A helicoidal transfer matrix model for inhomogeneous DNA melting

An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically stressed DNA with a fixed linking number constraint. Without loss of accuracy, the continuous degrees of freedom can be discretized using a minimal number of discretization points, yielding an effective transfer matrix model of modest dimension (d=36). The resulting algorithms to compute DNA melting profiles are both simple and efficient.Comment: v3: Matlab toolbox included with source file; article unchanged, 12 pages, 11 figures, RevTe

A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils

Background: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. Methods: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs. Results: In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and beta-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r=-0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events. Conclusions: ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments

The Effects of Stress on the Lives of Emerging Adult College Students: An Exploratory Analysis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113775/1/adsp12007.pd

Individualistic vs. collectivistic perspectives: Silent vs. oral poetry reading

Poetry originates in social orality, as people started to read silently only in the 18th century. Nowadays we are witnessing a return to its oral and public nature, evidenced by popularity of online and live slam festivals. However, we remain largely unaware of whether silent and oral reading modes make any emotional difference in poetry reception. We will report the results of two reading experiments in which we probed, through Likert scales, the reactions of university students and faculty to poems of different genres. The results indicate that the response differs more when poems are read aloud

Semigroup evolution in Wigner Weisskopf pole approximation with Markovian spectral coupling

We establish the relation between the Wigner-Weisskopf theory for the description of an unstable system and the theory of coupling to an environment. According to the Wigner-Weisskopf general approach, even within the pole approximation (neglecting the background contribution) the evolution of a total system subspace is not an exact semigroup for the multi-channel decay, unless the projectors into eigesntates of the reduced evolution generator $W(z)$ are orthogonal. In this case these projectors must be evaluated at different pole locations $z_\alpha\neq z_\beta$. Since the orthogonality relation does not generally hold at different values of $z$, for example, when there is symmetry breaking, the semigroup evolution is a poor approximation for the multi-channel decay, even for a very weak coupling. Nevertheless, there exists a possibility not only to ensure the orthogonality of the $W(z)$ projectors regardless the number of the poles, but also to simultaneously suppress the effect of the background contribution. This possibility arises when the theory is generalized to take into account interactions with an environment. In this case $W(z)$, and hence its eigenvectors as well, are {\it independent} of $z$, which corresponds to a structure of the coupling to the continuum spectrum associated with the Markovian limit.Comment: 9 pages, 3 figure

Aesthetics and literature : a problematic relation?

The paper argues that there is a proper place for literature within aesthetics but that care must be taken in identifying just what the relation is. In characterising aesthetic pleasure associated with literature it is all too easy to fall into reductive accounts, for example, of literature as merely "fine writing". Belleslettrist or formalistic accounts of literature are rejected, as are two other kinds of reduction, to pure meaning properties and to a kind of narrative realism. The idea is developed that literature-both poetry and prose fiction-invites its own distinctive kind of aesthetic appreciation which far from being at odds with critical practice, in fact chimes well with it

Multi-Target Prediction: A Unifying View on Problems and Methods

Multi-target prediction (MTP) is concerned with the simultaneous prediction of multiple target variables of diverse type. Due to its enormous application potential, it has developed into an active and rapidly expanding research field that combines several subfields of machine learning, including multivariate regression, multi-label classification, multi-task learning, dyadic prediction, zero-shot learning, network inference, and matrix completion. In this paper, we present a unifying view on MTP problems and methods. First, we formally discuss commonalities and differences between existing MTP problems. To this end, we introduce a general framework that covers the above subfields as special cases. As a second contribution, we provide a structured overview of MTP methods. This is accomplished by identifying a number of key properties, which distinguish such methods and determine their suitability for different types of problems. Finally, we also discuss a few challenges for future research

Post-contrast acute kidney injury \u2013 Part 1: Definition, clinical features, incidence, role of contrast medium and risk factors: Recommendations for updated ESUR Contrast Medium Safety Committee guidelines

Purpose: The Contrast Media Safety Committee (CMSC) of the European Society of Urogenital Radiology (ESUR) has updated its 2011 guidelines on the prevention of post-contrast acute kidney injury (PC-AKI). The results of the literature review and the recommendations based on it, which were used to prepare the new guidelines, are presented in two papers. Areas covered in part 1: Topics reviewed include the terminology used, the best way to measure eGFR, the definition of PC-AKI, and the risk factors for PC-AKI, including whether the risk with intravenous and intra-arterial contrast medium differs. Key Points: \u2022 PC-AKI is the preferred term for renal function deterioration after contrast medium. \u2022 PC-AKI has many possible causes. \u2022 The risk of AKI caused by intravascular contrast medium has been overstated. \u2022 Important patient risk factors for PC-AKI are CKD and dehydration