PCA and K-Means decipher genome

In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of genetic text of a bacterial genome and analyze its structure. By means of principal component analysis they ``discover'' that the information in the genome is encoded by non-overlapping triplets. Next, they learn how to find gene positions. This exercise on PCA and K-Means clustering enables active study of the basic bioinformatics notions. Appendix 1 contains program listings that go along with this exercise. Appendix 2 includes 2D PCA plots of triplet usage in moving frame for a series of bacterial genomes from GC-poor to GC-rich ones. Animated 3D PCA plots are attached as separate gif files. Topology (cluster structure) and geometry (mutual positions of clusters) of these plots depends clearly on GC-content.Comment: 18 pages, with program listings for MatLab, PCA analysis of genomes and additional animated 3D PCA plot

Forms of capital and career benefits of the MBA in china and the UK

This paper sets out the results of a research project which compares benefits from the MBA in China and the UK. Drawing on and modifying Bourdieu’s forms of capital theory, it highlights areas of commonality and difference. In particular it demonstrates that some forms of capital (e.g. institutional, social) transcend national boundaries and are equally valued in both contexts. Significant differences emerge within categories of cultural capital with Chinese respondents placing a higher value on more technical and UK respondents placing a higher value on personal and interpersonal skill components. Implications for the transferability of Western based management education to China are evaluated and discussed

Improving dialysis adherence for high risk patients using automated messaging: Proof of concept

AbstractComorbidities and socioeconomic barriers often limit patient adherence and self-management with hemodialysis. Missed sessions, often associated with communication barriers, can result in emergency dialysis and avoidable hospitalizations. This proof of concept study explored using a novel digital-messaging platform, EpxDialysis, to improve patient-to-dialysis center communication via widely available text messaging and telephone technology. A randomized controlled trial was conducted through Washington University-affiliated hemodialysis centers involving ESRD patients with poor attendance, defined as missing 2–6 sessions over the preceding 12 weeks. A cross-over study design evaluated appointment adherence between intervention and control groups. Comparing nonadherence rates eight weeks prior to enrollment, median appointment adherence after using the system increased by 75%, and median number of unintended hospitalization days fell by 31%. A conservative cost-benefit analysis of EpxDialysis demonstrates a 1:36 savings ratio from appointment adherence. EpxDialysis is a low-risk, cost-effective, intervention for increasing hemodialysis adherence in high-risk patients, especially at centers caring for vulnerable and low-income patients.</jats:p

Conceptual modelling: Towards detecting modelling errors in engineering applications

Rapid advancements of modern technologies put high demands on mathematical modelling of engineering systems. Typically, systems are no longer “simple” objects, but rather coupled systems involving multiphysics phenomena, the modelling of which involves coupling of models that describe different phenomena. After constructing a mathematical model, it is essential to analyse the correctness of the coupled models and to detect modelling errors compromising the final modelling result. Broadly, there are two classes of modelling errors: (a) errors related to abstract modelling, eg, conceptual errors concerning the coherence of a model as a whole and (b) errors related to concrete modelling or instance modelling, eg, questions of approximation quality and implementation. Instance modelling errors, on the one hand, are relatively well understood. Abstract modelling errors, on the other, are not appropriately addressed by modern modelling methodologies. The aim of this paper is to initiate a discussion on abstract approaches and their usability for mathematical modelling of engineering systems with the goal of making it possible to catch conceptual modelling errors early and automatically by computer assistant tools. To that end, we argue that it is necessary to identify and employ suitable mathematical abstractions to capture an accurate conceptual description of the process of modelling engineering systems

An open systems approach to calculating time dependent spectra

A new method to calculate the spectrum using cascaded open systems and master equations is presented. The method uses two state analyzer atoms which are coupled to the system of interest, whose spectrum of radiation is read from the excitation of these analyzer atoms. The ordinary definitions of a spectrum uses two-time averages and Fourier-transforms. The present method uses only one-time averages. The method can be used to calculate time dependent as well as stationary spectra.Comment: 8 pages, revtex, 18 figures, to be published in J.Mod.Op

Binary pulsars as probes of a Galactic dark matter disk

As a binary pulsar moves through a wind of dark matter particles, the resulting dynamical friction modifies the binary's orbit. We study this effect for the double disk dark matter (DDDM) scenario, where a fraction of the dark matter is dissipative and settles into a thin disk. For binaries within the dark disk, this effect is enhanced due to the higher dark matter density and lower velocity dispersion of the dark disk, and due to its co-rotation with the baryonic disk.We estimate the effect and compare it with observations for two different limits in the Knudsen number ($Kn$). First, in the case where DDDM is effectively collisionless within the characteristic scale of the binary ($Kn\gg1$) and ignoring the possible interaction between the pair of dark matter wakes. Second, in the fully collisional case ($Kn\ll1$), where a fluid description can be adopted and the interaction of the pair of wakes is taken into account. We find that the change in the orbital period is of the same order of magnitude in both limits. A comparison with observations reveals good prospects to probe currently allowed DDDM models with timing data from binary pulsars in the near future. We finally comment on the possibility of extending the analysis to the intermediate (rarefied gas) case with $Kn\sim1$.Comment: 15 pages, 6 figures. Few comments and references added, version accepted for publication in Physics of the Dark Universe (PDU

The Fate of the Accelerating Universe

The presently accelerating universe may keep accelerating forever, eventually run into the event horizon problem, and thus be in conflict with the superstring idea. In the other way around, the current accelerating phase as well as the fate of the universe may be swayed by a negative cosmological constant, which dictates a big crunch. Based on the current observational data, in this paper we investigate how large the magnitude of a negative cosmological constant is allowed to be. In addition, for distinguishing the sign of the cosmological constant via observations, we point out that a measure of the evolution of the dark energy equation of state may be a good discriminator. Hopefully future observations will provide much more detailed information about dark energy and thereby indicates the sign of the cosmological constant as well as the fate of the presently accelerating universe.Comment: 16 pages, 5 figures, LaTe

One Dimensional Magnetized TG Gas Properties in an External Magnetic Field

With Girardeau's Fermi-Bose mapping, we have constructed the eigenstates of a TG gas in an external magnetic field. When the number of bosons $N$ is commensurate with the number of potential cycles $M$, the probability of this TG gas in the ground state is bigger than the TG gas raised by Girardeau in 1960. Through the comparison of properties between this TG gas and Fermi gas, we find that the following issues are always of the same: their average value of particle's coordinate and potential energy, system's total momentum, single-particle density and the pair distribution function. But the reduced single-particle matrices and their momentum distributions between them are different.Comment: 6 pages, 4 figure