Canonical Templates Research Articles

"Warm," "cool," and the colors.

Participants judged affective cooler/warmer gradients around a 12-step color circle. Each pair of adjacent colors was presented twice (left-right reversed), all in random order. Participants readily performed the task, but their settings do not correlate very well. Individual responses were compared with a small number of canonical templates. For a little less than one-half of the participants responses or judgements correlate with such a template. We find a warm pole (in the orange environment) and a cool pole (in the teal environment) connected with two tracks that tend to have one or more gaps or weak, even inverted links. We conclude that the common artistic cool-warm polarity is only weakly reflected in responses of our observers. If it does, the observers apparently use categorical warm and cool poles and may be uncertain in relating adjacent hue steps along the 12-step color circle.

All-night spectral and microstate EEG analysis in patients with recurrent isolated sleep paralysis.

The pathophysiology of recurrent isolated sleep paralysis (RISP) has yet to be fully clarified. Very little research has been performed on electroencephalographic (EEG) signatures outside RISP episodes. This study aimed to investigate whether sleep is disturbed even without the occurrence of a RISP episode and in a stage different than conventional REM sleep. 17 RISP patients and 17 control subjects underwent two consecutive full-night video-polysomnography recordings. Spectral analysis was performed on all sleep stages in the delta, theta, and alpha band. EEG microstate (MS) analysis was performed on the NREM 3 phase due to the overall high correlation of subject template maps with canonical templates. Spectral analysis showed a significantly higher power of theta band activity in REM and NREM 2 sleep stages in RISP patients. The observed rise was also apparent in other sleep stages. Conversely, alpha power showed a downward trend in RISP patients' deep sleep. MS maps similar to canonical topographies were obtained indicating the preservation of prototypical EEG generators in RISP patients. RISP patients showed significant differences in the temporal dynamics of MS, expressed by different transitions between MS C and D and between MS A and B. Both spectral analysis and MS characteristics showed abnormalities in the sleep of non-episodic RISP subjects. Our findings suggest that in order to understand the neurobiological background of RISP, there is a need to extend the analyzes beyond REM-related processes and highlight the value of EEG microstate dynamics as promising functional biomarkers of RISP.

Canonical template tracking: Measuring the activation state of specific neural representations.

Multivariate analyses of neural data have become increasingly influential in cognitive neuroscience since they allow to address questions about the representational signatures of neurocognitive phenomena. Here, we describe Canonical Template Tracking: a multivariate approach that employs independent localizer tasks to assess the activation state of specific representations during the execution of cognitive paradigms. We illustrate the benefits of this methodology in characterizing the particular content and format of task-induced representations, comparing it with standard (cross-)decoding and representational similarity analyses. Then, we discuss relevant design decisions for experiments using this analysis approach, focusing on the nature of the localizer tasks from which the canonical templates are derived. We further provide a step-by-step tutorial of this method, stressing the relevant analysis choices for functional magnetic resonance imaging and magneto/electroencephalography data. Importantly, we point out the potential pitfalls linked to canonical template tracking implementation and interpretation of the results, together with recommendations to mitigate them. To conclude, we provide some examples from previous literature that highlight the potential of this analysis to address relevant theoretical questions in cognitive neuroscience.

Parkinson's disease medication state and severity assessment based on coordination during walking.

Walking is a complex motor function requiring coordination of all body parts. Parkinson’s disease (PD) motor signs such as rigidity, bradykinesia, and impaired balance affect movements including walking. Here, we propose a computational method to objectively assess the effects of Parkinson’s disease pathology on coordination between trunk, shoulder and limbs during the gait cycle to assess medication state and disease severity. Movements during a scripted walking task were extracted from wearable devices placed at six different body locations in participants with PD and healthy participants. Three-axis accelerometer data from each device was synchronized at the beginning of either left or right steps. Canonical templates of movements were then extracted from each body location. Movements projected on those templates created a reduced dimensionality space, where complex movements are represented as discrete values. These projections enabled us to relate the body coordination in people with PD to disease severity. Our results show that the velocity profile of the right wrist and right foot during right steps correlated with the participant’s total score on the gold standard Unified Parkinson’s Disease Rating Scale (UPRDS) with an r2 up to 0.46. Left-right symmetry of feet, trunk and wrists also correlated with the total UPDRS score with an r2 up to 0.3. In addition, we demonstrate that binary dopamine replacement therapy medication states (self-reported ‘ON’ or ‘OFF’) can be discriminated in PD participants. In conclusion, we showed that during walking, the movement of body parts individually and in coordination with one another changes in predictable ways that vary with disease severity and medication state.

Cranial growth in isolated sagittal craniosynostosis compared with normal growth in the first 6 months of age.

Sagittal craniosynostosis (SCS), the most common type of premature perinatal cranial suture fusion, results in abnormal head shape that requires extensive surgery to correct. It is important to find objective and repeatable measures of severity and surgical outcome to examine the effect of timing and technique on different SCS surgeries. The purpose of this study was to develop statistical models of infant (0-6months old) skull growth in both normative and SCS subjects (prior to surgery). Our goal was to apply these models to the assessment of differences between these two groups in overall post-natal growth patterns and sutural growth rates as a first step to develop methods for predictive models of surgical outcome. We identified 81 patients with isolated, non-syndromic SCS from Seattle Children's Craniofacial Center patient database who had a preoperative CT exam before the age of 6months. As a control group, we identified 117 CT exams without any craniofacial abnormalities or bone fractures in the same age group. We first created population-level templates from the CT images of the SCS and normal groups. All CT images from both groups, as well as the canonical templates of both cohorts, were annotated with anatomical landmarks, which were used in a growth model that predicted the locations of these landmarks at a given age based on each population. Using the template images and the landmark positions predicted by the growth models, we created 3D meshes for each week of age up to 6months for both populations. To analyze the growth patterns at the suture sites, we annotated both templates with additional semi-landmarks equally spaced along the metopic, coronal, sagittal and lambdoidal cranial sutures. By transferring these semi-landmarks to meshes produced from the growth model, we measured the displacement of the bone borders and suture closure rates. We found that the growth at the metopic and coronal sutures were more rapid in the SCS cohort than in the normal cohort. The antero-posterior displacement of the semi-landmarks also indicated a more rapid growth in the sagittal plane in the SCS model than in the normal model. Statistical templates and geometric morphometrics are promising tools for understanding the growth patterns in normal and synostotic populations and to produce objective and reproducible measurements of severity and outcome. Our study is the first of its kind to quantify the bone growth for the first 6months of life in both normal and sagittal synostosis patients.

Disjoint combinations profiling (DCP): a new method for the prediction of antibody CDR conformation from sequence.

The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in antibody variable regions. It relies on canonical templates which detail allowed residues at key positions in the variable region framework or in the CDR itself for 5 of the 6 CDRs. While no templates have as yet been defined for the hypervariable CDR-H3, instead, reliable sequence rules have been devised for predicting the base of the CDR-H3 loop. Here a new method termed Disjoint Combinations Profiling (DCP) is presented, which contributes a considerable advance in the prediction of CDR conformations. This novel method is explained and compared with canonical templates and sequence rules in a 3-way blind prediction. DCP achieved 93% accuracy over 951 blind predictions and showed an improvement in cumulative accuracy compared to predictions with canonical templates or sequence rules. In addition to its overall improvement in prediction accuracy, it is suggested that DCP is open to better implementations in the future and that it can improve as more antibody structures are deposited in the databank. In contrast, it is argued that canonical templates and sequence rules may have reached their peak.

The role of default constructions in the processing of mismatch: The case of possessive free relatives

Townsend and Bever (2001) and Ferreira (2003) argue that simple templates representing the most commonly used orderings of arguments within a clause (e.g., NP-V-NP = Agent-Action-Patient) are used early in sentence comprehension to derive a preliminary interpretation before a full parse is completed. Sentences which match these templates (e.g., active sentences, subject clefts) are understood quickly and accurately, while sentences which deviate from the templates (e.g. passive sentences, object clefts) require additional processing to arrive at the correct interpretation. The present study extends the idea of canonical templates to the domain of noun phrases. I report on two experiments showing that possessive free relative clauses in English, which involve a non-canonical ordering of the head noun, are more difficult to understand than canonically headed noun phrases. I propose two reasons for this finding: (1) possessive free relatives deviate from the canonical template for interpreting noun phrases; and (2) the formal cues for interpreting possessive free relatives are relatively subtle. More generally I suggest that canonical templates help constrain mismatch in language by making certain kinds of mismatches costly for language users. Finally, I argue that evidence for canonical templates fits best within a parallel-architecture, constructionist theory of grammar.

An Escherichia coli Strain Producing a Leaderless mRNA from the Chromosomal lac Promoter

A special Escherichia coli strain capable of producing a leaderless lacZ mRNA from the chromosomal lac promoter was constructed to study the mechanism of leaderless mRNA translation. The translation efficiency of this noncanonical mRNA is very low in comparison with the canonical cellular templates, but it increases by one order of magnitude in the presence of chromosomal mutations in the genes encoding the ribosomal S1 and S2 proteins. The new strain possesses obvious advantages over the commonly used plasmid constructs (first of all, due to the constant dosage of lacZ gene in the cell) and opens possibilities for investigation of the specific conditions for leaderless mRNA translation in vivo using molecular genetic approaches.

Reading a population code: a multi-scale neural model for representing binocular disparity

Although binocular neurons in the primary visual cortex are sensitive to retinal disparity, their activity does not constitute an unambiguous disparity signal. A multi-spatial-scale neural model for disparity computation is developed to examine how population activity might be interpreted to overcome ambiguities at the single neuron level. The model incorporates a front end that encodes disparity by a family of complex cell-like energy units and a second stage that reads the population activity. Disparity is recovered by matching the population response to a set of canonical templates, derived from the mean response to white noise stimuli at a range of disparities. Model predictions are qualitatively consistent with a variety of psychophysical results in the literature, including the effects of spatial frequency on stereoacuity and bias in perceived depths, and the effect of standing disparity on increment thresholds. Model predictions are also consistent with data on qualitative appearance of complex stimuli, including depth averaging, transparency, and corrugation. The model also accounts for the non-linear interaction of disparities in compound grating stimuli. These results show that a template-match approach reduces ambiguities in individual and pooled neuronal responses, and allows for a broader range of percepts, consistent with psychophysics, than other models. Thus, the pattern of neural population activity across spatial scales is a better candidate for the neural correlate of depth perception than the activity of single neurons or the pooled activity of multiple neurons.

Arguments or macroroles? : Two functional approaches to Old English quirky case

After comparing two functional approaches to the question of Old English deviant accusatives, genitives and datives, this paper follows Martín Arista (2001a, b) with respect to Old English prototypical verbal constructions: the prototypical transitive construction is defined as the active accomplishment version of verbs like writan 'write', the activity implementation of creation and consumption verbs representing the less-prototypical transitive construction; the active accomplishment use of verbs such as faran 'go' characterize the prototypical intransitive construction, whereas the activity version of motion verbs define the less-prototypical intransitive construction. The conclusion is reached that quirky case is not a feature of the morphosyntax of certain intransitive verbs of state and causative state, but a characteristic of verbal constructions that, deviating from both the transitive and the intransitive prototypes, show not only case-marking irregularity but also more case-marking choices than verbs that abide by the transitive or intransitive prototype. Since marked morphosyntax -including quirky case- is considered in this paper a consequence of the non-prototypical character of argument structure, it is claimed that the relationship between canonical lexical templates and their configurations should be semantically and syntactically motivated. The Principle of Lexical Template Instantiation guarantees the suitable degree of implementation of a lexical template by stipulating that, prototypically, all the internal variables of the instantiations of lexical templates are fully specified

Sparse Representations for Image Decompositions

We are given an image I and a library of templates {\cal L} , such that {\cal L} is an overcomplete basis for I. The templates can represent objects, faces, features, analytical functions, or be single pixel templates (canonical templates). There are infinitely many ways to decompose I as a linear combination of the library templates. Each decomposition defines a representation for the image I, given {\cal L} . What is an optimal representation for I given {\cal L} and how to select it? We are motivated to select a sparse/compact representation for I, and to account for occlusions and noise in the image. We present a concave cost function criterion on the linear decomposition coefficients that satisfies our requirements. More specifically, we study a “weighted L norm” with 0 < p < 1. We prove a result that allows us to generate all local minima for the L norm, and the global minimum is obtained by searching through the local ones. Due to the computational complexity, i.e., the large number of local minima, we also study a greedy and iterative “weighted L Matching Pursuit” strategy.