Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.

A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range

Factors associated with invasive lung aspergillosis and the significance of positive aspergillus culture after liver transplantation

From January 1981 to December 1990, 2180 patients underwent orthotopic liver transplantation at the University of Pittsburgh. Thirty-two patients (1.5%) were identified with invasive aspergillosis (29 lung, 2 intraabdominal, 1 meningitis). Of 29 patients with invasive lung disease, only 23 (79%) had positive culture (Aspergillus fumigatus, 20; Aspergillus flavus, 3). Forty-eight variables were analyzed and compared in 23 patients with invasive disease with positive cultures and 9 patients with colonization only. The variables associated with pulmonary invasive disease, by univariate analysis, were surgical time (P =.03), presence of laparotomies (P =.02), higher creatinine level at time of Aspergillus isolation (P =.01), and use of OKT3 (P =.02). However, in a multivariate analysis, only the last two (creatinine, OKT3) were associated with invasive lung aspergillosis. Of 4 patients with positive abdominal wound culture, 2 had local invasive aspergillosis. Therefore, positive cultures of Aspergillus organisms from respiratory secretions and wound drainage may represent invasive disease and should not be ignored. © 1992 the University of Chicago

Evidence for validity and reliability of a french version of the FAAM

BACKGROUND: The Foot and Ankle Ability Measure (FAAM) is a self reported questionnaire for patients with foot and ankle disorders available in English, German, and Persian. This study plans to translate the FAAM from English to French (FAAM-F) and assess the validity and reliability of this new version.METHODS: The FAAM-F Activities of Daily Living (ADL) and sports subscales were completed by 105 French-speaking patients (average age 50.5 years) presenting various chronic foot and ankle disorders. Convergent and divergent validity was assessed by Pearson's correlation coefficients between the FAAM-F subscales and the SF-36 scales: Physical Functioning (PF), Physical Component Summary (PCS), Mental Health (MH) and Mental Component Summary (MCS). Internal consistency was calculated by Cronbach's Alpha (CA). To assess test re-test reliability, 22 patients filled out the questionnaire a second time to estimate minimal detectable changes (MDC) and intraclass correlation coefficients (ICC).RESULTS: Correlations for FAAM-F ADL subscale were 0.85 with PF, 0.81 with PCS, 0.26 with MH, 0.37 with MCS. Correlations for FAAM-F Sports subscale were 0.72 with PF, 0.72 with PCS, 0.21 with MH, 0.29 with MCS. CA estimates were 0.97 for both subscales. Respectively for the ADL and Sports subscales, ICC were 0.97 and 0.94, errors for a single measure were 8 and 10 points at 95% confidence and the MDC values at 95% confidence were 7 and 18 points.CONCLUSION: The FAAM-F is valid and reliable for the self-assessment of physical function in French-speaking patients with a wide range of chronic foot and ankle disorders

Collaboration and teamwork: immersion and presence in an online learning environment

In the world of OTIS, an online Internet School for occupational therapists, students from four European countries were encouraged to work collaboratively through problem-based learning by interacting with each other in a virtual semi-immersive environment. This paper describes, often in their own words, the experience of European occupational therapy students working together across national and cultural boundaries. Collaboration and teamwork were facilitated exclusively through an online environment, since the students never met each other physically during the OTIS pilot course. The aim of the paper is to explore the observations that here was little interaction between students from different tutorial groups and virtual teamwork developed in each of the cross-cultural tutorial groups. Synchronous data from the students was captured during tutorial sessions and peer-booked meetings and analysed using the qualitative constructs of ‘immersion’, ‘presence’ and ‘reflection in learning’. The findings indicate that ‘immersion’ was experienced only to a certain extent. However, both ‘presence’ and shared presence were found by the students, within their tutorial groups, to help collaboration and teamwork. Other evidence suggests that communities of interest were established. Further study is proposed to support group work in an online learning environment. It is possible to conclude that collaborative systems can be designed, which encourage students to build trust and teamwork in a cross cultural online learning environment.</p

Microscopic origin of universality in Casimir forces

The microscopic mechanisms for universality of Casimir forces between macroscopic conductors are displayed in a model of classical charged fluids. The model consists of two slabs in empty space at distance $d$ containing classical charged particles in thermal equilibrium (plasma, electrolyte). A direct computation of the average force per unit surface yields, at large distance, the usual form of the Casimir force in the classical limit (up to a factor 2 due to the fact that the model does not incorporate the magnetic part of the force). Universality originates from perfect screening sum rules obeyed by the microscopic charge correlations in conductors. If one of the slabs is replaced by a macroscopic dielectric medium, the result of Lifshitz theory for the force is retrieved. The techniques used are Mayer expansions and integral equations for charged fluids.Comment: 31 pages, 0 figures, submitted to Journal of Statistical Physic

MC-Simulation of the Transverse Double Spin Asymmetry for RHIC

Using {\sc Sphinx tt}, a new MC simulation program for transverse polarized nucleon--nucleon scattering based on {\sc Pythia~5.6}, we calculate the transverse double spin asymmetry $A^{TT}$ in the Drell-Yan process. If one assumes (quite arbitrarily) that the transversity parton distribution $\delta q(x,Q^2)$ equals the helicity distribution $\Delta q(x,Q^2)$ at some low $Q_0^2$ scale, the resulting asymmetry is of order 1\%. In this case is $A^{TT}$ would hardly be be measurable with PHENIX at RHIC.Comment: 17 pages, 5 figure

Quantifying similarity of pore-geometry in nanoporous materials

In most applications of nanoporous materials the pore structure is as important as the chemical composition as a determinant of performance. For example, one can alter performance in applications like carbon capture or methane storage by orders of magnitude by only modifying the pore structure. For these applications it is therefore important to identify the optimal pore geometry and use this information to find similar materials. However, the mathematical language and tools to identify materials with similar pore structures, but different composition, has been lacking. We develop a pore recognition approach to quantify similarity of pore structures and classify them using topological data analysis. This allows us to identify materials with similar pore geometries, and to screen for materials that are similar to given top-performing structures. Using methane storage as a case study, we also show that materials can be divided into topologically distinct classes requiring different optimization strategies

Cardiovascular magnetic resonance of myocardial infarction after blunt chest trauma: a heartbreaking soccer-shot

Cardiac injury occasionally occurs as a result of blunt chest trauma. Most cardiac complications in chest trauma are due to myocardial contusion rather than direct damage to the coronary arteries. However, traumatic coronary injury has been reported, and a variety of underlying pathophysiological mechanisms have been proposed. We present a 26 year old patient presenting with an acute coronary syndrome as a consequence of a soccer-shot impact to the chest. CMR showed apical inferior infarction, as well as multiple small septal lesions which were presumed to have resulted from embolization. The culprit lesion was a proximal 75% LAD stenosis with a prominent plaque-rupture and thrombus-formation, and the distal LAD was occluded by thromboembolic material

Automatically extracting functionally equivalent proteins from SwissProt

In summary, FOSTA provides an automated analysis of annotations in UniProtKB/Swiss-Prot to enable groups of proteins already annotated as functionally equivalent, to be extracted. Our results demonstrate that the vast majority of UniProtKB/Swiss-Prot functional annotations are of high quality, and that FOSTA can interpret annotations successfully. Where FOSTA is not successful, we are able to highlight inconsistencies in UniProtKB/Swiss-Prot annotation. Most of these would have presented equal difficulties for manual interpretation of annotations. We discuss limitations and possible future extensions to FOSTA, and recommend changes to the UniProtKB/Swiss-Prot format, which would facilitate text-mining of UniProtKB/Swiss-Prot