EST-PAC HPC - a web portal for high-throughput EST annotation and protein sequence prediction

Expressed Sequence Tags (ESTs) are short DNA sequences generated by sequencing the transcribed cDNAs coming from a gene expression. They can provide significant functional, structural and evolutionary information and thus are a primary resource for gene discovery. EST annotation basically refers to the analysis of unknown ESTs that can be performed by database similarity search for possible identities and database search for functional prediction of translation products. Such kind of annotation typically consists of a series of repetitive tasks which should be automated, and be customizable and amenable to using distributed computing resources. Furthermore, processing of EST data should be done efficiently using a high performance computing platform. In this paper, we describe an EST annotator, EST-PACHPC, which has been developed for harnessing HPC resources potentially from Grid and Cloud systems for high throughput EST annotations. The performance analysis of EST-PACHPC has shown that it provides substantial performance gain in EST annotation.

Degradation of phenanthrene and pyrene in soil slurry reactors with immobilized bacteria Zoogloea sp.

The environmental fate of polycyclic aromatic hydrocarbons (PAHs) in soils is motivated by their wide distribution, high persistence, and potentially deleterious effect on human health. Polycyclic aromatic hydrocarbons constitute the largest group of environmental contaminants released in the environment. Therefore, the potential biodegradation of these compounds is of vital importance. A biocarrier suitable for the colonization by micro-organisms for the purpose of purifying soil contaminated by polycyclic aromatic hydrocarbons was developed. The optimized composition of the biocarrier was polyvinyl alcohol (PVA) 10%, sodium alginate (SA) 0.5%, and powdered activated carbon (PAC) 5%. There was no observable cytotoxicity of biocarriers on immobilized cells and a viable cell population of 1.86 × 10¹⁰ g^–1 was maintained for immobilized bacterium. Biocarriers made from chemical methods had a higher biodegradation but lower mechanical strengths. Immobilized bacterium Zoogloea sp. had an ideal capability of biodegradation for phenanthrene and pyrene over a relative wide concentration range. The study results showed that the biodegradation of phenanthrene and pyrene reached 87.0 and 75.4%, respectively, by using the optimal immobilized method of Zoogloea sp. cultivated in a sterilized soil. Immobilized Zoogloea sp. was found to be effective for biodegrading the soil contaminated with phenanthrene and pyrene. Even in "natural" (unsterilized) soil, the biodegradation of phenanthrene and pyrene using immobilized Zoogloea sp. reached 85.0 and 67.1%, respectively, after 168 h of cultivation, more than twice that achieved if the cells were not immobilized on the biocarrier. Therefore, the immobilization technology enhanced the competitive ability of introduced micro-organisms and represents an effective method for the biotreatment of soil contaminated with phenanthrene and pyrene.

Individual variation in the pup attraction call produced by female Australian fur seals during early lactation

Otariid seals (fur seals and sea lions) are colonial breeders with large numbers of females giving birth on land during a synchronous breeding period. Once pups are born, females alternate between feeding their young ashore and foraging at sea. Upon return, both mother and pup must relocate each other and it is thought to be primarily facilitated by vocal recognition. Vocalizations of thirteen female Australian fur seals (Arctocephalus pusillus doriferus) were recorded during the breeding seasons of December 2000 and 2001, when pups are aged from newborns to one month. The pup attraction call was examined to determine whether females produce individually distinct calls which could be used by pups as a basis for vocal recognition. Potential for individual coding, discriminant function analysis (DFA), and classification and regression tree analysis were used to determine which call features were important in separating individuals. Using the results from all three analyses: F0, MIN F and DUR were considered important in separating individuals. In 76% of cases, the PAC was classified to the correct caller, using DFA, suggesting that there is sufficient stereotypy within individual calls, and sufficient variation between them, to enable vocal recognition by pups of this species.

Coagulation and nano-filtration: a hybrid system for the removal of lower molecular weight organic compounds (LMWOC)

The removal of lower molecular weight organic compounds (LMWOC) from water is of increasing concern. While, nano-fi ltration (NF) is a good option, it removes only a fraction of the LMWOC. In this paper, NF experiments were conducted to remove oxalic acid and diuron in combination with coagulation using poly-aluminum chloride (PAC) as the coagulant. The results showed that this hybrid treatment system was effective in removing oxalic acid where almost a 100% removal effi ciency of oxalic acid was achieved. However, using PAC as coagulant to remove diuron from water was not effective. In order to improve the removal efficiency of diuron, 0.02 M NaCl was added to diuron and a 40% increase in the removal of diuron was achieved. Higher removal of diuron was achieved when the solution was treated with reverse osmosis (RO) when compared to the nano-filtration.

Biological treatment of oily wastewater from gas stations by membrane bioreactor

In many Asian countries, rapid industrialization and urbanization has led to an increased number of cars, making wastewater from gas stations an important issue of concern in urban environment. This wastewater is characterized by high concentration of oil-water emulsion, which cannot be effectively removed by a conventional gravity separator. An experimental investigation on the treatability of oily wastewater from gas stations using a membrane bioreactor (MBR) system revealed that MBR system could achieve good removal efficiency with stability against shock loading. Optimum operating conditions were found to be at a hydraulic retention time of 4 h and an oil-loading rate of 1.8 kg oil m^sup -3^.d^sup -1^. It was anticipated that adding powdered activated carbon (PAC) in the MBR could help to adsorb the oils. However, operating the MBR with only microbial flocs has an advantage over adding PAC particles into the MBR, since the former condition could provide a prolonged cycle of filtration with a relatively lesser increase in transmembrane pressure.

Powdered activated carbon for fouling reduction of membrane in a pilot-scale recirculation aquaculture system

Recirculating aquaculture systems (RAS) are essential for the reduction in fresh water usage as well as the discharge of nutrients along with aquaculture effluents. A RAS consisting of an anoxic reactor, a membrane bioreactor (MBR) and a UV-disinfection unit was used to process 10,000 L/d of aquaculture effluent providing high-quality treated water for recirculation to a Barramundi fish culture. The system maintained low levels of nitrate (<20 mg/L), nitrite (<3 mg/L) and ammonia (<0.6 mg/L) in the fish tank. Permeate from the membrane that was recirculated to the fish tank contained <21 mg/L of nitrate, <2 mg/L of nitrite and 0 mg/L of ammonia. However, the rate of fouling of the membrane in the MBR was around 1.47 kPa/d, and the membrane in the MBR required cleaning due to fouling after 16 days. Cleaning of the membrane was initiated when the TMP reached around 25 to 30 kPa. In order to reduce the rate of fouling, 500 mg of powdered activated carbon (PAC) per litre of MBR volume was introduced, which decreased the rate of fouling to 0.90 kPa/d. Cleaning of membrane was needed only after 31 days of operation while maintaining the treated effluent quality. Thus the frequency of cleaning could be halved due to the introduction of PAC into the MBR.

Activity preferences and participation of school-age children living in urban and rural environments

It is important for therapists to be knowledgeable about the impact of the environment on children’s participation patterns and activity preferences. This study investigated the activity preference and participation among school-age children living in urban and rural locations. The participation patterns and preferences for activities of 58 typically developing children (32 males and 26 females; response rate of 38.7%) aged 8–12 years were assessed across both urban (n = 24) and rural (n = 34) regions of southwest Victoria, Australia. The participation patterns and preferences for activities were assessed using the Children’s Assessment of Participation and Enjoyment and Preferences for Activities of Children (CAPE/PAC).An independent samples t-test was used to determinewhether significant differences existed for theCAPE/PACscores for urban and rurally based children as well as boys and girls. Significant differences were found between the scores of children living in urban and rural areas on the following subscales: CAPE Diversity, CAPE Intensity, CAPE Whom, CAPE Where, PAC Physical Preference, and PACSocial Preference.Asignificant difference for rural and urban groups was found on the following CAPE activity types:Recreation Diversity,Recreation Intensity, Social Diversity, Social Intensity, Self-Improvement Diversity, and Self-Improvement Intensity. Rurally based children were engaged in a broader range of activities and did so more frequently than urban children. Differences in gender were identified with girls preferring to participate in social and skill-based activities and being more likely to participate with friends or people outside their home. However, there were no significant differences in the participation patterns of boys and girls. Physical, social, and structural aspects of the location where a child lives impact the frequency, type of activities, and whom a child participates with most frequently in out-of-school activities. The activity participation of boys and girls in Australia has become quite similar.

Simplifying gene expression microarray comparative analysis.

Gene Expression Comparative Analysis allows bioinformatics researchers to discover the conserved or specific functional regulation of genes. This is achieved through comparisons between quantitative gene expression measurements obtained in different species on different platforms to address a particular biological system. Comparisons are made more difficult due to the need to map orthologous genes between species, pre-processing of data (normalization) and post-analysis (statistical and correlation analysis). In this paper we introduce a web-based software package called EXP-PAC which provides on line interfaces for database construction and query of data, and makes use of a high performance computing platform of computer clusters to run gene sequence mapping and normalization methods in parallel. Thus, EXP-PAC facilitates the integration of gene expression data for comparative analysis and the online sharing, retrieval and visualization of complex multi-specific and multi-platform gene expression results.

Training skills of divided attention among older adults

The current study examined whether video game training would help improve divided attention skills among older adults. Twenty-nine (4 males, 25 females) participants aged 50 to 84 years (M = 70) were tested for their skills of divided attention using a memory and reaction time task. Participants were randomly allocated to the experimental group and control group and only those in the experimental group trained with the computer game, Pac-Man Adventures in Time for three hours. Results show that three hours of training are not sufficient to enhance skills of divided attention amongst older adults as the differences in these skills were not significantly different between control and experimental groups. These findings suggest that greater amounts or other methods of training may be required to enhance older adults’ ability to perform dual tasks.

Experienced teachers and multiple intelligences

In the world of the Information Age, digital natives (students) are being taught by digital immigrants (experienced teachers). These digital immigrants prefer to employ a number of abilities or multiple intelligences (Gardner 1983) to learn about software that can be beneficial to their students. As experienced teachers with limited ICT exposure, they are interested in: learning how to push buttons (P), thinking how to apply software to their practice (A) and are willing to change their practice using ICT (C). This paper discusses a study of experienced teachers with limited ICT exposure and their preferred way of learning, as they PAC for the information age.

Video Game Training and Reaction Time Skills Among Older Adults

The aim of the current study was to examine whether reaction time (RT) among older adults could be improved through video game training. Twenty-nine participants between the ages of 50 and 84 either played (N = 14) or did not play (N = 15) a video game, Pac-Man: Adventures in Time. All participants completed a pre- and postassessment of RT. Results from this study showed that there were no significant differences between the control and experimental groups on RT performance across time. These findings indicate that the amount of training provided may have been inadequate to improve RT skills. It is therefore important to investigate the amount of training required to allow older adults to respond faster to environmental stimuli and transfer skills to activities of daily living.