Discussion of Likelihood Inference for Models with Unobservables: Another View

Discussion of "Likelihood Inference for Models with Unobservables: Another View" by Youngjo Lee and John A. Nelder [arXiv:1010.0303]Comment: Published in at http://dx.doi.org/10.1214/09-STS277A the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

It's not what you play, it's how you play it: timbre affects perception of emotion in music.

Salient sensory experiences often have a strong emotional tone, but the neuropsychological relations between perceptual characteristics of sensory objects and the affective information they convey remain poorly defined. Here we addressed the relationship between sound identity and emotional information using music. In two experiments, we investigated whether perception of emotions is influenced by altering the musical instrument on which the music is played, independently of other musical features. In the first experiment, 40 novel melodies each representing one of four emotions (happiness, sadness, fear, or anger) were each recorded on four different instruments (an electronic synthesizer, a piano, a violin, and a trumpet), controlling for melody, tempo, and loudness between instruments. Healthy participants (23 young adults aged 18-30 years, 24 older adults aged 58-75 years) were asked to select which emotion they thought each musical stimulus represented in a four-alternative forced-choice task. Using a generalized linear mixed model we found a significant interaction between instrument and emotion judgement with a similar pattern in young and older adults (p < .0001 for each age group). The effect was not attributable to musical expertise. In the second experiment using the same melodies and experimental design, the interaction between timbre and perceived emotion was replicated (p < .05) in another group of young adults for novel synthetic timbres designed to incorporate timbral cues to particular emotions. Our findings show that timbre (instrument identity) independently affects the perception of emotions in music after controlling for other acoustic, cognitive, and performance factors

Preliminary archaeoentomological analyses of permafrost-preserved cultural layers from the pre-contact Yup’ik Eskimo site of Nunalleq, Alaska : implications, potential and methodological considerations

Acknowledgements Site excavation and samples collection were conducted by archaeologists from the University of Aberdeen, with the help of archaeologists and student excavators from the University of Aberdeen University of Alaska Fairbanks and Bryn Mawr College, Kuskokwim Campus, College of Rural Alaska and residents of Quinhagak and Mekoryuk. This study is funded through AHRC grant to the project ‘Understanding Cultural Resilience and Climate Change on the Bering Sea through Yup’ik Ecological Knowledge, Lifeways, Learning and Archaeology’ to Rick Knecht, Kate Britton and Charlotta Hillderal (University of Aberdeen; AH/K006029/1). Thanks are due to Qanirtuuq Inc. and Quinhagak, Alaska for sampling permissions and to entomologists working at the CNC in Ottawa for allowing access to reference collections of beetles, lice and fleas. Yves Bousquet, Ales Smetana and Anthony E. Davies are specially acknowledged for their help with the identification of coleopteran specimens. Finally, we would also like to thank Scott Elias for useful comments on the original manuscript.Peer reviewedPublisher PD

Estimation of the linear mixed integrated Ornstein-Uhlenbeck model.

The linear mixed model with an added integrated Ornstein-Uhlenbeck (IOU) process (linear mixed IOU model) allows for serial correlation and estimation of the degree of derivative tracking. It is rarely used, partly due to the lack of available software. We implemented the linear mixed IOU model in Stata and using simulations we assessed the feasibility of fitting the model by restricted maximum likelihood when applied to balanced and unbalanced data. We compared different (1) optimization algorithms, (2) parameterizations of the IOU process, (3) data structures and (4) random-effects structures. Fitting the model was practical and feasible when applied to large and moderately sized balanced datasets (20,000 and 500 observations), and large unbalanced datasets with (non-informative) dropout and intermittent missingness. Analysis of a real dataset showed that the linear mixed IOU model was a better fit to the data than the standard linear mixed model (i.e. independent within-subject errors with constant variance)

Infants Help a Non-Human Agent

Young children can be motivated to help adults by sympathetic concern based upon empathy, but the underlying mechanisms are unknown. One account of empathy-based sympathetic helping in adults states that it arises due to direct-matching mirror-system mechanisms which allow the observer to vicariously experience the situation of the individual in need of help. This mechanism could not account for helping of a geometric-shape agent lacking human-isomorphic bodyparts. Here 17-month-olds observed a ball-shaped non-human agent trying to reach a goal but failing because it was blocked by a barrier. Infants helped the agent by lifting it over the barrier. They performed this action less frequently in a control condition in which the barrier could not be construed as blocking the agent. Direct matching is therefore not required for motivating helping in infants, indicating that at least some of our early helpful tendencies do not depend on human-specific mechanisms. Empathy-based mechanisms that do not require direct-matching provide one plausible basis for the observed helping. A second possibility is that rather than being based on empathy, the observed helping occurred as a result of a goal-contagion process in which the infants were primed with the unfulfilled goal

Autonomy dimensions and care seeking for delivery in Zambia; the prevailing importance of cluster-level measurement.

It is widely held that decisions whether or when to attend health facilities for childbirth are not only influenced by risk awareness and household wealth, but also by factors such as autonomy or a woman's ability to act upon her own preferences. How autonomy should be constructed and measured - namely, as an individual or cluster-level variable - has been less examined. We drew on household survey data from Zambia to study the effect of several autonomy dimensions (financial, relationship, freedom of movement, health care seeking and violence) on place of delivery for 3200 births across 203 rural clusters (villages). In multilevel logistic regression, two autonomy dimensions (relationship and health care seeking) were strongly associated with facility delivery when measured at the cluster level (OR 1.27 and 1.57, respectively), though not at the individual level. This suggests that power relations and gender norms at the community level may override an individual woman's autonomy, and cluster-level measurement may prove critical to understanding the interplay between autonomy and care seeking in this and similar contexts

Clustering of contacts relevant to the spread of infectious disease.

OBJECTIVE: Infectious disease spread depends on contact rates between infectious and susceptible individuals. Transmission models are commonly informed using empirically collected contact data, but the relevance of different contact types to transmission is still not well understood. Some studies select contacts based on a single characteristic such as proximity (physical/non-physical), location, duration or frequency. This study aimed to explore whether clusters of contacts similar to each other across multiple characteristics could better explain disease transmission. METHODS: Individual contact data from the POLYMOD survey in Poland, Great Britain, Belgium, Finland and Italy were grouped into clusters by the k medoids clustering algorithm with a Manhattan distance metric to stratify contacts using all four characteristics. Contact clusters were then used to fit a transmission model to sero-epidemiological data for varicella-zoster virus (VZV) in each country. RESULTS AND DISCUSSION: Across the five countries, 9-15 clusters were found to optimise both quality of clustering (measured using average silhouette width) and quality of fit (measured using several information criteria). Of these, 2-3 clusters were most relevant to VZV transmission, characterised by (i) 1-2 clusters of age-assortative contacts in schools, (ii) a cluster of less age-assortative contacts in non-school settings. Quality of fit was similar to using contacts stratified by a single characteristic, providing validation that single stratifications are appropriate. However, using clustering to stratify contacts using multiple characteristics provided insight into the structures underlying infection transmission, particularly the role of age-assortative contacts, involving school age children, for VZV transmission between households

Can Internet-Based Sexual Health Services Increase Diagnoses of Sexually Transmitted Infections (STI)? Protocol for a Randomized Evaluation of an Internet-Based STI Testing and Results Service.

BACKGROUND: Ensuring rapid access to high quality sexual health services is a key public health objective, both in the United Kingdom and internationally. Internet-based testing services for sexually transmitted infections (STIs) are considered to be a promising way to achieve this goal. This study will evaluate a nascent online STI testing and results service in South East London, delivered alongside standard face-to-face STI testing services. OBJECTIVE: The aim of this study is to establish whether an online testing and results services can (1) increase diagnoses of STIs and (2) increase uptake of STI testing, when delivered alongside standard face-to-face STI testing services. METHODS: This is a single-blind randomized controlled trial. We will recruit 3000 participants who meet the following eligibility criteria: 16-30 years of age, resident in the London boroughs of Lambeth and Southwark, having at least one sexual partner in the last 12 months, having access to the Internet and willing to take an STI test. People unable to provide informed consent and unable to read and understand English (the websites will be in English) will be excluded. Baseline data will be collected at enrolment. This includes participant contact details, demographic data (date of birth, gender, ethnicity, and sexual orientation), and sexual health behaviors (last STI test, service used at last STI test and number of sexual partners in the last 12 months). Once enrolled, participants will be randomly allocated either (1) to an online STI testing and results service (Sexual Health 24) offering postal self-administered STI kits for chlamydia, gonorrhoea, syphilis, and HIV; results via text message (short message service, SMS), except positive results for HIV, which will be delivered by phone; and direct referrals to local clinics for treatment or (2) to a conventional sexual health information website with signposting to local clinic-based sexual health services. Participants will be free to use any other interventions or services during the trial period. At 6 weeks from randomization we will collect self-reported follow-up data on service use, STI tests and results, treatment prescribed, and acceptability of STI testing services. We will also collect objective data from participating STI testing services on uptake of STI testing, STI diagnoses and treatment. We hypothesise that uptake of STI testing and STI diagnoses will be higher in the intervention arm. Our hypothesis is based on the assumption that the intervention is less time-consuming, more convenient, more private, and incur less stigma and embarrassment than face-to-face STI testing pathways. The primary outcome measure is diagnosis of any STI at 6 weeks from randomization and our co-primary outcome is completion of any STI test at 6 weeks from randomization. We define completion of a test, as samples returned, processed, and results delivered to the intervention and/or clinic settings. We will use risk ratios to calculate the effect of the intervention on our primary outcomes with 95% confidence intervals. All analyses will be based on the intention-to-treat (ITT) principle. RESULTS: This study is funded by Guy's and St Thomas' Charity and it has received ethical approval from NRES Committee London-Camberwell St Giles (Ref 14/LO/1477). Research and Development approval has been obtained from Kings College Hospital NHS Foundation Trust and Guy's and St Thomas' NHS Foundation Trust. Results are expected in June 2016. CONCLUSIONS: This study will provide evidence on the effectiveness of an online STI testing and results service in South East London. Our findings may also be generalizable to similar populations in the United Kingdom. TRIAL REGISTRATION: International Standard Randomized Controlled Trial Number (ISRCTN): 13354298; http://www.isrctn.com/ISRCTN13354298 (Archived by WebCite at http://www.webcitation.org/6d9xT2bPj)

Murine immune responses to virus-like particle-associated pre- and postfusion forms of the respiratory syncytial virus F protein

Virus-like particles (VLPs) built on the Newcastle disease virus (NDV) core proteins, NP and M, and containing two chimeric proteins, F/F and H/G, composed of respiratory syncytial virus (RSV) fusion protein (F) and glycoprotein (G) ectodomains fused to the transmembrane and cytoplasmic domains of the NDV F and HN proteins, respectively, stimulate durable, protective RSV neutralizing antibodies in mice. Here, we report the properties of VLPs constructed to contain mutant RSV F protein ectodomains stabilized in prefusion (pre-F/F) or postfusion (post-F/F) configurations. The structures of the chimeric proteins assembled into VLPs were verified immunologically by their reactivities with a conformationally restricted anti-F protein monoclonal antibody. Following immunization of mice, without adjuvant, pre-F/F-containing VLPs induced significantly higher neutralizing antibody titers than the post-F/F-containing VLPs or the wild-type F/F-containing VLPs after a single immunization but not after prime and boost immunization. The specificities of anti-F IgG induced by the two mutant VLPs were assessed by enzyme-linked immunosorbent assay (ELISA) using soluble forms of the prefusion and postfusion forms of the F protein as targets. While both types of VLPs stimulated similar levels of IgG specific for the soluble postfusion F protein, titers of IgG specific for prefusion F induced by the pre-F/F-containing VLPs were higher than those induced by post-F/F-containing VLPs. Thus, VLPs containing a stabilized prefusion form of the RSV F protein represent a promising RSV vaccine candidate. IMPORTANCE: The development of vaccines for respiratory syncytial virus has been hampered by a lack of understanding of the requirements for eliciting high titers of neutralizing antibodies. The results of this study suggest that particle-associated RSV F protein containing mutations that stabilize the structure in a prefusion conformation may stimulate higher titers of protective antibodies than particles containing F protein in a wild-type or postfusion conformation. These findings indicate that the prefusion F protein assembled into VLPs has the potential to produce a successful RSV vaccine candidate