A Web-based system enabling the integration, analysis, and 3D sub-surface visualization of groundwater monitoring data and geological models

The 3D Water Chemistry Atlas is an intuitive, open source, Web-based system that enables the three-dimensional (3D) sub-surface visualization of ground water monitoring data, overlaid on the local geological model (formation and aquifer strata). This paper firstly describes the results of evaluating existing virtual globe technologies, which led to the decision to use the Cesium open source WebGL Virtual Globe and Map Engine as the underlying platform. Next it describes the backend database and search, filtering, browse and analysis tools that were developed to enable users to interactively explore the groundwater monitoring data and interpret it spatially and temporally relative to the local geological formations and aquifers via the Cesium interface. The result is an integrated 3D visualization system that enables environmental managers and regulators to assess groundwater conditions, identify inconsistencies in the data, manage impacts and risks and make more informed decisions about coal seam gas extraction, waste water extraction, and water reuse.

Genetic structure of invasive weed Parthenium hysterophorus in Australia and Pakistan

Understanding the patterns of genetic structure in the introduced range of invasive species can help elucidate invasion histories and levels of gene flow among populations. Parthenium weed (Parthenium hysterophorus L.; PW) is native to the Gulf of Mexico and central South America but has become globally invasive during the last three decades and little is known about the genetics of this species in its invasive range. The present study was conducted to determine the genetic structure of 95 individual samples from 11 populations (9 from Pakistan and 2 from Australia) of PW using ISSR fingerprinting. A total of 30 ISSR primers were screened; of which eight were selected due to their high polymorphism and reproducibility. In toto 147 bands were amplified, which ranged in size from 200-2000 bp; among which 97 were polymorphic. Genetic diversity within the populations both from Pakistan and Australia ranged between 0.193-0.278. Approximately 18% of genetic variation occurred among and 82% within populations. Principal Coordinate Analysis showed that within the 95 samples two groups were present: one contained samples collected mainly from Pakistan and the second group included the Australian samples along with two populations from Pakistan. Overall, there was limited gene flow among PW populations in Pakistan, although the genetic diversity within populations was high. The degree of genetic variation inferred from various population diversity measures can predict different events of founding populations, which have passed through complicated processes of invasion, experiencing genetic bottlenecks. Taken together, results showed that PW in Pakistan is genetically heterogeneous and may have been the result of multiple introductions.

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.

Comparison of visual inspection and structural-health monitoring as bridge condition assessment methods

This paper presents the results of a research project aimed at examining the capabilities and challenges of two distinct but not mutually exclusive approaches to in-service bridge assessment: visual inspection and installed monitoring systems. In this study, the intended functionality of both approaches was evaluated on its ability to identify potential structural damage and to provide decision-making support. Inspection and monitoring are compared in terms of their functional performance, cost, and barriers (real and perceived) to implementation. Both methods have strengths and weaknesses across the metrics analyzed, and it is likely that a hybrid evaluation technique that adopts both approaches will optimize efficiency of condition assessment and ultimately lead to better decision making.

The ADMIN-ICU survey: A survey on antimicrobial dosing and monitoring in ICUs

Objectives: There is little evidence and few guidelines to inform the most appropriate dosing and monitoring for antimicrobials in the ICU. We aimed to survey current practices around the world. Methods: An online structured questionnaire was developed and sent by e-mail to obtain information on local antimicrobial prescribing practices for glycopeptides, piperacillin/tazobactam, carbapenems, aminoglycosides and colistin. Results: A total of 402 professionals from 328 hospitals in 53 countries responded, of whom 78% were specialists in intensive care medicine (41% intensive care, 30% anaesthesiology, 14% internal medicine) and 12% were pharmacists. Vancomycin was used as a continuous infusion in 31% of units at a median (IQR) daily dose of 25 (25–30) mg/kg. Piperacillin/tazobactam was used as an extended infusion by 22% and as a continuous infusion by 7%. An extended infusion of carbapenem (meropenem or imipenem) was used by 27% and a continuous infusion by 5%. Colistin was used at a daily dose of 7.5 (3.9–9) million IU (MIU)/day, predominantly as a short infusion. The most commonly used aminoglycosides were gentamicin (55%) followed by amikacin (40%), with administration as a single daily dose reported in 94% of the cases. Gentamicin was used at a daily dose of 5 (5–6) mg/day and amikacin at a daily dose of 15 (15–20) mg/day. Therapeutic drug monitoring of vancomycin, piperacillin/tazobactam and meropenem was used by 74%, 1% and 2% of the respondents, respectively. Peak aminoglycoside concentrations were sampled daily by 28% and trough concentrations in all patients by 61% of the respondents. Conclusions: We found wide variability in reported practices for antibiotic dosing and monitoring. Research is required to develop evidence-based guidelines to standardize practices.

Myriad genetics: Patent law and genetic testing

This paper considers the legal challenges to the legal validity of the patents held by Myriad Genetics in respect of genetic testing for breast cancer and ovarian cancer. It argues that broad-based patents on gene sequences and medical diagnostics will have a harmful effect upon access to patient care, genetic research, and the administration of public health care.

Identification of genetic variants contributing to the migraine phenotype in different Australian populations

This project aimed to identify novel genetic risk variants associated with migraine in the Norfolk Island population. Statistical analysis and bioinformatics approaches such as polygenic modeling and gene clustering methods were carried out to explore genotypic and expression data from high-throughput techniques. This project had a particular focus on hormonal genes and other genetic variants and identified a modest effect size on the migraine phenotype.

Complex Symbolic Sequence Encodings for Predictive Monitoring of Business Processes

This paper addresses the problem of predicting the outcome of an ongoing case of a business process based on event logs. In this setting, the outcome of a case may refer for example to the achievement of a performance objective or the fulfillment of a compliance rule upon completion of the case. Given a log consisting of traces of completed cases, given a trace of an ongoing case, and given two or more possible out- comes (e.g., a positive and a negative outcome), the paper addresses the problem of determining the most likely outcome for the case in question. Previous approaches to this problem are largely based on simple symbolic sequence classification, meaning that they extract features from traces seen as sequences of event labels, and use these features to construct a classifier for runtime prediction. In doing so, these approaches ignore the data payload associated to each event. This paper approaches the problem from a different angle by treating traces as complex symbolic sequences, that is, sequences of events each carrying a data payload. In this context, the paper outlines different feature encodings of complex symbolic sequences and compares their predictive accuracy on real-life business process event logs.

Genetic evidence for natural hybridization between Red Snow Crab (Chionoecetes japonicus) and Snow Crab (Chionoecetes opilio) in Korea

Both red snow crab (Chionoecetes japonicus Rathbun, 1932) and snow crab (Chionoecetes opilio Fabricius, 1788) are commercially important species in Korea. The geographical ranges of the two species overlap in the East Sea, where both species are fished commercially. Morphological identification of the two species and putative hybrids can be difficult because of their overlapping morphological characteristics. The presence of putative hybrids can affect the total allowable catch (TAC) of C. japonicus and C. opilio, and causes problems managing C. japonicus and C. opilio wild resources. To date, however, no natural hybridization has been reported between C. japonicus and C. opilio, despite their overlapping distributions along the coast of the East Sea. In this study, the internal transcribed spacer (ITS) region of major ribosomal RNA genes from the nuclear genome and the cytochrome oxidase I (CO I) gene from the mitochondrial genome were sequenced to determine whether natural hybridization occurs between the two species. Our results revealed that all putative hybrids identified using morphological traits had two distinct types of ITS sequences corresponding to those of both parental species. Mitochondrial CO I gene sequencing showed that all putative hybrids had sequences identical to C. japonicus. A genotyping assay based on single nucleotide polymorphisms in the ITS1 region and the CO I gene produced the most efficient and accurate identification of all hybrid individuals. Molecular data clearly demonstrate that natural hybridization does occur between C. japonicus and C. opilio, but only with C. japonicus as the maternal parent.

Isolation and inheritance of microsatellite loci for the oily bittering (Acheilognathus koreensis): applications for analysis of genetic diversity of wild populations

The oily bittering Acheilognathus koreensis is a freshwater species that is endemic to Korea and is experiencing severe declines in natural populations as a result of habitat fragmentation and water pollution. For the conservation and restoration of this species, it is necessary to assess its genetic diversity at the population level. We developed 13 polymorphic microsatellite loci that were used to analyze the genetic diversity of two populations collected from the Kum River and the Tamjin River in Korea. All loci exhibited Mendelian inheritance patterns when examined in controlled crosses. Both populations revealed high levels of variability, with the number of alleles ranging from 3 to 20 and observed and expected heterozygosities ranging from 0.500 to 0.969 and from 0.529 to 0.938, respectively. None of the loci showed significant deviation from Hardy–Weinberg equilibrium, and one pair of loci showed significant linkage disequilibrium after Bonferroni correction. Pairwise F ST and genetic distance estimation showed significant differences between two populations. These results suggest that the microsatellites developed herein can be used to study the genetic diversity, population structure and conservation measure of A. koreensis.

Development of polymorphic microsatellite markers suitable for genetic linkage mapping of olive flounder Paralichthys olivaceus

Microsatellite markers are important for gene mapping and for marker-assisted selection. Sixty-five polymorphic microsatellite markers were developed with an enriched partial genomic library from olive flounder Paralichthys olivaceus an important commercial fish species in Korea. The variability of these markers was tested in 30 individuals collected from the East Sea (Korea). The number of alleles for each locus ranged from 2 to 33 (mean, 17.1). Observed and expected heterozygosity as well as polymorphism information content varied from 0.313 to 1.000 (mean, 0.788), from 0.323 to 0.977 (mean, 0.820), and from 0.277 to 0.960 (mean, 0.787), respectively. Nine loci showed significant deviation from the Hardy-Weinberg equilibrium after sequential Bonferroni correction. Analysis with MICROCHECKER suggested the presence of null alleles at five of these loci with estimated null allele frequencies of 0.126-0.285. These new microsatellite markers from genomic libraries will be useful for constructing a P. olivaceus linkage map.

Mitochondrial DNA sequence analysis from multiple gene fragments reveals genetic heterogeneity of Crassostrea ariakensis in East Asia

The native Asian oyster, Crassostrea ariakensis is one of the most common and important Crassostrea species that occur naturally along the coast of East Asia. Molecular species diagnosis is a prerequisite for population genetic analysis of wild oyster populations because oyster species cannot be discriminated reliably using external morphological characters alone due to character ambiguity. To date there have been few phylogeographic studies of natural edible oyster populations in East Asia, in particular this is true of the common species in Korea C. ariakensis. We therefore assessed the levels and patterns of molecular genetic variation in East Asian wild populations of C. ariakensis from Korea, Japan, and China using DNA sequence analysis of five concatenated mtDNA regions namely; 16S rRNA, cytochrome oxidase I, cytochrome oxidase II, cytochrome oxidase III, and cytochrome b. Two divergent C. ariakensis clades were identified between southern China and remaining sites from the northern region. In addition, hierarchical AMOVA and pairwise UST analyses showed that genetic diversity was discontinuous among wild populations of C. ariakensis in East Asia. Biogeographical and historical sea level changes are discussed as potential factors that may have influenced the genetic heterogeneity of wild C. ariakensis stocks across this region.

Transferability of cupped oyster EST (Expressed Sequence Tag)-derived SNP (Single Nucleotide Polymorphism) markers to related crassostrea and ostrea species

Single nucleotide polymorphisms (SNPs) are widely acknowledged as the marker of choice for many genetic and genomic applications because they show co-dominant inheritance, are highly abundant across genomes and are suitable for high-throughput genotyping. Here we evaluated the applicability of SNP markers developed from Crassostrea gigas and C. virginica expressed sequence tags (ESTs) in closely related Crassostrea and Ostrea species. A total of 213 putative interspecific level SNPs were identified from re-sequencing data in six amplicons, yielding on average of one interspecific level SNP per seven bp. High polymorphism levels were observed and the high success rate of transferability show that genic EST-derived SNP markers provide an efficient method for rapid marker development and SNP discovery in closely related oyster species. The six EST-SNP markers identified here will provide useful molecular tools for addressing questions in molecular ecology and evolution studies including for stock analysis (pedigree monitoring) in related oyster taxa.

QUT structural health monitoring system and the capture of recent Queensland earthquakes

This article reports the main features of an innovative full-scale Structural Health Monitoring (SHM) system which has been implemented onto a landmark building on QUT Gardens Point Campus and its efficacy in capturing the recent Queensland earthquakes although they occurred almost 300 km away from where the system is located.

Using genetic algorithm in profile-based assignment of applications to virtual machines for greener data centers

The increase in data center dependent services has made energy optimization of data centers one of the most exigent challenges in today's Information Age. The necessity of green and energy-efficient measures is very high for reducing carbon footprint and exorbitant energy costs. However, inefficient application management of data centers results in high energy consumption and low resource utilization efficiency. Unfortunately, in most cases, deploying an energy-efficient application management solution inevitably degrades the resource utilization efficiency of the data centers. To address this problem, a Penalty-based Genetic Algorithm (GA) is presented in this paper to solve a defined profile-based application assignment problem whilst maintaining a trade-off between the power consumption performance and resource utilization performance. Case studies show that the penalty-based GA is highly scalable and provides 16% to 32% better solutions than a greedy algorithm.