Intercomparability of X_(CO_2) and X_(CH_4) from the United States TCCON sites

The Total Carbon Column Observing Network (TCCON) has become the standard for long-term column-averaged measurements of CO_2 and CH_4. Here, we use a pair of portable spectrometers to test for intra-network bias among the four currently operating TCCON sites in the United States (US). A previous analytical error analysis has suggested that the maximum 2σ site-to-site relative (absolute) bias of TCCON should be less than 0.2% (0.8ppm) in X_(CO_2) and 0.4% (7ppb) in X_(CH_4). We find here experimentally that the 95% confidence intervals for maximum pairwise site-to-site bias among the four US TCCON sites are 0.05–0.14% for X_(CO_2) and 0.08–0.24% for X_(CH_4). This is close to the limit of the bias we can detect using this methodology

Quality controls, bias, and seasonality of CO2columns in the boreal forest with Orbiting Carbon Observatory-2, Total Carbon Column Observing Network, and EM27/SUN measurements

Seasonal CO$_{2}$ exchange in the boreal forest plays an important role in the global carbon budget and in driving interannual variability in seasonal cycles of atmospheric CO$_{2}$. Satellite-based observations from polar orbiting satellites like the Orbiting Carbon Observatory-2 (OCO-2) offer an opportunity to characterize boreal forest seasonal cycles across longitudes with a spatially and temporally rich data set, but data quality controls and biases still require vetting at high latitudes. With the objective of improving data availability at northern, terrestrial high latitudes, this study evaluates quality control methods and biases of OCO-2 retrievals of atmospheric column-averaged dry air mole fractions of CO$_{2}$ (X$_{CO2}$) in boreal forest regions. In addition to the standard quality control (QC) filters recommended for the Atmospheric Carbon Observations from Space (ACOS) B8 (B8 QC) and ACOS B9 (B9 QC) OCO-2 retrievals, a third set of quality control filters were specifically tailored to boreal forest observations (boreal QC) with the goal of increasing data availability at high latitudes without sacrificing data quality. Ground-based reference measurements of X$_{CO2}$ include observations from two sites in the Total Carbon Column Observing Network (TCCON) at East Trout Lake, Saskatchewan, Canada, and Sodankylä, Finland. OCO-2 retrievals were also compared to ground-based observations from two Bruker EM27/SUN Fourier transform infrared spectrometers (FTSs) at Fairbanks, Alaska, USA. The EM27/SUN spectrometers that were deployed in Fairbanks were carefully monitored for instrument performance and were bias corrected to TCCON using observations at the Caltech TCCON site. The B9 QC were found to pass approximately twice as many OCO-2 retrievals over land north of 50° N than the B8 QC, and the boreal QC were found to pass approximately twice as many retrievals in May, August, and September as the B9 QC. While boreal QC results in a substantial increase in passable retrievals, this is accompanied by increases in the standard deviations in biases at boreal forest sites from ∼1.4 parts per million (ppm) with B9 QC to ∼1.6 ppm with boreal QC. Total average biases for coincident OCO-2 retrievals at the three sites considered did not consistently increase or decrease with different QC methods, and instead, responses to changes in QC varied according to site and satellite viewing geometries. Regardless of the quality control method used, seasonal variability in biases was observed, and this variability was more pronounced at Sodankylä and East Trout Lake than at Fairbanks. Long-term coincident observations from TCCON, EM27/SUN, and satellites from multiple locations would be necessary to determine whether the reduced seasonal variability in bias at Fairbanks is due to geography or instrumentation. Monthly average biases generally varied between −1 and +1 ppm at the three sites considered, with more negative biases in spring (March, April, and May – MAM) and autumn (September and October – SO) but more positive biases in the summer months (June, July, and August – JJA). Monthly standard deviations in biases ranged from approximately 1.0 to 2.0 ppm and did not exhibit strong seasonal dependence, apart from exceptionally high standard deviation observed with all three QC methods at Sodankylä in June. There was no evidence found to suggest that seasonal variability in bias is a direct result of air mass dependence in ground-based retrievals or of proximity bias from coincidence criteria, but there were a number of retrieval parameters used as quality control filters that exhibit seasonality and could contribute to seasonal dependence in OCO-2 bias. Furthermore, it was found that OCO-2 retrievals of X$_{CO2}$ without the standard OCO-2 bias correction exhibit almost no perceptible seasonal dependence in average monthly bias at these boreal forest sites, suggesting that seasonal variability in bias is introduced by the bias correction. Overall, we found that modified quality controls can allow for significant increases in passable OCO-2 retrievals with only marginal compromises in data quality, but seasonal dependence in biases still warrants further exploration

Intercomparability of X_(CO_2) and X_(CH_4) from the United States TCCON sites

The Total Carbon Column Observing Network (TCCON) has become the standard for long-term column-averaged measurements of CO_2 and CH_4. Here, we use a pair of portable spectrometers to test for intra-network bias among the four currently operating TCCON sites in the United States (US). A previous analytical error analysis has suggested that the maximum 2σ site-to-site relative (absolute) bias of TCCON should be less than 0.2% (0.8ppm) in X_(CO_2) and 0.4% (7ppb) in X_(CH_4). We find here experimentally that the 95% confidence intervals for maximum pairwise site-to-site bias among the four US TCCON sites are 0.05–0.14% for X_(CO_2) and 0.08–0.24% for X_(CH_4). This is close to the limit of the bias we can detect using this methodology

Catching Element Formation In The Act

Gamma-ray astronomy explores the most energetic photons in nature to address some of the most pressing puzzles in contemporary astrophysics. It encompasses a wide range of objects and phenomena: stars, supernovae, novae, neutron stars, stellar-mass black holes, nucleosynthesis, the interstellar medium, cosmic rays and relativistic-particle acceleration, and the evolution of galaxies. MeV gamma-rays provide a unique probe of nuclear processes in astronomy, directly measuring radioactive decay, nuclear de-excitation, and positron annihilation. The substantial information carried by gamma-ray photons allows us to see deeper into these objects, the bulk of the power is often emitted at gamma-ray energies, and radioactivity provides a natural physical clock that adds unique information. New science will be driven by time-domain population studies at gamma-ray energies. This science is enabled by next-generation gamma-ray instruments with one to two orders of magnitude better sensitivity, larger sky coverage, and faster cadence than all previous gamma-ray instruments. This transformative capability permits: (a) the accurate identification of the gamma-ray emitting objects and correlations with observations taken at other wavelengths and with other messengers; (b) construction of new gamma-ray maps of the Milky Way and other nearby galaxies where extended regions are distinguished from point sources; and (c) considerable serendipitous science of scarce events -- nearby neutron star mergers, for example. Advances in technology push the performance of new gamma-ray instruments to address a wide set of astrophysical questions.Comment: 14 pages including 3 figure

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

Salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics. We used Multilocus Sequence Typing (MLST) to assign 4,257 isolates from 554 serovars to 1092 sequence types (STs). The majority of the isolates and many STs were grouped into 138 genetically closely related clusters called eBurstGroups (eBGs). Many eBGs correspond to a serovar, for example most Typhimurium are in eBG1 and most Enteritidis are in eBG4, but many eBGs contained more than one serovar. Furthermore, most serovars were polyphyletic and are distributed across multiple unrelated eBGs. Thus, serovar designations confounded genetically unrelated isolates and failed to recognize natural evolutionary groupings. An inability of serotyping to correctly group isolates was most apparent for Paratyphi B and its variant Java. Most Paratyphi B were included within a sub-cluster of STs belonging to eBG5, which also encompasses a separate sub-cluster of Java STs. However, diphasic Java variants were also found in two other eBGs and monophasic Java variants were in four other eBGs or STs, one of which is in subspecies salamae and a second of which includes isolates assigned to Enteritidis, Dublin and monophasic Paratyphi B. Similarly, Choleraesuis was found in eBG6 and is closely related to Paratyphi C, which is in eBG20. However, Choleraesuis var. Decatur consists of isolates from seven other, unrelated eBGs or STs. The serological assignment of these Decatur isolates to Choleraesuis likely reflects lateral gene transfer of flagellar genes between unrelated bacteria plus purifying selection. By confounding multiple evolutionary groups, serotyping can be misleading about the disease potential of S. enterica. Unlike serotyping, MLST recognizes evolutionary groupings and we recommend that Salmonella classification by serotyping should be replaced by MLST or its equivalents

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta