theorems

Testing carbon farming opportunities for salinity management

An emerging prospect for farm revenue from revegetation of saline and other lands that are marginal or non-productive for agriculture is the sale of carbon credits. Australian Government schemes for carbon credits include the Carbon Farming Initiative (CFI) and the proposed Emissions Reduction Fund (ERF) Therefore, this study aimed to assess the potential for woody vegetation (trees and shrubs) established on and around salt-affected lands in the Northern Agricultural Region (NAR) to remove carbon dioxide from the atmosphere and store (sequester) the carbon in new growth. Revegetation plantings on six farms were selected for the study after the landowners expressed interest in participating in the study. Criteria for selection included: minimum of 5 ha planted on and around salt-affected land; a variety of native trees and shrub species planted; and that the plantings must be at least 10 years old. Across the six farms a total of nine sites were selected for the study. The estimates of carbon stocks in species and sites were projected forwards and backwards from the measurement ages (11 - 22 years)to age 15 years to \u27age standardise\u27 the results and facilitate comparison between species and sites. This was done using the national carbon accounting model, FullCAM

The symbiosis of concurrency and verification: teaching and case studies

Concurrency is beginning to be accepted as a core knowledge area in the undergraduate CS curriculum—no longer isolated, for example, as a support mechanism in a module on operating systems or reserved as an advanced discipline for later study. Formal verification of system properties is often considered a difficult subject area, requiring significant mathematical knowledge and generally restricted to smaller systems employing sequential logic only. This paper presents materials, methods and experiences of teaching concurrency and verification as a unified subject, as early as possible in the curriculum, so that they become fundamental elements of our software engineering tool kit—to be used together every day as a matter of course. Concurrency and verification should live in symbiosis. Verification is essential for concurrent systems as testing becomes especially inadequate in the face of complex non-deterministic (and, therefore, hard to repeat) behaviours. Concurrency should simplify the expression of most scales and forms of computer system by reflecting the concurrency of the worlds in which they operate (and, therefore, have to model); simplified expression leads to simplified reasoning and, hence, verification. Our approach lets these skills be developed without requiring students to be trained in the underlying formal mathematics. Instead, we build on the work of those who have engineered that necessary mathematics into the concurrency models we use (CSP, ?-calculus), the model checker (FDR) that lets us explore and verify those systems, and the programming languages/libraries (occam-?, Go, JCSP, ProcessJ) that let us design and build efficient executable systems within these models. This paper introduces a workflow methodology for the development and verification of concurrent systems; it also presents and reflects on two open-ended case studies, using this workflow, developed at the authors’ two universities. Concerns analysed include safety (don’t do bad things), liveness (do good things) and low probability deadlock (that testing fails to discover). The necessary technical background is given to make this paper self-contained and its work simple to reproduce and extend

The Next Generation Event Horizon Telescope Collaboration: History, Philosophy, and Culture

This white paper outlines the plans of the History Philosophy Culture Working Group of the Next Generation Event Horizon Telescope Collaboration.Comment: 23 pages, 1 figur

Bacterial Acquisition in Juveniles of Several Broadcast Spawning Coral Species

Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH) using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals

The Use of Preoperative Prophylactic Systemic Antibiotics for the Prevention of Endopthalmitis in Open Globe Injuries:A Meta-Analysis

Topic:This study reports the effect of systemic prophylactic antibiotics (and their route) on the risk of endophthalmitis after open globe injury. Clinical relevance:Endophthalmitis is a major complication of open globe injury, it can lead to rapid sight loss in the affected eye. The administration of systemic antibiotic prophylaxis is common practice in some health care systems, although there is no consensus on their use. PubMed, CENTRAL, Web of Science, CINAHL and Embase were searched. This was completed 6th July 2021 and updated 10th Dec 2022. We included randomised and non-randomised prospective studies which reported the rate of post-open globe injury endophthalmitis, when systemic pre-operative antibiotic prophylaxis (via the oral or intravenous route) was given. The Cochrane Risk of Bias tool and ROBINS-I tool were used for assessing the risk of bias. Where meta-analysis was performed results were reported as odds ratio. PROSPERO registration: CRD42021271271. Three studies were included. One prospective observational study compared outcomes of patients who had received systemic or no systemic pre-operative antibiotics. The endophthalmitis rates reported were 3.75% and 4.91% in the systemic and no systemic pre-operative antibiotics groups, a non-significant difference (p = 0.68). Two randomised controlled trials were included (1,555 patients). The rates of endophthalmitis were 17 events in 751 patients (2.26%) and 17 events in 804 patients (2.11%) in the oral antibiotics and intravenous (+/- oral) antibiotics groups, respectively. Meta-analysis demonstrated no significant differences between groups (OR 1.07 [95% confidence interval 0.54 – 2.12]). The incidences of endophthalmitis after open globe injury were low with and without systemic antibiotic prophylaxis, although high risk cases were excluded in the included studies. When antibiotic prophylaxis is considered, there is moderate evidence that oral antibiotic administration is non-inferior to intravenous

Induction of Larval Metamorphosis of the Coral Acropora millepora by Tetrabromopyrrole Isolated from a Pseudoalteromonas Bacterium

The induction of larval attachment and metamorphosis of benthic marine invertebrates is widely considered to rely on habitat specific cues. While microbial biofilms on marine hard substrates have received considerable attention as specific signals for a wide and phylogenetically diverse array of marine invertebrates, the presumed chemical settlement signals produced by the bacteria have to date not been characterized. Here we isolated and fully characterized the first chemical signal from bacteria that induced larval metamorphosis of acroporid coral larvae (Acropora millepora). The metamorphic cue was identified as tetrabromopyrrole (TBP) in four bacterial Pseudoalteromonas strains among a culture library of 225 isolates obtained from the crustose coralline algae Neogoniolithon fosliei and Hydrolithon onkodes. Coral planulae transformed into fully developed polyps within 6 h, but only a small proportion of these polyps attached to the substratum. The biofilm cell density of the four bacterial strains had no influence on the ratio of attached vs. non-attached polyps. Larval bioassays with ethanolic extracts of the bacterial isolates, as well as synthetic TBP resulted in consistent responses of coral planulae to various doses of TBP. The lowest bacterial density of one of the Pseudoalteromonas strains which induced metamorphosis was 7,000 cells mm−2 in laboratory assays, which is on the order of 0.1 –1% of the total numbers of bacteria typically found on such surfaces. These results, in which an actual cue from bacteria has been characterized for the first time, contribute significantly towards understanding the complex process of acroporid coral larval settlement mediated through epibiotic microbial biofilms on crustose coralline algae

Growth, yield and carbon sequestration of Pinus pinaster established on farmland in south-western Australia

© 2004 Dr. Peter Ritson.The objective of this study was to develop integrated systems for measurement and modelling of site quality, timber yields and carbon sequestration of Pinus pinaster established on farms in south-west Australia. Established farm plantings were identified for the necessary sampling and measurements but, as broadscale P.pinaster planting on farms is a relatively new venture, those available for study were mostly small-scale and not managed for current timber production objectives. Therefore new methods for sampling, data analysis and modelling were developed or adapted to indicate the growth and carbon sequestration that will be achieved in the new plantations. The system developed for site quality assessment is a two-stage process. Firstly, survival rate is predicted from annual pan evaporation and soil salinity. Then, site index (SI) is predicted from annual rainfall and six soil variables: soil salinity, depth to bedrock, depth to gravel layer, depth of pale soil, presence of high watertable, and soil colour at 5 cm soil depth. A difference equation form of the Chapman-Richards growth model is applied to predict future stemwood volume yield from measurement of current or past stemwood volume. Alternatively, in the case where P.pinaster has not been grown at a site, or no growth measurements are available, yield is predicted from SI. In both cases the yield prediction models were developed for fully-stocked block plantings, wider-spaced block plantings and belt plantings. A thinning model simulates the response of stemwood volume to thinning operations in block plantings. Equations were developed to predict biomass and carbon mass in individual trees (from stem diameter and height to crown base) and stands (from stand age, SI, stocking density and planting layout) from destructive sampling of above- and belowground biomass of 148 P. pinaster trees from 18 farm plantations. A simulation model Farm Wood was developed to forecast carbon sequestration trends at stand- to project-scale over one or more rotations of P. pinaster on farms. This includes carbon in live trees (tops and roots), harvest residues, wood products and soil organic matter