Wave data assimilation using a hybrid approach in the Persian Gulf

The main goal of this study is to develop an efficient approach for the assimilation of the hindcasted wave parameters in the Persian Gulf. Hence, the third generation SWAN model was employed for wave modeling forced by the 6-h ECMWF wind data with a resolution of 0.5஠In situ wave measurements at two stations were utilized to evaluate the assimilation approaches. It was found that since the model errors are not the same for wave height and period, adaptation of model parameter does not result in simultaneous and comprehensive improvement of them. Therefore, an approach based on the error prediction and updating of output variables was employed to modify wave height and period. In this approach, artificial neural networks (ANNs) were used to estimate the deviations between the simulated and measured wave parameters. The results showed that updating of output variables leads to significant improvement in a wide range of the predicted wave characteristics. It was revealed that the best input parameters for error prediction networks are mean wind speed, mean wind direction, wind duration, and the wave parameters. In addition, combination of the ANN estimated error with numerically modeled wave parameters leads to further improvement in the predicted wave parameters in contrast to direct estimation of the parameters by ANN.Full Tex

A simple approximation for larval retention around reefs

Estimating larval retention at individual reefs by local scale three-dimensional flows is a significant problem for understanding, and predicting, larval dispersal. Determining larval dispersal commonly involves the use of computationally demanding and expensively calibrated/validated hydrodynamic models that resolve reef wake eddies. This study models variation in larval retention times for a range of reef shapes and circulation regimes, using a reef-scale three-dimensional hydrodynamic model. It also explores how well larval retention time can be estimated based on the "Island Wake Parameter", a measure of the degree of flow turbulence in the wake of reefs that is a simple function of flow speed, reef dimension, and vertical diffusion. The mean residence times found in the present study (0.48–5.64 days) indicate substantial potential for self-recruitment of species whose larvae are passive, or weak swimmers, for the first several days after release. Results also reveal strong and significant relationships between the Island Wake Parameter and mean residence time, explaining 81–92% of the variability in retention among reefs across a range of unidirectional flow speeds and tidal regimes. These findings suggest that good estimates of larval retention may be obtained from relatively coarse-scale characteristics of the flow, and basic features of reef geomorphology. Such approximations may be a valuable tool for modeling connectivity and meta-population dynamics over large spatial scales, where explicitly characterizing fine-scale flows around reef requires a prohibitive amount of computation and extensive model calibration

Effects of Hierarchical Roost Removal on Northern Long-Eared Bat (Myotis septentrionalis) Maternity Colonies

Forest roosting bats use a variety of ephemeral roosts such as snags and declining live trees. Although conservation of summer maternity habitat is considered critical for forest-roosting bats, bat response to roost loss still is poorly understood. To address this, we monitored 3 northern long-eared bat (Myotis septentrionalis) maternity colonies on Fort Knox Military Reservation, Kentucky, USA, before and after targeted roost removal during the dormant season when bats were hibernating in caves. We used 2 treatments: removal of a single highly used (primary) roost and removal of 24% of less used (secondary) roosts, and an un-manipulated control. Neither treatment altered the number of roosts used by individual bats, but secondary roost removal doubled the distances moved between sequentially used roosts. However, overall space use by and location of colonies was similar pre- and post-treatment. Patterns of roost use before and after removal treatments also were similar but bats maintained closer social connections after our treatments. Roost height, diameter at breast height, percent canopy openness, and roost species composition were similar pre- and post-treatment. We detected differences in the distribution of roosts among decay stages and crown classes pre- and post-roost removal, but this may have been a result of temperature differences between treatment years. Our results suggest that loss of a primary roost or ≤ 20% of secondary roosts in the dormant season may not cause northern long-eared bats to abandon roosting areas or substantially alter some roosting behaviors in the following active season when tree-roosts are used. Critically, tolerance limits to roost loss may be dependent upon local forest conditions, and continued research on this topic will be necessary for conservation of the northern long-eared bat across its range

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

Transmission of SARS-CoV-2 is uncontrolled in many parts of the world; control is compounded in some areas by the higher transmission potential of the B.1.1.7 variant1, which has now been reported in 94 countries. It is unclear whether the response of the virus to vaccines against SARS-CoV-2 on the basis of the prototypic strain will be affected by the mutations found in B.1.1.7. Here we assess the immune responses of individuals after vaccination with the mRNA-based vaccine BNT162b22. We measured neutralizing antibody responses after the first and second immunizations using pseudoviruses that expressed the wild-type spike protein or a mutated spike protein that contained the eight amino acid changes found in the B.1.1.7 variant. The sera from individuals who received the vaccine exhibited a broad range of neutralizing titres against the wild-type pseudoviruses that were modestly reduced against the B.1.1.7 variant. This reduction was also evident in sera from some patients who had recovered from COVID-19. Decreased neutralization of the B.1.1.7 variant was also observed for monoclonal antibodies that target the N-terminal domain (9 out of 10) and the receptor-binding motif (5 out of 31), but not for monoclonal antibodies that recognize the receptor-binding domain that bind outside the receptor-binding motif. Introduction of the mutation that encodes the E484K substitution in the B.1.1.7 background to reflect a newly emerged variant of concern (VOC 202102/02) led to a more-substantial loss of neutralizing activity by vaccine-elicited antibodies and monoclonal antibodies (19 out of 31) compared with the loss of neutralizing activity conferred by the mutations in B.1.1.7 alone. The emergence of the E484K substitution in a B.1.1.7 background represents a threat to the efficacy of the BNT162b2 vaccine

SARS-CoV-2 evolution during treatment of chronic infection

The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals