Semi-automated dialogue act classification for situated social agents in games

As a step toward simulating dynamic dialogue between agents and humans in virtual environments, we describe learning a model of social behavior composed of interleaved utterances and physical actions. In our model, utterances are abstracted as {speech act, propositional content, referent} triples. After training a classifier on 100 gameplay logs from The Restaurant Game annotated with dialogue act triples, we have automatically classified utterances in an additional 5,000 logs. A quantitative evaluation of statistical models learned from the gameplay logs demonstrates that semi-automatically classified dialogue acts yield significantly more predictive power than automatically clustered utterances, and serve as a better common currency for modeling interleaved actions and utterances

Ozone-depleting substances (ODSs) and related chemicals

The amended and adjusted Montreal Protocol continues to be successful at reducing emissions and atmospheric abundances of most controlled ozone-depleting substances (ODSs).Global Ozone Research and Monitoring Projec

South African national household survey of HIV/AIDS prevalence, behavioural risks and mass media impact-detailed methodology and response rate results

Objectives. To describe the methodology used in a recent survey of HIV/AIDS in South Africa and to present the response rates.Methods. A cross-sectional, national household-based survey was conducted using second-generation surveillance procedures. A complex multistage sampling technique was used to create a master sample of 1 000 census enumerator areas out of a total of 86 000 nationally. Aerial photographs were taken and used to randomly select more than 10 197 households and ultimately 13 518 individuals from a sampling frame of 31 321 people. Phase 1 of the study involved notifying the household residents about the study and collecting key demographic information on respondents aged 2 years and older. This information was used to randomly select up to 3 respondents from each household: 1 adult (25 years and older), 1 youth (15- 24 years), and 1 child (2- 14 years). In phase 2 nurses interviewed respondents and collected oral fluid specimens for HIV testing. In the case of children aged 2 - 11 years, parents or guardians were interviewed, but HIV testing was performed on the selected children. Questionnaire data were anonymously linked with HIV test results.Results. A total of 9 963 persons agreed to be interviewed and 8 840 were tested for HIV, yielding a response rate of 73.7% and 65.4% respectively. However, only 8 428 (62.3%) HIV test results were correctly matched with behavioural data. The results showed that those tested for HIV did not differ from those not tested in terms of key determinants.Conclusion. It is possible to use community-based surveys to study the prevalence of HIV in the general population

Recently Integrated Alu Elements In Capuchin Monkeys: A Resource For Cebus/Sapajus Genomics

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships

Recently Integrated \u3cem\u3eAlu\u3c/em\u3e Elements in Capuchin Monkeys: A Resource for \u3cem\u3eCebus\u3c/em\u3e/\u3cem\u3eSapajus\u3c/em\u3e Genomics

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae fam-ily. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phy-logenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. There are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships

Euarchontan opsin variation brings new focus to primate origins

Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecological pressures. A problem with this approach is that opsin gene variation is incompletely known in the grandorder Euarchonta, i.e., the orders Scandentia (treeshrews), Dermoptera (colugos), and Primates. The ancestral state of primate color vision is therefore uncertain. Here we report on the genes (OPN1SW and OPN1LW) that encode SWS1 and M/LWS opsins in seven species of treeshrew, including the sole nocturnal scandentian Ptilocercus lowii. In addition, we examined the opsin genes of the Central American woolly opossum (Caluromys derbianus), an enduring ecological analogue in the debate on primate origins. Our results indicate: 1) retention of ultraviolet (UV) sensitivity in C. derbianus and a shift from UV to blue spectral sensitivities at the base of Euarchonta; 2) ancient pseudogenization of OPN1SW in the ancestors of P. lowii, but a signature of purifying selection in those of C. derbianus; and, 3) the absence of OPN1LW polymorphism among diurnal treeshrews. These findings suggest functional variation in color vision of nocturnal mammals and a distinctive visual ecology of early primates, perhaps one that demanded greater spatial resolution under light levels that could support cone-mediated color discrimination

Reactivation of a developmentally silenced embryonic globin gene

The α- and β-globin loci harbor developmentally expressed genes, which are silenced throughout post-natal life. Reactivation of these genes may offer therapeutic approaches for the hemoglobinopathies, the most common single gene disorders. Here, we address mechanisms regulating the embryonically expressed α-like globin, termed ζ-globin. We show that in embryonic erythroid cells, the ζ-gene lies within a ~65 kb sub-TAD (topologically associating domain) of open, acetylated chromatin and interacts with the α-globin super-enhancer. By contrast, in adult erythroid cells, the ζ-gene is packaged within a small (~10 kb) sub-domain of hypoacetylated, facultative heterochromatin within the acetylated sub-TAD and that it no longer interacts with its enhancers. The ζ-gene can be partially re-activated by acetylation and inhibition of histone de-acetylases. In addition to suggesting therapies for severe α-thalassemia, these findings illustrate the general principles by which reactivation of developmental genes may rescue abnormalities arising from mutations in their adult paralogues

Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage

Platy-1 elements are Platyrrhine-specific, short interspersed elements (SINEs) originally discovered in the Callithrix jacchus (common marmoset) genome. To date, only the marmoset genome has been analyzed for Platy-1 repeat content. Here, we report full-length Platy-1 insertions in other New World monkey (NWM) genomes (Saimiri boliviensis, squirrel monkey; Cebus imitator, capuchin monkey; and Aotus nancymaae, owl monkey) and analyze the amplification dynamics of lineage-specific Platy-1 insertions. A relatively small number of full-length and lineage-specific Platy-1 elements were found in the squirrel, capuchin, and owl monkey genomes compared to the marmoset genome. In addition, only a few older Platy-1 subfamilies were recovered in this study, with no Platy-1 subfamilies younger than Platy-1-6. By contrast, 62 Platy-1 subfamilies were discovered in the marmoset genome. All of the lineage-specific insertions found in the squirrel and capuchin monkeys were fixed present. However, ∼15% of the lineage-specific Platy-1 loci in Aotus were polymorphic for insertion presence/absence. In addition, two new Platy-1 subfamilies were identified in the owl monkey genome with low nucleotide divergences compared to their respective consensus sequences, suggesting minimal ongoing retrotransposition in Aotus genus and no current activity in the Saimiri, Cebus and Sapajus genera. These comparative analyses highlight the finding that the high number of Platy-1 elements discovered in the marmoset genome is an exception among NWM analyzed thus far, rather than the rule. Future studies are needed to expand upon our knowledge of Platy-1 amplification in other NWM genomes