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We explore the application of phase diversity to calibrate the non common path aberrations (NCPA) in the Gemini Planet Imager (GPI). This is first investigated in simulation in order to characterize the ideal technique parameters with simulated GPI calibration source data. The best working simulation parameters are derived and we establish the algorithm's capability to recover an injected astigmatism. Furthermore, the real data appear to exhibit signs of de-centering between the in and out of focus images that are required by phase diversity; this effect can arise when the diverse images are acquired in closed loop and are close to the non-linear regime of the wavefront sensor. We show in simulation that this effect can inhibit our algorithm, which does not take into account the impact of de-centering between images. To mitigate this effect, we validate the technique of using a single diverse image with our algorithm; this is first demonstrated in simulation and then applied to the real GPI data. Following this approach, we find that we can successfully recover a known astigmatism injection using the real GPI data and subsequently apply an NCPA correction to GPI (in the format of offset reference slopes) to improve the relative Strehl ratio by 5%; we note this NCPA correction application is rudimentary and a more thorough application will be investigated in the near future. Finally, the estimated NCPA in the form of astigmatism and coma agree well with the magnitude of the same modes reported by Poyneer et al. 2016.

ABSTRACT Perturbations to the vaginal microbiota can lead to dysbiosis, including bacterial vaginosis (BV), which affects a large portion of the female population. In a healthy state, the vaginal microbiota is characterized by low diversity and colonization by Lactobacillus spp., whereas in BV, these species are displaced by a highly diverse population of bacteria associated with adverse vaginal health outcomes. Since prebiotic ingestion has been a highly effective approach to invigorate lactobacilli for improved intestinal health, we hypothesized that these compounds could stimulate lactobacilli at the expense of BV organisms to maintain vaginal health. Monocultures of commensal Lactobacillus crispatus , Lactobacillus vaginalis , Lactobacillus gasseri , Lactobacillus johnsonii , Lactobacillus jensenii , and Lactobacillus iners , in addition to BV-associated organisms and Candida albicans , were tested for their ability to utilize a representative group of prebiotics consisting of lactitol, lactulose, raffinose, and oligofructose. The disaccharide lactulose was found to most broadly and specifically stimulate vaginal lactobacilli, including the strongly health-associated species L. crispatus , and importantly, not to stimulate BV organisms or C. albicans . Using freshly collected vaginal samples, we showed that exposure to lactulose promoted commensal Lactobacillus growth and dominance and resulted in healthy acidity partially through lactic acid production. This provides support for further testing of lactulose to prevent dysbiosis and potentially to reduce the need for antimicrobial agents in managing vaginal health. IMPORTANCE Bacterial vaginosis (BV) and other dysbioses of the vaginal microbiota significantly affect the quality of life of millions of women. Antimicrobial therapy is often poorly effective, causes side effects, and does not prevent recurrences. We report one of very few studies that have evaluated how prebiotics—compounds that are selectively fermented by beneficial bacteria such as Lactobacillus spp.—can modulate the vaginal microbiota. We also report use of a novel in vitro polymicrobial model to study the impact of prebiotics on the vaginal microbiota. The identification of prebiotic lactulose as enhancing Lactobacillus growth but not that of BV organisms or Candida albicans has direct application for retention of homeostasis and prevention of vaginal dysbiosis and infection.

Scattering amplitudes of partons in QCD contain infrared divergences which can be resummed to all orders in terms of an anomalous dimension. Independently, in the limit of high-energy forward scattering, large logarithms of the energy can be resummed using Balitsky-Fadin-Kuraev-Lipatov theory. We use the latter to analyze the infrared-singular part of amplitudes to all orders in perturbation theory and to next-to-leading-logarithm accuracy in the high-energy limit, resumming the two-Reggeon contribution. Remarkably, we find a closed form for the infrared-singular part, predicting the Regge limit of the soft anomalous dimension to any loop order. Comment: 35 pages, 8 figures

The kidney sessions of the 2017 Banff Conference focused on 2 areas: clinical implications of inflammation in areas of interstitial fibrosis and tubular atrophy (i‐IFTA) and its relationship to T cell–mediated rejection (TCMR), and the continued evolution of molecular diagnostics, particularly in the diagnosis of antibody‐mediated rejection (ABMR). In confirmation of previous studies, it was independently demonstrated by 2 groups that i‐IFTA is associated with reduced graft survival. Furthermore, these groups presented that i‐IFTA, particularly when involving >25% of sclerotic cortex in association with tubulitis, is often a sequela of acute TCMR in association with underimmunosuppression. The classification was thus revised to include moderate i‐IFTA plus moderate or severe tubulitis as diagnostic of chronic active TCMR. Other studies demonstrated that certain molecular classifiers improve diagnosis of ABMR beyond what is possible with histology, C4d, and detection of donor‐specific antibodies (DSAs) and that both C4d and validated molecular assays can serve as potential alternatives and/or complements to DSAs in the diagnosis of ABMR. The Banff ABMR criteria are thus updated to include these alternatives. Finally, the present report paves the way for the Banff scheme to be part of an integrative approach for defining surrogate endpoints in next‐generation clinical trials. The Banff consortium presents revisions to the diagnostic criteria for T cell– and antibody‐mediated kidney transplant rejection, including specific criteria for chronic active T cell–mediated rejection, plus prospects for integrative endpoints in clinical trials. See related articles on pages 321, 364, and 377.

Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis. Communications Biology, 3 (1) ISSN:2399-3642

Nutrient enrichment can simultaneously increase and destabilise plant biomass production, with co-limitation by multiple nutrients potentially intensifying these effects. Here, we test how factorial additions of nitrogen (N), phosphorus (P) and potassium with essential nutrients (K+) affect the stability (mean/standard deviation) of aboveground biomass in 34 grasslands over 7 years. Destabilisation with fertilisation was prevalent but was driven by single nutrients, not synergistic nutrient interactions. On average, N-based treatments increased mean biomass production by 21-51% but increased its standard deviation by 40-68% and so consistently reduced stability. Adding P increased interannual variability and reduced stability without altering mean biomass, while K+ had no general effects. Declines in stability were largest in the most nutrient-limited grasslands, or where nutrients reduced species richness or intensified species synchrony. We show that nutrients can differentially impact the stability of biomass production, with N and P in particular disproportionately increasing its interannual variability.

What are the psychological consequences of the increasingly politicized nature of the COVID-19 pandemic in the United States relative to similar Western countries? In a two-wave study completed early (March) and later (December) in the pandemic, we found that polarization was greater in the United States ( N = 1,339) than in Canada ( N = 644) and the United Kingdom. ( N = 1,283). Political conservatism in the United States was strongly associated with engaging in weaker mitigation behaviors, lower COVID-19 risk perceptions, greater misperceptions, and stronger vaccination hesitancy. Although there was some evidence that cognitive sophistication was associated with increased polarization in the United States in December (but not March), cognitive sophistication was nonetheless consistently negatively correlated with misperceptions and vaccination hesitancy across time, countries, and party lines. Furthermore, COVID-19 skepticism in the United States was strongly correlated with distrust in liberal-leaning mainstream news outlets and trust in conservative-leaning news outlets, suggesting that polarization may be driven by differences in information environments.

Background Patient preference is pivotal for widespread adoption of tests in clinical practice. Patient preferences for invasive versus other noninvasive tests for coronary artery disease are not known. Purpose To compare patient acceptance and preferences for noninvasive and invasive cardiac imaging in North and South America, Asia, and Europe. Materials and Methods This was a prospective 16-center trial in 381 study participants undergoing coronary CT angiography with stress perfusion, SPECT, and invasive coronary angiography (ICA). Patient preferences were collected by using a previously validated questionnaire translated into eight languages. Responses were converted to ordinal scales and were modeled with generalized linear mixed models. Results In patients in whom at least one test was associated with pain, CT and SPECT showed reduced median pain levels, reported on 0-100 visual analog scales, from 20 for ICA (interquartile range [IQR], 4-50) to 6 for CT (IQR, 0-27.5) and 5 for SPECT (IQR, 0-25) (P < .001). Patients from Asia reported significantly more pain than patients from other continents for ICA (median, 25; IQR, 10-50; P = .01), CT (median, 10; IQR, 0-30; P = .02), and SPECT (median, 7; IQR, 0-28; P = .03). Satisfaction with preparation differed by continent and test (P = .01), with patients from Asia reporting generally lower ratings. Patients from North America had greater percentages of "very high" or "high" satisfaction than patients from other continents for ICA (96% vs 82%, respectively; P < .001) and SPECT (95% vs 79%, respectively; P = .04) but not for CT (89% vs 86%, respectively; P = .70). Among all patients, CT was preferred by 54% of patients, compared with 18% for SPECT and 28% for ICA (P < .001). Conclusion For cardiac imaging, patients generally favored CT angiography with stress perfusion, while study participants from Asia generally reported lowest satisfaction. © RSNA, 2019 Online supplemental material is available for this article. See also the editorial by Woodard and Nguyen in this issue.

Studies of experimentally deformed rocks and small-scale natural shear zones have demonstrated that volumetrically minor phases can control strain localisation by limiting grain growth and promoting grain-size sensitive deformation mechanisms. These small-scale studies are often used to infer a critical role for minor phases in the development of plate boundaries. However, the role of minor phases in strain localisation at an actual plate boundary remains to be tested by direct observation. In order to test the hypothesis that minor phases control strain localisation at plate boundaries, we conducted microstructural analyses of peridotite samples collected along a ∼1 km transect across the base of the Oman-United Arab Emirates (UAE) ophiolite. The base of the ophiolite is marked by the Semail thrust, which represents the now exhumed contact between subducted oceanic crust and the overlying mantle wedge. As such, the base of the ophiolite provides the opportunity to directly examine a former plate boundary. Our results demonstrate that the mean olivine grain size is inversely proportional to the abundance of minor phases (primarily orthopyroxene, as well as clinopyroxene, hornblende, and spinel), consistent with suppression of grain growth by grain-boundary pinning. Our results also reveal that mean olivine grain size is proportional to CPO strength (both of which generally decrease towards the metamorphic sole), suggesting that the fraction of strain produced by different deformation mechanisms varied spatially. Experimentally-derived flow laws indicate that under the inferred deformation conditions, the viscosity of olivine was grain-size sensitive. As such, grain size, and thereby the abundance of minor phases, influenced viscosity during subduction-related deformation along the base of the mantle wedge. We calculate an order of magnitude decrease in the viscosity of olivine towards the base of the ophiolite, which suggests strain was localised near the subduction interface. Our data indicate that this rheological weakening was primarily the result of more abundant minor phases near the base of the ophiolite. Our interpretations are consistent with those of previous studies on experimentally deformed rocks and smaller-scale natural shear zones that indicate minor phases can exert the primary control on strain localisation. However, our study demonstrates for the first time that minor phases can control strain localisation at the scales relevant to a major plate boundary.