Surveillance of Ruminant Diseases in the Nordic Countries

<p/> <p>All the Nordic countries have a basis for their surveillance and disease control in ruminants in national legislation and regulations listing notifiable diseases of concern to the countries. The Nordic countries are a disease-free zone comparing to other parts of the world and the aim of the surveillance is to keep that status and be able to document it. Following is a short summary from each country.</p

Finding Multiple Reaction Pathways of Ligand Unbinding

Searching for reaction pathways describing rare events in large systems presents a long-standing challenge in chemistry and physics. Incorrectly computed reaction pathways result in the degeneracy of microscopic configurations and inability to sample hidden energy barriers. To this aim, we present a general enhanced sampling method to find multiple diverse reaction pathways of ligand unbinding through non-convex optimization of a loss function describing ligand-protein interactions. The method successfully overcomes large energy barriers using an adaptive bias potential, and constructs possible reaction pathways along transient tunnels without the initial guesses of intermediate or final states, requiring crystallographic information only. We examine the method on the T4 lysozyme L99A mutant which is often used as a model system to study ligand binding to proteins, provide a previously unknown reaction pathway, and show that using the bias potential and the tunnel widths it is possible to capture heterogeneity of the unbinding mechanisms between the found transient protein tunnels

Gas-Phase Retinal Spectroscopy: Temperature Effects Are But a Mirage

We employ state-of-the-art first-principle approaches to investigate whether temperature effects are responsible for the unusually broad and flat spectrum of protonated Schiff base retinal observed in photodissociation spectroscopy, as has recently been proposed. We first carefully calibrate how to construct a realistic geometrical model of retinal and show that the exchange–correlation M06-2X functional yields an accurate description while the commonly used complete active space self-consistent field method (CASSCF) is not adequate. Using modern multiconfigurational perturbative methods (NEVPT2) to compute the excitations, we then demonstrate that conformations with different orientations of the β-ionone ring are characterized by similar excitations. Moreover, other degrees of freedom identified as active in room-temperature molecular dynamics simulations do not yield the shift required to explain the anomalous spectral shape. Our findings indicate that photodissociation experiments are not representative of the optical spectrum of retinal in the gas phase and call for further experimental characterization of the dissociation spectr

Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials

[Image: see text] Collective variable-based enhanced sampling methods are routinely used on systems with metastable states, where high free energy barriers impede the proper sampling of the free energy landscapes when using conventional molecular dynamics simulations. One such method is variationally enhanced sampling (VES), which is based on a variational principle where a bias potential in the space of some chosen slow degrees of freedom, or collective variables, is constructed by minimizing a convex functional. In practice, the bias potential is taken as a linear expansion in some basis function set. So far, primarily basis functions delocalized in the collective variable space, like plane waves, Chebyshev, or Legendre polynomials, have been used. However, there has not been an extensive study of how the convergence behavior is affected by the choice of the basis functions. In particular, it remains an open question if localized basis functions might perform better. In this work, we implement, tune, and validate Daubechies wavelets as basis functions for VES. The wavelets construct orthogonal and localized bases that exhibit an attractive multiresolution property. We evaluate the performance of wavelet and other basis functions on various systems, going from model potentials to the calcium carbonate association process in water. We observe that wavelets exhibit excellent performance and much more robust convergence behavior than all other basis functions, as well as better performance than metadynamics. In particular, using wavelet bases yields far smaller fluctuations of the bias potential within individual runs and smaller differences between independent runs. Based on our overall results, we can recommend wavelets as basis functions for VES

Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling

Machine learning methods provide a general framework for automatically finding and representing the essential characteristics of simulation data. This task is particularly crucial in enhanced sampling simulations. There we seek a few generalized degrees of freedom, referred to as collective variables (CVs), to represent and drive the sampling of the free energy landscape. In theory, these CVs should separate different metastable states and correspond to the slow degrees of freedom of the studied physical process. To this aim, we propose a new method that we call multiscale reweighted stochastic embedding (MRSE). Our work builds upon a parametric version of stochastic neighbor embedding. The technique automatically learns CVs that map a high-dimensional feature space to a low-dimensional latent space via a deep neural network. We introduce several new advancements to stochastic neighbor embedding methods that make MRSE especially suitable for enhanced sampling simulations: (1) weight-tempered random sampling as a landmark selection scheme to obtain training data sets that strike a balance between equilibrium representation and capturing important metastable states lying higher in free energy; (2) a multiscale representation of the high-dimensional feature space via a Gaussian mixture probability model; and (3) a reweighting procedure to account for training data from a biased probability distribution. We show that MRSE constructs low-dimensional CVs that can correctly characterize the different metastable states in three model systems: the M\"uller-Brown potential, alanine dipeptide, and alanine tetrapeptide

Excitation energies of retinal chromophores: Critical role of the structural model

We employ a variety of highly-correlated approaches including quantum Monte Carlo (QMC) and the n-electron valence state perturbation theory (NEVPT2) to compute the vertical excitation energies of retinal protonated Schiff base (RPSB) models in the gas phase. We find that the NEVPT2 excitation energies are in good agreement with the QMC values and confirm our previous findings that the complete-active-space perturbation (CASPT2) approach yields accurate excitations for RPSB models only when the more recent zero-order IPEA Hamiltonian is employed. The excitations computed with the original zero-order formulation of CASPT2 are instead systematically red-shifted by more than 0.3 eV. We then focus on the full 11-cis retinal chromophore and show that the M06-2X and MP2 approaches provide reliable ground-state equilibrium structures for this system while the complete-active-space self-consistent field (CASSCF) geometry is characterized by significantly higher ground-state energies at the NEVPT2 and CASPT2 level. Our calibration of the structural model together with the general agreement of all highly-correlated excited-state methods allows us to reliably assign a value of about 2.3 eV to the vertical excitation of 11-cis RPSB in the gas-phase

Hringja - hnoða : tillaga að einfölduðum viðbrögðum almennings við hjartastoppi utan sjúkrahúss

Neðst á síðunni er hægt að nálgast greinina í heild sinni með því að smella á hlekkinn Skoða/Opna(view/open)Hjartastopp hjá fullorðnum er í miklum meirihluta tilfella orsakað af sleglahraðtakti (ventricular tachycardia) eða sleglatifi (ventricular fibrillation). Ef sleglatif er orsökin er rafstuð á brjóstholið það eina sem dugar til að koma aftur á reglulegum sínustakti. Þegar hjartastopp verða utan sjúkrahúss líður hins vegar oft einhver tími þar til rafstuðsgjafi kemur á vettvang, yfirleitt með sjúkrabifreið. Ef vitni eru að hjartastoppi utan sjúkrahúss skiptir gríðarlega miklu máli að hefja grunnendurlífgun sem allra fyrst eftir að kallað hefur verið á aðstoð. Slík viðbrögð geta lengt þann tíma sem sjúklingur er í sleglatifi eða sleglahraðtakti og auka þannig líkur á að mögulegt sé að koma aftur á sínustakti með rafstuði (1). Jafnframt getur þetta dregið úr hættu á heilaskaða ef einstaklingurinn lifir hjartastoppið af (2). Mikilvægi þess er augljóst þar sem hæfni þeirra sem lifa af hjartastopp fer að miklu leyti eftir því hvort heilastarfsemi hefur orðið fyrir varanlegum skaða eða ekki