FragBuilder:an efficient Python library to setup quantum chemistry calculations on peptides models

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in a variety of useful formats, such as XYZ or PDB formats, or directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license

Dannelse og ingeniørfaglighed

International interdisciplinary research on engineering education and practice (Christensen et al., 2007, 2009, 2019, and 2022 forthcoming) points to the fact, that the engineer’s understanding of the ‘social’ is underprioritized and discursively enacted as soft versus hard technical disciplines. As a result, it has often contributed to a cultural impoverishment of our lifeworld. Hence there is a need for a Bildung perspective in engineering degree programs. A perspective taking its point of departure in the democratic, cultural, and human challenges of society. The discourse on Bildung has primarily taken place in relation to the pedagogical professions, whereas the engineering profession has often been overlooked. In this contribution we make up for this by considering a contribution with potential for supplying a concept of Bildung suitable for the engineering profession and engineering degree programs. The article brings forth the social and ethical responsibility embedded in engineering work in democratic societies and calls to mind John Dewey´s democratic understanding of Bildung (Dewey, 2011 [1916]). The article projects, how this understanding of Bildung might offer an opportunity for rethinking engineering and engineering activity capable of contributing to democratic and responsible resolutions of societal challenges.&nbsp

Bayesian inference of protein structure from chemical shift data

Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction

Home care providers to the rescue:a novel first-responder programme

To describe the implementation of a novel first-responder programme in which home care providers equipped with automated external defibrillators (AEDs) were dispatched in parallel with existing emergency medical services in the event of a suspected out-of-hospital cardiac arrest (OHCA).We evaluated a one-year prospective study that trained home care providers in performing cardiopulmonary resuscitation (CPR) and using an AED in cases of suspected OHCA. Data were collected from cardiac arrest case files, case files from each provider dispatch and a survey among dispatched providers. The study was conducted in a rural district in Denmark.Home care providers were dispatched to 28 of the 60 OHCAs that occurred in the study period. In ten cases the providers arrived before the ambulance service and subsequently performed CPR. AED analysis was executed in three cases and shock was delivered in one case. For 26 of the 28 cases, the cardiac arrest occurred in a private home. Ninety-five per cent of the providers who had been dispatched to a cardiac arrest reported feeling prepared for managing the initial resuscitation, including use of AED.Home care providers are suited to act as first-responders in predominantly rural and residential districts. Future follow-up will allow further evaluation of home care provider arrivals and patient survival

Q Fever in Greenland

We report a patient with Q fever endocarditis in a settlement in eastern Greenland (Isortoq, Ammassalik area). Likely animal sources include sled dogs and seals. Q fever may be underdiagnosed in Arctic areas but may also represent an emerging infection

A 16-Week Aerobic Exercise Intervention Does Not Affect Hippocampal Volume and Cortical Thickness in Mild to Moderate Alzheimer’s Disease

Introduction: Brain imaging studies in healthy elderly subjects suggest a positive effect of aerobic exercise on both brain structure and function, while the effects of aerobic exercise in Alzheimer’s Disease (AD) has been scarcely investigated.Methods: In a single-blinded randomized MRI study, we assessed the effects of an aerobic exercise intervention on brain volume as measured by magnetic resonance imaging (MRI) and its correlation to cognitive functioning in patients with AD. The study was a sub-study of a larger randomized controlled trial (ADEX study). Forty-one patients were assigned to a control or exercise group. The exercise group performed 60-min of aerobic exercise three times per week for 16 weeks. All participants underwent whole-brain MRI at 3 Tesla and cognitive assessment at baseline and after 16 weeks. Attendance and intensity were monitored providing a total exercise load. Changes in regional brain volumes and cortical thickness were analyzed using Freesurfer software.Results: There was no effect of the type of intervention on MRI-derived brain volumes. In the entire group with and without training, Exercise load showed a positive correlation with changes in volume in the hippocampus, as well as frontal cortical thickness. Volume changes in frontal cortical thickness correlated with changes in measures of mental speed and attention and exercise load in the exercise group.Conclusion: We did not find evidence to support an effect of 16 weeks of aerobic exercise on brain volume changes in patients with AD. Longer intervention periods may be needed to affect brain structure as measured with volumetric MRI.Clinical Trial registration:ClinicalTrials.gov Identifier: NCT01681602, registered September 10th, 2012 (Retrospectively registered)