Prevalence of alkane monooxygenase genes in Arctic and Antarctic hydrocarbon-contaminated and pristine soils

The prevalence of four alkane monooxygenase genotypes (Pseudomonas putida GPo1, Pp alkB; Rhodococcus sp. strain Q15, Rh alkB1 and Rh alkB2; and Acinetobacter sp. strain ADP-1, Ac alkM) in hydrocarbon-contaminated and pristine soils from the Arctic and Antarctica were determined by both culture-independent (PCR hybridization analyses) and culture-dependent (colony hybridization analyses) molecular methods, using oligonucleotide primers and DNA probes specific for each of the alk genotypes. PCR hybridization of total soil community DNA detected the rhodococcal alkB genotypes in most of the contaminated (Rh alkB1, 18/20 soils; Rh alkB2, 13/20) and many pristine soils (Rh alkB1, 9/10 soils; Rh alkB2, 7/10), while Pp alkB was generally detected in the contaminated soils (15/20) but less often in pristine soils (5/10). Ac alkM was rarely detected in the soils (1/30). The colony hybridization technique was used to determine the prevalence of each of the alk genes and determine their relative abundance in culturable cold-adapted (5°C) and mesophilic populations (37°C) from eight of the polar soils. The cold-adapted populations, in general, possessed relatively higher percentages of the Rh alkB genotypes (Rh alkB1, 1.9% (0.55); Rh alkB2, 2.47% (0.89)), followed by the Pp alkB (1.13% (0.50)), and then the Ac alkM (0.53% (0.36)). The Rh alkB1 genotype was clearly more prevalent in culturable cold-adapted bacteria (1.9% (0.55)) than in culturable mesophiles (0.41 (0.55)), suggesting that cold-adapted bacteria are the predominant organisms possessing this genotype. Overall, these results indicated that (i) Acinetobacter spp. are not predominant members of polar alkane degradative microbial communities, (ii) Pseudomonas spp. may become enriched in polar soils following contamination events, and (iii) Rhodococcus spp. may be the predominant alkane-degradative bacteria in both pristine and contaminated polar soil

Momentum-resolved electronic structure at a buried interface from soft x-ray standing-wave angle-resolved photoemission

Angle-resolved photoemission spectroscopy (ARPES) is a powerful technique for the study of electronic structure, but it lacks a direct ability to study buried interfaces between two materials. We address this limitation by combining ARPES with soft x-ray standing-wave (SW) excitation (SWARPES), in which the SW profile is scanned through the depth of the sample. We have studied the buried interface in a prototypical magnetic tunnel junction La0.7Sr0.3MnO3/SrTiO3. Depth- and momentum-resolved maps of Mn 3d eg and t2g states from the central, bulk-like and interface-like regions of La0.7Sr0.3MnO3 exhibit distinctly different behavior consistent with a change in the Mn bonding at the interface. We compare the experimental results to state-of-the-art density-functional and one-step photoemission theory, with encouraging agreement that suggests wide future applications of this technique.Comment: 18 pages, 4 figures and Supplementary Informatio

Attentive Learning of Sequential Handwriting Movements: A Neural Network Model

Defense Advanced research Projects Agency and the Office of Naval Research (N00014-95-1-0409, N00014-92-J-1309); National Science Foundation (IRI-97-20333); National Institutes of Health (I-R29-DC02952-01)

On a coupled PDE model for image restoration

In this paper, we consider a new coupled PDE model for image restoration. Both the image and the edge variables are incorporated by coupling them into two different PDEs. It is shown that the initial-boundary value problem has global in time dissipative solutions (in a sense going back to P.-L. Lions), and several properties of these solutions are established. This is a rough draft, and the final version of the paper will contain a modelling part and numerical experiments

The ELFIN mission

The Electron Loss and Fields Investigation with a Spatio-Temporal Ambiguity-Resolving option (ELFIN-STAR, or heretoforth simply: ELFIN) mission comprises two identical 3-Unit (3U) CubeSats on a polar (∼93∘ inclination), nearly circular, low-Earth (∼450 km altitude) orbit. Launched on September 15, 2018, ELFIN is expected to have a >2.5 year lifetime. Its primary science objective is to resolve the mechanism of storm-time relativistic electron precipitation, for which electromagnetic ion cyclotron (EMIC) waves are a prime candidate. From its ionospheric vantage point, ELFIN uses its unique pitch-angle-resolving capability to determine whether measured relativistic electron pitch-angle and energy spectra within the loss cone bear the characteristic signatures of scattering by EMIC waves or whether such scattering may be due to other processes. Pairing identical ELFIN satellites with slowly-variable along-track separation allows disambiguation of spatial and temporal evolution of the precipitation over minutes-to-tens-of-minutes timescales, faster than the orbit period of a single low-altitude satellite (Torbit ∼ 90 min). Each satellite carries an energetic particle detector for electrons (EPDE) that measures 50 keV to 5 MeV electrons with Δ E/E 1 MeV. This broad energy range of precipitation indicates that multiple waves are providing scattering concurrently. Many observed events show significant backscattered fluxes, which in the past were hard to resolve by equatorial spacecraft or non-pitch-angle-resolving ionospheric missions. These observations suggest that the ionosphere plays a significant role in modifying magnetospheric electron fluxes and wave-particle interactions. Routine data captures starting in February 2020 and lasting for at least another year, approximately the remainder of the mission lifetime, are expected to provide a very rich dataset to address questions even beyond the primary mission science objective.Published versio

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease