Discriminating antigen and non-antigen using proteome dissimilarity III:tumour and parasite antigens

Computational genome analysis enables systematic identification of potential immunogenic proteins within a pathogen. Immunogenicity is a system property that arises through the interaction of host and pathogen as mediated through the medium of a immunogenic protein. The overt dissimilarity of pathogenic proteins when compared to the host proteome is conjectured by some to be the determining principal of immunogenicity. Previously, we explored this idea in the context of Bacterial, Viral, and Fungal antigen. In this paper, we broaden and extend our analysis to include complex antigens of eukaryotic origin, arising from tumours and from parasite pathogens. For both types of antigen, known antigenic and non-antigenic protein sequences were compared to human and mouse proteomes. In contrast to our previous results, both visual inspection and statistical evaluation indicate a much wider range of homologues and a significant level of discrimination; but, as before, we could not determine a viable threshold capable of properly separating non-antigen from antigen. In concert with our previous work, we conclude that global proteome dissimilarity is not a useful metric for immunogenicity for presently available antigens arising from Bacteria, viruses, fungi, parasites, and tumours. While we see some signal for certain antigen types, using dissimilarity is not a useful approach to identifying antigenic molecules within pathogen genomes.

Developmental trajectories of part-based and configural object recognition in adolescence.

Three experiments assessed the development of children's part and configural (part-relational) processing in object recognition during adolescence. In total, 312 school children aged 7-16 years and 80 adults were tested in 3-alternative forced choice (3-AFC) tasks. They judged the correct appearance of upright and inverted presented familiar animals, artifacts, and newly learned multipart objects, which had been manipulated either in terms of individual parts or part relations. Manipulation of part relations was constrained to either metric (animals, artifacts, and multipart objects) or categorical (multipart objects only) changes. For animals and artifacts, even the youngest children were close to adult levels for the correct recognition of an individual part change. By contrast, it was not until 11-12 years of age that they achieved similar levels of performance with regard to altered metric part relations. For the newly learned multipart objects, performance was equivalent throughout the tested age range for upright presented stimuli in the case of categorical part-specific and part-relational changes. In the case of metric manipulations, the results confirmed the data pattern observed for animals and artifacts. Together, the results provide converging evidence, with studies of face recognition, for a surprisingly late consolidation of configural-metric relative to part-based object recognition.

Nonlinear speech analysis algorithms mapped to a standard metric achieve clinically useful quantification of average Parkinson's disease symptom severity

The standard reference clinical score quantifying average Parkinson's disease (PD) symptom severity is the Unified Parkinson's Disease Rating Scale (UPDRS). At present, UPDRS is determined by the subjective clinical evaluation of the patient's ability to adequately cope with a range of tasks. In this study, we extend recent findings that UPDRS can be objectively assessed to clinically useful accuracy using simple, self-administered speech tests, without requiring the patient's physical presence in the clinic. We apply a wide range of known speech signal processing algorithms to a large database (approx. 6000 recordings from 42 PD patients, recruited to a six-month, multi-centre trial) and propose a number of novel, nonlinear signal processing algorithms which reveal pathological characteristics in PD more accurately than existing approaches. Robust feature selection algorithms select the optimal subset of these algorithms, which is fed into non-parametric regression and classification algorithms, mapping the signal processing algorithm outputs to UPDRS. We demonstrate rapid, accurate replication of the UPDRS assessment with clinically useful accuracy (about 2 UPDRS points difference from the clinicians' estimates, p < 0.001). This study supports the viability of frequent, remote, cost-effective, objective, accurate UPDRS telemonitoring based on self-administered speech tests. This technology could facilitate large-scale clinical trials into novel PD treatments.

Interactions between landcover pattern and geospatial processing methods:effects on landscape metrics and classification accuracy

Remote sensing data is routinely used in ecology to investigate the relationship between landscape pattern as characterised by land use and land cover maps, and ecological processes. Multiple factors related to the representation of geographic phenomenon have been shown to affect characterisation of landscape pattern resulting in spatial uncertainty. This study investigated the effect of the interaction between landscape spatial pattern and geospatial processing methods statistically; unlike most papers which consider the effect of each factor in isolation only. This is important since data used to calculate landscape metrics typically undergo a series of data abstraction processing tasks and are rarely performed in isolation. The geospatial processing methods tested were the aggregation method and the choice of pixel size used to aggregate data. These were compared to two components of landscape pattern, spatial heterogeneity and the proportion of landcover class area. The interactions and their effect on the final landcover map were described using landscape metrics to measure landscape pattern and classification accuracy (response variables). All landscape metrics and classification accuracy were shown to be affected by both landscape pattern and by processing methods. Large variability in the response of those variables and interactions between the explanatory variables were observed. However, even though interactions occurred, this only affected the magnitude of the difference in landscape metric values. Thus, provided that the same processing methods are used, landscapes should retain their ranking when their landscape metrics are compared. For example, highly fragmented landscapes will always have larger values for the landscape metric "number of patches" than less fragmented landscapes. But the magnitude of difference between the landscapes may change and therefore absolute values of landscape metrics may need to be interpreted with caution. The explanatory variables which had the largest effects were spatial heterogeneity and pixel size. These explanatory variables tended to result in large main effects and large interactions. The high variability in the response variables and the interaction of the explanatory variables indicate it would be difficult to make generalisations about the impact of processing on landscape pattern as only two processing methods were tested and it is likely that untested processing methods will potentially result in even greater spatial uncertainty. © 2013 Elsevier B.V.

Ageing factor:a potential altmetric for observing events and attention spans in microblogs

We present an initial examination of the (alt)metric ageing factor to study posts in Twitter. Ageing factor was used to characterize a sample of tweets, which contained a variety of astronomical terms. It was found that ageing factor can detect topics that both cause people to retweet faster than baseline values, and topics that hold people’s attention for longer than baseline values.

Late development of metric part-relational processing in object recognition

Four experiments with unfamiliar objects examined the remarkably late consolidation of part-relational relative to part-based object recognition (Jüttner, Wakui, Petters, Kaur, & Davidoff, 2013). Our results indicate a particularly protracted developmental trajectory for the processing of metric part relations. Schoolchildren aged 7 to 14 years and adults were tested in 3-Alternative-Forced-Choice tasks to judge the correct appearance of upright and inverted newly learned multipart objects that had been manipulated in terms of individual parts or part relations. Experiment 1 showed that even the youngest tested children were close to adult levels of performance for recognizing categorical changes of individual parts and relative part position. By contrast, Experiment 2 demonstrated that performance for detecting metric changes of relative part position was distinctly reduced in young children compared with recognizing metric changes of individual parts, and did not approach the latter until 11 to 12 years. A similar developmental dissociation was observed in Experiment 3, which contrasted the detection of metric relative-size changes and metric part changes. Experiment 4 showed that manipulations of metric size that were perceived as part (rather than part-relational) changes eliminated this dissociation. Implications for theories of object recognition and similarities to the development of face perception are discussed. © 2014 American Psychological Association.

Multi-frequency segmental bio-impedance device:design, development and applications

Bio-impedance analysis (BIA) provides a rapid, non-invasive technique for body composition estimation. BIA offers a convenient alternative to standard techniques such as MRI, CT scan or DEXA scan for selected types of body composition analysis. The accuracy of BIA is limited because it is an indirect method of composition analysis. It relies on linear relationships between measured impedance and morphological parameters such as height and weight to derive estimates. To overcome these underlying limitations of BIA, a multi-frequency segmental bio-impedance device was constructed through a series of iterative enhancements and improvements of existing BIA instrumentation. Key features of the design included an easy to construct current-source and compact PCB design. The final device was trialled with 22 human volunteers and measured impedance was compared against body composition estimates obtained by DEXA scan. This enabled the development of newer techniques to make BIA predictions. To add a ‘visual aspect’ to BIA, volunteers were scanned in 3D using an inexpensive scattered light gadget (Xbox Kinect controller) and 3D volumes of their limbs were compared with BIA measurements to further improve BIA predictions. A three-stage digital filtering scheme was also implemented to enable extraction of heart-rate data from recorded bio-electrical signals. Additionally modifications have been introduced to measure change in bio-impedance with motion, this could be adapted to further improve accuracy and veracity for limb composition analysis. The findings in this thesis aim to give new direction to the prediction of body composition using BIA. The design development and refinement applied to BIA in this research programme suggest new opportunities to enhance the accuracy and clinical utility of BIA for the prediction of body composition analysis. In particular, the use of bio-impedance to predict limb volumes which would provide an additional metric for body composition measurement and help distinguish between fat and muscle content.

Applying A Normalized Compression Metric To The Measurement Of Dialect Distance

The paper discusses the application of a similarity metric based on compression to the measurement of the distance among Bulgarian dia- lects. The similarity metric is de ned on the basis of the notion of Kolmo- gorov complexity of a le (or binary string). The application of Kolmogorov complexity in practice is not possible because its calculation over a le is an undecidable problem. Thus, the actual similarity metric is based on a real life compressor which only approximates the Kolmogorov complexity. To use the metric for distance measurement of Bulgarian dialects we rst represent the dialectological data in such a way that the metric is applicable. We propose two such representations which are compared to a baseline distance between dialects. Then we conclude the paper with an outline of our future work.

Dense Continuity and Selections of Set-Valued Mappings

∗ The first and third author were partially supported by National Fund for Scientific Research at the Bulgarian Ministry of Science and Education under grant MM-701/97.

Coincidence of Vietoris and Wijsman Topologies: A New Proof

Let (X, d) be a metric space and CL(X) the family of all nonempty closed subsets of X. We provide a new proof of the fact that the coincidence of the Vietoris and Wijsman topologies induced by the metric d forces X to be a compact space. In the literature only a more involved and indirect proof using the proximal topology is known. Here we do not need this intermediate step. Moreover we prove that (X, d) is boundedly compact if and only if the bounded Vietoris and Wijsman topologies on CL(X) coincide.

A Note on Coercivity of Lower Semicontinuous Functions and Nonsmooth Critical Point Theory

The first motivation for this note is to obtain a general version of the following result: let E be a Banach space and f : E → R be a differentiable function, bounded below and satisfying the Palais-Smale condition; then, f is coercive, i.e., f(x) goes to infinity as ||x|| goes to infinity. In recent years, many variants and extensions of this result appeared, see [3], [5], [6], [9], [14], [18], [19] and the references therein. A general result of this type was given in [3, Theorem 5.1] for a lower semicontinuous function defined on a Banach space, through an approach based on an abstract notion of subdifferential operator, and taking into account the “smoothness” of the Banach space. Here, we give (Theorem 1) an extension in a metric setting, based on the notion of slope from [11] and coercivity is considered in a generalized sense, inspired by [9]; our result allows to recover, for example, the coercivity result of [19], where a weakened version of the Palais-Smale condition is used. Our main tool (Proposition 1) is a consequence of Ekeland’s variational principle extending [12, Corollary 3.4], and deals with a function f which is, in some sense, the “uniform” Γ-limit of a sequence of functions.

A Partition Metric for Clustering Features Analysis

A new distance function to compare arbitrary partitions is proposed. Clustering of image collections and image segmentation give objects to be matched. Offered metric intends for combination of visual features and metadata analysis to solve a semantic gap between low-level visual features and high-level human concept.

A Sensitive Metric of Class Cohesion

Metrics estimate the quality of different aspects of software. In particular, cohesion indicates how well the parts of a system hold together. A metric to evaluate class cohesion is important in object-oriented programming because it gives an indication of a good design of classes. There are several proposals of metrics for class cohesion but they have several problems (for instance, low discrimination). In this paper, a new metric to evaluate class cohesion is proposed, called SCOM, which has several relevant features. It has an intuitive and analytical formulation, what is necessary to apply it to large-size software systems. It is normalized to produce values in the range [0..1], thus yielding meaningful values. It is also more sensitive than those previously reported in the literature. The attributes and methods used to evaluate SCOM are unambiguously stated. SCOM has an analytical threshold, which is a very useful but rare feature in software metrics. We assess the metric with several sample cases, showing that it gives more sensitive values than other well know cohesion metrics.

Collocation, interpretation and explanation:the case of just any

This article discusses the question of compositionality by examining whether the indiscriminacy reading of the collocation of just with any can be shown to be a consequence of the schematic meaning-potential of each of these two items. A comparison of justwith other restrictive focus particles allows its schematic meaning to be defined as that of goodness of fit. Any is defined as representing an indefinite member of a set as extractable from the set in exactly the same way as each of the other members thereof. The collocation just any often gives rise to a scalar reading oriented towards the lowest value on the scale due to the fact that focus on the unconstrained extractability of a random indefinite item brings into consideration even marginal cases and the latter tend to be interpreted as situated on the lower end of the scale. The attention to low-end values also explains why just any is regularly found with the adjective old, the prepositional phrase at all and various devaluating expressions. It is concluded that the meanings of the component parts of this collocation do indeed account for the meaning of the whole, and that an appropriate methodology allows identification of linguistic meanings and their interrelations. © 2011 Elsevier B.V.

Bounds for Fractional Powers of Operators in a Hilbert Space and Constants in Moment Inequalities

Mathematics Subject Classification: 47A56, 47A57,47A63