Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission

If open reading frames (ORFs) have been transmitted primarily by vertical descent, the distributional profile of orthologues of each ORF should be congruent with the organismal tree or a subtree thereof. Distributional patterns not reconciled parsimoniously with tree-like descent and loss are prima facie evidence of lateral gene transfer. Herein, a rigorous criterion for recognizing ORF distributions is described and implemented; it does not require the inference of phylogenetic trees, nor does it assume any specific tree. Because lineage-specific differences in rates of sequence change can also generate unexpected distributional patterns, rate artefacts, were controlled for by requiring pairwise matches between ORFs to exceed a rigorous inclusion threshold, but absence of a match was assessed against a more-permissive exclusion threshold. Applying this dual-threshold criterion to cross-domain and cross-phylum distributional patterns for ORFs in 23 bacterial genomes, a relative abundance of ORFs was observed that find a match in exactly seven other bacterial phyla; 94-99% of these ORFs also find matches among the Archaea and/or Eukarya. In the larger (and some smaller) bacterial genomes, ORFs that find matches in exactly one other bacterial phylum are also relatively abundant, but fewer of these have non-bacterial homologues; most of their matches within the Bacteria are to the Proteobacteria and/or Firmicutes, which cannot be sister lineages to all bacteria. ORFs that are neither distributed universally among the Bacteria, nor necessarily shared with topologically adjacent lineages, are preferentially enriched in large bacterial genomes.

Communicative repair strategies and problem behaviours of children with autism

The use of strategies by children with developmental disabilities to repair communicative breakdowns has received little attention in the research literature to date. The research that is available suggests that children with severe communication impairments may be more likely to experience communicative breakdowns than their typically developing peers. These children may also have fewer strategies available to them to repair these breakdowns. The present article reviews some of the research in this area and discusses the possible links between communicative breakdowns and the emergence of problem behaviour in children with autism. Theoretical and practical implications are considered and areas for future research are highlighted.

Teacher responses to the communicative attempts of children with autism

We assessed teacher responses to the communicative attempts of children with autism. Teachers were first interviewed using the Inventory of Potential Communicative Acts (IPCA) to identify behaviors in each child's repertoire that the teachers considered to be communicative. Interview results suggested that the teachers interpreted many of the children's prelinguistic gestures, body movements, and facial expressions, as forms of communication. Naturalistic observations were then conducted in the child's classroom to determine how teachers responded to the children's identified forms of prelinguistic behaviors. The results of these naturalistic observations suggested that the teachers often did not respond to the child's prelinguistic behaviors in ways that acknowledged their communicative intent. Implications of the results on the child's communication development and for intervention efforts are discussed.

Communicating continuous quantum variables between different Lorentz frames

We show how to communicate Heisenberg-limited continuous (quantum) variables between Alice and Bob in the case where they occupy two inertial reference frames that differ by an unknown Lorentz boost. There are two effects that need to be overcome: the Doppler shift and the absence of synchronized clocks. Furthermore, we show how Alice and Bob can share Doppler-invariant entanglement, and we demonstrate that the protocol is robust under photon loss.

Aboriginal self-determination in Australia - The effects of minority-majority frames and target universalism on majority collective guilt and compensation attitudes

In the context of Aboriginal-Anglo Australian relations, we tested the effect of framing (multiculturalism versus separatism) and majority group members' social values (universalism) on the persuasiveness of Aboriginal group rhetoric, majority collective guilt, attitudes toward compensation, and reparations for Aboriginals. As predicted, Anglo Australians who are low on universalism report more collective guilt when presented with a multiculturalist than a separatist Aboriginal frame, whereas those high on universalism report high levels of guilt independent of frame. The same pattern was predicted and found for the persuasiveness of the rhetoric and attitudes toward compensation. Our data suggest that (a) for individuals low in universalism, framing produces attitudes consonant with compensation because it produces collective guilt and (b) the reason that universalists are more in favor of compensation and reparation is because of high collective guilt. We discuss the strategic use of language to create power through the manipulation of collective guilt in political contexts.

Aphasia websites: An examination of their quality and communicative accessibility

Background: Studies have examined Internet use as a source of information by various populations, however no study has examined the quality and accessibility of websites for people with aphasia, or their use of such sites. Aims: This study aimed to describe the quality, communicative accessibility, and readability of a sample of aphasia websites and to determine whether sites preferred by people with aphasia were those rated highly on measures of accessibility and quality. The perceptions of people with aphasia regarding the accessibility of the sites were compared with those of speech pathologists. The relationship between the quality and communicative accessibility of websites was analysed. Factors that may influence use of the Internet by people with aphasia and speech pathologists were explored. Methods & Procedures: Tools for measuring quality and communicative accessibility were developed and a sample of five websites was selected. Two participant groups (18 speech pathologists and 6 people with aphasia) assessed aphasia websites in terms of communicative accessibility. Speech pathologists also rated website quality. Spearman's rho was used to determine levels of agreement between variables. Outcomes & Results: People with aphasia and speech pathologists showed minimal agreement on their perceptions of communicative accessibility. However, when the preferences of websites (Aphasia Help and Speakability) were of a very high standard. There was a weak relationship between quality and communicative accessibility, however it was not statistically significant. Conclusions: Accessible websites are not necessarily of high quality, and quality websites are not guaranteed to be easily accessible. People with aphasia did not agree with speech pathologists as to what makes a good aphasia website. Therefore, people with aphasia should be involved in the design of aphasia websites since they are often the intended users. If Internet use by people with aphasia increases in line with other health populations, speech pathologist need to have the skills and confidence to recommend appropriate sites to their clients.

Communicative practices in online communication: A case of agreeing to disagree

Online communities have evolved beyond the realm of social phenomenon to become important knowledge-sharing media with real economic consequences. However, the sharing of knowledge and the communication of meaning through Internet technology presents many difficulties. This is particularly so for online finance forums where market-sensitive information and disinformation about exchange-traded stocks is regularly disseminated. The development of trust and the effect of misinformation in this environment are important in the growth of this communication medium. Forum administrators need to better understand and handle the development of trust. In this article, we analyze and discuss the communicative practices of a group of investors and members of an online community of interest. We found that conflict as a driver of knowledge sharing is an important consideration for forum administrators and designers.

Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides

Background: Approximately 40% of mammalian mRNA sequences contain AUG trinucleotides upstream of the main coding sequence, with a quarter of these AUGs demarcating open reading frames of 20 or more codons. In order to investigate whether these open reading frames may encode functional peptides, we have carried out a comparative genomic analysis of human and mouse mRNA 'untranslated regions' using sequences from the RefSeq mRNA sequence database. Results: We have identified over 200 upstream open reading frames which are strongly conserved between the human and mouse genomes. Consensus sequences associated with efficient initiation of translation are overrepresented at the AUG trinucleotides of these upstream open reading frames, while comparative analysis of their DNA and putative peptide sequences shows evidence of purifying selection. Conclusion: The occurrence of a large number of conserved upstream open reading frames, in association with features consistent with protein translation, strongly suggests evolutionary maintenance of the coding sequence and indicates probable functional expression of the peptides encoded within these upstream open reading frames.