Multiple Transition States and Roaming in Ion-Molecule Reactions: a Phase Space Perspective

We provide a dynamical interpretation of the recently identified `roaming' mechanism for molecular dissociation reactions in terms of geometrical structures in phase space. These are NHIMs (Normally Hyperbolic Invariant Manifolds) and their stable/unstable manifolds that define transition states for ion-molecule association or dissociation reactions. The associated dividing surfaces rigorously define a roaming region of phase space, in which both reactive and nonreactive trajectories can be trapped for arbitrarily long times.Comment: 20 pages, 6 figure

Non-Markovian Stochastic Resonance

The phenomenological linear response theory of non-Markovian Stochastic Resonance (SR) is put forward for stationary two-state renewal processes. In terms of a derivation of a non-Markov regression theorem we evaluate the characteristic SR-quantifiers; i.e. the spectral power amplification (SPA) and the signal-to-noise ratio (SNR), respectively. In clear contrast to Markovian SR, a characteristic benchmark of genuine non-Markovian SR is its distinctive dependence of the SPA and SNR on small (adiabatic) driving frequencies; particularly, the adiabatic SNR becomes strongly suppressed over its Markovian counterpart. This non-Markovian SR theory is elucidated for a fractal gating dynamics of a potassium ion channel possessing an infinite variance of closed sojourn times.Comment: 4 pages, 1 figur

Genetic recombination during coinfection of two mutants of human respiratory syncytial virus

Recombination between coinfecting viruses had not been documented previously for a nonsegmented negative-strand RNA virus (mononegavirus). We investigated the potential of intermolecular recombination by respiratory syncytial virus (RSV) by coinfecting HEp-2 cells with two recombinant RSV (rRSV) mutants lacking either the G gene (DeltaG/HEK) or the NS1 and NS2 genes (DeltaNS1/2). These viruses replicate inefficiently and form pinpoint plaques in HEp-2 cells. Therefore, potential recombined viruses with a growth and/or plaque formation advantage should easily be identified and differentiated from the two parental viruses. Further identification of potential recombinants was aided by the inclusion of point mutation markers in the F and L genes of DeltaG/HEK and the design of reverse transcription-PCR (RT-PCR) primers capable of detecting these markers. Independent coinfections and control single infections by these two rRSV mutants were performed. In one of six coinfections, an RSV variant was identified that produced plaques slightly larger than those of wild-type RSV in HEp-2 cells. RT-PCR and sequencing provided evidence that this variant was a recombined RSV (rec-RSV). The rec-RSV appeared to have been generated by a polymerase jump from the DeltaG/HEK genome to that of DeltaNS1/2 and back again in the vicinity of the SH-G-F genes. This apparently involved nonhomologous and homologous recombination events, respectively. The recombined genome was identical to that of the DeltaG/HEK mutant except that all but the first 12 nucleotides of the SH gene were deleted and replaced by an insert consisting of the last 91 nucleotides of the G gene and its downstream intergenic region. This insert could have come only from the coinfecting DeltaNS1/2 virus. This resulted in the formation of a short chimeric SH:G gene. Northern and Western blot analysis confirmed that the rec-RSV did not express the normal SH and G mRNAs and proteins but did express the aberrant SH:G mRNA. This provides an experimental demonstration of intermolecular recombination yielding a viable, helper-independent mononegavirus. However, the isolation of only a single rec-RSV under these optimized conditions supports the idea that RSV recombination is rare indeed

Molecular characterization and complete genome sequence of avian paramyxovirus type 4 prototype strain duck/Hong Kong/D3/75

<p>Abstract</p> <p>Background</p> <p>Avian paramyxoviruses (APMVs) are frequently isolated from domestic and wild birds throughout the world. All APMVs, except avian metapneumovirus, are classified in the genus <it>Avulavirus </it>of the family <it>Paramyxoviridae</it>. At present, the APMVs of genus <it>Avulavirus </it>are divided into nine serological types (APMV 1–9). Newcastle disease virus represents APMV-1 and is the most characterized among all APMV types. Very little is known about the molecular characteristics and pathogenicity of APMV 2–9.</p> <p>Results</p> <p>As a first step towards understanding the molecular genetics and pathogenicity of APMV-4, we have sequenced the complete genome of APMV-4 strain duck/Hong Kong/D3/75 and determined its pathogenicity in embryonated chicken eggs. The genome of APMV-4 is 15,054 nucleotides (nt) in length, which is consistent with the "rule of six". The genome contains six non-overlapping genes in the order 3'-N-P/V-M-F-HN-L-5'. The genes are flanked on either side by highly conserved transcription start and stop signals and have intergenic sequences varying in length from 9 to 42 nt. The genome contains a 55 nt leader region at 3' end. The 5' trailer region is 17 nt, which is the shortest in the family <it>Paramyxoviridae</it>. Analysis of mRNAs transcribed from the P gene showed that 35% of the transcripts were edited by insertion of one non-templated G residue at an editing site leading to production of V mRNAs. No message was detected that contained insertion of two non-templated G residues, indicating that the W mRNAs are inefficiently produced in APMV-4 infected cells. The cleavage site of the F protein (DIPQR↓F) does not conform to the preferred cleavage site of the ubiquitous intracellular protease furin. However, exogenous proteases were not required for the growth of APMV-4 in cell culture, indicating that the cleavage does not depend on a furin site.</p> <p>Conclusion</p> <p>Phylogenic analysis of the nucleotide sequences of viruses of all five genera of the family <it>Paramyxoviridae </it>showed that APMV-4 is more closely related to the APMVs than to other paramyxoviruses, reinforcing the classification of all APMVs in the genus <it>Avulavirus </it>of the family <it>Paramyxoviridae</it>.</p

Impairment of the CD8+ T cell response in lungs following infection with human respiratory syncytial virus is specific to the anatomical site rather than the virus, antigen, or route of infection

<p>Abstract</p> <p>Background</p> <p>A subset of the virus-specific CD8+ cytotoxic T lymphocytes (CTL) isolated from the lungs of mice infected with human respiratory syncytial virus (RSV) is impaired in the ability to secrete interferon γ (IFNγ), a measure of functionality. It was suggested that the impairment specifically suppressed the host cellular immune response, a finding that could help explain the ability of RSV to re-infect throughout life.</p> <p>Results</p> <p>To determine whether this effect is dependent on the virus, the route of infection, or the type of infection (respiratory, disseminated, or localized dermal), we compared the CTL responses in mice following intranasal (IN) infection with RSV or influenza virus or IN or intradermal (ID) infection with vaccinia virus expressing an RSV CTL antigen. The impairment was observed in the lungs after IN infection with RSV, influenza or vaccinia virus, and after a localized ID infection with vaccinia virus. In contrast, we observed a much higher percentage of IFNγ secreting CD8+ lymphocytes in the spleens of infected mice in every case.</p> <p>Conclusion</p> <p>The decreased functionality of CD8+ CTL is specific to the lungs and is not dependent on the specific virus, viral antigen, or route of infection.</p

Why Users (Don’t) Use Password Managers at a Large Educational Institution

We quantitatively investigated the current state of Password Manager (PM) usage and general password habits at a large, private university in the United States. Building on prior qualitative findings from SOUPS 2019, we survey n=277 faculty, staff, and students, finding that 77% of our participants already use PMs, but users of third-party PMs, as opposed to browser-based PMs, were significantly less likely to reuse their passwords across accounts. The largest factor encouraging PM adoption is perceived ease-of-use, indicating that communication and institutional campaigns should focus more on usability factors. Additionally, our work indicates the need for design improvements for browser-based PMs to encourage less password reuse as they are more widely adopted

SRRs Embedded with MEMS Cantilevers to Enable Electrostatic Tuning of the Resonant Frequency

A microelectromechanical systems (MEMS) cantilever array was monolithically fabricated in the gap region of a split ring resonator (SRR) to enable electrostatic tuning of the resonant frequency. The design consisted of two concentric SRRs each with a set of cantilevers extending across the split region. The cantilever array consisted of five beams that varied in length from 300 to 400 μm, with each beam adding about 2 pF to the capacitance as it actuated. The entire structure was fabricated monolithically to reduce its size and minimize losses from externally wire bonded components. The beams actuate one at a time, longest to shortest with an applied voltage ranging from 30–60 V. The MEMS embedded SRRs displayed dual resonant frequencies at 7.3 and 14.2 GHz or 8.4 and 13.5 GHz depending on the design details. As the beams on the inner SRR actuated the 14.2 GHz resonance displayed tuning, while the cantilevers on the outer SRR tuned the 8.4 GHz resonance. The 14.2 GHz resonant frequency shifts 1.6 GHz to 12.6 GHz as all the cantilevers pulled-in. Only the first two beams on the outer cantilever array pulled-in, tuning the resonant frequency 0.4 GHz from 8.4 to 8.0 GHz

Experimental infection of hamsters with avian paramyxovirus serotypes 1 to 9

Avian paramyxoviruses (APMVs) are frequently isolated from domestic and wild birds throughout the world and are separated into nine serotypes (APMV-1 to -9). Only in the case of APMV-1, the infection of non-avian species has been investigated. The APMVs presently are being considered as human vaccine vectors. In this study, we evaluated the replication and pathogenicity of all nine APMV serotypes in hamsters. The hamsters were inoculated intranasally with each virus and monitored for clinical disease, pathology, histopathology, virus replication, and seroconversion. On the basis of one or more of these criteria, each of the APMV serotypes was found to replicate in hamsters. The APMVs produced mild or inapparent clinical signs in hamsters except for APMV-9, which produced moderate disease. Gross lesions were observed over the pulmonary surface of hamsters infected with APMV-2 & -3, which showed petechial and ecchymotic hemorrhages, respectively. Replication of all of the APMVs except APMV-5 was confirmed in the nasal turbinates and lungs, indicating a tropism for the respiratory tract. Histologically, the infection resulted in lung lesions consistent with bronchointerstitial pneumonia of varying severity and nasal turbinates with blunting or loss of cilia of the epithelium lining the nasal septa. The majority of APMV-infected hamsters exhibited transient histological lesions that self resolved by 14 days post infection (dpi). All of the hamsters infected with the APMVs produced serotype-specific HI or neutralizing antibodies, confirming virus replication. Taken together, these results demonstrate that all nine known APMV serotypes are capable of replicating in hamsters with minimal disease and pathology

Evaluation of Pneumonia Virus of Mice as a Possible Human Pathogen

Pneumonia virus of mice (PVM), a relative of human respiratory syncytial virus (RSV), causes respiratory disease in mice. There is serologic evidence suggesting widespread exposure of humans to PVM. To investigate replication in primates, African green monkeys (AGM) and rhesus macaques (n=4) were inoculated with PVM by the respiratory route. Virus was shed intermittently at low levels by a subset of animals, suggesting poor permissiveness. PVM efficiently replicated in cultured human cells and inhibited the type I interferon (IFN) response in these cells. This suggests that poor replication in nonhuman primates was not due to a general nonpermissiveness of primate cells or poor control of the IFN response. Seroprevalence in humans was examined by screening sera from 30 adults and 17 young children for PVM-neutralizing activity. Sera from a single child (6%) and 40% of adults had low neutralizing activity against PVM, which could be consistent with increasing incidence of exposure following early childhood. There was no cross-reaction of human or AGM sera between RSV and PVM and no cross-protection in the mouse model. In native Western blots, human sera reacted with RSV but not PVM proteins under conditions in which AGM immune sera reacted strongly. Serum reactivity was further evaluated by flow cytometry using unfixed Vero cells infected with PVM or RSV expressing green fluorescent protein (GFP) as a measure of viral gene expression. The reactivity of human sera against RSV-infected cells correlated with GFP expression, whereas reactivity against PVM-infected cells was low and uncorrelated with GFP expression. Thus, PVM specificity was not evident. Our results indicate that the PVM-neutralizing activity of human sera is not due to RSV- or PVM-specific antibodies but may be due to low-affinity, polyreactive natural antibodies of the IgG subclass. The absence of PVM-specific antibodies and restriction in nonhuman primates makes PVM unlikely to be a human pathogen

Respiratory Syncytial Virus Interferon Antagonist NS1 Protein Suppresses and Skews the Human T Lymphocyte Response

We recently demonstrated that the respiratory syncytial virus (RSV) NS1 protein, an antagonist of host type I interferon (IFN-I) production and signaling, has a suppressive effect on the maturation of human dendritic cells (DC) that was only partly dependent on released IFN-I. Here we investigated whether NS1 affects the ability of DC to activate CD8+ and CD4+ T cells. Human DC were infected with RSV deletion mutants lacking the NS1 and/or NS2 genes and assayed for the ability to activate autologous T cells in vitro, which were analyzed by multi-color flow cytometry. Deletion of the NS1, but not NS2, protein resulted in three major effects: (i) an increased activation and proliferation of CD8+ T cells that express CD103, a tissue homing integrin that directs CD8+ T cells to mucosal epithelial cells of the respiratory tract and triggers cytolytic activity; (ii) an increased activation and proliferation of Th17 cells, which have recently been shown to have anti-viral effects and also indirectly attract neutrophils; and (iii) decreased activation of IL-4-producing CD4+ T cells - which are associated with enhanced RSV disease - and reduced proliferation of total CD4+ T cells. Except for total CD4+ T cell proliferation, none of the T cell effects appeared to be due to increased IFN-I signaling. In the infected DC, deletion of the NS1 and NS2 genes strongly up-regulated the expression of cytokines and other molecules involved in DC maturation. This was partly IFN-I-independent, and thus might account for the T cell effects. Taken together, these data demonstrate that the NS1 protein suppresses proliferation and activation of two of the protective cell populations (CD103+ CD8+ T cells and Th17 cells), and promotes proliferation and activation of Th2 cells that can enhance RSV disease