Solution chemistry impacts on the seawater neutralisation process: Benefits of nanofiltered seawater and reverse osmosis brine

It is well known that the neutralisation of Bayer liquor with seawater causes the precipitation of stable alkaline products and a reduction in pH and dissolved metal concentrations in the effluent. However, there is limited information available on solution chemistry effects on the stability and reaction kinetics of these precipitates. This investigation shows the influence of reactive species (magnesium and calcium) in seawater on precipitate stabilities and volumetric efficiencies during the neutralisation of bauxite refinery residues. Correlations between synthetic seawater solutions and real samples of seawater (filtered seawater, nanofiltered seawater and reverse osmosis brine) have been made. These investigations have been used to confirm that alternative seawater sources can be used to increase the productivity potential of the neutralisation process with minimal implications on the composition and stability of precipitates formed. The volume efficiency of the neutralisation process using synthetic analogues has been shown to be almost directly proportional with the concentration of magnesium. This was further confirmed in the nanofiltered seawater and reverse osmosis brine that showed increases in the efficiency of neutralisation by factors of 3 and 2 compared to seawater, which corresponds with relatively the same increase in the concentration of magnesium in these alternative seawater sources. An assessment of the chemical stability of the precipitates, volumetric efficiency, and discharge water quality have been determined using numerous techniques that include pH, conductivity, inductively coupled plasma optical emission spectroscopy, infrared spectroscopy, thermogravimetric analysis coupled to mass spectrometry and X-ray diffraction. Correlations between synthetic solution compositions and alternative seawater sources have been used to determine if alternative seawater sources are potential substitutes for seawater based on improvements in productivity, implementation costs, savings to operations and environmental benefits.

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.

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.

Genetic structure of the Korean black scraper Thamnaconus modestus inferred from microsatellite marker analysis

The Korean black scraper, Thamnaconus modestus, is one of the most economically important maricultural fish species in Korea. However, the annual catch of this fish has been continuously declining over the past several decades. In this study, the genetic diversity and relationships among four wild populations and two hatchery stocks of Korean black scraper were assessed based on 16 microsatellite (MS) markers. A total of 319 different alleles were detected over all loci with an average of 19.94 alleles per locus. The hatchery stocks [mean number of alleles (N A) = 12, allelic richness (A R) = 12, expected heterozygosity (He) = 0.834] showed a slight reduction (P > 0.05) in genetic variability in comparison with wild populations (mean N A = 13.86, A R = 12.35, He = 0.844), suggesting a sufficient level of genetic variation in the hatchery populations. Similarly low levels of inbreeding and significant Hardy–Weinberg equilibrium deviations were detected in both wild and hatchery populations. The genetic subdivision among all six populations was low but significant (overall F ST = 0.008, P < 0.01). Pairwise F ST, a phylogenetic tree, and multidimensional scaling analysis suggested the existence of three geographically structured populations based on different sea basin origins, although the isolation-by-distance model was rejected. This result was corroborated by an analysis of molecular variance. This genetic differentiation may result from the co-effects of various factors, such as historical dispersal, local environment and ocean currents. These three geographical groups can be considered as independent management units. Our results show that MS markers may be suitable not only for the genetic monitoring of hatchery stocks but also for revealing the population structure of Korean black scraper populations. These results will provide critical information for breeding programs, the management of cultured stocks and the conservation of this species.

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.

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.

A penalty-based genetic algorithm for the migration cost-aware virtual machine placement problem in cloud data centers

In the past few years, the virtual machine (VM) placement problem has been studied intensively and many algorithms for the VM placement problem have been proposed. However, those proposed VM placement algorithms have not been widely used in today's cloud data centers as they do not consider the migration cost from current VM placement to the new optimal VM placement. As a result, the gain from optimizing VM placement may be less than the loss of the migration cost from current VM placement to the new VM placement. To address this issue, this paper presents a penalty-based genetic algorithm (GA) for the VM placement problem that considers the migration cost in addition to the energy-consumption of the new VM placement and the total inter-VM traffic flow in the new VM placement. The GA has been implemented and evaluated by experiments, and the experimental results show that the GA outperforms two well known algorithms for the VM placement problem.

A systematic review of hepatitis C clinical practice guidelines: Benefits, limitations and harms

Background Hepatitis C (HCV) was described as a “viral time bomb” due to its prevalence and potential for causing serious, life-threatening complications. The Australian’s National Hepatitis C Strategy calls for a coordinated, evidence-based approach to testing, management, care and support of HCV. This review aimed to systematically and comparatively appraise existing international HCV clinical guidelines. Methods A systematic search of bibliographic databases and reference lists from selected papers were the source of data. Inclusion criteria were latest clinical guidelines as defined by Institute of Medicine, published in English, between January 2002 and November 2014. Quality of the guidelines was independently assessed using the iCAHE instrument. Results Twenty-eight international clinical practice guidelines were included. The majority of the international guidelines were based on the same primary studies however clinical recommendations on pre- and in-treatment assessments, choice of pharmaceuticals, and dosages and duration of the same pharmaceutical agents varied considerably. This diversity was beyond what would be considered reasonable practice context variations. Furthermore, there is limited guidance on post-treatment surveillance and care. Conclusions/implications There is a need for a harmonised international consensus on the clinical management of HCV. Key message A lack of consistency among international HCV clinical guidelines may impede effective and efficient patient care.

Generating benefits and negotiating tensions through an international doctoral forum: A sociological analysis

Workshops and seminars are widely-used forms of doctoral training. However, research with a particular focus on these forms of doctoral training is sporadic in the literature. There is no, if any, such research concerning the international context and participants’ own voices. Mindful of these lacunae in the literature, we write the current paper as a group of participants in one of a series of doctoral forums co-organised annually by Beijing Normal University, China and Queensland University of Technology, Australia. The paper voices our own experiences of participation in the doctoral forum. Data were drawn from reflections, journals, and group discussions of all 12 student and academic participants. These qualitative data were organised and analysed through Bourdieu’s notions of capital and field. Findings indicate that the doctoral forum created enabling and challenging social fields where participants accrued and exchanged various forms of capital and negotiated transient and complex power relations. In this respect, the sociological framework used provides a distinctive theoretical tool to conceptualise and analyse the benefits and tensions of participation in the doctoral forum. Knowledge built and lessons learned through our paper will provide implications and recommendations for future planning of, and participation in, the doctoral forum series and similar activities elsewhere.

Phylogeographical relationships of Sicilian brown trout and the effects of genetic introgression on morphospace occupation

Genetic introgression of aquaculture stocks in local forms is well documented in many fish species but their evolutionary consequences for the local populations have not been thoroughly explored. Due to its wide geographical range, the existence of many locally adapted forms and the frequent occurrence of introgression of aquaculture stocks in local forms, brown trout represents the ideal system to study the effects of such introgressions. Here, we focus on a group of rivers and streams in Sicily (Italy), and, by using molecular tools, we show that autochthonous populations are probably derived from the Southern Atlantic clade, which is present in the Iberian peninsula and North Africa. Three out of the four studied rivers reveal signs of genetic introgression of domestic stocks. Finally, by using advanced geometric morphometric analyses, we show that genetic introgression produces a higher degree of morphological variability relative to that observed in non-introgressed populations.

Association of variants at 1q32 and STAT3 with ankylosing spondylitis suggests genetic overlap with Crohn's disease

Ankylosing spondylitis (AS) is a common inflammatory arthritic condition. Overt inflammatory bowel disease (IBD) occurs in about 10% of AS patients, and in addition 70% of AS cases may have subclinical terminal ileitis. Spondyloarthritis is also common in IBD patients. We therefore tested Crohn's disease susceptibility genes for association with AS, aiming to identify pleiotropic genetic associations with both diseases. Genotyping was carried out using Sequenom and Applied Biosystems TaqMan and OpenArray technologies on 53 markers selected from 30 Crohn's disease associated genomic regions. We tested genotypes in a population of unrelated individual cases (n = 2,773) and controls (n = 2,215) of white European ancestry for association with AS. Statistical analysis was carried out using a Cochran-Armitage test for trend in PLINK. Strong association was detected at chr1q32 near KIF21B (rs11584383, P = 1.66 x 10-10, odds ratio (OR) = 0.74, 95% CI:0.68-0.82). Association with disease was also detected for 2 variants within STAT3 (rs6503695, P = 4.6×10-4. OR = 0.86 (95% CI:0.79-0.93); rs744166, P = 2.6×10-5, OR = 0.84 (95% CI:0.77-0.91)). Association was confirmed for IL23R (rs11465804, P = 1.2×10-5, OR = 0.65 (95% CI:0.54-0.79)), and further associations were detected for IL12B (rs10045431, P = 5.261025, OR = 0.83 (95% CI:0.76-0.91)), CDKAL1 (rs6908425, P = 1.1×10-4, OR = 0.82 (95% CI:0.74-0.91)), LRRK2/MUC19 (rs11175593, P = 9.9×10-5, OR = 1.92 (95% CI: 1.38-2.67)), and chr13q14 (rs3764147, P = 5.9×10-4, OR = 1.19 (95% CI: 1.08-1.31)). Excluding cases with clinical IBD did not significantly affect these findings. This study identifies chr1q32 and STAT3 as ankylosing spondylitis susceptibility loci. It also further confirms association for IL23R and detects suggestive association with another 4 loci. STAT3 is a key signaling molecule within the Th17 lymphocyte differentiation pathway and further enhances the case for a major role of this T-lymphocyte subset in ankylosing spondylitis. Finally these findings suggest common aetiopathogenic pathways for AS and Crohn's disease and further highlight the involvement of common risk variants across multiple diseases.

Whole-genome screening in ankylosing spondylitis: Evidence of non-MHC genetic-susceptibility loci

Ankylosing spondylitis (AS) is a common inflammatory arthritis predominantly affecting the axial skeleton. Susceptibility to the disease is thought to be oligogenic. To identify the genes involved, we have performed a genomewide scan in 185 families containing 255 affected sibling pairs. Two-point and multipoint nonparametric linkage analysis was performed. Regions were identified showing "suggestive" or stronger linkage with the disease on chromosomes 1p, 2q, 6p, 9q, 10q, 16q, and 19q. The MHC locus was identified as encoding the greatest component of susceptibility, with an overall LOD score of 15.6. The strongest non-MHC linkage lies on chromosome 16q (overall LOD score 4.7). These results strongly support the presence of non-MHC genetic-susceptibility factors in AS and point to their likely locations.

Recurrence risk modelling of the genetic susceptibility to ankylosing spondylitis

Objectives - It has long been suspected that susceptibility to ankylosing spondylitis (AS) is influenced by genes lying distant to the major histocompatibility complex. This study compares genetic models of AS to assess the most likely mode of inheritance, using recurrence risk ratios in relatives of affected subjects. Methods - Recurrence risk ratios in different degrees of relatives were determined using published data from studies specifically designed to address the question. The methods of Risch were used to determine the expected recurrence risk ratios in different degrees of relatives, assuming equal first degree relative recurrence risk between models. Goodness of fit was determined by χ2 comparison of the expected number of affected subjects with the observed number, given equal numbers of each type of relative studied. Results - The recurrence risks in different degrees of relatives were: monozygotic (MZ) twins 63% (17/27), first degree relatives 8.2% (441/5390), second degree relatives 1.0% (8/834), and third degree relatives 0.7% (7/997). Parent-child recurrence risk (7.9%, 37/466) was not significantly different from the sibling recurrence risk (8.2%, 404/4924), excluding a significant dominance genetic component to susceptibility. Poor fitting models included single gene, genetic heterogeneity, additive, two locus multiplicative, and one locus and residual polygenes (χ2 > 32 (two degrees of freedom), p < 10-6 for all models). The best fitting model studied was a five locus model with multiplicative interaction between loci (χ2 = 1.4 (two degrees of freedom), p = 0.5). Oligogenic multiplicative models were the best fitting over a range of population prevalences and first degree recurrence risk rates. Conclusions - This study suggests that of the genetic models tested, the most likely model operating in AS is an oligogenic model with predominantly multiplicative interaction between loci.