Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis

Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we introduce tools from topological data analysis to characterize the frequency and scale of lateral gene transfer in bacteria, focusing on a set of pathogens of significant public health relevance. As a case study, we examine the spread of antibiotic resistance in Staphylococcus aureus. Finally, we consider the possible role of the human microbiome as a reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on Advanced Methods of Interactive Data Mining for Personalized Medicin

Coherence of qubits based on single Ca+^+ ions

Two-level ionic systems, where quantum information is encoded in long lived states (qubits), are discussed extensively for quantum information processing. We present a collection of measurements which characterize the stability of a qubit based on the $S_{1/2}$--$D_{5/2}$ transition of single $^{40}$Ca$^+$ ions in a linear Paul trap. We find coherence times of $\simeq$1 ms, discuss the main technical limitations and outline possible improvements.Comment: Proceedings of "Trapped charged particles and fundamental interactions" submitted to Journal of Physics B (IoP

First passage times and distances along critical curves

We propose a model for anomalous transport in inhomogeneous environments, such as fractured rocks, in which particles move only along pre-existing self-similar curves (cracks). The stochastic Loewner equation is used to efficiently generate such curves with tunable fractal dimension $d_f$. We numerically compute the probability of first passage (in length or time) from one point on the edge of the semi-infinite plane to any point on the semi-circle of radius $R$. The scaled probability distributions have a variance which increases with $d_f$, a non-monotonic skewness, and tails that decay faster than a simple exponential. The latter is in sharp contrast to predictions based on fractional dynamics and provides an experimental signature for our model.Comment: 5 pages, 5 figure

Ultrafast modulation of the chemical potential in BaFe2As2 by coherent phonons

Time- and angle-resolved extreme ultraviolet photoemission spectroscopy is used to study the electronic structure dynamics in BaFe2As2 around the high-symmetry points Γ and M. A global oscillation of the Fermi level at the frequency of the A1g(As) phonon mode is observed. It is argued that this behavior reflects a modulation of the effective chemical potential in the photoexcited surface region that arises from the high sensitivity of the band structure near the Fermi level to the A1g(As) phonon mode combined with a low electron diffusivity perpendicular to the layers. The results establish a novel way to tune the electronic properties of iron pnictides: coherent control of the effective chemical potential. The results further suggest that the equilibration time for the effective chemical potential needs to be considered in the ultrafast electronic structure dynamics of materials with weak interlayer coupling. © 2014 American Physical Society

Ultrafast modulation of the chemical potential in BaFe2_2As2_2 by coherent phonons

Time- and angle-resolved extreme ultraviolet photoemission spectroscopy is used to study the electronic structure dynamics in BaFe$_2$As$_2$ around the high-symmetry points $\Gamma$ and $M$. A global oscillation of the Fermi level at the frequency of the $A_{1g}$(As) phonon mode is observed. It is argued that this behavior reflects a modulation of the effective chemical potential in the photoexcited surface region that arises from the high sensitivity of the band structure near the Fermi level to the $A_{1g}$ phonon mode combined with a low electron diffusivity perpendicular to the layers. The results establish a novel way to tune the electronic properties of iron pnictides: coherent control of the effective chemical potential. The results further suggest that the equilibration time for the effective chemical potential needs to be considered in the ultrafast electronic structure dynamics of materials with weak interlayer coupling.Comment: 6 pages, 3 figure

Engaging with graduate attributes through encouraging accurate student self-assessment

Self-assessment can be conceptualised as the involvement of students in identifying assessment criteria and standards that they can apply to their work in order to make judgements about whether they have met these criteria (Boud, 1995). It is a process that promotes student learning rather than just grade allocation. However, self-assessment does not have obvious face validity for students; and many students find that making an objective assessment of their work difficult (Lindblom-ylanne, Pihlajamak & Kotkas, 2006). Previous business education research has also found that self-assessment does not closely reflect either peer or instructor assessments (Campbell, et al., 2001). The current study aimed to explore: (a) the relationship between self-assessment grading and teacher assessment; and (b) the effect of self-assessment in engaging students with graduate attributes, in order to explore the tenets of self-assessment This process of self-assessment was investigated through application of an online assessment system, Re View, to encourage more effective self-assessment in business education. Data collected from two groups (student and teacher) demonstrated that: (1) initial self-assessment results between the teaching academics and the students' self-assessment, were significantly different with students overestimating their ability on every criterion; (2) however, the variation diminished with time to the point that there was no significant difference between the two assessments; and (3) students' awareness of the graduate attributes for their degree program increased from the beginning to the end of the subject (Note 1)

Sociocultural Competence Training in Higher Engineering Education: The Role of Gaming Simulation

The present study focuses on competency-based approach in higher engineering education. Today engineers are required to be socially, culturally and communicatively skilled and able to act in constantly changing sociocultural environment. Presently the development of engineers’ sociocultural competency is of great importance, which is seen from the criteria for accrediting engineering programs of numerous international organizations, e.g. ABET. The paper presents some methods of sociocultural competency training based on the techniques of gaming simulation. Here we describe the educational games “Intercultural communication” and “The art of presentation” for the students of Elite Education Department of National Research Tomsk Polytechnic University. The results of incorporating the gaming technologies in education contribute to the effectiveness of engineers’ sociocultural competency training. The paper ends by pointing out gaming simulation which is a cutting-edge pedagogical approach which allows students to participate in realistic scenarios and develop sociocultural competency