An Ensemble of Bayesian Neural Networks for Exoplanetary Atmospheric Retrieval

Machine learning is now used in many areas of astrophysics, from detecting exoplanets in Kepler transit signals to removing telescope systematics. Recent work demonstrated the potential of using machine learning algorithms for atmospheric retrieval by implementing a random forest to perform retrievals in seconds that are consistent with the traditional, computationally-expensive nested-sampling retrieval method. We expand upon their approach by presenting a new machine learning model, \texttt{plan-net}, based on an ensemble of Bayesian neural networks that yields more accurate inferences than the random forest for the same data set of synthetic transmission spectra. We demonstrate that an ensemble provides greater accuracy and more robust uncertainties than a single model. In addition to being the first to use Bayesian neural networks for atmospheric retrieval, we also introduce a new loss function for Bayesian neural networks that learns correlations between the model outputs. Importantly, we show that designing machine learning models to explicitly incorporate domain-specific knowledge both improves performance and provides additional insight by inferring the covariance of the retrieved atmospheric parameters. We apply \texttt{plan-net} to the Hubble Space Telescope Wide Field Camera 3 transmission spectrum for WASP-12b and retrieve an isothermal temperature and water abundance consistent with the literature. We highlight that our method is flexible and can be expanded to higher-resolution spectra and a larger number of atmospheric parameters

The use of dithiothreitol for the quantitative analysis of elemental sulfur concentrations and isotopes in environmental samples

Determining the concentration and isotopic composition of elemental sulfur in modern and ancient environments is essential to improved interpretation of the mechanisms and pathways of sulfur utilization in biogeochemical cycles. Elemental sulfur can be extracted from sediment or water samples and quantified by converting to hydrogen sulfide. Alternatively, elemental sulfur concentrations can themselves be analyzed using HPLC and other methodologies; however, the preparation and analysis times can be long and these methods are not amenable to stable isotopic analysis. Current reduction methods involve the use of costly and specialized glassware in addition to toxins such as chromium chloride or cyanide to reduce the sulfur to hydrogen sulfide. The novel reduction method presented here uses dithiothreitol (DTT) as a less toxic reducing agent to obtain both elemental sulfur concentrations and isotopic composition from the same sample. The sample is dissolved in an aqueous or organic liquid medium and upon reaction with DTT, the elemental sulfur is volatilized as hydrogen sulfide and collected in a sulfide trap using an inexpensive gas extraction apparatus. The evolved sulfide concentrations can easily be measured for concentration, by absorbance spectrophotometery or voltammetry techniques, and then analyzed for sulfur isotopic composition. The procedure is quantitative at >93% recovery to dissolved elemental sulfur with no observed sulfur isotope fractionation during reduction and recovery. Controlled experiments also demonstrate that DTT is not reactive to sulfate, sulfite, pyrite, or organic sulfur

Liver collagen proportionate area predicts decompensation in patients with recurrent hepatitis C virus cirrhosis after liver transplantation

Background and Aims: Current histological scoring systems do not subclassify cirrhosis. Computer-assisted digital image analysis (DIA) of Sirius Red-stained sections measures fibrosis morphologically producing a fibrosis ratio (collagen proportionate area [CPA]). CPA could have prognostic value within a disease stage, such as cirrhosis. The aim of the present study was to evaluate CPA in patients with recurrent hepatitis C virus (HCV) allograft cirrhosis and assess its relationship with hepatic venous pressure gradient (HVPG). Methods: In 121 consecutively-transplanted HCV patients with HVPG, measured contemporaneously with transjugular liver biopsies, 65 had Ishak stage 5 or 6 disease (43 with HVPG measurement). Biopsies were stained with Sirius Red for DIA, and the collagen content was expressed as a CPA. In three cases, a tissue for Sirius Red staining was not obtained, and the patients were excluded. Results: Sixty-two patients were analyzed. The median HVPG was 8mmHg (interquartile range [IQR]: 5-10). Portal hypertension (HVPG ≥6<10mmHg) was present in 30 (69.8%), and HVPG ≥10mmHg in 13 (30.2%). The median CPA was 16% (IQR 10.75-23.25). Median Child-Pugh score and HVPG were not significantly different between Ishak fibrosis stage 5 or 6, whereas CPA was statistically different: 13% in stage 5 (IQR 8.3-12.4) versus 23% in stage 6 (IQR 17-33.7, P<0.001). In the multivariate analysis, CPA was the only variable significantly associated with clinically-significant portal hypertension (HVPG ≥10mmHg, odds ratio: 1.085, confidence interval: 1.004-1.172, P=0.040). A CPA of 14% was the best cut-off value for clinically-significant portal hypertension (CSPH) and liver decompensation, which occurred in 24 patients. Event-free survival was significantly shorter in patients with CSPH or with a CPA value ≥14%, or with a combination of both. Conclusion: In Ishak stages 5 and 6, CPA correlated with HVPG, but had a wider range of values, suggesting a greater sensitivity for distinguishing "early" from "late" severe fibrosis/cirrhosis. CPA was a unique, independent predictor of HVPG ≥10mmHg. CPA can be used to subclassify cirrhosis and for prognostic stratification. © 2012 Journal of Gastroenterology and Hepatology Foundation and Blackwell Publishing Asia Pty Ltd

Effects of oxygen-depleted atmospheres on survival and growth of Listeria monocytogenes on fresh-cut Iceberg lettuce stored at mild abuse commercial temperatures

The effects of oxygen-depleted atmospheres, 0.25% O2 þ 12% CO2 (balance N2) and 2% O2 þ 6% CO2 (balance N2), on growth of Listeria monocytogenes on fresh-cut Iceberg lettuce were determined. The study was carried out at mild abuse temperatures using controlled atmosphere chambers. During storage at a constant temperature of 7 C, growth was enhanced at the lower oxygen level of 0.25% O2 by Day 10. Over 17 days of storage at temperatures designed to mimic mild abuse commercial conditions, there were again significantly higher counts under 0.25% O2 from Day 10 onwards. These were 0.9 and 0.7 log cycles higher on Days 14 and 17, respectively. When a model lettuce agar medium was used to eliminate possible interactions with competing flora the direct effects of the atmosphere enhancing the growth of L. monocytogenes was also observed. It is concluded that use of very O2-depleted atmospheres for control of enzymatic browning of fresh-cut Iceberg lettuce may introduce a potential hazard under some commercial conditions. There is a need for greater vigilance and possibly additional measures to ensure consumer safety.Ciencias de la Alimentació

Accurate Machine Learning Atmospheric Retrieval via a Neural Network Surrogate Model for Radiative Transfer

Atmospheric retrieval determines the properties of an atmosphere based on its measured spectrum. The low signal-to-noise ratio of exoplanet observations require a Bayesian approach to determine posterior probability distributions of each model parameter, given observed spectra. This inference is computationally expensive, as it requires many executions of a costly radiative transfer (RT) simulation for each set of sampled model parameters. Machine learning (ML) has recently been shown to provide a significant reduction in runtime for retrievals, mainly by training inverse ML models that predict parameter distributions, given observed spectra, albeit with reduced posterior accuracy. Here we present a novel approach to retrieval by training a forward ML surrogate model that predicts spectra given model parameters, providing a fast approximate RT simulation that can be used in a conventional Bayesian retrieval framework without significant loss of accuracy. We demonstrate our method on the emission spectrum of HD 189733 b and find good agreement with a traditional retrieval from the Bayesian Atmospheric Radiative Transfer (BART) code (Bhattacharyya coefficients of 0.9843--0.9972, with a mean of 0.9925, between 1D marginalized posteriors). This accuracy comes while still offering significant speed enhancements over traditional RT, albeit not as much as ML methods with lower posterior accuracy. Our method is ~9x faster per parallel chain than BART when run on an AMD EPYC 7402P central processing unit (CPU). Neural-network computation using an NVIDIA Titan Xp graphics processing unit is 90--180x faster per chain than BART on that CPU.Comment: 16 pages, 4 figures, submitted to PSJ 3/4/2020, revised 1/22/2021. Text restructured and updated for clarity, model updated and expanded to work for range of hot Jupiters, results/plots updated, two new appendices to further justify model selection and methodolog

Review article: the role of the microcirculation in liver cirrhosis

BACKGROUND: Intrahepatic microvascular derangements and microcirculatory dysfunction are key in the development of liver cirrhosis and its associated complications. While much has been documented relating to cirrhosis and the dysfunction of the microcirculation in the liver parenchyma, far less is known about the state of the extrahepatic microcirculation and the role this may have in the pathogenesis of multiple organ failure in end stage liver cirrhosis. AIM: To provide an update on the role of the microcirculation in the pathophysiology of cirrhosis and its associated complications and briefly discuss some of the imaging techniques which may be used to directly investigate the microcirculation. METHODS: A Medline literature search was conducted using the following search terms: ‘cirrhosis’, ‘microcirculation’, ‘circulation’, ‘systemic’, ‘inflammation’, ‘peripheral’, ‘hepatorenal’ and ‘hepatopulmonary’. RESULTS: Significant heterogeneous microvascular alterations exist in patients with cirrhosis. Data suggest that the systemic inflammation, associated with advanced cirrhosis, induces microcirculatory dysregulation and contributes to haemodynamic derangement. The resultant vasoconstriction and hypoperfusion in the systemic extrahepatic microvasculature, is likely to be instrumental in the pathophysiology of organ failure in decompensated cirrhosis, however the mechanistic action of vasoactive agents used to correct the circulatory disturbance of advanced cirrhosis is poorly understood. CONCLUSIONS: Further research into the role of the microcirculation in patients with liver cirrhosis, will improve physicians understanding of the pathophysiology of cirrhosis, and may provide a platform for real time evaluation of an individual's microcirculatory response to vasoactive mediators, thus guiding their therapy

Digital image analysis of liver collagen predicts clinical outcome of recurrent hepatitis C virus 1 year after liver transplantation.

Clinical outcomes of recurrent hepatitis C virus after liver transplantation are difficult to predict. We evaluated collagen proportionate area (CPA), a quantitative histological index, at 1 year with respect to the first episode of clinical decompensation. Patients with biopsies at 1 year after liver transplantation were evaluated by Ishak stage/grade, and biopsy samples stained with Sirius red for digital image analysis were evaluated for CPA. Cox regression was used to evaluate variables associated with first appearance of clinical decompensation. Receiver operating characteristic (ROC) curves were also used. A total of 135 patients with median follow-up of 76 months were evaluated. At 1 year, median CPA was 4.6% (0.2%-36%) and Ishak stage was 0-2 in 101 patients, 3-4 in 23 patients, and 5-6 in 11 patients. Decompensation occurred in 26 (19.3%) at a median of 61 months (15-138). Univariately, CPA, tacrolimus monotherapy, and Ishak stage/grade at 1 year were associated with decompensation; upon multivariate analysis, only CPA was associated with decompensation (P = 0.010; Exp(B) = 1.169; 95%CI, 1.037-1.317). Area under the ROC curve was 0.97 (95%CI, 0.94-0.99). A cutoff value of 6% of CPA had 82% sensitivity and 95% specificity for decompensation. In the 89 patients with hepatic venous pressure gradient (HVPG) measurement, similar results were obtained. When both cutoffs of CPA > 6% and HVPG >= 6 mm Hg were used, all patients decompensated. Thus, CPA at 1-year biopsy after liver transplantation was highly predictive of clinical outcome in patients infected with hepatitis C virus who underwent transplantation, better than Ishak stage or HVPG. Liver Transpl 17:178-188, 2011. (C) 2011 AASLD

Bacterial Infections Change Natural History of Cirrhosis Irrespective of Liver Disease Severity

OBJECTIVES: We assessed the prognostic significance of infections in relation to current prognostic scores and explored if infection could be considered per se a distinct clinical stage in the natural history of cirrhosis. METHODS: We included consecutive patients with cirrhosis admitted to a tertiary referral liver unit for at least 48 h over a 2-year period. Diagnosis of infection was based on positive cultures or strict established criteria. We used competing risk analysis and propensity score matching for data analysis. RESULTS: 501 patients (63% male, 48% alcoholic liver disease, median Model of End-stage Liver Disease (MELD)=17) underwent 781 admissions over the study period. Portal hypertensive bleeding and complicated ascites were the commonest reasons of admission. The incidence of proven bacterial infection was 25.6% (60% community acquired and 40% nosocomial). Survival rates at 3, 6, 12, and 30 months were 83%, 77%, 71%, and 62% in patients without diagnosis of infection, vs. 50%, 46%, 41%, and 34% in patients with diagnosis of infection. Overall survival was independently associated with MELD score (hazards ratio (HR) 1.099), intensive care (ITU) stay (HR 1.967) and bacterial infection (HR 2.226). Bacterial infection was an independent predictor of survival even when patients who died within the first 30 days were excluded from the analysis in Cox regression (HR 2.013) and competing risk Cox models in all patients (HR 1.46) and propensity risk score-matched infected and non-infected patients (HR 1.67). CONCLUSIONS: Infection most likely represents a distinct prognostic stage of cirrhosis, which affects survival irrespective of disease severity, even after recovery from the infective episode

Validation of the Baveno Vi Criteria to Identify Low Risk Cirrhotic Patients not Requiring Endoscopic Surveillance for Varices

BACKGROUND: The Baveno VI guidelines propose that cirrhotic patients with a liver stiffness measurement (LSM) 150000/μL can avoid screening endoscopy as their combination is highly specific for excluding clinically significant varices. The aim of the study was to validate these criteria. METHODS: Transient elastography data was collected from two institutions from 2006-2015. Inclusion criteria were a LSM ⩾10kPa and an upper gastrointestinal endoscopy within 12 months, with a diagnosis of compensated chronic liver disease. Exclusion criteria were porto-mesenteric-splenic vein thrombosis and non-cirrhotic portal hypertension. Varices were graded as low risk (grade 150) are at low risk of having varices and do not need a screening endoscopy. Varices are a complication of cirrhosis, confer a risk of serious bleeding, and can be diagnosed and treated by endoscopy. Our study reviewed the clinical records of patients who have had liver stiffness scans and endoscopy over a 9 year period at two hospitals. The results show that only about 2% of patients who meet the Baveno VI criteria will be miss classified as not having varices