Cluster-based network model for time-course gene expression data

We propose a model-based approach to unify clustering and network modeling using time-course gene expression data. Specifically, our approach uses a mixture model to cluster genes. Genes within the same cluster share a similar expression profile. The network is built over cluster-specific expression profiles using state-space models. We discuss the application of our model to simulated data as well as to time-course gene expression data arising from animal models on prostate cancer progression. The latter application shows that with a combined statistical/bioinformatics analyses, we are able to extract gene-to-gene relationships supported by the literature as well as new plausible relationships.

N2O emissions from agricultural lands: a synthesis of simulation approaches

Nitrous oxide (N2O) is primarily produced by the microbially-mediated nitrification and denitrification processes in soils. It is influenced by a suite of climate (i.e. temperature and rainfall) and soil (physical and chemical) variables, interacting soil and plant nitrogen (N) transformations (either competing or supplying substrates) as well as land management practices. It is not surprising that N2O emissions are highly variable both spatially and temporally. Computer simulation models, which can integrate all of these variables, are required for the complex task of providing quantitative determinations of N2O emissions. Numerous simulation models have been developed to predict N2O production. Each model has its own philosophy in constructing simulation components as well as performance strengths. The models range from those that attempt to comprehensively simulate all soil processes to more empirical approaches requiring minimal input data. These N2O simulation models can be classified into three categories: laboratory, field and regional/global levels. Process-based field-scale N2O simulation models, which simulate whole agroecosystems and can be used to develop N2O mitigation measures, are the most widely used. The current challenge is how to scale up the relatively more robust field-scale model to catchment, regional and national scales. This paper reviews the development history, main construction components, strengths, limitations and applications of N2O emissions models, which have been published in the literature. The three scale levels are considered and the current knowledge gaps and challenges in modelling N2O emissions from soils are discussed.

Encryption safe harbours and data breach notification laws

Data breach notification laws require organisations to notify affected persons or regulatory authorities when an unauthorised acquisition of personal data occurs. Most laws provide a safe harbour to this obligation if acquired data has been encrypted. There are three types of safe harbour: an exemption; a rebuttable presumption and factor-based analysis. We demonstrate, using three condition-based scenarios, that the broad formulation of most encryption safe harbours is based on the flawed assumption that encryption is the silver bullet for personal information protection. We then contend that reliance upon an encryption safe harbour should be dependent upon a rigorous and competent risk-based review that is required on a case-by-case basis. Finally, we recommend the use of both an encryption safe harbour and a notification trigger as our preferred choice for a data breach notification regulatory framework.

Stakeholder perspectives regarding the mandatory notification of Australian data breaches

The advent of data breach notification laws in the United States (US) has unearthed a significant problem involving the mismanagement of personal information by a range of public and private sector organisations. At present, there is currently no statutory obligation under Australian law requiring public or private sector organisations to report a data breach of personal information to law enforcement agencies or affected persons. However, following a comprehensive review of Australian privacy law, the Australian Law Reform Commission (ALRC) has recommended the introduction of a mandatory data breach notification scheme. The issue of data breach notification has ignited fierce debate amongst stakeholders, especially larger private sector entities. The purpose of this article is to document the perspectives of key industry and government representatives to identify their standpoints regarding an appropriate regulatory approach to data breach notification in Australia.

The mandatory notification of data breaches : issues arising for Australian and EU legal developments

Public and private sector organisations are now able to capture and utilise data on a vast scale, thus heightening the importance of adequate measures for protecting unauthorised disclosure of personal information. In this respect, data breach notification has emerged as an issue of increasing importance throughout the world. It has been the subject of law reform in the United States and in other jurisdictions. This article reviews US, Australian and EU legal developments regarding the mandatory notification of data breaches. The authors highlight areas of concern based on the extant US experience that require further consideration in Australia and in the EU.

Grassland management activity data : current sources and future needs

Estimates of potential and actual C sequestration require areal information about various types of management activities. Forest surveys, land use data, and agricultural statistics contribute information enabling calculation of the impacts of current and historical land management on C sequestration in biomass (in forests) or in soil (in agricultural systems). Unfortunately little information exists on the distribution of various management activities that can impact soil C content in grassland systems. Limited information of this type restricts our ability to carry out bottom-up estimates of the current C balance of grasslands or to assess the potential for grasslands to act as C sinks with changes in management. Here we review currently available information about grassland management, how that information could be related to information about the impacts of management on soil C stocks, information that may be available in the future, and needs that remain to be filled before in-depth assessments may be carried out. We also evaluate constraints induced by variability in information sources within and between countries. It is readily apparent that activity data for grassland management is collected less frequently and on a coarser scale than data for forest or agricultural inventories and that grassland activity data cannot be directly translated into IPCC-type factors as is done for IPCC inventories of agricultural soils. However, those management data that are available can serve to delineate broad-scale differences in management activities within regions in which soil C is likely to change in response to changes in management. This, coupled with the distinct possibility of more intensive surveys planned in the future, may enable more accurate assessments of grassland C dynamics with higher resolution both spatially and in the number management activities.

Using digital rights management for securing data in a medical research environment

We propose a digital rights management approach for sharing electronic health records in a health research facility and argue advantages of the approach. We also give an outline of the system under development and our implementation of the security features and discuss challenges that we faced and future directions.

Assessment of the suitability of public mobile data networks for aircraft telemetry and control purposes

This paper provides a review of the state of the art relevant work on the use of public mobile data networks for aircraft telemetry and control proposes. Moreover, it describes the characterisation for airborne uses of the public mobile data communication systems known broadly as 3G. The motivation for this study was the explore how this mature public communication systems could be used for aviation purposes. An experimental system was fitted to a light aircraft to record communication latency, line speed, RF level, packet loss and cell tower identifier. Communications was established using internet protocols and connection was made to a local server. The aircraft was flown in both remote and populous areas at altitudes up to 8500 ft in a region located in South East Queensland, Australia. Results show that the average airborne RF levels are better than those on the ground by 21% and in the order of - 77dbm. Latencies were in the order of 500ms (1/2 the latency of Iridium), an average download speed of 0.48Mb/s, average uplink speed of 0.85Mb/s, a packet of information loss of 6.5%. The maximum communication range was also observed to be 70km from a single cell station. The paper also describes possible limitations and utility of using such communications architecture for both manned and unmanned aircraft systems.

Determination of a set of surrogate parameters to assess urban stormwater quality

This paper presents the outcomes of a research project, which focused on developing a set of surrogate parameters to evaluate urban stormwater quality using simulated rainfall. Use of surrogate parameters has the potential to enhance the rapid generation of urban stormwater quality data based on on-site measurements and thereby reduce resource intensive laboratory analysis. The samples collected from rainfall simulations were tested for a range of physico-chemical parameters which are key indicators of nutrients, solids and organic matter. The analysis revealed that [total dissolved solids (TDS) and dissolved organic carbon (DOC)]; [total solids (TS) and total organic carbon (TOC)]; [turbidity (TTU)]; [electrical conductivity (EC)]; [TTU and EC] as appropriate surrogate parameters for dissolved total nitrogen (DTN), total phosphorus (TP), total suspended solids (TSS), TDS and TS respectively. Relationships obtained for DTN-TDS, DTN-DOC, and TP-TS demonstrated good portability potential. The portability of the relationship developed for TP and TOC was found to be unsatisfactory. The relationship developed for TDS-EC and TS-EC also demonstrated poor portability.

Incorporating weather into regionwide safety planning prediction models

Predicting safety on roadways is standard practice for road safety professionals and has a corresponding extensive literature. The majority of safety prediction models are estimated using roadway segment and intersection (microscale) data, while more recently efforts have been undertaken to predict safety at the planning level (macroscale). Safety prediction models typically include roadway, operations, and exposure variables—factors known to affect safety in fundamental ways. Environmental variables, in particular variables attempting to capture the effect of rain on road safety, are difficult to obtain and have rarely been considered. In the few cases weather variables have been included, historical averages rather than actual weather conditions during which crashes are observed have been used. Without the inclusion of weather related variables researchers have had difficulty explaining regional differences in the safety performance of various entities (e.g. intersections, road segments, highways, etc.) As part of the NCHRP 8-44 research effort, researchers developed PLANSAFE, or planning level safety prediction models. These models make use of socio-economic, demographic, and roadway variables for predicting planning level safety. Accounting for regional differences - similar to the experience for microscale safety models - has been problematic during the development of planning level safety prediction models. More specifically, without weather related variables there is an insufficient set of variables for explaining safety differences across regions and states. Furthermore, omitted variable bias resulting from excluding these important variables may adversely impact the coefficients of included variables, thus contributing to difficulty in model interpretation and accuracy. This paper summarizes the results of an effort to include weather related variables, particularly various measures of rainfall, into accident frequency prediction and the prediction of the frequency of fatal and/or injury degree of severity crash models. The purpose of the study was to determine whether these variables do in fact improve overall goodness of fit of the models, whether these variables may explain some or all of observed regional differences, and identifying the estimated effects of rainfall on safety. The models are based on Traffic Analysis Zone level datasets from Michigan, and Pima and Maricopa Counties in Arizona. Numerous rain-related variables were found to be statistically significant, selected rain related variables improved the overall goodness of fit, and inclusion of these variables reduced the portion of the model explained by the constant in the base models without weather variables. Rain tends to diminish safety, as expected, in fairly complex ways, depending on rain frequency and intensity.

Statistical and Econometric Methods for Transportation Data Analysis, 2nd edition

Now in its second edition, this book describes tools that are commonly used in transportation data analysis. The first part of the text provides statistical fundamentals while the second part presents continuous dependent variable models. With a focus on count and discrete dependent variable models, the third part features new chapters on mixed logit models, logistic regression, and ordered probability models. The last section provides additional coverage of Bayesian statistical modeling, including Bayesian inference and Markov chain Monte Carlo methods. Data sets are available online to use with the modeling techniques discussed.

Quality of child abuse information for measurement and surveillance : linking hospital and child welfare data

National estimates of the prevalence of child abuse-related injuries are obtained from a variety of sectors including welfare, justice, and health resulting in inconsistent estimates across sectors. The International Classification of Diseases (ICD) is used as the international standard for categorising health data and aggregating data for statistical purposes, though there has been limited validation of the quality, completeness or concordance of these data with other sectors. This research study examined the quality of documentation and coding of child abuse recorded in hospital records in Queensland and the concordance of these data with child welfare records. A retrospective medical record review was used to examine the clinical documentation of over 1000 hospitalised injured children from 20 hospitals in Queensland. A data linkage methodology was used to link these records with records in the child welfare database. Cases were sampled from three sub-groups according to the presence of target ICD codes: Definite abuse, Possible abuse, unintentional injury. Less than 2% of cases coded as being unintentional were recoded after review as being possible abuse, and only 5% of cases coded as possible abuse cases were reclassified as unintentional, though there was greater variation in the classification of cases as definite abuse compared to possible abuse. Concordance of health data with child welfare data varied across patient subgroups. This study will inform the development of strategies to improve the quality, consistency and concordance of information between health and welfare agencies to ensure adequate system responses to children at risk of abuse.

Quality of child abuse information in emergency department injury surveillance data : linking hospital and child welfare data

Emergency departments (EDs) are often the first point of contact with an abused child. Despite legal mandate, the reporting of definite or suspected abusive injury to child safety authorities by ED clinicians varies due to a number of factors including training, access to child safety professionals, departmental culture and a fear of ‘getting it wrong’. This study examined the quality of documentation and coding of child abuse captured by ED based injury surveillance data and ED medical records in the state of Queensland and the concordance of these data with child welfare records. A retrospective medical record review was used to examine the clinical documentation of almost 1000 injured children included in the Queensland Injury Surveillance Unit database (QISU) from 10 hospitals in urban and rural centres. Independent experts re-coded the records based on their review of the notes. A data linkage methodology was then used to link these records with records in the state government’s child welfare database. Cases were sampled from three sub-groups according to the surveillance intent codes: Maltreatment by parent, Undetermined and Unintentional injury. Only 0.1% of cases coded as unintentional injury were recoded to maltreatment by parent, while 1.2% of cases coded as maltreatment by parent were reclassified as unintentional and 5% of cases where the intent was undetermined by the triage nurse were recoded as maltreatment by parent. Quality of documentation varied across type of hospital (tertiary referral centre, children’s, urban, regional and remote). Concordance of health data with child welfare data varied across patient subgroups. Outcomes from this research will guide initiatives to improve the quality of intentional child injury surveillance systems.

Component reliability estimations without field data

Maintenance activities in a large-scale engineering system are usually scheduled according to the lifetimes of various components in order to ensure the overall reliability of the system. Lifetimes of components can be deduced by the corresponding probability distributions with parameters estimated from past failure data. While failure data of the components is not always readily available, the engineers have to be content with the primitive information from the manufacturers only, such as the mean and standard deviation of lifetime, to plan for the maintenance activities. In this paper, the moment-based piecewise polynomial model (MPPM) are proposed to estimate the parameters of the reliability probability distribution of the products when only the mean and standard deviation of the product lifetime are known. This method employs a group of polynomial functions to estimate the two parameters of the Weibull Distribution according to the mathematical relationship between the shape parameter of two-parameters Weibull Distribution and the ratio of mean and standard deviation. Tests are carried out to evaluate the validity and accuracy of the proposed methods with discussions on its suitability of applications. The proposed method is particularly useful for reliability-critical systems, such as railway and power systems, in which the maintenance activities are scheduled according to the expected lifetimes of the system components.