Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2

Mutations drive viral evolution and genome variability that causes viruses to escape host immunity and to develop drug resistance. SARS-CoV-2 has considerably higher mutation rate. SARS-CoV-2 possesses a RNA dependent RNA polymerase (RdRp) which helps to replicate its genome. The mutation P323L in RdRp is associated with the loss of a particular epitope (321-327) from this protein. We consider the effects of mutations in some of the epitope region including the naturally occurring mutation P323L on the structure of the epitope and their interface with paratope using all-atom molecular dynamics (MD) simulation studies. We observe that the mutations cause conformational changes in the epitope region by opening up the region associated with increase in the radius of gyration and intramolecular hydrogen bonds, making the region less accessible. Moreover, we study the conformational stability of the epitope region and epitope:paratope interface under the mutation from the fluctuations in the dihedral angles. We observe that the mutation renders the epitope and the epitope:paratope interface unstable compared to the corresponding wild type ones. Thus, the mutations may help in escaping antibody mediated immunity of the hostCommunicated by Ramaswamy H. Sarma.

Fragmentation dynamics of doubly charged camphor molecule following C 1s Auger decay

The fragmentation dynamics of the gas-phase, doubly charged camphor molecule, formed by Auger decay following carbon 1s ionisation, using soft X-ray synchrotron radiation, is presented in this work. The technique of velocity map imaging combined with a photoelectron-photoion-photoion coincidence (VMI-PEPIPICO) is used for both electron energy and ion momentum (in-sequence) measurements. The experimental study is complemented by molecular dynamics simulation, performed with an NVT (moles, volume, and temperature) ensemble. Velocity Verlet algorithms were used for time integration at various internal energies. These simulations validate observed dissociation pathways. From these, we successfully deduce that the internal energy of the doubly charged molecular ion has a significant contribution to the fragmentation mechanism. Notably, a prominent signature of the internal energy was observed in the experimentally determined energies of the neutral fragment in these deferred charge separation pathways, entailing a more detailed theoretical study to uncover the exact dissociation dynamics.

Coincident angle-resolved state-selective photoelectron spectroscopy of acetylene molecules: a candidate system for time-resolved dynamics

The acetylene-vinylidene system serves as a benchmark for investigations of ultrafast dynamical processes where the coupling of the electronic and nuclear degrees of freedom provides a fertile playground to explore the femto- and sub-femto-second physics with coherent extreme-ultraviolet (EUV) photon sources both on the table-top as well as free-electron lasers. We focus on detailed investigations of this molecular system in the photon energy range 19-40 eV where EUV pulses can probe the dynamics effectively. We employ photoelectron-photoion coincidence (PEPICO) spectroscopy to uncover hitherto unrevealed aspects of this system. In this work, the role of excited states of the C2H2+ cation, the primary photoion, is specifically addressed. From photoelectron energy spectra and angular distributions, the nature of the dissociation and isomerization channels is discerned. Exploiting the 4π-collection geometry of the velocity map imaging spectrometer, we not only probe pathways where the efficiency of photoionization is inherently high but also perform PEPICO spectroscopy on relatively weak channels.

Scanning of a Double-Sided Germanium Strip Detector

This work presents the results from the characterization of a Position-Sensitive Planar Germanium (PSPGe) detector. The PSPGe detector is a double-sided orthogonal strip detector consisting of 10x10 electrical segmentation along the horizontal and vertical directions. The characterization was performed using the coincidence setup between the PSPGe detector and the well-characterized scanning system employing the positron annihilation correlation principle. The scanning system consists of a Position Sensitive Detector (PSD) and 22Na positron source. The main objective of this study is to deploy PSPGe detector for future decay experiments at the Facility for Antiproton and Ion Research (FAIR), Germany. The measurements have been performed to find the depth of gamma-ray interaction in the planar segmented detector. The 2-Dimensional image obtained from the PSD has been used to find the depth of gamma-ray interaction in the planar strip detector using pulse shape analysis. In addition, the sensitivity of PSPGe detector has been investigated by calculating the rise-time from pulse shapes for the front and back strips of the detector.

Antifeedant Activity of Pyrazolin-5-One Derivatives

A series of substituted 4-{1-aza-2-[(aryl) amino)]}-3-methyl-2-pyrazolin-5-ones has been synthesized and evaluated for their biological activity. The title compounds (4a-l) were prepared by the diazotization of substituted anilines (1a-l) to form substituted phenyl hydrazine derivatives (2a-l) which synthesized substituted 4-{1-aza-2-[(aryl) amino)]}-3-methyl-2-pyrazolin-5-ones (4a-l) by Michael addition reaction, which is a nucleophilic addition of enolate anion to the carbon-carbon double bond of a α, β–unsaturated carboxylic acid derivatives. Twelve different pyrazolinone derivatives (4a to 4l) were synthesized. Structural assignments of these compounds have been made by elemental analysis, FTIR, 1HNMR and Mass spectral data and the purity of the compounds was determined by TLC. The antifeedant activity of the newly isolated heterocyclic compounds was evaluated against agriculture pest Achoea janata. Compound 4d found to be very effective as antifeedant while rest of the compounds showed a moderate to good degree of antifeedant activity.

Nonreciprocal Transport of Exciton Polaritons in a Non-Hermitian Chain

We consider exciton polaritons in a zigzag chain of coupled elliptical micropillars subjected to incoherent excitation. The driven-dissipative nature of the system along with the naturally present polarization splitting inside the pillars gives rise to nonreciprocal dynamics, which eventually leads to the non-Hermitian skin effect, where all the modes of the system collapse to one edge. As a result, the polaritons propagate only in one direction along the chain, independent of the excitation position, and the propagation in the opposite direction is suppressed. The system shows robustness against disorder and, using the bistable nature of polaritons to encode information, we show one-way information transfer. This paves the way for compact and robust feedback-free one-dimensional polariton transmission channels without the need for external magnetic field, which are compatible with proposals for polaritonic circuits.

Monitoring liver transplant rates in persons diagnosed with hepatitis C: a data linkage study, England 2008 to 2017

Introduction

Liver transplantation is an important measure of burden from hepatitis C virus (HCV)-associated liver disease.

Aims

To describe transplant rates and survival in individuals with HCV infection from 2008 to 2017 in England through data linkage.

Methods

This is a retrospective observational cohort study. Laboratory reports of HCV infection were linked to the Liver Transplant Registry for individuals aged 15 years and over, first diagnosed between 1998 and 2017. We estimated age-sex standardised incidence rates and used Poisson regression to investigate predictors of liver transplantation and test for a change in incidence after introduction of direct-acting antivirals (DAAs) in 2014. Kaplan-Meier survival analysis was used to calculate post-transplant survival rates.

Results

Of 124,238 individuals diagnosed with HCV infection, 1,480 were registered and 1,217 received a liver transplant. Of individuals registered, 1,395 had post-HCV cirrhosis and 636 had hepatocellular carcinoma (618 also had post-HCV cirrhosis). Median time from HCV diagnosis to transplant was 3.4 years (interquartile range: 1.3–6.8 years). Liver transplant rates were lower 2014–17 compared with 2011–13 (incidence rate ratio: 0.64; 95% confidence interval: 0.55–0.76). Survival rates were 93.4%, 79.9% and 67.9% at 1, 5 and 10 years, respectively. Data linkage showed minimal under-reporting of HCV in the transplant registry.

Conclusion

In the post-DAA era, liver transplant rates have fallen in individuals with HCV infection, showing early impact of HCV treatment scale-up; but the short time from HCV diagnosis to liver transplant suggests late diagnosis is a problem.

Penning spectroscopy and structure of acetylene oligomers in He nanodroplets

Embedded atoms or molecules in a photoexcited He nanodroplet are well-known to be ionized through inter-atomic relaxation in a Penning process. In this work, we investigate the Penning ionization of acetylene oligomers occurring from the photoexcitation bands of He nanodroplets. In close analogy to conventional Penning electron spectroscopy by thermal atomic collisions, the n = 2 photoexcitation band plays the role of the metastable atomic 1s2s 3,1S He*. This facilitates electron spectroscopy of acetylene aggregates in the sub-Kelvin He environment, providing the following insight into their structure: the molecules in the dopant cluster are loosely bound van der Waals complexes rather than forming covalent compounds. In addition, this work reveals a Penning process stemming from the n = 4 band where charge-transfer from autoionized He in the droplets is known to be the dominant relaxation channel. This allows for excited states of the remnant dopant oligomer Penning-ions to be studied. Hence, we demonstrate Penning ionization electron spectroscopy of doped droplets as an effective technique for investigating dopant oligomers which are easily formed by attachment to the host cluster.

International Nosocomial Infection Control Consortium (INICC) report, data summary of 45 countries for 2012-2017: Device-associated module

BACKGROUND

We report the results of International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2012 to December 2017 in 523 intensive care units (ICUs) in 45 countries from Latin America, Europe, Eastern Mediterranean, Southeast Asia, and Western Pacific.

METHODS

During the 6-year study period, prospective data from 532,483 ICU patients hospitalized in 242 hospitals, for an aggregate of 2,197,304 patient days, were collected through the INICC Surveillance Online System (ISOS). The Centers for Disease Control and Prevention-National Healthcare Safety Network (CDC-NHSN) definitions for device-associated health care-associated infection (DA-HAI) were applied.

RESULTS

Although device use in INICC ICUs was similar to that reported from CDC-NHSN ICUs, DA-HAI rates were higher in the INICC ICUs: in the medical-surgical ICUs, the pooled central line-associated bloodstream infection rate was higher (5.05 vs 0.8 per 1,000 central line-days); the ventilator-associated pneumonia rate was also higher (14.1 vs 0.9 per 1,000 ventilator-days,), as well as the rate of catheter-associated urinary tract infection (5.1 vs 1.7 per 1,000 catheter-days). From blood cultures samples, frequencies of resistance, such as of Pseudomonas aeruginosa to piperacillin-tazobactam (33.0% vs 18.3%), were also higher.

CONCLUSIONS

Despite a significant trend toward the reduction in INICC ICUs, DA-HAI rates are still much higher compared with CDC-NHSN's ICUs representing the developed world. It is INICC's main goal to provide basic and cost-effective resources, through the INICC Surveillance Online System to tackle the burden of DA-HAIs effectively.

Coupling between Exciton-Polariton Corner Modes through Edge States

Recently realized higher order topological insulators have taken a surge of interest among the theoretical and experimental condensed matter community. The two-dimensional second order topological insulators give rise to zero-dimensional localized corner modes that reside within the band gap of the system along with edge modes that inhabit a band edge next to bulk modes. Thanks to the topological nature, information can be trapped at the corners of these systems, which will be unhampered even in the presence of disorder. Being localized at the corners, the exchange of information among the corner states is an issue. Here we show that the nonlinearity in an exciton polariton system can allow the coupling between the different corners through the edge states based on optical parametric scattering, realizing a system of multiple connectible topological modes.

Electron transfer mediated decay of alkali dimers attached to He nanodroplets

Double ionization of alkali dimers attached to He nanodroplets by electron transfer mediated decay (ETMD).

A 15 Year's Experience with Minimally Invasive Mitral Valve Replacement in Bangladesh

This study was aimed to compare the long-term outcomes and survival rate among mitral valve replacement using thoracotomy and standard median sternotomy in a single surgeon's practice. Total 250 patients were evaluated; Group I (n=65) patients had anterolateral thoracotomy and Group II (n=185) had standard median sternotomy for valve replacement. Mean age was 25.1±5 years in Group I and 41.8±10.5 years in Group II. Female was predominant in Group I. Total operative time and bypass time was statistically significant in Group I (235.5±25.8 minutes; 84.2±12.75 minutes) in contrast to Group II (203.8±15.5 minutes; 71.5±10.5 minutes). Incision scar was not visible in females in Group I but full incision scar was visible in Group II. Post-operative ICU stay duration was significant high in Group II. Though, wound infection incidence was 0% in Group I; however, 9.73% patient had wound infection in Group II. Only 1.62% patient developed unstable sternum in Group II. Most of the patients from both study group were in regular follow up and 1-year mortality rate was 4.62% and 5.94% in Group I and Group II respectively. Mitral valve replacement through a right anterolateral thoracotomy is easy and safe to perform; while getting maximum benefits for the patients. Besides satisfactory cosmetic outcome especially in female, this approach provides better exposure to mitral apparatus even in patients with small left atrium, cost effectiveness, less duration of hospital stays and absence of the risk for unstable sternum.