The effect of inversion on the encoding of normal and “thatcherized” faces

In the "Thatcher illusion" a face, in which the eyes and mouth are inverted relative to the rest of the face, looks grotesque when shown upright but not when inverted. In four experiments we investigated the contribution of local and global processing to this illusion in normal observers. We examined inversion effects (i.e., better performance for upright than for inverted faces) in a task requiring discrimination of whether faces were or were not "thatcherized". Observers made same/different judgements to isolated face parts (Experiments 1-2) and to whole faces (Experiments 3-4). Face pairs had the same or different identity, allowing for different processing strategies using feature-based or configural information, respectively. In Experiment 1, feature-based matching of same-person face parts yielded only a small inversion effect for normal face parts. However, when feature-based matching was prevented by using the face parts of different people on all trials (Experiment 2) an inversion effect occurred for normal but not for thatcherized parts. In Experiments 3 and 4, inversion effects occurred with normal but not with thatcherized whole faces, on both same- and different-person matching tasks. This suggests that a common configural strategy was used with whole (normal) faces. Face context facilitated attention to misoriented parts in same-person but not in different-person matching. The results indicate that (1) face inversion disrupts local configural processing, but not the processing of image features, and (2) thatcherization disrupts local configural processing in upright faces.

Ingroup categorization affects the structural encoding of other-race faces:evidence from the N170 event-related potential

The current research examined the influence of ingroup/outgroup categorization on brain event-related potentials measured during perceptual processing of own- and other-race faces. White participants performed a sequential matching task with upright and inverted faces belonging either to their own race (White) or to another race (Black) and affiliated with either their own university or another university by a preceding visual prime. Results demonstrated that the right-lateralized N170 component evoked by test faces was modulated by race and by social category: the N170 to own-race faces showed a larger inversion effect (i.e., latency delay for inverted faces) when the faces were categorized as other-university rather than own-university members; the N170 to other-race faces showed no modulation of its inversion effect by university affiliation. These results suggest that neural correlates of structural face encoding (as evidenced by the N170 inversion effects) can be modulated by both visual (racial) and nonvisual (social) ingroup/outgroup status. © 2014 © 2014 Taylor & Francis.

A computational model of prosody for Yorùbá text-to-speech synthesis

This work examines prosody modelling for the Standard Yorùbá (SY) language in the context of computer text-to-speech synthesis applications. The thesis of this research is that it is possible to develop a practical prosody model by using appropriate computational tools and techniques which combines acoustic data with an encoding of the phonological and phonetic knowledge provided by experts. Our prosody model is conceptualised around a modular holistic framework. The framework is implemented using the Relational Tree (R-Tree) techniques (Ehrich and Foith, 1976). R-Tree is a sophisticated data structure that provides a multi-dimensional description of a waveform. A Skeletal Tree (S-Tree) is first generated using algorithms based on the tone phonological rules of SY. Subsequent steps update the S-Tree by computing the numerical values of the prosody dimensions. To implement the intonation dimension, fuzzy control rules where developed based on data from native speakers of Yorùbá. The Classification And Regression Tree (CART) and the Fuzzy Decision Tree (FDT) techniques were tested in modelling the duration dimension. The FDT was selected based on its better performance. An important feature of our R-Tree framework is its flexibility in that it facilitates the independent implementation of the different dimensions of prosody, i.e. duration and intonation, using different techniques and their subsequent integration. Our approach provides us with a flexible and extendible model that can also be used to implement, study and explain the theory behind aspects of the phenomena observed in speech prosody.

Reading without central vision:effects of text spacing on reading in patients with macular disease

Abstract: Loss of central vision caused by age-related macular degeneration (AMD) is a problem affecting increasingly large numbers of people within the ageing population. AMD is the leading cause of blindness in the developed world, with estimates of over 600,000 people affected in the UK . Central vision loss can be devastating for the sufferer, with vision loss impacting on the ability to carry out daily activities. In particular, inability to read is linked to higher rates of depression in AMD sufferers compared to age-matched controls. Methods to improve reading ability in the presence of central vision loss will help maintain independence and quality of life for those affected. Various attempts to improve reading with central vision loss have been made. Most textual manipulations, including font size, have led to only modest gains in reading speed. Previous experimental work and theoretical arguments on spatial integrative properties of the peripheral retina suggest that ‘visual crowding’ may be a major factor contributing to inefficient reading. Crowding refers to the phenomena in which juxtaposed targets viewed eccentrically may be difficult to identify. Manipulating text spacing of reading material may be a simple method that reduces crowding and benefits reading ability in macular disease patients. In this thesis the effect of textual manipulation on reading speed was investigated, firstly for normally sighted observers using eccentric viewing, and secondly for observers with central vision loss. Test stimuli mimicked normal reading conditions by using whole sentences that required normal saccadic eye movements and observer comprehension. Preliminary measures on normally-sighted observers (n = 2) used forced-choice procedures in conjunction with the method of constant stimuli. Psychometric functions relating the proportion of correct responses to exposure time were determined for text size, font type (Lucida Sans and Times New Roman) and text spacing, with threshold exposure time (75% correct responses) used as a measure of reading performance. The results of these initial measures were used to derive an appropriate search space, in terms of text spacing, for assessing reading performance in AMD patients. The main clinical measures were completed on a group of macular disease sufferers (n=24). Firstly, high and low contrast reading acuity and critical print size were measured using modified MNREAD test charts, and secondly, the effect of word and line spacing was investigated using a new test, designed specifically for this study, called the Equal Readability Passages (ERP) test. The results from normally-sighted observers were in close agreement with those from the group of macular disease sufferers. Results show that: (i) optimum reading performance was achieved when using both double line and double word spacing; (ii) the effect of line spacing was greater than the effect of word spacing (iii) a text size of approximately 0.85o is sufficiently large for reading at 5o eccentricity. In conclusion, the results suggest that crowding is detrimental to reading with peripheral vision, and its effects can be minimized with a modest increase in text spacing.

In search of a theory of list memory: an inquiry into the efects of long-term information on short-term recall

Over recent years, evidence has been accumulating in favour of the importance of long-term information as a variable which can affect the success of short-term recall. Lexicality, word frequency, imagery and meaning have all been shown to augment short term recall performance. Two competing theories as to the causes of this long-term memory influence are outlined and tested in this thesis. The first approach is the order-encoding account, which ascribes the effect to the usage of resources at encoding, hypothesising that word lists which require less effort to process will benefit from increased levels of order encoding, in turn enhancing recall success. The alternative view, trace redintegration theory, suggests that order is automatically encoded phonologically, and that long-term information can only influence the interpretation of the resultant memory trace. The free recall experiments reported here attempted to determine the importance of order encoding as a facilitatory framework and to determine the locus of the effects of long-term information in free recall. Experiments 1 and 2 examined the effects of word frequency and semantic categorisation over a filled delay, and experiments 3 and 4 did the same for immediate recall. Free recall was improved by both long-term factors tested. Order information was not used over a short filled delay, but was evident in immediate recall. Furthermore, it was found that both long-term factors increased the amount of order information retained. Experiment 5 induced an order encoding effect over a filled delay, leaving a picture of short-term processes which are closely associated with long-term processes, and which fit conceptions of short-term memory being part of language processes rather better than either the encoding or the retrieval-based models. Experiments 6 and 7 aimed to determine to what extent phonological processes were responsible for the pattern of results observed. Articulatory suppression affected the encoding of order information where speech rate had no direct influence, suggesting that it is ease of lexical access which is the most important factor in the influence of long-term memory on immediate recall tasks. The evidence presented in this thesis does not offer complete support for either the retrieval-based account or the order encoding account of long-term influence. Instead, the evidence sits best with models that are based upon language-processing. The path urged for future research is to find ways in which this diffuse model can be better specified, and which can take account of the versatility of the human brain.

A modular holistic approach to prosody modelling for Standard Yorùbá speech synthesis

This paper presents a novel prosody model in the context of computer text-to-speech synthesis applications for tone languages. We have demonstrated its applicability using the Standard Yorùbá (SY) language. Our approach is motivated by the theory that abstract and realised forms of various prosody dimensions should be modelled within a modular and unified framework [Coleman, J.S., 1994. Polysyllabic words in the YorkTalk synthesis system. In: Keating, P.A. (Ed.), Phonological Structure and Forms: Papers in Laboratory Phonology III, Cambridge University Press, Cambridge, pp. 293–324]. We have implemented this framework using the Relational Tree (R-Tree) technique. R-Tree is a sophisticated data structure for representing a multi-dimensional waveform in the form of a tree. The underlying assumption of this research is that it is possible to develop a practical prosody model by using appropriate computational tools and techniques which combine acoustic data with an encoding of the phonological and phonetic knowledge provided by experts. To implement the intonation dimension, fuzzy logic based rules were developed using speech data from native speakers of Yorùbá. The Fuzzy Decision Tree (FDT) and the Classification and Regression Tree (CART) techniques were tested in modelling the duration dimension. For practical reasons, we have selected the FDT for implementing the duration dimension of our prosody model. To establish the effectiveness of our prosody model, we have also developed a Stem-ML prosody model for SY. We have performed both quantitative and qualitative evaluations on our implemented prosody models. The results suggest that, although the R-Tree model does not predict the numerical speech prosody data as accurately as the Stem-ML model, it produces synthetic speech prosody with better intelligibility and naturalness. The R-Tree model is particularly suitable for speech prosody modelling for languages with limited language resources and expertise, e.g. African languages. Furthermore, the R-Tree model is easy to implement, interpret and analyse.

Editorial overview:new protein production tools for structural biology

Full text: The idea of producing proteins from recombinant DNA hatched almost half a century ago. In his PhD thesis, Peter Lobban foresaw the prospect of inserting foreign DNA (from any source, including mammalian cells) into the genome of a λ phage in order to detect and recover protein products from Escherichia coli [ 1 and 2]. Only a few years later, in 1977, Herbert Boyer and his colleagues succeeded in the first ever expression of a peptide-coding gene in E. coli — they produced recombinant somatostatin [ 3] followed shortly after by human insulin. The field has advanced enormously since those early days and today recombinant proteins have become indispensable in advancing research and development in all fields of the life sciences. Structural biology, in particular, has benefitted tremendously from recombinant protein biotechnology, and an overwhelming proportion of the entries in the Protein Data Bank (PDB) are based on heterologously expressed proteins. Nonetheless, synthesizing, purifying and stabilizing recombinant proteins can still be thoroughly challenging. For example, the soluble proteome is organized to a large part into multicomponent complexes (in humans often comprising ten or more subunits), posing critical challenges for recombinant production. A third of all proteins in cells are located in the membrane, and pose special challenges that require a more bespoke approach. Recent advances may now mean that even these most recalcitrant of proteins could become tenable structural biology targets on a more routine basis. In this special issue, we examine progress in key areas that suggests this is indeed the case. Our first contribution examines the importance of understanding quality control in the host cell during recombinant protein production, and pays particular attention to the synthesis of recombinant membrane proteins. A major challenge faced by any host cell factory is the balance it must strike between its own requirements for growth and the fact that its cellular machinery has essentially been hijacked by an expression construct. In this context, Bill and von der Haar examine emerging insights into the role of the dependent pathways of translation and protein folding in defining high-yielding recombinant membrane protein production experiments for the common prokaryotic and eukaryotic expression hosts. Rather than acting as isolated entities, many membrane proteins form complexes to carry out their functions. To understand their biological mechanisms, it is essential to study the molecular structure of the intact membrane protein assemblies. Recombinant production of membrane protein complexes is still a formidable, at times insurmountable, challenge. In these cases, extraction from natural sources is the only option to prepare samples for structural and functional studies. Zorman and co-workers, in our second contribution, provide an overview of recent advances in the production of multi-subunit membrane protein complexes and highlight recent achievements in membrane protein structural research brought about by state-of-the-art near-atomic resolution cryo-electron microscopy techniques. E. coli has been the dominant host cell for recombinant protein production. Nonetheless, eukaryotic expression systems, including yeasts, insect cells and mammalian cells, are increasingly gaining prominence in the field. The yeast species Pichia pastoris, is a well-established recombinant expression system for a number of applications, including the production of a range of different membrane proteins. Byrne reviews high-resolution structures that have been determined using this methylotroph as an expression host. Although it is not yet clear why P. pastoris is suited to producing such a wide range of membrane proteins, its ease of use and the availability of diverse tools that can be readily implemented in standard bioscience laboratories mean that it is likely to become an increasingly popular option in structural biology pipelines. The contribution by Columbus concludes the membrane protein section of this volume. In her overview of post-expression strategies, Columbus surveys the four most common biochemical approaches for the structural investigation of membrane proteins. Limited proteolysis has successfully aided structure determination of membrane proteins in many cases. Deglycosylation of membrane proteins following production and purification analysis has also facilitated membrane protein structure analysis. Moreover, chemical modifications, such as lysine methylation and cysteine alkylation, have proven their worth to facilitate crystallization of membrane proteins, as well as NMR investigations of membrane protein conformational sampling. Together these approaches have greatly facilitated the structure determination of more than 40 membrane proteins to date. It may be an advantage to produce a target protein in mammalian cells, especially if authentic post-translational modifications such as glycosylation are required for proper activity. Chinese Hamster Ovary (CHO) cells and Human Embryonic Kidney (HEK) 293 cell lines have emerged as excellent hosts for heterologous production. The generation of stable cell-lines is often an aspiration for synthesizing proteins expressed in mammalian cells, in particular if high volumetric yields are to be achieved. In his report, Buessow surveys recent structures of proteins produced using stable mammalian cells and summarizes both well-established and novel approaches to facilitate stable cell-line generation for structural biology applications. The ambition of many biologists is to observe a protein's structure in the native environment of the cell itself. Until recently, this seemed to be more of a dream than a reality. Advances in nuclear magnetic resonance (NMR) spectroscopy techniques, however, have now made possible the observation of mechanistic events at the molecular level of protein structure. Smith and colleagues, in an exciting contribution, review emerging ‘in-cell NMR’ techniques that demonstrate the potential to monitor biological activities by NMR in real time in native physiological environments. A current drawback of NMR as a structure determination tool derives from size limitations of the molecule under investigation and the structures of large proteins and their complexes are therefore typically intractable by NMR. A solution to this challenge is the use of selective isotope labeling of the target protein, which results in a marked reduction of the complexity of NMR spectra and allows dynamic processes even in very large proteins and even ribosomes to be investigated. Kerfah and co-workers introduce methyl-specific isotopic labeling as a molecular tool-box, and review its applications to the solution NMR analysis of large proteins. Tyagi and Lemke next examine single-molecule FRET and crosslinking following the co-translational incorporation of non-canonical amino acids (ncAAs); the goal here is to move beyond static snap-shots of proteins and their complexes and to observe them as dynamic entities. The encoding of ncAAs through codon-suppression technology allows biomolecules to be investigated with diverse structural biology methods. In their article, Tyagi and Lemke discuss these approaches and speculate on the design of improved host organisms for ‘integrative structural biology research’. Our volume concludes with two contributions that resolve particular bottlenecks in the protein structure determination pipeline. The contribution by Crepin and co-workers introduces the concept of polyproteins in contemporary structural biology. Polyproteins are widespread in nature. They represent long polypeptide chains in which individual smaller proteins with different biological function are covalently linked together. Highly specific proteases then tailor the polyprotein into its constituent proteins. Many viruses use polyproteins as a means of organizing their proteome. The concept of polyproteins has now been exploited successfully to produce hitherto inaccessible recombinant protein complexes. For instance, by means of a self-processing synthetic polyprotein, the influenza polymerase, a high-value drug target that had remained elusive for decades, has been produced, and its high-resolution structure determined. In the contribution by Desmyter and co-workers, a further, often imposing, bottleneck in high-resolution protein structure determination is addressed: The requirement to form stable three-dimensional crystal lattices that diffract incident X-ray radiation to high resolution. Nanobodies have proven to be uniquely useful as crystallization chaperones, to coax challenging targets into suitable crystal lattices. Desmyter and co-workers review the generation of nanobodies by immunization, and highlight the application of this powerful technology to the crystallography of important protein specimens including G protein-coupled receptors (GPCRs). Recombinant protein production has come a long way since Peter Lobban's hypothesis in the late 1960s, with recombinant proteins now a dominant force in structural biology. The contributions in this volume showcase an impressive array of inventive approaches that are being developed and implemented, ever increasing the scope of recombinant technology to facilitate the determination of elusive protein structures. Powerful new methods from synthetic biology are further accelerating progress. Structure determination is now reaching into the living cell with the ultimate goal of observing functional molecular architectures in action in their native physiological environment. We anticipate that even the most challenging protein assemblies will be tackled by recombinant technology in the near future.