We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets ...of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its own symmetric distance matrix class that, besides the fact that it can be used as a regular matrix, helps to save memory and increases memory access speed. This last feature can dramatically improve the overall performance of any Python algorithm using it. In addition, its extensibility, testing suites and documentation make it a good choice to those in need of a workbench for developing or testing new algorithms.
The source code (under MIT license), installer, test suites and benchmarks can be found at https://pele.bsc.es/ under the tools section.
victor.guallar@bsc.es
Supplementary data are available at Bioinformatics online.
This paper studies and provides a performance analysis for the atmospheric influence on the visibility in Free Space Optical Communications (FSOC). With a focus on ground station-satellite links, it ...aims to present and analyse the most commonly used attenuation models for the main atmospheric events, establish relationships and dependence never analyzed before, such as for example in the case of rain and snow. As the characterisation of atmospheric attenuation is far from following a pattern in different locations, this work is intended to simplify and unify all the atmospheric events, proposing the visibility as the main single parameter to compare and analyze them. This parameter is available in most of the measurements, including in the fog scenarios. Besides, the effects of clouds are also analyzed, establishing relationships to visibility, in the case of attenuation calculations, suggesting the use of certain attenuation models and providing a new technique for the calculation of the link blockage in the presence of clouds, which are reported by aviation codes in meteorological stations. Besides, all the sites accessed to obtain the meteorological parameters and tools used for the study in this paper are listed in <xref ref-type="sec" rid="sec2">section II .
Tick-borne encephalitis virus (TBEV) is a leading cause of human neuroinfections in Europe and Northeast Asia. There are no antiviral therapies for treating TBEV infection. A series of nucleoside ...analogues was tested for the ability to inhibit the replication of TBEV in porcine kidney cells and human neuroblastoma cells. The interactions of three nucleoside analogues with viral polymerase were simulated using advanced computational methods. The nucleoside analogues 7-deaza-2'-C-methyladenosine (7-deaza-2'-CMA), 2'-C-methyladenosine (2'-CMA), and 2'-C-methylcytidine (2'-CMC) inhibited TBEV replication. These compounds showed dose-dependent inhibition of TBEV-induced cytopathic effects, TBEV replication (50% effective concentrations EC50of 5.1 ± 0.4 μM for 7-deaza-2'-CMA, 7.1 ± 1.2 μM for 2'-CMA, and 14.2 ± 1.9 μM for 2'-CMC) and viral antigen production. Notably, 2'-CMC was relatively cytotoxic to porcine kidney cells (50% cytotoxic concentration CC50 of ∼50 μM). The anti-TBEV effect of 2'-CMA in cell culture diminished gradually after day 3 posttreatment. 7-Deaza-2'-CMA showed no detectable cellular toxicity (CC50 > 50 μM), and the antiviral effect in culture was stable for >6 days posttreatment. Computational molecular analyses revealed that compared to the other two compounds, 7-deaza-2'-CMA formed a large cluster near the active site of the TBEV polymerase. High antiviral activity and low cytotoxicity suggest that 7-deaza-2'-CMA is a promising candidate for further investigation as a potential therapeutic agent in treating TBEV infection.
The circular economy model offers great opportunities to companies, as it not only allows them to capture additional value from their products and materials, but also reduce the fluctuations of ...price-related risks and material supply. These risks are present in all kind of businesses not based on the circular economy. The circular economy also enables economic growth without the need for more resources. This is because each unit has a higher value as a result of recycling and reuse of products and materials after use. Following this circular economics framework, the Polytechnic University of Madrid (Universidad Politécnica de Madrid, UPM) has adopted strategies aimed at improving the circularity of products. In particular, this article provides the result of obtaining recycled PLA filament from waste originating from university 3D FFF (fused filament fabrication) printers and waste generated by “Coronamakers” in the production of visors and parts for PPEs (Personal Protective Equipment) during the lockdown period of COVID-19 in Spain. This filament is used in the production of 3D printed parts that university students use in their classes, so the circular loop is closed. The obtained score of Material Circularity Indicator (MCI) of this material has been calculated, indicating its high level of circularity.
Age appropriateness of anticoagulants for stroke prevention in atrial fibrillation is uncertain.
To review oral anticoagulants for the treatment of atrial fibrillation in older (age >65 years) people ...and to classify appropriate and inappropriate drugs based on efficacy, safety and tolerability using the Fit-fOR-The-Aged (FORTA) classification.
We performed a structured comprehensive review of controlled clinical trials and summaries of individual product characteristics to assess study and total patient numbers, quality of major outcome data and data of geriatric relevance. The resulting evidence was discussed in a round table with an interdisciplinary panel of ten European experts. Decisions on age appropriateness were made using a Delphi process.
For the eight drugs included, 380 citations were identified. The primary outcome results were reported in 32 clinical trials with explicit and relevant data on older people. Though over 24,000 patients aged >75/80 years were studied for warfarin, data on geriatric syndromes were rare (two studies reporting on frailty/falls/mental status) and missing for all other compounds. Apixaban was rated FORTA-A (highly beneficial). Other non-vitamin K antagonist oral anticoagulants (including low/high-intensity dabigatran and high-intensity edoxaban) and warfarin were assigned to FORTA-B (beneficial). Phenprocoumon, acenocoumarol and fluindione were rated FORTA-C (questionable), mainly reflecting the absence of data.
All non-vitamin K antagonist oral anticoagulants and warfarin were classified as beneficial or very beneficial in older persons (FORTA-A or -B), underlining the overall positive assessment of the risk/benefit ratio for these drugs. For other vitamin-K antagonists regionally used in Europe, the lack of evidence should challenge current practice.
Direct current-biased optical orthogonal frequency division multiplexing (DCO-OFDM) signals used in visible light communications suffer from high peak-to-average-power ratio (PAPR) or cubic metric ...(CM). It strongly degrades the performance due to the great back-off necessary to avoid the clipping effect in the light-emitting diode. Thus, PAPR and CM reduction techniques become crucial to improve the system performance. In this paper, an adaptive network-based fuzzy inference system (ANFIS) is used to obtain efficient DCO-OFDM signals with a low power envelope profile. First, signals specially designed for DCO-OFDM with very low CM, as the ones obtained from the raw cubic metric (RCM)-active constellation extension method, are used to train the fuzzy systems in time and frequency domains. Second, after the off-line training, the ANFIS can generate a real-valued signal in a one-shot way with 8.9 dB of RCM reduction from the original real-valued signal, which involves a gain in the input power back off larger than 2.8 dB, an illumination-to-communication conversion efficiency gain of more than 35% and considerable improvements in bit error rate.
The Smart Grid is a modern power grid that relies on advanced technologies to provide reliable and sustainable electricity. However, its integration with various communication technologies and IoT ...devices makes it vulnerable to cyber-attacks. Such attacks can lead to significant damage, economic losses, and public safety hazards. To ensure the security of the smart grid, increasingly strong security solutions are needed. This paper provides a comprehensive analysis of the vulnerabilities of the smart grid and the different approaches for detecting cyber-attacks. It examines the different vulnerabilities of the smart grid, including system vulnerabilities and cyber-attacks, and discusses the vulnerabilities of all its elements. The paper also investigates various approaches for detecting cyber-attacks, including rule-based, signature-based, anomaly detection, and ma-chine learning-based methods, with a focus on their effectiveness and related research. Finally, prospective cybersecurity approaches for the smart grid, such as AI approaches and blockchain, are discussed along with the challenges and future prospects of cyberattacks on the smart grid. The paper's findings can help policymakers and stakeholders make informed decisions about the security of the smart grid and develop effective strategies to protect it from cyber-attacks.
Visible light communication (VLC) is capable of satisfying the escalating data rate demand in indoor scenarios. The lighting infrastructure may also be exploited in the downlink of a wireless local ...area network (WLAN), where light-emitting diodes are used for transmitting information. The backhaul of VLC access points (APs) constitutes a potential bottleneck in WLANs, especially in large rooms where the number of APs is high. Thus, an alternative reflection-based cooperative wireless system concept is proposed, where no wired connections are required for connecting the APs. Then, its data rate analysis is developed based on the signal-to-noise ratio attained. The results show that the performance of the cooperative wireless system advocated closely approximates the performance of the traditional wired backhaul. Finally, we demonstrate by using Jain's index of fairness that the proposed scheme provides fair coverage quality for all users.
Visible light communication (VLC) is a promising technology to achieve high data rates in heterogeneous scenarios. However, VLC strongly depends on the existence of a line-of-sight (LoS) link between ...transmitter and receiver to guarantee a good data rate performance, which is often a condition that is difficult to satisfy in practice. In this letter, a novel cooperative multicarrier transmission scheme is proposed, where neighboring attocells smartly cooperate to decrease the probability of blockage in the LoS link. This approach is compared to single-cell transmission schemes, obtaining notable gains in both received signal-to-interference-plus-noise ratio and cell data rate when blockage of the LoS link occurs toward the nearest base station.
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