An algorithm to predict 3 ' intron splice sites in Plasmodium falciparum genomic sequences

A new algorithm, PfAGSS, for predicting 3' splice sites in Plasmodium falciparum genomic sequences is described. Application of this program to the published P. falciparum chromosome 2 and 3 data suggests that existing programs result in a high error rate in assigning 3' intron boundaries. (C) 2001 Elsevier Science B.V. All rights reserved.

A simulated annealing algorithm for finding consensus sequences

Motivation: A consensus sequence for a family of related sequences is, as the name suggests, a sequence that captures the features common to most members of the family. Consensus sequences are important in various DNA sequencing applications and are a convenient way to characterize a family of molecules. Results: This paper describes a new algorithm for finding a consensus sequence, using the popular optimization method known as simulated annealing. Unlike the conventional approach of finding a consensus sequence by first forming a multiple sequence alignment, this algorithm searches for a sequence that minimises the sum of pairwise distances to each of the input sequences. The resulting consensus sequence can then be used to induce a multiple sequence alignment. The time required by the algorithm scales linearly with the number of input sequences and quadratically with the length of the consensus sequence. We present results demonstrating the high quality of the consensus sequences and alignments produced by the new algorithm. For comparison, we also present similar results obtained using ClustalW. The new algorithm outperforms ClustalW in many cases.

Economics teaching in Australian universities: Rewards and outcomes

This paper presents evidence from two survey's to help explain the poor ratings consistently given to the teaching of economics at Australian universities. The evidence suggests that the Poor ratings of economics teaching can be attributed to two related factors: inappropriate pedagogical practices and lack of rewards for allocating additional time to teaching. The survey data oil pedagogy, in economics consist of 205 responses from graduates from two Queensland universities. The time elapsed since graduation ranges from 1 to 10 years. The survey data on academics' time allocation consist of 290 responses from academic economists across a wide range of Australian universities.

Molecular phylogenetics of Lentibulariaceae inferred from plastid rps16 Intron and trnL-F DNA sequences: implications for character evolution and biogeography

Phylogenetic relationships among 75 species of Lentibulariaceae, representing the three recognized genera, were assessed by cladistic analysis of DNA sequences from the plastid rps16 intron and the trnL-F region. Sequence data from the two loci were analyzed both separately and in combination. Consensus trees from all analyses are congruent, and parsimony jackknife results demonstrate strong support for relationships both between and within each of the three demonstrably monophyletic genera. The genus Pinguicula is sister to a Genlisea-Utricularia clade, the phylogenetic structure within this clade closely follows Taylor's recent sectional delimitations based on morphology. Three principal clades are shown within Utricularia, with the basal sections Polypoinpholyx and Pleiochasia together forming the sister lineage of the remaining Utricularia species. Of the fundamental morphological specializations, the stoloniferous growth form apparently arose independently within Genlisea and Utricularia three times, and within Utricularia itself, perhaps more than once. The epiphytic habit has evolved independently at least three times, in Pinguicula, in Utricularia section Phyllaria, and within the two sections Orchidioides and Iperua (in the latter as bromeliad tank-epiphytes). The suspended aquatic habit may have evolved independently within sections Utricularia and Vesiculina. Biogeographic optimization on the phylogeny demonstrates patterns commonly associated with the boreotropics hypothesis and limits the spatial origin of Lentibulariaceae to temperate Eurasia or tropical America.

Teaching PSP: Challenges and lessons learned

Teaching the PSP: Challenges and Lessons Learned by Jurgen Borstler, David Carrington, Gregory W Hislop, Susan Lisack, Keith Olson, and Laurie Williams, pp. 42-48. Soft-ware engineering educators need to provide environments where students learn about the size and complexity of modern software systems and the techniques available for managing these difficulties. Five universities used the Personal Software Process to teach software engineering concepts in a variety of contexts.

Outcome of stroke patients admitted to intensive care: Experience from an Australian teaching hospital

The objective of this study was to determine the mortality rate and the functional outcomes of stroke patients admitted to the intensive care unit (ICU) and to identify predictors of poor outcome in this population. The records of all patients admitted to the ICU with the diagnosis of stroke between January 1994 and December 1999 were reviewed. Patients with subarachnoid haemorrhage were excluded. Data were collected on clinical and biological variables, risk factors for stroke and the presence of comorbidities. Mortality (ICU, in-hospital and three-month) and functional outcome were used as end-points. In the six-year-period, 61 patients were admitted to the ICU with either haemorrhagic or ischaemic stroke. Medical records were available for only 58 patients. There were 23 ischaemic and 35 haemorrhagic strokes. The ICU, in-hospital and three-month mortality rates were 36%, 47% and 52% respectively. There were no significant differences in the prevalence of premorbid risk factors between survivors and non-survivors. The mean Barthel score was significantly different between the independent and dependent survivors (94 +/- 6 vs 45 +/- 26, P < 0.001). A substantial number of patients with good functional outcomes had lower Rankin scores (92% vs 11%, P < 0.001). Only 46% of those who were alive at three months were functionally independent. Intensive care admission was associated with a high mortality rate and a high likelihood of dependent lifestyle after hospital discharge. Haemorrhagic stroke, fixed dilated pupil(s) and GCS < 10 during assessment were associated with increased mortality and poor functional outcome.

Veterinary parasitology teaching in eastern Australia

There are tendencies in universities globally to change undergraduate teaching in veterinary parasitology. To be able to give considered advice to universities, faculties, governmental bodies and professional societies about a discipline and to establish how particular changes may impact on the quality of a course, is the requirement to record and review its current status. The present paper contributes toward this objective by providing a snap-shot of the veterinary parasitology courses at the Universities of Melbourne, Sydney and Queensland in eastern Australia. It includes a description of the veterinary science curriculum in each institution, and provides an outline of its veterinary parasitology course, including objectives, topics covered, course delivery, student examination procedures and course evaluation. Student contact time in veterinary parasitology during the curriculum is currently higher in Melbourne (183 h) compared with Sydney and Queensland (106-110 h). In the teaching of parasitology, Melbourne adopts a taxonomic approach (in the pre-clinical period) followed by a combined disciplinary and problem-based approach in the clinical semesters, whereas both Sydney and Queensland focus more on presenting parasites on a host species-basis followed by a problem-based approach. (C) 2002 Elsevier Science B.V. All rights reserved.

Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

Engaging with theories of dialogue and voice: Using Bakhtin as a framework to understand teaching and learning Indigenous Australian women's performance

In this paper I explore the Indigenous Australian women's performance classroom (hereafter ANTH2120) as a dialectic and discursive space where the location of possibility is opened for female Indigenous performers to enter into a dialogue from and between both non-Indigenous and Indigenous voices. The work of Bakhtin on dialogue serves as a useful standpoint for understanding the multiple speaking positions and texts in the ANTH2120 context. Bakhtin emphasizes performance, history, actuality and the openness of dialogue to provide an important framework for analysing multiple speaking positions and ways of making meaning through dialogue between shifting and differing subjectivities. I begin by briefly critiquing Bakhtin's "dialogic imagination" and consider the application and usefulness of concepts such as dialogism, heteroglossia and the utterance to understanding the ANTH2120 classroom as a polyphonic and discursive space. I then turn to an analysis of dialogue in the ANTH2120 classroom and primarily situate my gaze on an examination of the interactions that took place between the voices of myself as family/teacher/student and senior Yanyuwa women from the r e m o t e N o r t h e r n T e r r i t o r y A b o r i g i n a l c o m m u n i t y o f B o r r o l o o l a as family/performers/teachers. The 2000 and 2001 Yanyuwa women's performance workshops will be used as examples of the way power is constantly shifting in this dialogue to allow particular voices to speak with authority, and for others to remain silent as roles and relationships between myself and the Yanyuwa women change. Conclusions will be drawn regarding how my subject positions and white race privilege affect who speaks, who listens and on whose terms, and further, the efficacy of this pedagogical platform for opening up the location of possibility for Indigenous Australian women to play a powerful part in the construction of knowledges about women's performance traditions.