Quantifying spatial structure in experimental observations and agent-based simulations using pair-correlation functions

We define a pair-correlation function that can be used to characterize spatiotemporal patterning in experimental images and snapshots from discrete simulations. Unlike previous pair-correlation functions, the pair-correlation functions developed here depend on the location and size of objects. The pair-correlation function can be used to indicate complete spatial randomness, aggregation or segregation over a range of length scales, and quantifies spatial structures such as the shape, size and distribution of clusters. Comparing pair-correlation data for various experimental and simulation images illustrates their potential use as a summary statistic for calibrating discrete models of various physical processes.

Mass spectrometry-based metabolomics towards understanding of gene functions with a diversity of biological contexts

Currently, mass spectrometry-based metabolomics studies extend beyond conventional chemical categorization and metabolic phenotype analysis to understanding gene function in various biological contexts (e.g., mammalian, plant, and microbial). These novel utilities have led to many innovative discoveries in the following areas: disease pathogenesis, therapeutic pathway or target identification, the biochemistry of animal and plant physiological and pathological activities in response to diverse stimuli, and molecular signatures of host-pathogen interactions during microbial infection. In this review, we critically evaluate the representative applications of mass spectrometry-based metabolomics to better understand gene function in diverse biological contexts, with special emphasis on working principles, study protocols, and possible future development of this technique. Collectively, this review raises awareness within the biomedical community of the scientific value and applicability of mass spectrometry-based metabolomics strategies to better understand gene function, thus advancing this application's utility in a broad range of biological fields

A family of Alltop functions that are EA-inequivalent to the cubic function

Sequences with optimal correlation properties are much sought after for applications in communication systems. In 1980, Alltop (\emph{IEEE Trans. Inf. Theory} 26(3):350-354, 1980) described a set of sequences based on a cubic function and showed that these sequences were optimal with respect to the known bounds on auto and crosscorrelation. Subsequently these sequences were used to construct mutually unbiased bases (MUBs), a structure of importance in quantum information theory. The key feature of this cubic function is that its difference function is a planar function. Functions with planar difference functions have been called \emph{Alltop functions}. This paper provides a new family of Alltop functions and establishes the use of Alltop functions for construction of sequence sets and MUBs.

A framework for security analysis of key derivation functions

This paper presents a comprehensive formal security framework for key derivation functions (KDF). The major security goal for a KDF is to produce cryptographic keys from a private seed value where the derived cryptographic keys are indistinguishable from random binary strings. We form a framework of five security models for KDFs. This consists of four security models that we propose: Known Public Inputs Attack (KPM, KPS), Adaptive Chosen Context Information Attack (CCM) and Adaptive Chosen Public Inputs Attack(CPM); and another security model, previously defined by Krawczyk [6], which we refer to as Adaptive Chosen Context Information Attack(CCS). These security models are simulated using an indistinguisibility game. In addition we prove the relationships between these five security models and analyse KDFs using the framework (in the random oracle model).

Proceedings of the 6th Knowledge Cities World Summit, KCWS 2013

In recent years, with the impact of global knowledge economy, a more comprehensive development approach has gained significant popularity. This new development approach, so called ‘knowledge-based urban development’, is different from its traditional predecessor. With a much more balanced focus on all of the four key development domains – economic, spatial, institutional, and socio-cultural – this contemporary approach, aims to bring economic prosperity, environmental sustainability and local institutional competence with a just socio-spatial order to our cities and regions. The ultimate goal of knowledgebased urban development is to produce a city purposefully designed to encourage the continuous production, circulation and commercialization of social and scientific knowledge – this will in turn establish a ‘knowledge city’. A city following the ‘knowledge city’ concept embarks on a strategic mission to firmly encourage and nurture locally focused innovation, science and creativity within the context of an expanding knowledge economy and society. In this regard a ‘knowledge city’ can be seen as an integrated city, which physically and institutionally combines the functions of a science and technology park with civic and residential functions and urban amenities. It also offers one of the effective paradigms for the sustainable cities of our time. This sixth edition of KCWS – The 6th Knowledge Cities World Summit 2013 – makes an important reminder that the ‘knowledge city’ concept is a key notion in the 21st Century development. Considering this notion, the Summit sheds light on the multifaceted dimensions and various scales of building a ‘knowledge city’ via ‘knowledge-based urban development’ paradigm by particularly focusing on the overall Summit theme of ‘Establishing Bridges’. At this summit, the theoretical and practical maturing of knowledge-based development paradigms are advanced through the interplay between the world’s leading academics’ theories and the practical models and strategies of practitioners’ and policy makers’ drawn from around the world. This summit proceeding is compiled in order to disseminate the knowledge generated and shared in KCWS 2013 with the wider research, governance, and practice communities the knowledge co-created in this summit. All papers of this proceeding have gone through a double-blind peer review process and been reviewed by our summit editorial review and advisory board members. We, organizers of the summit, cordially thank the members of the Summit Proceeding Editorial Review and Advisory Board for their diligent work in the review of the papers. Also we thank Prof.Dr. Ahmet Ademoğlu, Rector of İstanbul Şehir University, for providing all the support for the Summit. We hope the papers in this proceeding will inspire and make a significant contribution to the research, governance, and practice circles.

Laboratory measurement of hydraulic conductivity functions of two unsaturated sandy soils during drying and wetting processes

The importance of applying unsaturated soil mechanics to geotechnical engineering design has been well understood. However, the consumption of time and the necessity for a specific laboratory testing apparatus when measuring unsaturated soil properties have limited the application of unsaturated soil mechanics theories in practice. Although methods for predicting unsaturated soil properties have been developed, the verification of these methods for a wide range of soil types is required in order to increase the confidence of practicing engineers in using these methods. In this study, a new permeameter was developed to measure the hydraulic conductivity of unsaturated soils using the steady-state method and directly measured suction (negative pore-water pressure) values. The apparatus is instrumented with two tensiometers for the direct measurement of suction during the tests. The apparatus can be used to obtain the hydraulic conductivity function of sandy soil over a low suction range (0-10 kPa). Firstly, the repeatability of the unsaturated hydraulic conductivity measurement, using the new permeameter, was verified by conducting tests on two identical sandy soil specimens and obtaining similar results. The hydraulic conductivity functions of the two sandy soils were then measured during the drying and wetting processes of the soils. A significant hysteresis was observed when the hydraulic conductivity was plotted against the suction. However, the hysteresis effects were not apparent when the conductivity was plotted against the volumetric water content. Furthermore, the measured unsaturated hydraulic conductivity functions were compared with predictions using three different predictive methods that are widely incorporated into numerical software. The results suggest that these predictive methods are capable of capturing the measured behavior with reasonable agreement.

Continuous monitoring of reservoir water quality: The Wivenhoe Project

The Lake Wivenhoe Integrated Wireless Sensor Network is conceptually similar to traditional SCADA monitoring and control approaches. However, it is applied in an open system using wireless devices to monitor processes that affect water quality at both a high spatial and temporal frequency. This monitoring assists scientists to better understand drivers of key processes that influence water quality and provide the operators with an early warning system if below standard water enters the reservoir. Both of these aspects improve the safety and efficient delivery of drinking water to the end users.

Continuous production of Bi-2212 thick film on silver tape

Bi-2212 thick film on silver tapes are seen as a simple and low cost alternative to high temperature superconducting wires produced by the Powder In Thbe (PIT) technique, particularly in react and wind applications. A rig for the continuous production of Bi-2212 tapes for use in react and wind component manufacture has been developed and commissioned. The rig consists of several sections, each fully automatic, for task specific duties in the production of HTS tape. The major sections are: tape coating, sintering and annealing. High temperature superconducting tapes with engineering critical current densities of 10 kA/cm2 (77 K, self field), and lengths of up to 100 m have been produced using the rig. Properties of the finished tape are discussed and results are presented for current density versus bend radius and applied strain. Depending on tape content and thickness, irreversible strain tirrm varies between 0.04 and 0.1 %. Cyclic bending tests when applied strain does not exceed Eirrm showed negligible reduction in J c along the length of the tape.

Gemcitabine reactivates epigenetically silenced genes and functions as a DNA methyltransferase inhibitor

Gemcitabine is indicated in combination with cisplatin as first-line therapy for solid tumours including non-small cell lung cancer (NSCLC), bladder cancer and mesothelioma. Gemcitabine is an analogue of pyrimidine cytosine and functions as an anti-metabolite. Structurally, however, gemcitabine has similarities to 5-aza-2-deoxycytidine (decitabine/Dacogen®), a DNA methyltransferase inhibitor (DNMTi). NSCLC, mesothelioma and prostate cancer cell lines were treated with decitabine and gemcitabine. Reactivation of epigenetically silenced genes was examined by RT-PCR/qPCR. DNA methyltransferase activity in nuclear extracts and recombinant proteins was measured using a DNA methyltransferase assay, and alterations in DNA methylation status were examined using methylation-specific PCR (MS-PCR) and pyrosequencing. We observe a reactivation of several epigenetically silenced genes including GSTP1, IGFBP3 and RASSF1A. Gemcitabine functionally inhibited DNA methyltransferase activity in both nuclear extracts and recombinant proteins. Gemcitabine dramatically destabilised DNMT1 protein. However, DNA CpG methylation was for the most part unaffected by gemcitabine. In conclusion, gemcitabine both inhibits and destabilises DNA methyltransferases and reactivates epigenetically silenced genes having activity equivalent to decitabine at concentrations significantly lower than those achieved in the treatment of patients with solid tumours. This property may contribute to the anticancer activity of gemcitabine.

A RBF meshless approach for modeling a fractal mobile/immobile transport model

A fractional differential equation is used to describe a fractal model of mobile/immobile transport with a power law memory function. This equation is the limiting equation that governs continuous time random walks with heavy tailed random waiting times. In this paper, we firstly propose a finite difference method to discretize the time variable and obtain a semi-discrete scheme. Then we discuss its stability and convergence. Secondly we consider a meshless method based on radial basis functions (RBFs) to discretize the space variable. In contrast to conventional FDM and FEM, the meshless method is demonstrated to have distinct advantages: calculations can be performed independent of a mesh, it is more accurate and it can be used to solve complex problems. Finally the convergence order is verified from a numerical example which is presented to describe a fractal model of mobile/immobile transport process with different problem domains. The numerical results indicate that the present meshless approach is very effective for modeling and simulating fractional differential equations, and it has good potential in the development of a robust simulation tool for problems in engineering and science that are governed by various types of fractional differential equations.

Continuous remote emissions monitoring – the lynchpin for air quality management

Diesel particulate matter (DPM), in particular, has been likened in a somewhat inflammatory manner to be the ‘next asbestos’. From the business change perspective, there are three areas holding the industry back from fully engaging with the issue: 1. There is no real feedback loop in any operational sense to assess the impact of investment or application of controls to manage diesel emissions. 2. DPM are getting ever smaller and more numerous, but there is no practical way of measuring them to regulate them in the field. Mass, the current basis of regulation, is becoming less and less relevant. 3. Diesel emissions management is generally wholly viewed as a cost, yet there are significant areas of benefit available from good management. This paper discusses a feedback approach to address these three areas to move the industry forward. The six main areas of benefit from providing a feedback loop by continuously monitoring diesel emissions have been identified: 1. Condition-based maintenance. Emissions change instantaneously if engine condition changes. 2. Operator performance. An operator can use a lot more fuel for little incremental work output through poor technique or discipline. 3. Vehicle utilisation. Operating hours achieved and ratios of idling to under power affect the proportion of emissions produced with no economic value. 4. Fuel efficiency. This allows visibility into other contributing configuration and environmental factors for the vehicle. 5. Emission rates. This allows scope to directly address the required ratio of ventilation to diesel emissions. 6. Total carbon emissions - for NGER-type reporting requirements, calculating the emissions individually from each vehicle rather than just reporting on fuel delivered to a site.

Continuous appearance-based localisation and mapping

This thesis presents a novel approach to mobile robot navigation using visual information towards the goal of long-term autonomy. A novel concept of a continuous appearance-based trajectory is proposed in order to solve the limitations of previous robot navigation systems, and two new algorithms for mobile robots, CAT-SLAM and CAT-Graph, are presented and evaluated. These algorithms yield performance exceeding state-of-the-art methods on public benchmark datasets and large-scale real-world environments, and will help enable widespread use of mobile robots in everyday applications.

Continuous positive air pressure treatment for obstructive sleep apnoea patients : effects on sleep quality and quantity as measured by actigraphy

Objectives Actigraphy can reliably assess sleep in healthy adults and be used to estimate total sleep time in suspected obstructive sleep apnoea (OSA) patients. We compared sleep quality for Continuous Positive Air Pressure (CPAP) treated OSA patients and controls, evaluating the impact of stopping CPAP for one night. Methods 11 men, aged 51–75 years (m = 65.6 years), compliant CPAP users, treated for 1–19 years (m = 7.8 years) wore Cambridge Neurotechnology Ltd actiwatches for one night while using CPAP and for one night sleeping without CPAP. A control group of 11 healthy men, aged 63–74 years (m = 64.1 years) slept normally whilst wearing an actiwatch. Subsequent daytime sleepiness was recorded using Karolinska sleepiness scores (KSS). Results Actimetry showed no significant differences between actual sleep time, sleep efficiency, sleep disturbance index or number of wake bouts when comparing OSA participants using CPAP, with controls; there was no difference in subsequent daytime sleepiness, control KSS = 4.21, OSA KSS = 4.17. Without CPAP there was no significant difference in sleep length or sleep onset latency compared with using CPAP, but there was a significant impact on sleep quality as shown by: increased sleep disturbance index from 7.9 to 13.8 [t(10) = 3.510, P < 0.05], decreased percent of actual sleep from 92.05% to 86.15% [t(10) = 3.51, P < 0.05], decreased sleep efficiency from 86.6% to 81% [t(10) = 2.204, P < 0.05] and increased number of wake bouts from 29 to 42.5 [t(10) = 3.877, P < 0.05]. Daytime sleepiness became significantly worse increasing from KSS 4.17 to 6.27 [t(10) = )4.96, P < 0.05]. Conclusion There was no disparity in sleep quality or KSS scores between CPAP treated OSA patients and healthy controls of a similar age. Treated OSA patients obtained quality sleep with no elevated day time sleepiness. However, cessation of treatment for one night caused sleep quality to deteriorate despite a comparable sleep time; the deterioration in sleep quality could explain the increase in daytime sleepiness. OSA patients need to know that even short-term noncompliance with CPAP treatment significantly impairs sleep quality, leading to excessive sleepiness during monotonous tasks such as driving. Actigraphy successfully identified nights of non-compliance in treated OSA patients; but did not differentiate between the sleep of CPAP treated OSA patients and healthy controls.

Sampling designs on stream networks using the pseudo-Bayesian approach

Monitoring stream networks through time provides important ecological information. The sampling design problem is to choose locations where measurements are taken so as to maximise information gathered about physicochemical and biological variables on the stream network. This paper uses a pseudo-Bayesian approach, averaging a utility function over a prior distribution, in finding a design which maximizes the average utility. We use models for correlations of observations on the stream network that are based on stream network distances and described by moving average error models. Utility functions used reflect the needs of the experimenter, such as prediction of location values or estimation of parameters. We propose an algorithmic approach to design with the mean utility of a design estimated using Monte Carlo techniques and an exchange algorithm to search for optimal sampling designs. In particular we focus on the problem of finding an optimal design from a set of fixed designs and finding an optimal subset of a given set of sampling locations. As there are many different variables to measure, such as chemical, physical and biological measurements at each location, designs are derived from models based on different types of response variables: continuous, counts and proportions. We apply the methodology to a synthetic example and the Lake Eacham stream network on the Atherton Tablelands in Queensland, Australia. We show that the optimal designs depend very much on the choice of utility function, varying from space filling to clustered designs and mixtures of these, but given the utility function, designs are relatively robust to the type of response variable.

Identifying Core Functions of Asset Management

It is widely acknowledged that effective asset management requires an interdisciplinary approach, in which synergies should exist between traditional disciplines such as: accounting, engineering, finance, humanities, logistics, and information systems technologies. Asset management is also an important, yet complex business practice. Business process modelling is proposed as an approach to manage the complexity of asset management through the modelling of asset management processes. A sound foundation for the systematic application and analysis of business process modelling in asset management is, however, yet to be developed. Fundamentally, a business process consists of activities (termed functions), events/states, and control flow logic. As both events/states and control flow logic are somewhat dependent on the functions themselves, it is a logical step to first identify the functions within a process. This research addresses the current gap in knowledge by developing a method to identify functions common to various industry types (termed core functions). This lays the foundation to extract such functions, so as to identify both commonalities and variation points in asset management processes. This method describes the use of a manual text mining and a taxonomy approach. An example is presented.