Designing protein β-sheet surfaces by Z-score optimization

Studies of lattice models of proteins have suggested that the appropriate energy expression for protein design may include nonthermodynamic terms to accommodate negative design concerns. One method, developed in lattice model studies, maximizes a quantity known as the "Z-score," which compares the lowest energy sequence whose ground state structure is the target structure to an ensemble of random sequences. Here we show that, in certain circumstances, the technique can be applied to real proteins. The resulting energy expression is used to design the β-sheet surfaces of two real proteins. We find experimentally that the designed proteins are stable and well folded, and in one case is even more thermostable than the wild type

The Value of Literacy Practices

The concepts of literacy events and practices have received considerable attention in educational research and policy. In comparison, the question of value, that is, ‘which literacy practices do people most value?’ has been neglected. With the current trend of cross-cultural adult literacy assessment, it is increasingly important to recognise locally valued literacy practices. In this paper we argue that measuring preferences and weighting of literacy practices provides an empirical and democratic basis for decisions in literacy assessment and curriculum development and could inform rapid educational adaptation to changes in the literacy environment. The paper examines the methodological basis for investigating literacy values and its potential to inform cross-cultural literacy assessments. The argument is illustrated with primary data from Mozambique. The correlation between individual values and respondents’ socio-economic and demographic characteristics is explored

Book Reviews

Book Reviews of: Jonathan Schell, The Fate of the Earth (Alfred A. Knopf) John Updike, Rabbit is Rich (Alfred A. Knopf) George Gilder, Wealth and Poverty (Basic Book, Inc.

Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function

To determine which of seven library design algorithms best introduces new protein function without destroying it altogether, seven combinatorial libraries of green fluorescent protein variants were designed and synthesized. Each was evaluated by distributions of emission intensity and color compiled from measurements made in vivo. Additional comparisons were made with a library constructed by error-prone PCR. Among the designed libraries, fluorescent function was preserved for the greatest fraction of samples in a library designed by using a structure-based computational method developed and described here. A trend was observed toward greater diversity of color in designed libraries that better preserved fluorescence. Contrary to trends observed among libraries constructed by error-prone PCR, preservation of function was observed to increase with a library's average mutation level among the four libraries designed with structure-based computational methods

Magnetic Field scaling of Relaxation curves in Small Particle Systems

We study the effects of the magnetic field on the relaxation of the magnetization of small monodomain non-interacting particles with random orientations and distribution of anisotropy constants. Starting from a master equation, we build up an expression for the time dependence of the magnetization which takes into account thermal activation only over barriers separating energy minima, which, in our model, can be computed exactly from analytical expressions. Numerical calculations of the relaxation curves for different distribution widths, and under different magnetic fields H and temperatures T, have been performed. We show how a \svar scaling of the curves, at different T and for a given H, can be carried out after proper normalization of the data to the equilibrium magnetization. The resulting master curves are shown to be closely related to what we call effective energy barrier distributions, which, in our model, can be computed exactly from analytical expressions. The concept of effective distribution serves us as a basis for finding a scaling variable to scale relaxation curves at different H and a given T, thus showing that the field dependence of energy barriers can be also extracted from relaxation measurements.Comment: 12 pages, 9 figures, submitted to Phys. Rev.

Distant echoes: evoking the soundscapes of the past in the radio documentary series Noise: a human history

This article asks whether radio can ever successfully evoke an accurate sense of the sound of the past. It does so through a reflective critical analysis of the 2013 BBC Radio 4 documentary series, Noise: A Human History, by its own writer and presenter. It explores how the ‘sound design’ of the series met the challenge of providing a longue durée history of sound without having recourse to authentic sound archive recordings for most of the period being covered. Through an analysis of key sequences, and by highlighting the significance of the broader context of production, it argues that it is possible for epistemologically valuable history to emerge, even via a medium that treats sound more as a device for evoking the imagination than as something possessing evidential status in itself. The article does this by invoking the series as a practical example of ‘historical acoustemology’, and by suggesting that in radio notions of subjectivity and perceptual mimesis are key to understanding the medium's success. In doing so, the article calls for a redefinition of the notion of the radiogenic – arguing for a move away from seeing ‘raw’ sound as the key ingredient of sound design, and towards greater attention to the influence of radio's other characteristics as a time-based, institutionally-produced mass medium

Ab initio estimate of temperature dependence of electrical conductivity in a model amorphous material: hydrogenated amorphous silicon

We present an ab initio calculation of the DC conductivity of amorphous silicon and hydrogenated amorphous silicon. The Kubo-Greenwood formula is used to obtain the DC conductivity, by thermal averaging over extended dynamical simulation. Its application to disordered solids is discussed. The conductivity is computed for a wide range of temperatures and doping is explored in a naive way by shifting the Fermi level. We observed the Meyer-Neldel rule for the electrical conductivity with E_MNR = 0.06 eV and a temperature coefficient of resistance, TCR ~ -2.0% K^-1 for a-Si:H. In general, experimental trends are reproduced by these calculations, and this suggests the possible utility of the approach for modeling carrier transport in other disordered systems.Comment: 9 pages, 8 figures, submitted to PRB Comments: corrected typos, referee's comments include

BMQ

BMQ: Boston Medical Quarterly was published from 1950-1966 by the Boston University School of Medicine and the Massachusetts Memorial Hospitals

The (im)materiality of literacy : the significance of subjectivity to new literacies research.

This article deconstructs the online and offline experience to show its complexities and idiosyncratic nature. It proposes a theoretical framework designed to conceptualise aspects of meaning-making across on- and offline contexts. In arguing for the ‘(im)materiality’ of literacy, it makes four propositions which highlight the complex and diverse relationships between the immaterial and material associated with meaning-making. Complementing existing sociocultural perspectives on literacy, the article draws attention to the significance of relationships between space, mediation, materiality and embodiment to literacy practices. This in turn emphasises the importance of the subjective in understanding how different locations, experiences and so forth inflect literacy practice. The article concludes by drawing on the Deleuzian concept of the ‘baroque’ to suggest that this focus on articulations between the material and immaterial helps us to see literacy as multiply and flexibly situated

A review of clinical decision-making: Models and current research

Aims and objectives: The aim of this paper was to review the current literature with respect to clinical decision-making models and the educational application of models to clinical practice. This was achieved by exploring the function and related research of the three available models of clinical decision making: information processing model, the intuitive-humanist model and the clinical decision making model. Background: Clinical decision-making is a unique process that involves the interplay between knowledge of pre-existing pathological conditions, explicit patient information, nursing care and experiential learning. Historically, two models of clinical decision making are recognised from the literature; the information processing model and the intuitive-humanist model. The usefulness and application of both models has been examined in relation the provision of nursing care and care related outcomes. More recently a third model of clinical decision making has been proposed. This new multidimensional model contains elements of the information processing model but also examines patient specific elements that are necessary for cue and pattern recognition. Design: Literature review Methods: Evaluation of the literature generated from MEDLINE, CINAHL, OVID, PUBMED and EBESCO systems and the Internet from 1980 – November 2005