Data preprocessing for anomaly based network intrusion detection : a review

Data preprocessing is widely recognized as an important stage in anomaly detection. This paper reviews the data preprocessing techniques used by anomaly-based network intrusion detection systems (NIDS), concentrating on which aspects of the network traffic are analyzed, and what feature construction and selection methods have been used. Motivation for the paper comes from the large impact data preprocessing has on the accuracy and capability of anomaly-based NIDS. The review finds that many NIDS limit their view of network traffic to the TCP/IP packet headers. Time-based statistics can be derived from these headers to detect network scans, network worm behavior, and denial of service attacks. A number of other NIDS perform deeper inspection of request packets to detect attacks against network services and network applications. More recent approaches analyze full service responses to detect attacks targeting clients. The review covers a wide range of NIDS, highlighting which classes of attack are detectable by each of these approaches. Data preprocessing is found to predominantly rely on expert domain knowledge for identifying the most relevant parts of network traffic and for constructing the initial candidate set of traffic features. On the other hand, automated methods have been widely used for feature extraction to reduce data dimensionality, and feature selection to find the most relevant subset of features from this candidate set. The review shows a trend toward deeper packet inspection to construct more relevant features through targeted content parsing. These context sensitive features are required to detect current attacks.

Improving trust and securing data accessibility for e-health decision making by using data encryption techniques

In the medical and healthcare arena, patients‟ data is not just their own personal history but also a valuable large dataset for finding solutions for diseases. While electronic medical records are becoming popular and are used in healthcare work places like hospitals, as well as insurance companies, and by major stakeholders such as physicians and their patients, the accessibility of such information should be dealt with in a way that preserves privacy and security. Thus, finding the best way to keep the data secure has become an important issue in the area of database security. Sensitive medical data should be encrypted in databases. There are many encryption/ decryption techniques and algorithms with regard to preserving privacy and security. Currently their performance is an important factor while the medical data is being managed in databases. Another important factor is that the stakeholders should decide more cost-effective ways to reduce the total cost of ownership. As an alternative, DAS (Data as Service) is a popular outsourcing model to satisfy the cost-effectiveness but it takes a consideration that the encryption/ decryption modules needs to be handled by trustworthy stakeholders. This research project is focusing on the query response times in a DAS model (AES-DAS) and analyses the comparison between the outsourcing model and the in-house model which incorporates Microsoft built-in encryption scheme in a SQL Server. This research project includes building a prototype of medical database schemas. There are 2 types of simulations to carry out the project. The first stage includes 6 databases in order to carry out simulations to measure the performance between plain-text, Microsoft built-in encryption and AES-DAS (Data as Service). Particularly, the AES-DAS incorporates implementations of symmetric key encryption such as AES (Advanced Encryption Standard) and a Bucket indexing processor using Bloom filter. The results are categorised such as character type, numeric type, range queries, range queries using Bucket Index and aggregate queries. The second stage takes the scalability test from 5K to 2560K records. The main result of these simulations is that particularly as an outsourcing model, AES-DAS using the Bucket index shows around 3.32 times faster than a normal AES-DAS under the 70 partitions and 10K record-sized databases. Retrieving Numeric typed data takes shorter time than Character typed data in AES-DAS. The aggregation query response time in AES-DAS is not as consistent as that in MS built-in encryption scheme. The scalability test shows that the DBMS reaches in a certain threshold; the query response time becomes rapidly slower. However, there is more to investigate in order to bring about other outcomes and to construct a secured EMR (Electronic Medical Record) more efficiently from these simulations.

Validation of a new hand-held electronic data capture method for continuous monitoring of subjective appetite sensations

Background When large scale trials are investigating the effects of interventions on appetite, it is paramount to efficiently monitor large amounts of human data. The original hand-held Electronic Appetite Ratings System (EARS) was designed to facilitate the administering and data management of visual analogue scales (VAS) of subjective appetite sensations. The purpose of this study was to validate a novel hand-held method (EARS II (HP® iPAQ)) against the standard Pen and Paper (P&P) method and the previously validated EARS. Methods Twelve participants (5 male, 7 female, aged 18-40) were involved in a fully repeated measures design. Participants were randomly assigned in a crossover design, to either high fat (>48% fat) or low fat (<28% fat) meal days, one week apart and completed ratings using the three data capture methods ordered according to Latin Square. The first set of appetite sensations was completed in a fasted state, immediately before a fixed breakfast. Thereafter, appetite sensations were completed every thirty minutes for 4h. An ad libitum lunch was provided immediately before completing a final set of appetite sensations. Results Repeated measures ANOVAs were conducted for ratings of hunger, fullness and desire to eat. There were no significant differences between P&P compared with either EARS or EARS II (p > 0.05). Correlation coefficients between P&P and EARS II, controlling for age and gender, were performed on Area Under the Curve ratings. R2 for Hunger (0.89), Fullness (0.96) and Desire to Eat (0.95) were statistically significant (p < 0.05). Conclusions EARS II was sensitive to the impact of a meal and recovery of appetite during the postprandial period and is therefore an effective device for monitoring appetite sensations. This study provides evidence and support for further validation of the novel EARS II method for monitoring appetite sensations during large scale studies. The added versatility means that future uses of the system provides the potential to monitor a range of other behavioural and physiological measures often important in clinical and free living trials.

A six-year descriptive analysis of hospitalisations for ambulatory care sensitive conditions among people born in refugee-source countries

Background: Hospitalisation for ambulatory care sensitive conditions (ACSHs) has become a recognised tool to measure access to primary care. Timely and effective outpatient care is highly relevant to refugee populations given the past exposure to torture and trauma, and poor access to adequate health care in their countries of origin and during flight. Little is known about ACSHs among resettled refugee populations. With the aim of examining the hypothesis that people from refugee backgrounds have higher ACSHs than people born in the country of hospitalisation, this study analysed a six-year state-wide hospital discharge dataset to estimate ACSH rates for residents born in refugee-source countries and compared them with the Australia-born population. Methods: Hospital discharge data between 1 July 1998 and 30 June 2004 from the Victorian Admitted Episodes Dataset were used to assess ACSH rates among residents born in eight refugee-source countries, and compare them with the Australia-born average. Rate ratios and 95% confidence levels were used to illustrate these comparisons. Four categories of ambulatory care sensitive conditions were measured: total, acute, chronic and vaccine-preventable. Country of birth was used as a proxy indicator of refugee status. Results: When compared with the Australia-born population, hospitalisations for total and acute ambulatory care sensitive conditions were lower among refugee-born persons over the six-year period. Chronic and vaccine-preventable ACSHs were largely similar between the two population groups. Conclusion: Contrary to our hypothesis, preventable hospitalisation rates among people born in refugee-source countries were no higher than Australia-born population averages. More research is needed to elucidate whether low rates of preventable hospitalisation indicate better health status, appropriate health habits, timely and effective care-seeking behaviour and outpatient care, or overall low levels of health care-seeking due to other more pressing needs during the initial period of resettlement. It is important to unpack dimensions of health status and health care access in refugee populations through ad-hoc surveys as the refugee population is not a homogenous group despite sharing a common experience of forced displacement and violence-related trauma.

Water Sensitive Urban Design (WSUD) application auditing

Background WSUD implementation in the Gold Coast City Council area commenced more than a decade ago. As a result, Council is expected to be in possession of WSUD assets valued at over tens of million dollars. The Gold Coast City Council is responsible for the maintenance and long-term management of these WSUD assets. Any shortcoming in implementation of best WSUD practices can potentially result in substantial liabilities and ineffective expenditure for the Council in addition to reduced efficiencies and outcomes. This highlights the importance of periodic auditing of WSUD implementation. Project scope The overall study entailed the following tasks: * A state-of-the-art literature review of the conceptual hydraulic and water quality treatment principles, current state of knowledge in relation to industry standards, best practice and identification of knowledge gaps in relation to maintenance and management practices and potential barriers to the implementation of WSUD. * Council stakeholder interviews to understand current practical issues in relation to the implementation of WSUD and the process of WSUD application from development application approval to asset management. * Field auditing of selected WSUD systems for condition assessment and identification of possible strengths and weaknesses in implementation. * Review of the Land Development Guidelines in order to identify any gaps and to propose recommendations for improvement. Conclusions Given below is a consolidated summary of the findings of the study undertaken. State-of-the-art literature review Though the conceptual framework for WSUD implementation is well established, the underlying theoretical knowledge underpinning the treatment processes and maintenance regimes and life cycle costing are still not well understood. Essentially, these are the recurring themes in the literature, namely, the inadequate understanding of treatment processes and lack of guidance to ensure specificity of maintenance regimes and life cycle costing of WSUDs. The fundamental barriers to successful WSUD implementation are: * Lack of knowledge transfer – This essentially relates to the lack of appropriate dissemination of research outcomes and the common absence of protocols for knowledge transfer within the same organisation. * Cultural barriers – These relate to social and institutional factors, including institutional inertia and the lack of clear understanding of the benefits. * Fragmented responsibilities – This results from poor administrative integration within local councils in relation to WSUDs. * Technical barriers – These relate to lack of knowledge on operational and maintenance practices which is compounded by model limitations and the lack of long-term quantitative performance evaluation data. * Lack of engineering standards – Despite the availability of numerous guidelines which are non-enforceable and can sometimes be confusing, there is a need for stringent engineering standards. The knowledge gaps in relation to WSUDs are only closing very slowly. Some of the common knowledge gaps identified in recent publications have been recognised almost a decade ago. The key knowledge gaps identified in the published literature are: * lack of knowledge on operational and maintenance practices; * lack of reliable methodology for identifying life cycle issues including costs; * lack of technical knowledge on system performance; * lack of guidance on retrofitting in existing developments. Based on the review of barriers to WSUD implementation and current knowledge gaps, the following were identified as core areas for further investigation: * performance evaluation of WSUD devices to enhance model development and to assess their viability in the context of environmental, economic and social drivers; establishing realistic life cycle costs to strengthen maintenance and asset management practices; * development of guidelines specific to retrofitting in view of the unique challenges posed by existing urban precincts together with guidance to ensure site specificity; establishment of a process for knowledge translation for enhancing currently available best practice guidelines; * identification of drivers and overcoming of barriers in the areas of institutional fragmentation, knowledge gaps and awareness of WSUD practices. GCCC stakeholder interviews Fourteen staff members involved in WSUD systems management in the Gold Coast City Council, representing four Directorates were interviewed using a standard questionnaire. The primary issues identified by the stakeholders were: * standardisation of WSUD terminology; * clear protocols for safeguarding devices during the construction phase; * engagement of all council stakeholders in the WSUD process from the initial phase; * limitations in the Land Development Guidelines; * ensuring public safety through design; * system siting to avoid conflicts with environmental and public use of open space; * provision of adequate access for maintenance; * integration of social and ecosystem issues to ensure long-term viability of systems in relation to both, vandalism and visual recreation; * lack of performance monitoring and inadequacy of the maintenance budget; * lack of technical training for staff involved in WSUD design approvals and maintenance; incentives for developers for acting responsibly in stormwater management. Field auditing of WSUD systems A representative cross section of WSUD systems in the Gold Coast were audited in the field. The following strengths and weaknesses in WSUD implementation were noted: * The implementation of WSUD systems in the field is not consistent. * The concerns raised by the stakeholders during the interviews in relation to WSUD implementation was validated from the observations from the field auditing, particularly in relation to the following: * safeguarding of devices during the construction phase * public safety * accessibility for maintenance * lack of performance monitoring by Council to assess system performance * inadequate maintenance of existing systems to suit site specific requirements. * A treatment train approach is not being consistently adopted. * Most of the systems audited have satisfactorily catered for public safety. Accessibility for maintenance has been satisfactorily catered for in most of the systems that were audited. * Systems are being commissioned prior to construction activities being substantially completed. * The hydraulic design of most systems appears to be satisfactory. * The design intent of the systems is not always clear. Review of Land Development Guidelines The Land Development Guidelines (TDG) was extensively reviewed and the following primary issues were noted in relation to WSUD implementation: * the LDG appears to have been prepared primarily to provide guidance to developers. It is not clear to what extent the guidelines are applicable to Council staff involved in WSUD maintenance and management; * Section 13 is very voluminous and appears to be a compilation of a series of individual documents resulting in difficulties in locating specific information, a lack of integration and duplication of information; * the LDG has been developed with a primary focus on new urban precinct development and the retrofitting of systems in existing developments has not been specifically discussed; * WSUDs are discussed in two different sections in the LDG and it is not clear which section takes precedence as there are inconsistencies between the two sections; there is inconsistent terminology being used; * there is a need for consolidation of information provided in different sections in the LDG; * there are inconsistencies in the design criteria provided; * there is a need for regular updating of the LDG to ensure that the information provided encompasses the state-of-the-art; * there is limited guidance provided for the preparation of maintenance plans and life cycle costing to assist developers in asset handover and to assist Council staff in assessment. * Based on these observations, eleven recommendations have been provided which are discussed below. Additionally, the stakeholder provided the following specific comments during the interviews in relation to the LDG: * lack of flexibility to cover the different stages of the life cycle of the systems; * no differentiation in projects undertaken by developers and Council; * inadequate information with regards to safety issues such as maximum standing water depth, fencing and safety barriers and public access; * lack of detailed design criteria in relation to Crime Prevention through Environmental Design, safety, amenity, environment, surrounding uses and impacts on surroundings; * inadequate information regarding maintenance requirements specific to the assessment and compliance phases; * recommendations for plantings are based primarily on landscape requirements rather than pollutant uptake capability. Recommendations With regards to the Land Development Guidelines, the following specific recommendations are provided: 1. the relevant sections and their extent of applicability to Council should be clearly identified; 2. integration of the different subsections within Section 13 and re-formatting the document for easy reference; 3. the maintenance guidelines provided in Section 13 should be translated to a maintenance manual for guidance of Council staff; 4. should consider extending the Guidelines to specifically encompass retrofitting of WSUD systems to existing urban precincts; 5. Section 3 needs to be revised to be made consistent with Section 13, to ensure priority for WSUD practices in urban precincts and to move away from conventional stormwater drainage design such as kerb and channelling; 6. it would also be good to specify as to which Section takes predominance in relation to stormwater drainage. It is expected that Section 13 would take predominance over the other sections in the LDG; 7. terminology needs to be made consistent to avoid confusion among developers and Council staff. Water Sensitive Urban Design is the term commonly used in Australia for stormwater quality treatment, rather than Stormwater Quality Improvement Devices. This once again underlines the need for ensuring consistency between Section 3 and Section 13; 8. it would also be good if there is a glossary of commonly used terms in relation to WSUD for use by all stakeholders and which should also be reflected in the LDG; 9. consolidation of all WSUD information into one section should be considered together with appropriate indicators in other LDG Sections regarding the availability of WSUD information. Ensuring consistency in the information provided is implied; 10. Section 13 should be updated at regular intervals to ensure the incorporation of the latest in research outcomes and incorporating criteria and guidance based on the state-of-the-art knowledge. The updating could be undertaken, say, in five year cycles. This would help to overcome the current lack of knowledge transfer; 11. the Council should consider commissioning specialised studies to extend the current knowledge base in relation to WSUD maintenance and life cycle costing. Additionally, Recommendation 10 is also applicable in this instance. The following additional recommendations are made based on the state-of-the-art literature review, stakeholder interviews and field auditing of WSUD systems: 1. Performance monitoring of existing systems to assess improvements to water quality, identify modifications and enhancements to improve performance; 2. Appropriate and monitored maintenance during different phases of development of built assets over time is needed to investigate the most appropriate time/phase of development to commission the final WSUD asset. 3. Undertake focussed investigations in the areas of WSUD maintenance and asset management in order to establish more realistic life cycle costs of systems and maintenance schedules; 4. the engagement of all relevant Council stakeholders from the initial stage of concept planning through to asset handover, and ongoing monitoring. This close engagement of internal stakeholders will assist in building a greater understanding of responsibilities and contribute to overcoming constraints imposed by fragmented responsibilities; 5. the undertaking of a public education program to inform the community of the benefits and ecosystem functions of WSUD systems; 6. technical training to impart state-of-the-art knowledge to staff involved in the approval of designs and maintenance and management of WSUD projects; 7. during the construction phase, it is important to ensure that appropriate measures to safeguard WSUD devices are implemented; 8. risks associated with potential public access to open water zones should be minimised with the application of appropriate safety measures; 9. system siting should ensure that potential conflicts are avoided with respect to public and ecosystem needs; 10. integration of social and ecosystem issues to ensure long-term viability of systems; provide incentives to developers who are proactive and responsible in the area of stormwater management.

Probing second harmonic components of pH-sensitive Redox processes in a mesoporous TiO2-Nafion film electrode with Fourier-transformed large-amplitude sinusoidally modulated voltammetry

Electrochemical processes in mesoporous TiO2-Nafion thin films deposited on indium tin oxide (ITO) electrodes are inherently complex and affected by capacitance, Ohmic iR-drop, RC-time constant phenomena, and by potential and pH-dependent conductivity. In this study, large-amplitude sinusoidally modulated voltammetry (LASMV) is employed to provide access to almost purely Faradaic-based current data from second harmonic components, as well as capacitance and potential domain information from the fundamental harmonic for mesoporous TiO2-Nafion film electrodes. The LASMV response has been investigated with and without an immobilized one-electron redox system, ferrocenylmethyltrimethylammonium+. Results clearly demonstrate that the electron transfer associated with the immobilized ferrocene derivative follows two independent pathways i) electron hopping within the Nafion network and ii) conduction through the TiO2 backbone. The pH effect on the voltammetric response for the TiO2 reduction pathway (ii) can be clearly identified in the 2nd harmonic LASMV response with the diffusion controlled ferrocene response (i) acting as a pH independent reference. Application of second harmonic data derived from LASMV measurement, because of the minimal contribution from capacitance currents, may lead to reference-free pH sensing with systems like that found for ferrocene derivatives.

Controlled Monte Carlo data generation for statistical damage identification employing Mahalanobis squared distance

The use of Mahalanobis squared distance–based novelty detection in statistical damage identification has become increasingly popular in recent years. The merit of the Mahalanobis squared distance–based method is that it is simple and requires low computational effort to enable the use of a higher dimensional damage-sensitive feature, which is generally more sensitive to structural changes. Mahalanobis squared distance–based damage identification is also believed to be one of the most suitable methods for modern sensing systems such as wireless sensors. Although possessing such advantages, this method is rather strict with the input requirement as it assumes the training data to be multivariate normal, which is not always available particularly at an early monitoring stage. As a consequence, it may result in an ill-conditioned training model with erroneous novelty detection and damage identification outcomes. To date, there appears to be no study on how to systematically cope with such practical issues especially in the context of a statistical damage identification problem. To address this need, this article proposes a controlled data generation scheme, which is based upon the Monte Carlo simulation methodology with the addition of several controlling and evaluation tools to assess the condition of output data. By evaluating the convergence of the data condition indices, the proposed scheme is able to determine the optimal setups for the data generation process and subsequently avoid unnecessarily excessive data. The efficacy of this scheme is demonstrated via applications to a benchmark structure data in the field.

Changes in environmentally sensitive productivity and technological modernization in China's iron and steel industry in the 1990s

Technological modernization is widely believed to contribute positively both to economic development and to environmental and resource conservation, through improvements in productivity and strengthening of business competitiveness. However, this may not always be true, particularly in the short term, as it requires substantial investments and may impose financial burdens on firms undertaking such investments. This study empirically examines the effects of technological modernization in China's iron and steel industry in the 1990s on conventional economic productivity (CEP) and environmentally sensitive productivities (ESPs). We employ a directional distance function that can handle multiple inputs and outputs to compute relative production efficiencies. We apply these models to the data covering 27 iron and steel firms in China between 1990 and 1999-a period when the Chinese iron and steel industry modernized rapidly. We find that ESPs have continuously improved, even in the period when the CEP declined.

Locality-sensitive hashing for protein classification

Determination of sequence similarity is a central issue in computational biology, a problem addressed primarily through BLAST, an alignment based heuristic which has underpinned much of the analysis and annotation of the genomic era. Despite their success, alignment-based approaches scale poorly with increasing data set size, and are not robust under structural sequence rearrangements. Successive waves of innovation in sequencing technologies – so-called Next Generation Sequencing (NGS) approaches – have led to an explosion in data availability, challenging existing methods and motivating novel approaches to sequence representation and similarity scoring, including adaptation of existing methods from other domains such as information retrieval. In this work, we investigate locality-sensitive hashing of sequences through binary document signatures, applying the method to a bacterial protein classification task. Here, the goal is to predict the gene family to which a given query protein belongs. Experiments carried out on a pair of small but biologically realistic datasets (the full protein repertoires of families of Chlamydia and Staphylococcus aureus genomes respectively) show that a measure of similarity obtained by locality sensitive hashing gives highly accurate results while offering a number of avenues which will lead to substantial performance improvements over BLAST..

Assessment of the effects of CT dose in averaged x-ray CT images of a dose-sensitive polymer gel

The signal-to-noise ratio achievable in x-ray computed tomography (CT) images of polymer gels can be increased by averaging over multiple scans of each sample. However, repeated scanning delivers a small additional dose to the gel which may compromise the accuracy of the dose measurement. In this study, a NIPAM-based polymer gel was irradiated and then CT scanned 25 times, with the resulting data used to derive an averaged image and a "zero-scan" image of the gel. Comparison between these two results and the first scan of the gel showed that the averaged and zero-scan images provided better contrast, higher contrast-to- noise and higher signal-to-noise than the initial scan. The pixel values (Hounsfield units, HU) in the averaged image were not noticeably elevated, compared to the zero-scan result and the gradients used in the linear extrapolation of the zero-scan images were small and symmetrically distributed around zero. These results indicate that the averaged image was not artificially lightened by the small, additional dose delivered during CT scanning. This work demonstrates the broader usefulness of the zero-scan method as a means to verify the dosimetric accuracy of gel images derived from averaged x-ray CT data.

Molecular data extend Australian Cricotopus midge (Chironomidae) species diversity, and provide a phylogenetic hypothesis for biogeography and freshwater monitoring

Resolving species relationships and confirming diagnostic morphological characters for insect clades that are highly plastic, and/or include morphologically cryptic species, is crucial for both academic and applied reasons. Within the true fly (Diptera) family Chironomidae, a most ubiquitous freshwater insect group, the genera CricotopusWulp, 1874 and ParatrichocladiusSantos-Abreu, 1918 have long been taxonomically confusing. Indeed, until recently the Australian fauna had been examined in just two unpublished theses: most species were known by informal manuscript names only, with no concept of relationships. Understanding species limits, and the associated ecology and evolution, is essential to address taxonomic sufficiency in biomonitoring surveys. Immature stages are collected routinely, but tolerance is generalized at the genus level, despite marked variation among species. Here, we explored this issue using a multilocus molecular phylogenetic approach, including the standard mitochondrial barcode region, and tested explicitly for phylogenetic signal in ecological tolerance of species. Additionally, we addressed biogeographical patterns by conducting Bayesian divergence time estimation. We sampled all but one of the now recognized Australian Cricotopus species and tested monophyly using representatives from other austral and Asian locations. Cricotopus is revealed as paraphyletic by the inclusion of a nested monophyletic Paratrichocladius, with in-group diversification beginning in the Eocene. Previous morphological species concepts are largely corroborated, but some additional cryptic diversity is revealed. No significant relationship was observed between the phylogenetic position of a species and its ecology, implying either that tolerance to deleterious environmental impacts is a convergent trait among many Cricotopus species or that sensitive and restricted taxa have diversified into more narrow niches from a widely tolerant ancestor.

Whole exome sequencing is an efficient and sensitive method for detection of germline mutations in patients with phaeochromcytomas and paragangliomas

Background Genetic testing is recommended when the probability of a disease-associated germline mutation exceeds 10%. Germline mutations are found in approximately 25% of individuals with phaeochromcytoma (PCC) or paraganglioma (PGL); however, genetic heterogeneity for PCC/PGL means many genes may require sequencing. A phenotype-directed iterative approach may limit costs but may also delay diagnosis, and will not detect mutations in genes not previously associated with PCC/PGL. Objective To assess whether whole exome sequencing (WES) was efficient and sensitive for mutation detection in PCC/PGL. Methods Whole exome sequencing was performed on blinded samples from eleven individuals with PCC/PGL and known mutations. Illumina TruSeq™ (Illumina Inc, San Diego, CA, USA) was used for exome capture of seven samples, and NimbleGen SeqCap EZ v3.0 (Roche NimbleGen Inc, Basel, Switzerland) for five samples (one sample was repeated). Massive parallel sequencing was performed on multiplexed samples. Sequencing data were called using Genome Analysis Toolkit and annotated using annovar. Data were assessed for coding variants in RET, NF1, VHL, SDHD, SDHB, SDHC, SDHA, SDHAF2, KIF1B, TMEM127, EGLN1 and MAX. Target capture of five exome capture platforms was compared. Results Six of seven mutations were detected using Illumina TruSeq™ exome capture. All five mutations were detected using NimbleGen SeqCap EZ v3.0 platform, including the mutation missed using Illumina TruSeq™ capture. Target capture for exons in known PCC/PGL genes differs substantially between platforms. Exome sequencing was inexpensive (<$A800 per sample for reagents) and rapid (results <5 weeks from sample reception). Conclusion Whole exome sequencing is sensitive, rapid and efficient for detection of PCC/PGL germline mutations. However, capture platform selection is critical to maximize sensitivity.

Deriving optimal fishing effort for managing Australia's Moreton Bay multispecies trawl fishery with aggregated effort data

Deriving an estimate of optimal fishing effort or even an approximate estimate is very valuable for managing fisheries with multiple target species. The most challenging task associated with this is allocating effort to individual species when only the total effort is recorded. Spatial information on the distribution of each species within a fishery can be used to justify the allocations, but often such information is not available. To determine the long-term overall effort required to achieve maximum sustainable yield (MSY) and maximum economic yield (MEY), we consider three methods for allocating effort: (i) optimal allocation, which optimally allocates effort among target species; (ii) fixed proportions, which chooses proportions based on past catch data; and (iii) economic allocation, which splits effort based on the expected catch value of each species. Determining the overall fishing effort required to achieve these management objectives is a maximizing problem subject to constraints due to economic and social considerations. We illustrated the approaches using a case study of the Moreton Bay Prawn Trawl Fishery in Queensland (Australia). The results were consistent across the three methods. Importantly, our analysis demonstrated the optimal total effort was very sensitive to daily fishing costs-the effort ranged from 9500-11 500 to 6000-7000, 4000 and 2500 boat-days, using daily cost estimates of $0, $500, $750, and $950, respectively. The zero daily cost corresponds to the MSY, while a daily cost of $750 most closely represents the actual present fishing cost. Given the recent debate on which costs should be factored into the analyses for deriving MEY, our findings highlight the importance of including an appropriate cost function for practical management advice. The approaches developed here could be applied to other multispecies fisheries where only aggregated fishing effort data are recorded, as the literature on this type of modelling is sparse.