Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers

The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.

Representing traumatic space

This presentation will begin by the screening of Traum a Dream (2003, 7 mins, Digital Video, Sound)

A representation of traumatised space, depicting a person who is consumed by a body of pain, consumed by fire. Slowly something is remembered (Festival Catalogue: Transmediale.03. February 2003).

The screening will allow a discussion of some of the material embedded in and ideas used in the film's construction. This includes Atwood's view of the colony as victim, Peter pan and never-never-land, Kroker's concept of the panicked body as it relates to the cinema of Mike Hoolboom's hyper-collage and also the use of the abstract and repetition to depict the process of remembering, re-ordering and forgetting. It is also suggested that Random Access Memory as a method of information storage in Digital Media can provide a model for the architecture of traumatised space and Post Traumatic Stress Disorder.

AMC: an adaptive multi-level cache algorithm in hybrid storage systems

Hybrid storage systems that consist of flash-based solid state drives (SSDs) and traditional disks are now widely used. In hybrid storage systems, there exists a two-level cache hierarchy that regard dynamic random access memory (DRAM) as the first level cache and SSD as the second level cache for disk storage. However, this two-level cache hierarchy typically uses independent cache replacement policies for each level, which makes cache resource management inefficient and reduces system performance. In this paper, we propose a novel adaptive multi-level cache (AMC) replacement algorithm in hybrid storage systems. The AMC algorithm adaptively adjusts cache blocks between DRAM and SSD cache levels using an integrated solution. AMC uses combined selective promote and demote operations to dynamically determine the level in which the blocks are to be cached. In this manner, the AMC algorithm achieves multi-level cache exclusiveness and makes cache resource management more efficient. By using real-life storage traces, our evaluation shows the proposed algorithm improves hybrid multi-level cache performance and also increases the SSD lifetime compared with traditional multi-level cache replacement algorithms.

Pharmacy access to the emergency contraceptive pill : a national survey of a random sample of Australian women

Background : The emergency contraceptive pill (ECP) has the potential to assist in reducing unintended pregnancy and abortion rates. Since its rescheduling to pharmacy availability without prescription in Australia in January 2004, there is little information about Australian women's knowledge, attitudes and use of the ECP. The aim of this study was to measure the knowledge about the ECP and sociodemographic patterns of and barriers to use of the ECP.

Study Design : A cross-sectional study, using a computer-assisted telephone interview (CATI) survey conducted with a national random sample of 632 Australian women aged 16–35 years.

Results : Most women had heard of the ECP (95%) and 26% had used it. The majority of women agreed with pharmacy availability of the ECP (72%); however, only 48% were aware that it was available from pharmacies without a prescription. About a third (32%) believed the ECP to be an abortion pill. The most common reason for not using the ECP was that women did not think they were at risk of getting pregnant (57%). Logistic regression showed that women aged 20–29 years (OR 2.58; CI: 1.29–5.19) and 30–35 years (OR 3.16; CI: 1.47–6.80) were more likely to have used the ECP than those aged 16–19 years. Women with poor knowledge of the ECP were significantly less likely to have used it than those with very good knowledge (OR 0.28; CI: 0.09–0.77). Those in a de facto relationship (OR 2.21; CI: 1.27–3.85), in a relationship but not living with the partner (OR 2.46; 95% CI 1.31–4.63) or single women (OR 2.40; CI: 1.33–4.34) were more likely to have used the ECP than married women.

Conclusions : Women in Australia have a high level of awareness of the ECP, but more information and education about how to use it and where to obtain it are still needed.

Trauma and holocaust video testimony : the intersection of history, memory, and judgment in the interview process

This article analyzes video testimonies recorded at the Jewish Holocaust Museum and Research Centre in Melbourne,Australia, which address the highly complex and sensitive issue of “privileged” Jews. The so-called privileged Jews include prisoners in the Nazi-operated camps and ghettos who held positions that gave them access to material and other benefits, while compelling them to act in ways that have been judged detrimental to fellow inmates. Although the issue of “privileged” Jews has been largely neglected, it relates to a crucial facet of the Holocaust and has vast implications for its aftermath. The ethical dilemmas facing these victims may be closely linked to what Lawrence Langer has termed choiceless choices, which challenge conventional notions of “judgment” and “responsibility.” This problem is also the primary subject of Auschwitz survivor Primo Levi’s essay titled “The Grey Zone,” which is arguably the most influential essay ever written on the Holocaust. Levi argues that one should abstain from judging individuals who confronted such extreme circumstances, positioning prisoners with “privileged” positions at the threshold of representation and understanding. However, moral evaluations of “privileged” Jews have a strong impact on Holocaust testimonies, whether these were constructed during the war or recorded long after the survivors’ experiences. The examples of video testimonies explored in this article reveal that this is particularly the case when interviewees are former “privileged” Jews and interviewers are themselves Holocaust survivors. The article argues that when confronted with such an emotionally and morally fraught issue, judgment may itself be seen as a “limit of representation.”

Reduced food access due to a lack of money, inability to lift and lack of access to a car for food shopping : a multilevel study in Melbourne, Victoria

Objective: To describe associations between demographic and individual and arealevel socio-economic variables and restricted household food access due to lack of money, inability to lift groceries and lack of access to a car to do food shopping.
Design: Multilevel study of three measures of restricted food access, i.e. running out of money to buy food, inability to lift groceries and lack of access to a car for food shopping. Multilevel logistic regression was conducted to examine the risk of each of these outcomes according to demographic and socio-economic variables.
Setting: Random selection of households from fifty small areas in Melbourne, Australia, in 2003.
Subjects: The main food shoppers in each household (n 2564).
Results: A lack of money was significantly more likely among the young and in households with single adults. Difficultly lifting was more likely among the elderly and those born overseas. The youngest and highest age groups both reported reduced car access, as did those born overseas and single-adult households. All three factors were most likely among those with a lower individual or household socio-economic position. Increased levels of area disadvantage were independently associated with difficultly lifting and reduced car access.
Conclusions: In Melbourne, households with lower individual socio-economic position and area disadvantage have restricted access to food because of a lack of money and/or having physical limitations due difficulty lifting or lack of access to a car for food shopping. Further research is required to explore the relationship between physical restrictions and food access.

The impact of working memory load on task execution and online plan adjustment during multitasking in a virtual environment

Three experiments investigated the impact of working memory load on online plan adjustment during a test of multitasking in young, nonexpert, adult participants. Multitasking was assessed using the Edinburgh Virtual Errands Test (EVET). Participants were asked to memorize either good or poor plans for performing multiple errands and were assessed both on task completion and on the extent to which they modified their plans during EVET performance. EVET was performed twice, with and without a secondary task loading a component of working memory. In Experiment 1, articulatory suppression was used to load the phonological loop. In Experiment 2, oral random generation was used to load executive functions. In Experiment 3, spatial working memory was loaded with an auditory spatial localization task. EVET performance for both good- and poor-planning groups was disrupted by random generation and sound localization, but not by articulatory suppression. Additionally, people given a poor plan were able to overcome this initial disadvantage by modifying their plans online. It was concluded that, in addition to executive functions, multiple errands performance draws heavily on spatial, but not verbal, working memory resources but can be successfully completed on the basis of modifying plans online, despite a secondary task load.

Tree-based iterated local search for Markov random fields with applications in image analysis

The maximum a posteriori assignment for general structure Markov random fields is computationally intractable. In this paper, we exploit tree-based methods to efficiently address this problem. Our novel method, named Tree-based Iterated Local Search (T-ILS), takes advantage of the tractability of tree-structures embedded within MRFs to derive strong local search in an ILS framework. The method efficiently explores exponentially large neighborhoods using a limited memory without any requirement on the cost functions. We evaluate the T-ILS on a simulated Ising model and two real-world vision problems: stereo matching and image denoising. Experimental results demonstrate that our methods are competitive against state-of-the-art rivals with significant computational gain.

The National Perinatal Depression Initiative: An evaluation of access to general practitioners, psychologists and psychiatrists through the Medicare Benefits Schedule

OBJECTIVE: To evaluate the impact of the National Perinatal Depression Initiative on access to Medicare services for women at risk of perinatal mental illness. METHOD: Retrospective cohort study using difference-in-difference analytical methods to quantify the impact of the National Perinatal Depression Initiative policies on Medicare Benefits Schedule mental health usage by Australian women giving birth between 2006 and 2010. A random sample of women of reproductive age enrolled in Medicare who had not given birth where used as controls. The main outcome measures were the proportions of women giving birth each month who accessed a Medicare Benefits Schedule mental health items during the perinatal period (pregnancy through to the end of the first postnatal year) before and after the introduction of the National Perinatal Depression Initiative. RESULTS: The proportion of women giving birth who accessed at least one mental health item during the perinatal period increased from 88 to 141 per 1000 between 2007 and 2010. The difference-in-difference analysis showed that while there was an overall increase in Medicare Benefits Schedule mental health item access as a result of the National Perinatal Depression Initiative, this did not reach statistical significance. However, the National Perinatal Depression Initiative was found to significantly increase access in subpopulations of women, particularly those aged under 25 and over 34 years living in major cities. CONCLUSION: In the 2 years following its introduction, the National Perinatal Depression Initiative was found to have increased access to Medicare funded mental health services in particular groups of women. However, an overall increase across all groups did not reach statistical significance. Further studies are needed to assess the impact of the National Perinatal Depression Initiative on women during childbearing years, including access to tertiary care, the cost-effectiveness of the initiative, and mental health outcomes. It is recommended that new mental health policy initiatives incorporate a planned strategic approach to evaluation, which includes sufficient follow-up to assess the impact of public health strategies.

Spatial coordinated medium sharing: Optimal access control management in drive-thru internet

Driven by the ever-growing expectation of ubiquitous connectivity and the widespread adoption of IEEE 802.11 networks, it is not only highly demanded but also entirely possible for in-motion vehicles to establish convenient Internet access to roadside WiFi access points (APs) than ever before, which is referred to as Drive-Thru Internet. The performance of Drive-Thru Internet, however, would suffer from the high vehicle mobility, severe channel contentions, and instinct issues of the IEEE 802.11 MAC as it was originally designed for static scenarios. As an effort to address these problems, in this paper, we develop a unified analytical framework to evaluate the performance of Drive-Thru Internet, which can accommodate various vehicular traffic flow states, and to be compatible with IEEE 802.11a/b/g networks with a distributed coordination function (DCF). We first develop the mathematical analysis to evaluate the mean saturated throughput of vehicles and the transmitted data volume of a vehicle per drive-thru. We show that the throughput performance of Drive-Thru Internet can be enhanced by selecting an optimal transmission region within an AP's coverage for the coordinated medium sharing of all vehicles. We then develop a spatial access control management approach accordingly, which ensures the airtime fairness for medium sharing and boosts the throughput performance of Drive-Thru Internet in a practical, efficient, and distributed manner. Simulation results show that our optimal access control management approach can efficiently work in IEEE 802.11b and 802.11g networks. The maximal transmitted data volume per drive-thru can be enhanced by 113.1% and 59.5% for IEEE 802.11b and IEEE 802.11g networks with a DCF, respectively, compared with the normal IEEE 802.11 medium access with a DCF.

Academic outcomes 2 years after working memory training for children with low working memory: a randomized clinical trial

IMPORTANCE: Working memory training may help children with attention and learning difficulties, but robust evidence from population-level randomized controlled clinical trials is lacking.

OBJECTIVE: To test whether a computerized adaptive working memory intervention program improves long-term academic outcomes of children 6 to 7 years of age with low working memory compared with usual classroom teaching.

DESIGN, SETTING, AND PARTICIPANTS: Population-based randomized controlled clinical trial of first graders from 44 schools in Melbourne, Australia, who underwent a verbal and visuospatial working memory screening. Children were classified as having low working memory if their scores were below the 15th percentile on either the Backward Digit Recall or Mister X subtest from the Automated Working Memory Assessment, or if their scores were below the 25th percentile on both. These children were randomly assigned by an independent statistician to either an intervention or a control arm using a concealed computerized random number sequence. Researchers were blinded to group assignment at time of screening. We conducted our trial from March 1, 2012, to February 1, 2015; our final analysis was on October 30, 2015. We used intention-to-treat analyses.

INTERVENTION: Cogmed working memory training, comprising 20 to 25 training sessions of 45 minutes' duration at school.

MAIN OUTCOMES AND MEASURES: Directly assessed (at 12 and 24 months) academic outcomes (reading, math, and spelling scores as primary outcomes) and working memory (also assessed at 6 months); parent-, teacher-, and child-reported behavioral and social-emotional functioning and quality of life; and intervention costs.

RESULTS: Of 1723 children screened (mean [SD] age, 6.9 [0.4] years), 226 were randomized to each arm (452 total), with 90% retention at 1 year and 88% retention at 2 years; 90.3% of children in the intervention arm completed at least 20 sessions. Of the 4 short-term and working memory outcomes, 1 outcome (visuospatial short-term memory) benefited the children at 6 months (effect size, 0.43 [95% CI, 0.25-0.62]) and 12 months (effect size, 0.49 [95% CI, 0.28-0.70]), but not at 24 months. There were no benefits to any other outcomes; in fact, the math scores of the children in the intervention arm were worse at 2 years (mean difference, -3.0 [95% CI, -5.4 to -0.7]; P = .01). Intervention costs were A$1035 per child.

CONCLUSIONS AND RELEVANCE: Working memory screening of children 6 to 7 years of age is feasible, and an adaptive working memory training program may temporarily improve visuospatial short-term memory. Given the loss of classroom time, cost, and lack of lasting benefit, we cannot recommend population-based delivery of Cogmed within a screening paradigm.

Restricting access to invasion hubs enables sustained control of an invasive vertebrate

Biological invasions often occur through expansion of satellite populations that become established at 'invasion hubs'. Invasion hubs can result from random dispersal events, but frequently arise when invading individuals actively choose habitats using cues that signify high-quality environments where the fitness consequences are positive. Theoretical studies suggest that targeted control at invasion hubs can effectively suppress the populations and impacts of invaders. In arid Australia, small dams that provide water for livestock function as invasion hubs by providing an invasive vertebrate, the cane toad Rhinella marina, with refuge from extreme aridity during the annual dry season. Toads are attracted to dams and use them as stepping stone habitats from which they disperse during rainy periods. Here, we ask whether sustained control of this invasive vertebrate can be achieved by converting invasion hubs into ecological traps. We did this by manipulating invasion hub habitats to induce a mismatch between toads' habitat preference and the fitness consequences of their habitat choice to cause high mortality. We constructed fences to exclude toads from dams and maintained these fences for 1 year. This period encompassed periods of dry and wet seasonal climatic conditions. Our manipulation did not alter the attractive cues for invading toads which died en masse while attempting to settle at fenced dams that prevented toads from reaching water. Toad populations at the fenced dams were suppressed by 1-2 orders of magnitude compared to unfenced controls and procedural controls. Toad populations remained suppressed for a year after exclusion. By excluding toads from dams, we converted invasion hubs into ecological traps and effectively thwarted the reinvasion of cane toads. Our research suggests that water exclusion devices could be used to prevent toad invasion or to control cane toad populations in arid landscapes colonized by toads. Synthesis and applications. Our study demonstrates that sustained control of invader populations can be achieved by restricting their access to invasion hubs. Control of invasive species via elimination of invasion hubs could be conducted reactively, to control established populations of invaders, or conducted strategically, by rendering invasion hubs unsuitable for colonization ahead of the invasion front to prevent further population spread.

Improving access for community health and sub-acute outpatient services: protocol for a stepped wedge cluster randomised controlled trial

BACKGROUND: Waiting lists for treatment are common in outpatient and community services, Existing methods for managing access and triage to these services can lead to inequities in service delivery, inefficiencies and divert resources from frontline care. Evidence from two controlled studies indicates that an alternative to the traditional "waitlist and triage" model known as STAT (Specific Timely Appointments for Triage) may be successful in reducing waiting times without adversely affecting other aspects of patient care. This trial aims to test whether the model is cost effective in reducing waiting time across multiple services, and to measure the impact on service provision, health-related quality of life and patient satisfaction.

METHODS/DESIGN: A stepped wedge cluster randomised controlled trial has been designed to evaluate the impact of the STAT model in 8 community health and outpatient services. The primary outcome will be waiting time from referral to first appointment. Secondary outcomes will be nature and quantity of service received (collected from all patients attending the service during the study period and health-related quality of life (AQOL-8D), patient satisfaction, health care utilisation and cost data (collected from a subgroup of patients at initial assessment and after 12 weeks). Data will be analysed with a multiple multi-level random-effects regression model that allows for cluster effects. An economic evaluation will be undertaken alongside the clinical trial.

DISCUSSION: This paper outlines the study protocol for a fully powered prospective stepped wedge cluster randomised controlled trial (SWCRCT) to establish whether the STAT model of access and triage can reduce waiting times applied across multiple settings, without increasing health service costs or adversely impacting on other aspects of patient care. If successful, it will provide evidence for the effectiveness of a practical model of access that can substantially reduce waiting time for outpatient and community services with subsequent benefits for both efficiency of health systems and patient care.

Collaborative filtering via sparse Markov random fields

Recommender systems play a central role in providing individualized access to information and services. This paper focuses on collaborative filtering, an approach that exploits the shared structure among mind-liked users and similar items. In particular, we focus on a formal probabilistic framework known as Markov random fields (MRF). We address the open problem of structure learning and introduce a sparsity-inducing algorithm to automatically estimate the interaction structures between users and between items. Item-item and user-user correlation networks are obtained as a by-product. Large-scale experiments on movie recommendation and date matching datasets demonstrate the power of the proposed method.