APOLLO: a quality assessment service for single and multiple protein models

Summary: We built a web server named APOLLO, which can evaluate the absolute global and local qualities of a single protein model using machine learning methods or the global and local qualities of a pool of models using a pair-wise comparison approach. Based on our evaluations on 107 CASP9 (Critical Assessment of Techniques for Protein Structure Prediction) targets, the predicted quality scores generated from our machine learning and pair-wise methods have an average per-target correlation of 0.671 and 0.917, respectively, with the true model quality scores. Based on our test on 92 CASP9 targets, our predicted absolute local qualities have an average difference of 2.60 Å with the actual distances to native structure

Improving your target-template alignment with MODalign

Summary: MODalign is an interactive web-based tool aimed at helping protein structure modelers to inspect and manually modify the alignment between the sequences of a target protein and of its template(s). It interactively computes, displays and, upon modification of the target-template alignment, updates the multiple sequence alignments of the two protein families, their conservation score, secondary structure and solvent accessibility values, and local quality scores of the implied three-dimensional model(s). Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information

The ModFOLD4 server for the quality assessment of 3D protein models

Once you have generated a 3D model of a protein, how do you know whether it bears any resemblance to the actual structure? To determine the usefulness of 3D models of proteins, they must be assessed in terms of their quality by methods that predict their similarity to the native structure. The ModFOLD4 server is the latest version of our leading independent server for the estimation of both the global and local (per-residue) quality of 3D protein models. The server produces both machine readable and graphical output, providing users with intuitive visual reports on the quality of predicted protein tertiary structures. The ModFOLD4 server is freely available to all at: http://www.reading.ac.uk/bioinf/ModFOLD/

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Shifting new media: from content to consultancy, from heterarchy to hierarchy

This is a detailed case history of one of London’s iconic new media companies, AMX Studios. Some of the changes in this firm, we assume, are not untypical for other firms in this sector. Particularly we want to draw attention to two transformations. The first change in AMX and in London’s new media industry more generally refers to the field of industrial relations. What can be observed is a shift from a rather heterarchical towards a more hierarchical organized new media industry, a shift from short-term project networks to long-term client dependency. The second change refers to new media products and services. We want to argue for a shift from cool content production towards consultancy and interactive communications solutions

Ultrafast time-resolved spectroscopy of 1D metal-dielectric photonic crystals

We study the all-optical switching behavior of one-dimensional metal-dielectric photonic crystals due to the nonlinearity of the free metal electrons. A polychromatic pump-probe setup is used to determine the wavelength and pump intensity dependence of the ultrafast transmission suppression as well as the dynamics of the process on a subpicosecond timescale. We find ultrafast (sub-picosecond) as well as a slow (millisecond) behavior. We present a model of the ultrafast dynamics and nonlinear response which can fit the measured data well and allows us to separate the thermal and the electronic response of the system.Comment: 7 pages, 5 figure

Test of an interprofessional collaborative practice model to improve obesity-related health outcomes in Michigan

The purpose of the study was to test the effectiveness of an interprofessional collaborative practice (IPCP) education program on clinicians\u27 and students\u27 knowledge and attitudes toward IPCP and to determine the effectiveness of an IPCP weight loss program in two nurse-managed centers. The study team used the Midwest Interprofessional Practice, Education, and Research Center (MIPERC) collaborative practice education program that consists of online learning modules followed by daily huddles and collaborative care planning. The obesity intervention program was implemented by faculty and staff practitioners and students in two clinics with very different patient populations (community residents and college students). Staff/faculty practitioners and students demonstrated statistically significant knowledge gains as a result of online learning modules (Introduction to IPE p \u3c .05; Motivational Interviewing p \u3c .001; Safety Behaviors p \u3c .001; Team Dynamics p \u3c .001). Small, but not statistically significant changes in attitudes toward IPCP were seen with both groups. At program completion, enrolled patients showed statistical significant (p \u3c .001) weight losses and decreases in body mass indices. Other health outcomes showed no significant changes (blood pressure, prevalence of smoking, exercise frequency or duration p \u3e .05). The study demonstrated the potential of an IPCP program to affect weight loss in two populations

TRH: Pathophysiologic and clinical implications

Thyrotropin releasing hormone is thought to be a tonic stimulator of the pituitary TSH secretion regulating the setpoint of the thyrotrophs to the suppressive effect of thyroid hormones. The peptide stimulates the release of normal and elevated prolactin. ACTH and GH may increase in response to exogenous TRH in pituitary ACTH and GH hypersecretion syndromes and in some extrapituitary diseases. The pathophysiological implications of extrahypothalamic TRH in humans are essentially unknown. The TSH response to TRH is nowadays widely used as a diganostic amplifier in thyroid diseases being suppressed in borderline and overt hyperthyroid states and increased in primary thyroid failure. In hypothyroid states of hypothalamic origin, TSH increases in response to exogenous TRH often with a delayed and/or exaggerated time course. But in patients with pituitary tumors and suprasellar extension TSH may also respond to TRH despite secondary hypothyroidism. This TSH increase may indicate a suprasellar cause for the secondary hypothyroidism, probably due to portal vessel occlusion. The TSH released in these cases is shown to be biologically inactive

A new approach for the limit to tree height using a liquid nanolayer model

Liquids in contact with solids are submitted to intermolecular forces inferring density gradients at the walls. The van der Waals forces make liquid heterogeneous, the stress tensor is not any more spherical as in homogeneous bulks and it is possible to obtain stable thin liquid films wetting vertical walls up to altitudes that incompressible fluid models are not forecasting. Application to micro tubes of xylem enables to understand why the ascent of sap is possible for very high trees like sequoias or giant eucalyptus.Comment: In the conclusion is a complementary comment to the Continuum Mechanics and Thermodynamics paper. 21 pages, 4 figures. Continuum Mechanics and Thermodynamics 20, 5 (2008) to appea