Search

Summary: SARS-CoV-2 infection and vaccination elicit potent immune responses. Our study presents a comprehensive multimodal single-cell analysis of blood from COVID-19 patients and healthy volunteers receiving the SARS-CoV-2 vaccine and booster. We profiled immune responses via transcriptional analysis and lymphocyte repertoire reconstruction. COVID-19 patients displayed an enhanced interferon signature and cytotoxic gene upregulation, absent in vaccine recipients. B and T cell repertoire analysis revealed clonal expansion among effector cells in COVID-19 patients and memory cells in vaccine recipients. Furthermore, while clonal αβ T cell responses were observed in both COVID-19 patients and vaccine recipients, expansion of clonal γδ T cells was found only in infected individuals. Our dataset enables side-by-side comparison of immune responses to infection versus vaccination, including clonal B and T cell responses. Our comparative analysis shows that vaccination induces a robust, durable clonal B and T cell responses, without the severe inflammation associated with infection.

The bacterial microbiota promotes the life cycle of the intestine-dwelling whipworm Trichuris by mediating hatching of parasite eggs ingested by the mammalian host. Despite the enormous disease burden associated with Trichuris colonization, the mechanisms underlying this transkingdom interaction have been obscure. Here, we used a multiscale microscopy approach to define the structural events associated with bacteria-mediated hatching of eggs for the murine model parasite Trichuris muris. Through the combination of scanning electron microscopy (SEM) and serial block face SEM (SBFSEM), we visualized the outer surface morphology of the shell and generated 3D structures of the egg and larva during the hatching process. These images revealed that exposure to hatching-inducing bacteria catalyzed asymmetric degradation of the polar plugs prior to exit by the larva. Unrelated bacteria induced similar loss of electron density and dissolution of the structural integrity of the plugs. Egg hatching was most efficient when high densities of bacteria were bound to the poles. Consistent with the ability of taxonomically distant bacteria to induce hatching, additional results suggest chitinase released from larva within the eggs degrade the plugs from the inside instead of enzymes produced by bacteria in the external environment. These findings define at ultrastructure resolution the evolutionary adaptation of a parasite for the microbe-rich environment of the mammalian gut.

Here, the authors demonstrate a multi-momentum transformation metasurface. The orbital angular momentum meta-transformer reconstructs different vortex beams into on-axis distinct patterns, and the linear momentum meta-transformer converts red, green and blue beams to vivid color images.

Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Furthermore, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with inflammatory bowel disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn’s disease (CD) patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.

Abstract Background Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research. Results We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics. Conclusions WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.

Abstract We present here a compact metasurface lens element that enables simultaneous and spatially separated imaging of light of opposite circular polarization states. The design overcomes a limitation of previous chiral lenses reliant on the traditional geometric phase approach by allowing for independent focusing of both circular polarizations without a 50% efficiency trade-off. We demonstrate circular polarization-dependent imaging at visible wavelengths with polarization contrast greater than 20dB and efficiencies as high as 70%.

Conventional compact spectrometers have a fixed spectral resolution and cannot resolve the polarization properties of light without additional optical elements, while their larger counterparts are bulky and costly. Here, we demonstrate multiple off-axis meta-lenses in the visible integrated on a single planar substrate. They possess both focusing and strongly dispersive properties and are designed to provide different spectral resolutions as well as working wavelength ranges on the same chip. We realize a compact spectrometer using only these meta-lenses and a CMOS camera and achieve detector-limited spectral resolutions as small as 0.3 nm and a total working wavelength range exceeding 170 nm for a beam propagation length of only a few cm. In addition, this spectrometer has the capability to resolve different helicities of light in a single measurement. This chip-camera setup represents the most compact configuration so far achieved for a spectrometer with similar performance and functionality, and its compatibility with large-scale fabrication processes makes it broadly applicable.

The quiet-time coherent backscatter from the F-region observed by the Tasman International Geospace Environment Radar (TIGER) Bruny Island HF radar is analysed statistically in order to determine typical trends and controlling factors in the ionospheric echo occurrence. A comparison of the F-region peak density values from the IRI-2007 model and ionosonde measurements in the vicinity of the radar's footprint shows a very good agreement, particularly at subauroral and auroral latitudes, and model densities within the radar's footprint are used in the following analyses. The occurrence of F-region backscatter is shown to exhibit distinct diurnal, seasonal and solar cycle variations and these are compared with model trends in the F-region peak electron density and Pedersen conductance of the underlying ionosphere. The solar cycle effects in occurrence are demonstrated to be strong and more complex than a simple proportionality on a year-to-year basis. The diurnal and seasonal effects are strongly coupled to each other, with diurnal trends exhibiting a systematic gradual variation from month to month that can be explained when both electron density and conductance trends are considered. During the night, the echo occurrence is suggested to be controlled directly by the density conditions, with a direct proportionality observed between the occurrence and peak electron density. During the day, the echo occurrence appears to be controlled by both conductance and propagation conditions. It is shown that the range of echo occurrence values is smaller for larger conductances and that the electron density determines what value the echo occurrence takes in that range. These results suggest that the irregularity production rates are significantly reduced by the highly conducting E layer during the day while F-region density effects dominate during the night.

At 08:35 UT on 21 November 2004, the onset of an interval of substorm activity was captured in the southern hemisphere by the Far UltraViolet (FUV) instrument on board the IMAGE spacecraft. This was accompanied by the onset of Pi2 activity and subsequent magnetic bays, evident in ground magnetic data from both hemispheres. Further intensifications were then observed in both the auroral and ground magnetic data over the following ~3 h. During this interval the fields-of-view of the two southern hemisphere Tasman International Geospace Enviroment Radars (TIGER) moved through the evening sector towards midnight. Whilst initially low, the amount of backscatter from TIGER increased considerably during the early stages of the expansion phase such that by ~09:20 UT an enhanced dusk flow cell was clearly evident. During the expansion phase the equatorward portion of this flow cell developed into a narrow high-speed flow channel, indicative of the auroral and sub-auroral flows identified in previous studies (e.g. Freeman et al., 1992; Parkinson et al., 2003). At the same time, higher latitude transient flow features were observed and as the interval progressed the flow reversal region and Harang discontinuity became very well defined. Overall, this study has enabled the spatial and temporal development of many different elements of the substorm process to be resolved and placed within a simple conceptual framework of magnetospheric convection. Specifically, the detailed observations of ionospheric flows have illustrated the complex interplay between substorm electric fields and associated auroral dynamics. They have helped define the distinct nature of different substorm current systems such as the traditional substorm current wedge and the more equatorward currents associated with polarisation electric fields. Additionally, they have revealed a radar signature of nightside reconnection which provides the promise of quantifying nightside reconnection in a way which has already proved extremely successful in studies of the dayside magnetosphere.

Earthward injections of energetic ions and electrons mark the onset of magnetospheric substorms. In the inner magnetosphere (L4), the energetic ions drift westward and the electrons eastward, thereby enhancing the equatorial ring current. Wave-particle interactions can accelerate these particles to radiation belt energies. The ions are injected slightly closer to Earth in the pre-midnight sector, leading to the formation of a radial polarisation field in the inner magnetosphere. This maps to a poleward electric field just equatorward of the auroral oval in the ionosphere. The poleward electric field is subsequently amplified by ionospheric feedback, thereby producing auroral westward flow channels (AWFCs). In terms of electric field strength, AWFCs are the strongest manifestation of substorms in the ionosphere. Because geomagnetic flux tubes are essentially equi-potentials, similar AWFC signatures should be observed simultaneously in the Northern and Southern Hemispheres. Here we present magnetically conjugate SuperDARN radar observations of AWFC activity observed in the pre-midnight sector during two substorm intervals including multiple onsets during the evening of 30 November 2002. The Northern Hemisphere observations were made with the Japanese radar located at King Salmon, Alaska (57, and the Southern Hemisphere observations with the Tasman International Geospace Environment Radar (TIGER) located at Bruny Island, Tasmania (55. LANL geosynchronous satellite observations of energetic ion and electron fluxes monitored the effects of substorms in the inner magnetosphere (L6). The radar-observed AWFC activity was coincident with activity observed at geosynchronous orbit, as well as westward current surges in the ionosphere observed using ground-based magnetometers. The location of AWFCs with respect to the auroral oval was inferred from FUV auroral images recorded on board the IMAGE spacecraft. DMSP SSIES ion drift measurements confirmed the presence of AWFCs equatorward of the auroral oval. Systematic asymmetries in the interhemispheric signatures of the AWFCs probably arose because the magnetic flux tubes were distorted at L shells passing close to the substorm dipolarisation region. Transient asymmetries were attributed to the development of nearby field-aligned potential drops and currents.

Super Dual Auroral Radar Network (DARN) radars often detect a distinct transition in line-of-sight Doppler velocity spread, or spectral width, from –1 at lower latitude to >200ms–1 at higher latitude. They also detect a similar boundary, namely the range at which ionospheric scatter with large spectral width suddenly commences (i.e. without preceding scatter with low spectral width). The location and behaviour of the spectral width boundary (SWB) (and scatter boundary) and the open-closed magnetic field line boundary (OCB) are thought to be closely related. The location of the nightside OCB can be inferred from the poleward edge of the auroral oval determined using energy spectra of precipitating particles measured on board Defence Meteorology Satellite Program (DMSP) satellites. Observations made with the Halley SuperDARN radar (75.5° S, 26.6° W, geographic; –62.0°Λ) and the Tasman International Geospace Environment Radar (TIGER) (43.4° S, 147.2° E; –54.5°Λ) are used to compare the location of the SWB with the DMSP-inferred OCB during 08:00 to 22:00 UT on 1 April 2000. This study interval was chosen because it includes several moderate substorms, whilst the Halley radar provided almost continuous high-time resolution measurements of the dayside SWB location and shape, and TIGER provided the same in the nightside ionosphere. The behaviour of the day- and nightside SWB can be understood in terms of the expanding/contracting polar cap model of high-latitude convection change, and the behaviour of the nightside SWB can also be organised according to substorm phase. Previous comparisons with DMSP OCBs have proven that the radar SWB is often a reasonable proxy for the OCB from dusk to just past midnight (Chisham et al., 2004). However, the present case study actually suggests that the nightside SWB is often a better proxy for the poleward edge of Pedersen conductance enhanced by hot particle precipitation in the auroral zone. Simple modeling implies that the large spectral widths must be caused by ~10-km scale velocity fluctuations. Key words. Ionosphere (auroral ionosphere; ionospheremagnetosphere interactions) – Magnetospheric physics (storms and substorms)

The statistical occurrence of decametre-scale ionospheric irregularities, average line-of-sight (LOS) Doppler velocity, and Doppler spectral width in the sub-auroral, auroral, and polar cap ionosphere ( - 57°L to - 88°L) has been investigated using echoes recorded with the Tasman International Geospace Environment Radar (TIGER), a SuperDARN radar located on Bruny Island, Tasmania (147.2° E, 43.4° S geographic; - 54.6 °L). Results are shown for routine soundings made on the magnetic meridian beam 4 and the near zonal beam 15 during the sunspot maximum interval December 1999 to November 2000. Most echoes were observed in the nightside ionosphere, typically via 1.5-hop propagation near dusk and then via 0.5-hop propagation during pre-midnight to dawn. Peak occurrence rates on beam 4 were often > 60% near magnetic midnight and ~ - 70 °L. They increased and shifted equatorward and toward pre-midnight with increasing Kp (i.e. Bz southward). The occurrence rates remained very high for Kp > 4, de-spite enhanced D-region absorption due to particle precipitation. Average occurrence rates on beam 4 exhibited a relatively weak seasonal variation, consistent with known longitudinal variations in auroral zone magnetic activity (Basu, 1975). The average echo power was greatest between 23 and 07 MLT. Two populations of echoes were identified on both beams, those with low spectral width and a mode value of ~ 9 ms-1 (bin size of 2 ms-1) concentrated in the auroral and sub-auroral ionosphere (population A), and those with high spectral width and a mode value of ~ 70 ms-1 concentrated in the polar cap ionosphere (population B). The occurrence of population A echoes maximised post-midnight because of TIGER’s lower latitude, but the subset of the population A echoes observed near dusk had characteristics reminiscent of "dusk scatter" (Ruohoniemi et al., 1988). There was a dusk "bite out" of large spectral widths between ~ 15 and 21 MLT and poleward of - 67 °L, and a pre-dawn enhancement of large spectral widths between ~ 03 and 07 MLT, centred on ~ - 61 °L. The average LOS Doppler velocities revealed that frequent westward jets of plasma flow occurred equatorward of, but overlapping, the diffuse auroral oval in the pre-midnight sector.Key words. Ionosphere (auroral ionosphere; electric fields and currents, ionospheric irregularities)

A -190-nT negative bay in the geomagnetic X component measured at Macquarie Island ( -65° L) showed that an ionospheric substorm occurred during 09:58 to 11:10 UT on 27 February 2000. Signatures of an auroral westward flow channel (AWFC) were observed nearly simultaneously in the backscatter power, LOS Doppler velocity, and Doppler spectral width measured using the Tasman International Geospace Environment Radar (TIGER), a Southern Hemisphere HF SuperDARN radar. Many of the characteristics of the AWFC were similar to those occurring during a polarisation jet (PJ), or subauroral ion drift (SAID) event, and suggest that it may have been a pre-cursor to a fully developed, intense westward flow channel satisfying all of the criteria defining a PJ/SAID. A beam-swinging analysis showed that the westward drifts (poleward electric field) associated with the flow channel were very structured in time and space, but the smoothed velocities grew to ~ 800 ms-1 (47 mVm-1) during the 22-min substorm onset interval 09:56 to 10:18 UT. Maximum west-ward drifts of >1.3 km s-1 (>77 mVm-1) occurred during a ~ 5-min velocity spike, peaking at 10:40 UT during the expansion phase. The drifts decayed rapidly to ~ 300 ms-1 (18 mVm-1) during the 6-min recovery phase interval, 11:04 to 11:10 UT. Overall, the AWFC had a lifetime of 74 min, and was located near -65° L in the evening sector west of the Harang discontinuity. The large westward drifts were confined to a geographic zonal channel of longitudinal ex-tent >20° (>1.3 h magnetic local time), and latitudinal width ~2° L. Using a half-width of ~ 100 km in latitude, the peak electric potential was >7.7 kV. However, a transient velocity of >3.1 km s-1 with potential >18.4 kV was observed further poleward at the end of the recovery phase. Auroral oval boundaries determined using DMSP measurements suggest the main flow channel overlapped the equatorward boundary of the diffuse auroral oval. During the ~ 2-h interval following the flow channel, an ~ 3° L wide band of scatter was observed drifting slowly toward the west, with speeds gradually decaying to ~ 50 ms-1 (3 mVm -1). The scatter was observed extending past the Harang discontinuity, and had Doppler signatures characteristic of the main ionospheric trough, implicating the flow channel in the further depletion of F-region plasma. The character of this scatter was in contrast with the character of the scatter drifting toward the east at higher latitude.Key words. Ionosphere (auroral ionosphere; electric fields and currents; ionosphere-magnetospehere interactions) Magnetospheric physics (storms and substorms)

The geomagnetic conditions were moderately disturbed (Kp = 2) during magnetic midnight on 10 December 1999, when the Tasman International Geospace Environment Radar (TIGER), a Southern Hemisphere HF SuperDARN radar, observed a persistent, sharp latitudinal decrease (~ 90 km) in spectral width near - 69°L. The line-of-sight Doppler velocity also rapidly declined across this spectral width boundary (SWB). The region poleward of the SWB was characterized by high spectral widths (>200 m/s), and the start of bursty equatorward and eastward flows (>500 m/s), which rapidly expanded equatorward. The relationships between familiar ionospheric and magnetospheric regions were inferred by comparing TIGER data with spectrograms calculated from precipitating particles measured on board the Defence Meteorology Satellite Program (DMSP) F14 satellite. The high spectral width scatter is often observed, and on this evening it was associated with irregularities forming on the open (but soon to be reconnected) field lines threading the polar cap ionosphere to the southern tail lobe. The region equatorward of the SWB was characterized by very low spectral widths (L) and Hobart (- 54°L), and the ionograms recorded at the same stations, as well as at Bundoora (- 49°L), also helped to validate the interpretation.Key words. Ionosphere (auroral ionosphere; electric fields and currents; ionosphere-magnetosphere interactions)

How is positive emotion associated with our ability to empathize with others? Extant research provides support for two competing predictions about this question. An empathy amplification hypothesis suggests positive emotion would be associated with greater empathy, as it often enhances other prosocial processes. A contrasting empathy attenuation hypothesis suggests positive emotion would be associated with lower empathy, because positive emotion promotes self-focused or antisocial behaviors. The present investigation tested these competing perspectives by examining associations between dispositional positive emotion and both subjective (i.e., self-report) and objective (i.e., task performance) measures of empathy. Findings revealed that although trait positive emotion was associated with increased subjective beliefs about empathic tendencies, it was associated with both increases and decreases in task-based empathic performance depending on the target's emotional state. More specifically, trait positive emotion was linked to lower overall empathic accuracy toward a high-intensity negative target, but also a higher sensitivity to emotion upshifts (i.e., shifts in emotion from negative to positive) toward positive targets. This suggests that trait positive affect may be associated with decreased objective empathy in the context of mood incongruent (i.e., negative) emotional stimuli, but may increase some aspects of empathic performance in the context of mood congruent (i.e., positive) stimuli. Taken together, these findings suggest that trait positive emotion engenders a compelling subjective-objective gap regarding its association with empathy, in being related to a heightened perception of empathic tendencies, despite being linked to mixed abilities in regards to empathic performance. (Word count: 242).