TREATMENT RECOMMENDATION IN VIETNAMESE MEDICAL CONSULTATIONS

This study investigated the doctor’s recommendation of treatment to their adult patients in primary-care visits in the Vietnamese context. Data was gathered from 55 audio-recorded consultations at two public hospitals, and examined from a conversation-analytic perspective. We demonstrate that the participating doctors used two main approaches to treatment recommendation with their patients: general and detailed. In the latter case, the doctor recommended a treatment regime, sought the patient’s agreement, or offered choices regarding aspects of the treatment. Our overall contention is that, in the Vietnamese public hospital system, the doctor’s organisation of talk in the course of recommending treatment tends to be shaped by the institutional and cultural context in which it occurs, regardless of which type of treatment approach is being used

Follow-up visits in doctor-patient communication: the Vietnamese case

In a 'follow-up visit', a patient seeks medical attention for an existing health problem. Using data from the Vietnamese public hospital system, we present a more nuanced analysis of follow-ups in health communication than the one currently available. To be specific, we discriminate between 'same follow-ups', in which the doctor is the same one as in the last visit, and 'different follow-ups', in which the doctor has not treated the patient for their problem before. We then extend existing research on 'inappropriate follow-ups', in which the problem solicitation is more suitable for another type of visit, by teasing out additional typological distinctions within this category of follow-up. We go on to show that same and different follow-ups contrast with each other in terms of the format used for the problem solicitation. The broader implication of our findings is that the structure of a medical visit is not invariant, but is shaped by the cultural context in which it occurs

Estimates of the effect of natural selection on protein-coding content

Analysis of natural selection is key to understanding many core biological processes, including the emergence of competition, cooperation, and complexity, and has important applications in the targeted development of vaccines. Selection is hard to observe directly but can be inferred from molecular sequence variation. For protein-coding nucleotide sequences, the ratio of nonsynonymous to synonymous substitutions (ω) distinguishes neutrally evolving sequences (ω = 1) from those subjected to purifying (ω 1) selection. We show that current models used to estimate ω are substantially biased by naturally occurring sequence compositions. We present a novel model that weights substitutions by conditional nucleotide frequencies and which escapes these artifacts. Applying it to the genomes of pathogens causing malaria, leprosy, tuberculosis, and Lyme disease gave significant discrepancies in estimates with ∼10-30% of genes affected. Our work has substantial implications for how vaccine targets are chosen and for studying the molecular basis of adaptive evolution

The only known egg of the Night Parrot? A molecular and morphometric assessment of an alleged egg from the Tanami Desert

The Night Parrot Pezoporus occidentalis is a much sought-after, recently ‘rediscovered’, endangered nocturnal parrot, endemic to arid Central Australia. Very little is known of its ecology, and its eggs have never been formally described. The literature on the eggs of the Night Parrot is collated here, and the provenance of an alleged Night Parrot egg found in the Tanami Desert, Northern Territory, in 1983 was assessed using DNA analysis and physical characteristics. Anecdotal reports from the late 19th–early 20th Century indicate that the Night Parrot lays a clutch of two to six roundish, white eggs. We suggest that its eggs are probably similar to and slightly larger than those of its congener, the Ground Parrot P. wallicus. The alleged Night Parrot egg was definitively identified by mitochondrial DNA analysis to be from the Brown Quail Synoicus ypsilophorus. This represents the first evidence of breeding by this species in the Tanami Desert, and lays to rest a long-standing misconception regarding the parrot

PyEvolve: a toolkit for statistical modelling of molecular evolution

BACKGROUND: Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences – ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. RESULTS: Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from ~10 days to ~6 hours. CONCLUSION: PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be used interactively or by writing and executing scripts. The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. PyEvolve is released under the GPL and can be downloaded from http://cbis.anu.edu.au/software webcite

Asymmetries in L2 functional morphology: The Korean learner of English

Variability in the production of L2 functional morphology has long been recognised as a pervasive and entrenched characteristic of interlanguage development. As Trenkic (2007, p. 292) suggests, a potentially fruitful way of identifying the sources of this behaviour is to compare the rates at which a given morpheme (e.g., past tense) is omitted, substituted or oversupplied in two (or more) distinct contexts. The present thesis adds to earlier work exploring certain patterns of this type, while also seeking to address some of the main limitations of these studies. Using a combined elicited-imitation and story-recall task adapted from Snape (2006), I examine the production of various types of functional morpheme by Korean learners of English. Three experiments were conducted. In the first of these, I predicted asymmetries in the omission or substitution of definite articles in first- and second-mention DPs based on the effects of non-target form-meaning relationships plus communicative redundancy. The second experiment examined past tense, agreement and plural morphology, and investigated the claim that differences in stem length and (for tense inflection only) verb class would give rise to contrasting patterns of inflectional omission. The third experiment focused on various kinds of QP, and manipulated the effects of contrasts in quantifier type and syntactic structure on the omission of plural inflection in these phrases. The predictions of experiment 1 were not supported, while those of experiment 2 were not supported for tense inflection; however, I am able to suggest reasons for these unexpected results. The overall results of the thesis confirm that by systematically investigating asymmetries in the production of a given functional morpheme, we stand to gain an insight into the underlying causes of L2 variability

Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues

Background: More than 20% of human transcripts have naturally occurring antisense products (or natural antisense transcripts – NATs), some of which may play a key role in a range of human diseases. To date, several databases of in silico defined human sense-antisense (SAS) pairs have appeared, however no study has focused on differential expression of SAS pairs in breast tissue. We therefore investigated the expression levels of sense and antisense transcripts in normal and malignant human breast epithelia using the Affymetrix HG-U133 Plus 2.0 and Almac Diagnostics Breast Cancer DSA microarray technologies as well as massively parallel signature sequencing (MPSS) data. Results: The expression of more than 2500 antisense transcripts were detected in normal breast duct luminal cells and in primary breast tumors substantially enriched for their epithelial cell content by DSA microarray. Expression of 431 NATs were confirmed by either of the other two technologies. A corresponding sense transcript could be identified on DSA for 257 antisense transcripts. Of these SAS pairs, 163 have not been previously reported. A positive correlation of differential expression between normal and malignant breast samples was observed for most SAS pairs. Orientation specific RT-QPCR of selected SAS pairs validated their expression in several breast cancer cell lines and solid breast tumours. Conclusion: Disease-focused and antisense enriched microarray platforms (such as Breast Cancer DSA) confirm the assumption that antisense transcription in the human breast is more prevalent than previously anticipated. Expression of a proportion of these NATs has already been confirmed by other technologies while the true existence of the remaining ones has to be validated. Nevertheless, future studies will reveal whether the relative abundances of antisense and sense transcripts have regulatory influences on the translation of these mRNAs

Eliciting patients’ health concerns in consulting rooms and wards in Vietnamese public hospitals

This article examines the doctor’s elicitation of the patient’s presenting health concern in two clinical settings in the Vietnamese public hospital system: the consulting room and the ward. The data were taken from 66 audio-recorded consultations. Our analysis shows that the elicitors used by the doctor in the consulting room often communicate a weak epistemic stance towards the patient’s health issue, while those used in the ward tend to signal a strong epistemic stance. In addition, this contrast between the elicitors employed in the consulting room and the ward is evident in our data regardless of whether the consultation is a first visit or a same follow-up (in which the doctor is the same one that treated the patient on their last visit), though the contrast is less clear for different follow-ups (in which the doctor has not treated the patient before). An additional finding is that the clinical setting has some bearing on the use of inappropriate elicitation formats (in which the doctor opens the visit with an elicitor which is more appropriate for another type of visit). The precise way in which each of the consulting room and the ward operates is, of course, a feature of the Vietnamese public hospital system itself. Hence, the overall contrast between the elicitors and elicitation formats used in these two settings illustrates how, on a more general level, the institutional context can have an impact on doctor-patient communication

An asymmetry in the spoken production of number agreement in second language English : adjacency or locality?

In English, subject-verb agreement is deemed to be ‘local’ if the controller (i.e., the subject) and the target (i.e., the main verb) are adjacent, but ‘non-local’ if these items are separated by one or more terminal nodes. Previous research indicates that second language English learners whose first languages lack subject-verb agreement tend to supply inflection for this functional category less accurately in non-adjacent than adjacent contexts in spoken production. This asymmetry could be driven by either adjacency or locality, since, for subject-verb agreement at least, these two properties are aligned with each other. Phrase-internal agreement, by contrast, is local regardless of whether the controller (i.e., a determiner or quantifier) and the target (i.e., a noun) are adjacent or non-adjacent; hence, for this type of agreement, adjacency and locality are not aligned with each other. In the present study, we gave a sentence-construction task to 64 native speakers of Vietnamese, a language without inflection for number agreement. Suppliance of inflection was lower in non-adjacent than adjacent contexts phrase-internally, and therefore within the local domain itself. We concluded that what gave rise to the asymmetries in inflectional production in our study, and, by extension, also in previous research on subject-verb agreement, was not the distinction between local and non-local domains, but rather the one between adjacent and nonadjacent contexts for agreement. In so doing, we present a more parsimonious analysis of asymmetries in the spoken production of agreement inflection than the one currently available