Complex-linear invariants of biochemical networks

The nonlinearities found in molecular networks usually prevent mathematical analysis of network behaviour, which has largely been studied by numerical simulation. This can lead to difficult problems of parameter determination. However, molecular networks give rise, through mass-action kinetics, to polynomial dynamical systems, whose steady states are zeros of a set of polynomial equations. These equations may be analysed by algebraic methods, in which parameters are treated as symbolic expressions whose numerical values do not have to be known in advance. For instance, an "invariant" of a network is a polynomial expression on selected state variables that vanishes in any steady state. Invariants have been found that encode key network properties and that discriminate between different network structures. Although invariants may be calculated by computational algebraic methods, such as Gr\"obner bases, these become computationally infeasible for biologically realistic networks. Here, we exploit Chemical Reaction Network Theory (CRNT) to develop an efficient procedure for calculating invariants that are linear combinations of "complexes", or the monomials coming from mass action. We show how this procedure can be used in proving earlier results of Horn and Jackson and of Shinar and Feinberg for networks of deficiency at most one. We then apply our method to enzyme bifunctionality, including the bacterial EnvZ/OmpR osmolarity regulator and the mammalian 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase glycolytic regulator, whose networks have deficiencies up to four. We show that bifunctionality leads to different forms of concentration control that are robust to changes in initial conditions or total amounts. Finally, we outline a systematic procedure for using complex-linear invariants to analyse molecular networks of any deficiency.Comment: 36 pages, 6 figure

A Control Systems Perspective to Condition Monitoring and Fault Diagnosis

Modern industrial processors, engineering systems and structures, have grown significantly in complexity and in scale during the recent years. Therefore, there is an increase in the demand for automatic processors, to avoid faults and severe break downs, through predictive maintenance. In this context, the research into nonlinear systems analysis has attained much interest in recent years as linear models cannot be used to represent some of these systems. In the field of control systems, the analysis of such systems is conducted in the frequency domain using methods of Frequency Response Analysis. Generalised Frequency Response Functions (GFRFs) and the Nonlinear Output Frequency Response Functions (NOFRFs) are Frequency Response Analysis techniques used for the analysis of nonlinear dynamical behaviour in the frequency domain. The problem of Condition Monitoring and Fault Diagnosis has been investigated in the perspective of modelling, signal processing and multivariate statistical analysis, data-driven methods such as neural networks have gained significant popularity. This is because possible faulty conditions related to complex systems are often difficult to interpret. In such a background, recently, a new data-driven approach based on a systems perspective has been proposed. This approach uses a controls systems analysis method of System Identification and Frequency Response Analysis and has been shown before as a potential technique. However, this approach has certain practical concerns regarding real-world applications. Motivated by these concerns in this thesis, the following contributions are put forward: 1. The method of evaluating NOFRFs, using input-output data of a nonlinear system may experience numerical errors. This is a major concern, hence the development of a method to overcome these numerical issues effectively. 2. Frequency Response Analysis cannot be used in its current state for nonlinear systems that exhibit severe nonlinear behaviour. Although theoretically, it has been argued that this is possible, even though, it has been impossible in a practical point of view. Therefore, the possibility and the manner in which Frequency Response Analysis can be conducted for these types of systems is presented. 3. Development of a System Identification methodology to overcome the issues of inadequately exciting inputs and appropriately capturing system dynamics under general circumstances of Condition Monitoring and Fault Diagnosis. In addition to the above, the novel implementation of a control systems analysis approach is implemented in characterising corrosion, crack depth and crack length on metal samples. The approach is applied to the data collected, using a newly proposed non-invasive Structural Health Monitoring method called RFID (Radio Frequency IDentification) wireless eddy current probing. The control systems analysis approach along with the RFID wireless eddy current probing method shows the clear potential of being a new technology in non-invasive Structural Health Monitoring systems

Soil Loss Estimation from Kelani River Catchment, Sri Lanka

Soil erosion from land surfaces is a major problem worldwide including Sri Lanka, especially in the Kelani river catchment. Kelani river basin is home to around 25% of the Sri Lankan population. The river is primary source of drinking water to over 4 million people living in the capital city - greater Colombo and over 10,000 industries and businesses depend on the natural resources and services provided by the basin. The land of Kelani river catchment is 2,342.05 km2 of this area 1,211.67 km2 used for agricultural purposes including rubber, tea and paddy and for the home gardens 390.29 km2 have been used. Another 269.38 km2 are occupied for forest cover together with lowland rainforests, sub-montane forests and montane forests. In addition, 24.04 km2 are covered with streams and rivers. To address these issues proper understating of soil erosion from the catchment is a vital requirement. Therefore, a study was conducted with the objective of estimating the soil erosion from the Kelani river watershed using universal soil loss equation (USLE). ArcGIS 10.2.2 commercial software was used to calculate the soil loss from the catchment. The results indicate that the average soil loss ranges between 0 to 715-ton ha-1, which is considerably high soil loss from the catchment. Average soil loss is highest in urbanized areas (715-ton ha-1) due to increases of the slope length factor and the lowest soil loss were found in the forested areas (0-ton ha-1). The soil loss from agricultural areas (481-ton ha-1), had average soil loss. Therefore, immediate soil erosion control measures must be applied to the residential areas. Also, sustainable development strategies should give major consideration for soil conservation. Since, the forested areas have the lowest erosion rates, forest cover in the upper catchments must be protected and expansion of the forests must be promoted. Therefore, this study concludes, estimation and modeling of soil erosion from the Kelani river catchment is an important tool for development of environment conservation and management plans with in the catchment.Keywords: Catchment, GIS, Kelani River, Soil loss USL

Long term trend of selected halogenated hydrocarbons

The so-called 'Library of Background Air' at the Oregon Graduate Institute was used to determine the trend in volume mixing ratios of selected halogenated hydrocarbons in the time period 1977-1989. This library consists of background air samples most of them taken at Cape Meares (Oregon). For storage stainless steel containers are used. Tests have shown the gases under consideration to be stable in these containers. Analyses using a GC/MS-system were performed for the CFCs 11, 12, 12B1 (HALON 1211, CBrClF2), 22, 113, 114 and CH3Cl, CH3Br, CH3CCl3, CCl4. The advantage of this unique investigation: different aged air samples are analyzed at the same time with the same instrument. No calibrations or intercalibrations are needed. All data are presented in normalized mixing ratios versus time. We discuss the results, derive rate constants and present a formula to describe the nonlinear increases

The horofunction boundary of the Hilbert geometry

We investigate the horofunction boundary of the Hilbert geometry defined on an arbitrary finite-dimensional bounded convex domain D. We determine its set of Busemann points, which are those points that are the limits of `almost-geodesics'. In addition, we show that any sequence of points converging to a point in the horofunction boundary also converges in the usual sense to a point in the Euclidean boundary of D. We prove that all horofunctions are Busemann points if and only if the set of extreme sets of the polar of D is closed in the Painleve-Kuratowski topology.Comment: 24 pages, 2 figures; minor changes, examples adde

Introducing New Methodologies for Identifying Design Patterns for Internationalization and Localization

This paper describes a new methodology for deriving interaction design patterns from an analysis of ethnographic data. It suggests using inductive and deductive analysis processes to identify and articulate patterns that address the needs of culturally diverse users of interactive, collaborative systems. This might inform the internationalization and localization process of computer supported collaboration systems

Readiness of the Port of Colombo as a Mega Hub Port for Transshipment Containers

The Colombo Port has become a hub port for transshipment containers in the South-Asia region mainly due to its location advantage and have further carved out a niche linking feeder connections in the Indian subcontinent trade to main sea routes on the back of its access to the Indian Ocean. During past couple of decades major ports around the world have faced significant challenges due to rapid evolvement in marine technology and international logistical system. Primarily there were two major thrusts have been impacting the seaports which identified as ‘Increased specialization of ship design’ and the ‘Growth in ship size’. These two aspects of ship specialization and capacity enhancement that were continued to progress resulted a greater demand in Ports and container terminals to invest on improvements to equipment and ports infrastructure. Each subsequent generation of containership which evolved has not only created new challenges to ports around the world, but also limited the number of port calls. Presently only one deep water container terminal available in Port of Colombo to handle modern day Ultra large container carriers (ULCC’s)

Indoor residual spraying of insecticide and malaria morbidity in a high transmission intensity area of Uganda.

BackgroundRecently the use of indoor residual spraying of insecticide (IRS) has greatly increased in Africa; however, limited data exist on the quantitative impacts of IRS on health outcomes in highly malaria endemic areas.Methodology/principal findingsRoutine data were collected on more than 90,000 patient visits at a single health facility over a 56 month period covering five rounds of IRS using three different insecticides. Temporal associations between the timing of IRS and the probability of a patient referred for microscopy having laboratory confirmed malaria were estimated controlling for seasonality and age. Considering patients less than five years of age there was a modest decrease in the odds of malaria following the 1(st) round of IRS using DDT (OR = 0.76, p<0.001) and the 2(nd) round using alpha-cypermethrin (OR = 0.83, p = 0.002). Following rounds 3-5 using bendiocarb there was a much greater decrease in the odds of malaria (ORs 0.34, 0.16, 0.17 respectively, p<0.001 for all comparisons). Overall, the impact of IRS was less pronounced among patients 5 years or older.Conclusions/significanceIRS was associated with a reduction in malaria morbidity in an area of high transmission intensity in Uganda and the benefits appeared to be greatest after switching to a carbamate class of insecticide

Trace Spaces: an Efficient New Technique for State-Space Reduction

State-space reduction techniques, used primarily in model-checkers, all rely on the idea that some actions are independent, hence could be taken in any (respective) order while put in parallel, without changing the semantics. It is thus not necessary to consider all execution paths in the interleaving semantics of a concurrent program, but rather some equivalence classes. The purpose of this paper is to describe a new algorithm to compute such equivalence classes, and a representative per class, which is based on ideas originating in algebraic topology. We introduce a geometric semantics of concurrent languages, where programs are interpreted as directed topological spaces, and study its properties in order to devise an algorithm for computing dihomotopy classes of execution paths. In particular, our algorithm is able to compute a control-flow graph for concurrent programs, possibly containing loops, which is "as reduced as possible" in the sense that it generates traces modulo equivalence. A preliminary implementation was achieved, showing promising results towards efficient methods to analyze concurrent programs, with very promising results compared to partial-order reduction techniques

A discourse analysis of trainee teacher identity in online discussion forums

Teacher education involves an identity transformation for trainees from being a student to being a teacher. This discourse analysis examined the online discussion board communications of a cohort of trainee teachers to better understand the situated identities of the trainees and how they were presented online. Their discussion board posts were the primary method of communication during placement periods and, as such, provided insight into how the trainees situated their identities in terms of being a student or being a teacher. During the analysis, the community boundaries, language and culture were explored along with the tutor's power and role in the identity transformation process. This involved looking at the lexis used by the students, the use of pronouns to refer to themselves and others such as teachers and pupils, the types of messages allowed in the community and the effect of the tutor's messages on their communication. The research found that the trainees felt comfortable with teaching but did not feel like teachers during the course. Tutors and school teachers need to develop an awareness of the dual nature of trainees' identities and help promote the transition from student to teacher. In the beginning of the course, trainees should be familiarised with teacher vocabulary and practical concepts in addition to pedagogical theory. Towards the end of the course, trainee identity as teachers could be promoted through the use of authentic assessments that mirror real teacher tasks and requirements