A geometric approach to visualization of variability in functional data

We propose a new method for the construction and visualization of boxplot-type displays for functional data. We use a recent functional data analysis framework, based on a representation of functions called square-root slope functions, to decompose observed variation in functional data into three main components: amplitude, phase, and vertical translation. We then construct separate displays for each component, using the geometry and metric of each representation space, based on a novel definition of the median, the two quartiles, and extreme observations. The outlyingness of functional data is a very complex concept. Thus, we propose to identify outliers based on any of the three main components after decomposition. We provide a variety of visualization tools for the proposed boxplot-type displays including surface plots. We evaluate the proposed method using extensive simulations and then focus our attention on three real data applications including exploratory data analysis of sea surface temperature functions, electrocardiogram functions and growth curves

FlexPass: Symbiosis of Seamless User Authentication Schemes in IoT

This paper presents a new user authentication paradigm which is based on a flexible user authentication method, namely FlexPass. FlexPass relies on a single, user-selected secret that can be reflected in both textual and graphical authentication secrets. Such an approach facilitates adaptability in nowadays ubiquitous user interaction contexts within the Internet of Things (IoT), in which end-users authenticate multiple times per day through a variety of interaction device types. We present an initial evaluation of the new authentication method based on an in-lab experiment with 32 participants. Analysis of results reveal that the FlexPass paradigm is memorable and that users like the adaptable perspective of the new approach. Findings are expected to scaffold the design of more user-centric knowledge-based authentication mechanisms within nowadays ubiquitous computation realms

Optimal free descriptions of many-body theories

Interacting bosons or fermions give rise to some of the most fascinating phases of matter, including high-temperature superconductivity, the fractional quantum Hall effect, quantum spin liquids and Mott insulators. Although these systems are promising for technological applications, they also present conceptual challenges, as they require approaches beyond mean-field and perturbation theory. Here we develop a general framework for identifying the free theory that is closest to a given interacting model in terms of their ground-state correlations. Moreover, we quantify the distance between them using the entanglement spectrum. When this interaction distance is small, the optimal free theory provides an effective description of the low-energy physics of the interacting model. Our construction of the optimal free model is non-perturbative in nature; thus, it offers a theoretical framework for investigating strongly correlated systems

eIF2α Kinases Regulate Development through the BzpR Transcription Factor in Dictyostelium discoideum

A major mechanism of translational regulation in response to a variety of stresses is mediated by phosphorylation of eIF2α to reduce delivery of initiator tRNAs to scanning ribosomes. For some mRNAs, often encoding a bZIP transcription factor, eIF2α phosphorylation leads to enhanced translation due to delayed reinitiation at upstream open reading frames. Dictyostelium cells possess at least three eIF2α kinases that regulate various portions of the starvation-induced developmental program. Cells possessing an eIF2α that cannot be phosphorylated (BS167) show abnormalities in growth and development. We sought to identify a bZIP protein in Dictyostelium whose production is controlled by the eIF2α regulatory system.Cells disrupted in the bzpR gene had similar developmental defects as BS167 cells, including small entities, stalk defects, and reduced spore viability. β-galactosidase production was used to examine translation from mRNA containing the bzpR 5' UTR. While protein production was readily apparent and regulated temporally and spatially in wild type cells, essentially no β-galactosidase was produced in developing BS167 cells even though the lacZ mRNA levels were the same as those in wild type cells. Also, no protein production was observed in strains lacking IfkA or IfkB eIF2α kinases. GFP fusions, with appropriate internal controls, were used to directly demonstrate that the bzpR 5' UTR, possessing 7 uORFs, suppressed translation by 12 fold. Suppression occurred even when all but one uORF was deleted, and translational suppression was removed when the ATG of the single uORF was mutated.The findings indicate that BzpR regulates aspects of the development program in Dictyostelium, serving as a downstream effector of eIF2α phosphorylation. Its production is temporally and spatially regulated by eIF2α phosphorylation by IfkA and IfkB and through the use of uORFs within the bzpR 5' UTR

Estimating the evidence of selection and the reliability of inference in unigenic evolution

<p>Abstract</p> <p>Background</p> <p>Unigenic evolution is a large-scale mutagenesis experiment used to identify residues that are potentially important for protein function. Both currently-used methods for the analysis of unigenic evolution data analyze 'windows' of contiguous sites, a strategy that increases statistical power but incorrectly assumes that functionally-critical sites are contiguous. In addition, both methods require the questionable assumption of asymptotically-large sample size due to the presumption of approximate normality.</p> <p>Results</p> <p>We develop a novel approach, termed the Evidence of Selection (EoS), removing the assumption that functionally important sites are adjacent in sequence and and explicitly modelling the effects of limited sample-size. Precise statistical derivations show that the EoS score can be easily interpreted as an expected log-odds-ratio between two competing hypotheses, namely, the hypothetical presence or absence of functional selection for a given site. Using the EoS score, we then develop selection criteria by which functionally-important yet non-adjacent sites can be identified. An approximate power analysis is also developed to estimate the reliability of inference given the data. We validate and demonstrate the the practical utility of our method by analysis of the homing endonuclease <monospace>I-Bmol</monospace>, comparing our predictions with the results of existing methods.</p> <p>Conclusions</p> <p>Our method is able to assess both the evidence of selection at individual amino acid sites and estimate the reliability of those inferences. Experimental validation with <monospace>I-Bmol</monospace> proves its utility to identify functionally-important residues of poorly characterized proteins, demonstrating increased sensitivity over previous methods without loss of specificity. With the ability to guide the selection of precise experimental mutagenesis conditions, our method helps make unigenic analysis a more broadly applicable technique with which to probe protein function.</p> <p>Availability</p> <p>Software to compute, plot, and summarize EoS data is available as an open-source package called 'unigenic' for the 'R' programming language at <url>http://www.fernandes.org/txp/article/13/an-analytical-framework-for-unigenic-evolution</url>.</p

A shifting enemy: analysing the BBC’s representations of “al-Qaeda” in the aftermath of the September 11th 2001 attacks

This article seeks to explore how the BBC made sense of the al-Qaeda phenomenon in its flagship “News at Ten” bulletin during the aftermath of the September 11th 2001 attacks. Using Critical Multimodal Discourse Analysis, it shows how the BBC’s representations function as a dynamic and continually shifting site upon which a range of fears, identities, discourses and forms of knowledge and power struggle and contend, and through which a number of different “al-Qaedas” manifest themselves. In particular, three shifting modes of visual and verbal representation are identified within the BBC’s coverage which each correspond to a separate understanding of al-Qaeda: the “Islamic” mode, the “Personalised” mode and the “Elusive” mode. These representations both draw upon and challenge the dominant discourses surrounding Islam, non-state terrorism and the identities of terrorist suspects, providing audiences with a variety of often conflicting ways of seeing and speaking about this entity. As such, the article provides insight into the complex nature of the BBC’s representations of al-Qaeda during its coverage of the September 11th 2001 attacks, and shows how such complexity serves, albeit inadvertently, to legitimise the far-reaching counterterrorism policies that were enacted in the aftermath of these attacks

Raman Spectroscopy and Regenerative Medicine: A Review

The field of regenerative medicine spans a wide area of the biomedical landscape—from single cell culture in laboratories to human whole-organ transplantation. To ensure that research is transferrable from bench to bedside, it is critical that we are able to assess regenerative processes in cells, tissues, organs and patients at a biochemical level. Regeneration relies on a large number of biological factors, which can be perturbed using conventional bioanalytical techniques. A versatile, non-invasive, non-destructive technique for biochemical analysis would be invaluable for the study of regeneration; and Raman spectroscopy is a potential solution. Raman spectroscopy is an analytical method by which chemical data are obtained through the inelastic scattering of light. Since its discovery in the 1920s, physicists and chemists have used Raman scattering to investigate the chemical composition of a vast range of both liquid and solid materials. However, only in the last two decades has this form of spectroscopy been employed in biomedical research. Particularly relevant to regenerative medicine are recent studies illustrating its ability to characterise and discriminate between healthy and disease states in cells, tissue biopsies and in patients. This review will briefly outline the principles behind Raman spectroscopy and its variants, describe key examples of its applications to biomedicine, and consider areas of regenerative medicine that would benefit from this non-invasive bioanalytical tool