High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constantly evolving. Prior studies focused on high-case-density locations, such as the northern and western metropolitan areas of the United States. This study demonstrates continued SARS-CoV-2 evolution in a suburban southern region of the United States by high-density amplicon sequencing of symptomatic cases. 57% of strains carry the spike D614G variant, which is associated with higher genome copy numbers, and its prevalence expands with time. Four strains carry a deletion in a predicted stem loop of the 3′ UTR. The data are consistent with community spread within local populations and the larger continental United States. The data instill confidence in current testing sensitivity and validate “testing by sequencing” as an option to uncover cases, particularly nonstandard coronavirus disease 2019 (COVID-19) clinical presentations. This study contributes to the understanding of COVID-19 through an extensive set of genomes from a non-urban setting and informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the United States

The Earth: Plasma Sources, Losses, and Transport Processes

This paper reviews the state of knowledge concerning the source of magnetospheric plasma at Earth. Source of plasma, its acceleration and transport throughout the system, its consequences on system dynamics, and its loss are all discussed. Both observational and modeling advances since the last time this subject was covered in detail (Hultqvist et al., Magnetospheric Plasma Sources and Losses, 1999) are addressed

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

A case study of plasma structure in the dusk sector associated with enhanced magnetospheric convection

In a case study from June 8–9, 1982, data from ground whistler stations Siple and Halley, Antarctica, located at L ∼4.3 and spaced by ∼2 hours in MLT, and from satellites DE 1 and GEOS 2, have provided confirming evidence that the bulge region of the magnetosphere can exhibit an abrupt westward “edge,” as reported earlier from whistlers. The present data and previous MHD modeling work suggest that this distinctive feature develops during periods of steady or declining substorm activity, when dense plasma previously carried sunward under the influence of enhanced convection activity begins to rotate with the Earth at angular velocities that decrease with increasing L value and becomes spirallike in form. For the first time, whistler data have been used to identify a narrow dense plasma feature, separated from the main plasmasphere and extending sunward into the late afternoon sector at L values near the outer observed limits of the main plasmasphere bulge. The westward edge of the main bulge, found by both whistler stations to be at ∼1800 MLT, appeared to be quasi-stationary in Sun-Earth coordinates during the prevailing conditions of gradually declining geomagnetic agitation. It is possible that outlying dense plasma features such as the one observed develop as part of the process leading to the occurrence of the more readily detectable abrupt westward edge of the bulge. It was not possible in this case to determine the extent to which the outlying feature was smoothly attached to or isolated from the main bulge region

Plasmasphere dynamics in the duskside bulge region: a new look at an old topic

Data acquired during several multiday periods in 1982 at ground stations Siple, Halley, and Kerguelen and on satellites DE 1, ISEE 1, and GEOS 2 have been used to investigate thermal plasma structure and dynamics in the duskside plasmasphere bulge region of the Earth. The distribution of thermal plasma in the dusk bulge sector is difficult to describe realistically, in part because of the time integral manner in which the thermal plasma distribution depends upon the effects of bulk cross-B flow and interchange plasma flows along B. While relatively simple MHD models can be useful for qualitatively predicting certain effects of enhanced convection on a quiet plasmasphere, such as an initial sunward entrainment of the outer regions, they are of limited value in predicting the duskside thermal plasma structures that are observed. Furthermore, use of such models can be misleading if one fails to realize that they do not address the question of the formation of the steep plasmapause profile or provide for a possible role of instabilities or other irreversible processes in plasmapause formation. Our specific findings, which are based both upon the present case studies and upon earlier work, include the following: (1) during active periods the plasmasphere appears to become divided into two entities, a main plasmasphere and a duskside bulge region. The latter consists of outlying or outward extending plasmas that are the products of erosion of the main plasmasphere; (2) in the aftermath of an increase in convection activity, the main plasmasphere tends (from a statistical point of view) to become roughly circular in equatorial cross section, with only a slight bulge at dusk; (3) the abrupt westward edge of the duskside bulge observed from whistlers represents a state in the evolution of sunward extending streamers; (4) in the aftermath of a weak magnetic storm, 10 to 30% of the plasma ''removed'' from the outer plasmasphere appears to remain in the afternoon-dusk sector beyond the main plasmasphere. This suggests that plasma flow from the afternoon-dusk magnetosphere into the boundary layers is to some extent impeded, possibly through a mechanism that partially decouples the high altitude and ionospheric-level flow regimes; (5) outlying dense plasma structures may circulate in the outer duskside magnetosphere for many days following an increase in convection, unless there is extremely deep quieting; (6) a day-night plasmatrough boundary may be identified in equatorial satellite data; (7) factor-of-2-to-10 density irregularities appear near the plasmapause in the postdusk sector in the aftermath of weak magnetic storms; (8) during the refilling of the plasmatrough from the ionosphere at L = 4.6, predominantly bidirectional field aligned and equatorially trapped light ion pitch angle distributions give way to a predominantly isotropic distribution (as seen by DE 1) when the plasma density reaches a level a factor of about 3 below the saturated plasmasphere level; (9) some outlying dense plasma structures are effectively detached from the main plasmasphere, while others appear to be connected to that body

Recurrent Neural Networks as Local Models for Time Series Prediction

International audience"Local models" (Walter, J., et al. International Joint Conference on Neural Networks, vol. 1. (1990) 589-594), consists on dividing the data into homogeneous clusters by Vector Quantization (VQ (Gray, R. M., and Neuhoff, D.L. IEEE Trans. Inf. Theory 44(6) (1998) 2325-2383)) to simplify the prediction task on each cluster and mostly inspired from the Self-Organizing Maps algorithm (SOM (Kohonen, T. Self-Organization and associative memory, 3rd edn. (1989))). Since recurrent neural networks have demonstrated in many times a better results and specially for chaotic time series (Boné, R. Recurrent Neural Networks for Time Series Forecasting. (2000)), we propose in this paper a method to use the Recurrent Neural Networks in the local approach