ACO-Based Multi-User Detection in Cooperative CDMA Networks

In this paper, the cooperative diversity is investigated in the uplink of a Code Division Multiple Access (CDMA) network in which users cooperate by relaying each other’s messages toward the Base Station (BS). It is assumed that the spreading waveforms are not orthogonal and hence, Multiple Access Interference (MAI) exists at the relay nodes as well as the BS. MAI degrades the signal quality at both relays and BS and decreases the cooperative diversity gain. To alleviate this problem, an Ant Colony Optimization (ACO) based Multi-User Detector (MUD) has been proposed to efficiently combine the received signals from the direct and relay paths and sub-optimally extract transmitted bits at the BS. The computational complexity of proposed algorithm is significantly lower than that of the Maximum Likelihood (ML) detector. More explicitly, for a cooperative network supporting 15 users, the computational complexity of the proposed ACO algorithm is a factor of 103 lower than that of the optimum Bayesian detector. Simulation results show that the performance of the proposed ACO-based detector can closely approach the maximum diversity in terms of BER and efficiently cancel the MAI at the BS

Membrane mediated toppling mechanism of the folate energy coupling factor transporter

Energy coupling factor (ECF) transporters are responsible for the uptake of micronutrients in bacteria and archaea. They consist of an integral membrane unit, the S-component, and a tripartite ECF module. It has been proposed that the S-component mediates the substrate transport by toppling over in the membrane when docking onto an ECF module. Here, we present multi-scale molecular dynamics simulations and in vitro experiments to study the molecular toppling mechanism of the S-component of a folate-specific ECF transporter. Simulations reveal a strong bending of the membrane around the ECF module that provides a driving force for toppling of the S-component. The stability of the toppled state depends on the presence of non-bilayer forming lipids, as confirmed by folate transport activity mea- surements. Together, our data provide evidence for a lipid-dependent toppling-based mechanism for the folate-specific ECF transporter, a mechanism that might apply to other ECF transporters

Martini 3 : a general purpose force field for coarse-grained molecular dynamics

The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein-protein and protein-lipid interactions and material science applications as ionic liquids and aedamers.Peer reviewe

Titratable Martini model for constant pH simulations

In this work, we deliver a proof of concept for a fast method that introduces pH effects into classical coarse-grained (CG) molecular dynamics simulations. Our approach is based upon the latest version of the popular Martini CG model to which explicit proton mimicking particles are added. We verify our approach against experimental data involving several different molecules and different environmental conditions. In particular, we compute titration curves, pH dependent free energies of transfer, and lipid bilayer membrane affinities as a function of pH. Using oleic acid as an example compound, we further illustrate that our method can be used to study passive translocation in lipid bilayers via protonation. Finally, our model reproduces qualitatively the expansion of the macromolecule dendrimer poly(propylene imine) as well as the associated pKa shift of its different generations. This example demonstrates that our model is able to pick up collective interactions between titratable sites in large molecules comprising many titratable functional groups

The combination of sofosbuvir and daclatasvir is effective and safe in treating patients with hepatitis C and severe renal impairment

Background and Aim: Many of the treatment regimens available for hepatitis C include sofosbuvir. Unfortunately, sofosbuvir has not been recommended for use in patients with severe renal impairment leaving these group of patients with very few options. Nevertheless, there are many reports in which these patients have been treated with sofosbuvir-containing regiments without important adverse events. This study aims at determining the safety and effectiveness of a sofosbuvir-based treatment in patients with severe renal impairment, including those on hemodialysis. Method: We enrolled subjects with hepatitis C and estimated glomerular filtration rate under ml/min/1.73m2 from 13 centers in Iran. Patients were treated for 12 weeks with a single daily pill containing 400-mg sofosbuvir and 60-mg daclatasvir. Patients with cirrhosis were treated for 24 weeks. Response to treatment was evaluated 12 weeks after end of treatment (sustained viral response SVR). ClinicalTrials.gov identifier: NCT03063879. Results: A total of 103 patients were enrolled from 13 centers. Seventy-five patients were on hemodialysis. Thirty-nine had cirrhosis and eight were decompensated. Fifty-three were Genotype 1, and 27 Genotype 3. Twenty-seven patients had history of previous failed interferon-based treatment. Three patients died in which cause of death was not related to treatment. Six patients were lost to follow-up. The remaining 94 patients all achieved SVR. No adverse events leading to discontinuation of medicine was observed. Conclusions: The combination of sofosbuvir and daclatasvir is an effective and safe treatment for patients infected with all genotypes of hepatitis C who have severe renal impairment, including patients on hemodialysis. © 2020 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Lt