Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Rutgers' TREC-7 Interactive Track Experience

We present results of a study comparing two different interactive information retrieval systems: one which supports positive relevance feedback as a termsuggestion device; the other which supports both positive and negative relevance feedback in this same context. The purpose of the study was to investigate the effectiveness and usability of a specific implementation of negative relevance feedback in interactive information retrieval. A second purpose was to investigate the effectiveness and usability of relevance feedback implemented as a term-suggestion device. The results suggest that, although there was no benefit in terms of performance for the system with negative and positive relevance feedback, this might be due to specific implementation issues. 1.0 Introduction As in TREC-7, we continued the work begun in our TREC-6 experiments (Belkin, et al., 1998), investigating the effectiveness and usability of negative relevance feedback (RF) in interactive information retrieval (IR)...

The T2K experiment

The T2K experiment is a long baseline neutrino oscillation experiment. Its main goal is to measure the last unknown lepton sector mixing angle θ13 by observing νe appearance in a νμ beam. It also aims to make a precision measurement of the known oscillation parameters, and sin22θ23, via νμ disappearance studies. Other goals of the experiment include various neutrino cross-section measurements and sterile neutrino searches. The experiment uses an intense proton beam generated by the J-PARC accelerator in Tokai, Japan, and is composed of a neutrino beamline, a near detector complex (ND280), and a far detector (Super-Kamiokande) located 295 km away from J-PARC. This paper provides a comprehensive review of the instrumentation aspect of the T2K experiment and a summary of the vital information for each subsystem

Mechanisms for HIV Tat upregulation of IL-10 and other cytokine expression: Kinase signaling and PKR-mediated immune response

HIV Tat has been known to have multiple regulatory roles including replication of HIV and modulation of cellular kinases. We investigated whether signaling kinase PKR plays a critical role in mediating Tat-induced cytokine dysregulation. We showed Tat induction of IL-10 dysregulation is associated with PKR activation. To examine the mechanism involved, inhibition of PKR activity abrogated the Tat-induced cytokine induction. We next identified that the MAP kinases including ERK-1/2 and p38 are downstream of PKR in these Tat-induced pathways. Thus, PKR may play a critical role in mediating the subversive effects of HIV Tat resulting in IL-10 induction. © 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.link_to_subscribed_fulltex