The occlusion illusion: Partial modal completion or apparent distance?

In the occlusion illusion, the visible portion of a partly occluded object (eg a semicircle partly hidden behind a rectangle) appears to be significantly larger than a physically identical region that is fully visible. This illusion may occur either because the visual system 'fills in' a thin strip along the occluded border (the partial-modal-completion hypothesis) or because the partly occluded object is perceived as farther away (the apparent-distance hypothesis). We measured the magnitude of the occlusion illusion psychophysically in several experiments to investigate its causes. The results of experiments 1-3 are consistent with the general proposal that the magnitude of the illusion varies with the strength of the evidence for occlusion, supporting the inference that it is due to occlusion. Experiment 4 provides a critical test between apparent-distance and partial-modal-completion explanations by determining whether the increase in apparent size of the occluded region results from a change in its perceived shape (due to the modal extension of the occluded shape along the occluding edge, as predicted by the partial-modal-completion hypothesis) or from a change in its perceived overall size (as predicted by the apparent-distance hypothesis). The results more strongly support the partial-modal-completion hypothesis

Room reflections and constancy in speech-like sounds: within-band effects

The experiment asks whether constancy in hearing precedes or follows grouping. Listeners heard speech-like sounds comprising 8 auditory-filter shaped noise-bands that had temporal envelopes corresponding to those arising in these filters when a speech message is played. The „context‟ words in the message were “next you‟ll get _to click on”, into which a “sir” or “stir” test word was inserted. These test words were from an 11-step continuum that was formed by amplitude modulation. Listeners identified the test words appropriately and quite consistently, even though they had the „robotic‟ quality typical of this type of 8-band speech. The speech-like effects of these sounds appears to be a consequence of auditory grouping. Constancy was assessed by comparing the influence of room reflections on the test word across conditions where the context had either the same level of reflections, or where it had a much lower level. Constancy effects were obtained with these 8-band sounds, but only in „matched‟ conditions, where the room reflections were in the same bands in both the context and the test word. This was not the case in a comparison „mismatched‟ condition, and here, no constancy effects were found. It would appear that this type of constancy in hearing precedes the across-channel grouping whose effects are so apparent in these sounds. This result is discussed in terms of the ubiquity of grouping across different levels of representation

'Part'ly first among equals: Semantic part-based benchmarking for state-of-the-art object recognition systems

An examination of object recognition challenge leaderboards (ILSVRC, PASCAL-VOC) reveals that the top-performing classifiers typically exhibit small differences amongst themselves in terms of error rate/mAP. To better differentiate the top performers, additional criteria are required. Moreover, the (test) images, on which the performance scores are based, predominantly contain fully visible objects. Therefore, `harder' test images, mimicking the challenging conditions (e.g. occlusion) in which humans routinely recognize objects, need to be utilized for benchmarking. To address the concerns mentioned above, we make two contributions. First, we systematically vary the level of local object-part content, global detail and spatial context in images from PASCAL VOC 2010 to create a new benchmarking dataset dubbed PPSS-12. Second, we propose an object-part based benchmarking procedure which quantifies classifiers' robustness to a range of visibility and contextual settings. The benchmarking procedure relies on a semantic similarity measure that naturally addresses potential semantic granularity differences between the category labels in training and test datasets, thus eliminating manual mapping. We use our procedure on the PPSS-12 dataset to benchmark top-performing classifiers trained on the ILSVRC-2012 dataset. Our results show that the proposed benchmarking procedure enables additional differentiation among state-of-the-art object classifiers in terms of their ability to handle missing content and insufficient object detail. Given this capability for additional differentiation, our approach can potentially supplement existing benchmarking procedures used in object recognition challenge leaderboards.Comment: Extended version of our ACCV-2016 paper. Author formatting modifie

Investigating the role of a dynamin-actin interaction

Endocytosis is a fundamental cellular process which facilitates the uptake of lipids and proteins from the plasma membrane. During endocytosis, the plasma membrane is internalised through the formation of an invagination, which is then pinched off to form a vesicle. Endocytosed vesicles are then able to fuse with endosomal compartments allowing cargo to be sorted within the endo-lysosomal system. One of the most well characterised forms of endocytosis is clathrin mediated, which takes place in distinct stages. These include coat and clathrin recruitment, membrane invagination and finally scission which releases the vesicle into the cytoplasm. Cells require many different molecules to orchestrate each stage including the GTPase dynamin and cytoskeletal protein actin. Dynamin facilitates the scission stage of endocytosis where it oligomerises around the vesicle neck and, through the hydrolysis of GTP, enables scission. Furthermore dynamin-1 has been reported to bind directly to actin. In Saccharomyces cerevisiae (yeast) actin is essential to endocytic invagination in order to overcome turgor pressure. Yeast contain a dynamin-like protein Vps1 which acts during endocytic scission and has orthology with dynamin-1. In this thesis the direct interaction between Vps1 and actin was explored to elucidate how this interaction may be required during endocytosis. It is understood that both dynamin and actin are involved in other cellular processes and therefore the knowledge gained from investigating this interaction during endocytosis may well provide new insight into how these two molecules work together in other molecular systems. Thus, mutations found to perturb the Vps1-actin interaction were created in human dynamin-1 and preliminary results suggest this could have an effect on mammalian cell endocytosis and cell migration. This project has identified a novel Vps1-actin interaction which is required for the scission stage of yeast endocytosis. It also describes a point mutation in Vps1 E461K, which has been found to cause an early stage endocytic defect

Reduction of low- and high-grade cervical abnormalities associated with high uptake of the HPV bivalent vaccine in Scotland

In Scotland, a national HPV immunisation programme began in 2008 for 12-13 year olds, with a catch-up campaign from 2008-2011 for those under the age of 18. To monitor the impact of HPV immunisation on cervical disease at the population level, a programme of national surveillance was established.  We analysed colposcopy data from a cohort of women born between 1988-1992 who entered the Scottish Cervical Screening Programme (SCSP) and were aged 20-21 in 2008-2012.  By linking datasets from the SCSP and colposcopy services, we observed a significant reduction in diagnoses of cervical intraepithelial neoplasia 1 (CIN 1) (RR 0.71, 95% CI 0.58 to 0.87, p=0.0008), CIN 2 (RR 0.5, 95% CI 0.4, 0.63, p<0.0001) and CIN 3 (RR 0.45, 95% CI 0.35 to 0.58, p< 0.0001) for women who received 3 doses of vaccine compared with unvaccinated women.  To our knowledge, this is one of the first studies to show a reduction of low and high grade cervical intraepithelial neoplasia associated with high uptake of the HPV bivalent vaccine at the population level. These data are very encouraging for countries that have achieved high HPV vaccine uptake

The 1983 drought in the West Sahel: a case study

Some drought years over sub-Saharan west Africa (1972, 1977, 1984) have been previously related to a cross-equatorial Atlantic gradient pattern with anomalously warm sea surface temperatures (SSTs) south of 10°N and anomalously cold SSTs north of 10°N. This SST dipole-like pattern was not characteristic of 1983, the third driest summer of the twentieth century in the Sahel. This study presents evidence that the dry conditions that persisted over the west Sahel in 1983 were mainly forced by high Indian Ocean SSTs that were probably remanent from the strong 1982/1983 El Niño event. The synchronous Pacific impact of the 1982/1983 El Niño event on west African rainfall was however, quite weak. Prior studies have mainly suggested that the Indian Ocean SSTs impact the decadal-scale rainfall variability over the west Sahel. This study demonstrates that the Indian Ocean also significantly affects inter-annual rainfall variability over the west Sahel and that it was the main forcing for the drought over the west Sahel in 1983

Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis

The preterm gut microbiome is a complex dynamic community influenced by genetic and environmental factors and is implicated in the pathogenesis of necrotising enterocolitis (NEC) and sepsis. We aimed to explore the longitudinal development of the gut microbiome in preterm twins to determine how shared environmental and genetic factors may influence temporal changes and compared this to the expressed breast milk (EBM) microbiome. Stool samples (n = 173) from 27 infants (12 twin pairs and 1 triplet set) and EBM (n = 18) from 4 mothers were collected longitudinally. All samples underwent PCR-DGGE (denaturing gradient gel electrophoresis) analysis and a selected subset underwent 454 pyrosequencing. Stool and EBM shared a core microbiome dominated by Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae. The gut microbiome showed greater similarity between siblings compared to unrelated individuals. Pyrosequencing revealed a reduction in diversity and increasing dominance of Escherichia sp. preceding NEC that was not observed in the healthy twin. Antibiotic treatment had a substantial effect on the gut microbiome, reducing Escherichia sp. and increasing other Enterobacteriaceae. This study demonstrates related preterm twins share similar gut microbiome development, even within the complex environment of neonatal intensive care. This is likely a result of shared genetic and immunomodulatory factors as well as exposure to the same maternal microbiome during birth, skin contact and exposure to EBM. Environmental factors including antibiotic exposure and feeding are additional significant determinants of community structure, regardless of host genetics

The kinases MSK1 and MSK2 act as negative regulators of Toll-like receptor signaling

The kinases MSK1 and MSK2 are activated 'downstream' of the p38 and Erk1/2 mitogen-activated protein kinases. Here we found that MSK1 and MSK2 were needed to limit the production of proinflammatory cytokines in response to stimulation of primary macrophages with lipopolysaccharide. By inducing transcription of the mitogen-activated protein kinase phosphatase DUSP1 and the anti-inflammatory cytokine interleukin 10, MSK1 and MSK2 exerted many negative feedback mechanisms. Deficiency in MSK1 and MSK2 prevented the binding of phosphorylated transcription factors CREB and ATF1 to the promoters of the genes encoding interleukin 10 and DUSP1. Mice doubly deficient in MSK1 and MSK2 were hypersensitive to lipopolysaccharide-induced endotoxic shock and showed prolonged inflammation in a model of toxic contact eczema induced by phorbol 12-myristate 13-acetate. Our results establish MSK1 and MSK2 as key components of negative feedback mechanisms needed to limit Toll-like receptor-driven inflammation.</p

A multiproxy analysis of extreme wave deposits in a tropical coastal lagoon in Jamaica, West Indies

The Small Island Developing States (SIDS) of the Caribbean Region are vulnerable to natural hazards including earthquakes, tsunamis and tropical cyclones that can cause widespread devastation. Sedimentary archives of these hazards are often well-preserved in coastal lagoons; however, few studies in the Caribbean have adopted a multiproxy approach to their reconstruction. Here, we present a 1200-year multiproxy record of extreme washover events deposited within a coastal mangrove lagoon on the south coast of Jamaica. Manatee Bay lagoon is a permanent fresh-brackish-water mangrove lagoon separated from the Caribbean Sea by a low-elevation carbonate beach. Fifteen sediment cores recovered along five shore-normal transects contain ostracod-rich authigenic carbonate lake muds interspersed with beds of organic lake mud and mangrove peat. The cores contain evidence of multiple palaeo-washover deposits that are readily distinguished by their sedimentology, geochemistry and microfossil assemblages. Hypersaline conditions dominated the early part of the record (~ 800 to 900 CE), and we infer a freshening of lagoonal waters and the subsequent expansion of the mangrove community following an extreme wave event that occurred some time before ~ 1290 to 1400 CE. We constrain the primary historical-washover deposit to 1810–1924 CE (2σ; 71% probability), a period characterised by extreme tectonic and meteorological events, which include the Great Kingston Earthquake of 1907 and a local episode of enhanced hurricane activity. Whilst the balance of circumstantial evidence indicates that the deposit was probably emplaced during the tsunami generated by the 1907 earthquake, we are currently unable to differentiate between tectonically and meteorologically driven washover events based on their sedimentological characteristics

Should Research Ethics Encourage the Production of Cost-Effective Interventions?

This project considers whether and how research ethics can contribute to the provision of cost-effective medical interventions. Clinical research ethics represents an underexplored context for the promotion of cost-effectiveness. In particular, although scholars have recently argued that research on less-expensive, less-effective interventions can be ethical, there has been little or no discussion of whether ethical considerations justify curtailing research on more expensive, more effective interventions. Yet considering cost-effectiveness at the research stage can help ensure that scarce resources such as tissue samples or limited subject popula- tions are employed where they do the most good; can support parallel efforts by providers and insurers to promote cost-effectiveness; and can ensure that research has social value and benefits subjects. I discuss and rebut potential objections to the consideration of cost-effectiveness in research, including the difficulty of predicting effectiveness and cost at the research stage, concerns about limitations in cost-effectiveness analysis, and worries about overly limiting researchers’ freedom. I then consider the advantages and disadvantages of having certain participants in the research enterprise, including IRBs, advisory committees, sponsors, investigators, and subjects, consider cost-effectiveness. The project concludes by qualifiedly endorsing the consideration of cost-effectiveness at the research stage. While incorporating cost-effectiveness considerations into the ethical evaluation of human subjects research will not on its own ensure that the health care system realizes cost-effectiveness goals, doing so nonetheless represents an important part of a broader effort to control rising medical costs