Minibatch Markov chain Monte Carlo Algorithms for Fitting Gaussian Processes

Gaussian processes (GPs) are a highly flexible, nonparametric statistical model that are commonly used to fit nonlinear relationships or account for correlation between observations. However, the computational load of fitting a Gaussian process is $\mathcal{O}(n^3)$ making them infeasible for use on large datasets. To make GPs more feasible for large datasets, this research focuses on the use of minibatching to estimate GP parameters. Specifically, we outline both approximate and exact minibatch Markov chain Monte Carlo algorithms that substantially reduce the computation of fitting a GP by only considering small subsets of the data at a time. We demonstrate and compare this methodology using various simulations and real datasets.Comment: 19 Pages, 6 Figure

Isotopic fingerprint for phosphorus in drinking water supplies

Phosphate dosing of drinking water supplies, coupled with leakage from distribution networks, represents a significant input of phosphorus to the environment. The oxygen isotope composition of phosphate (δ18OPO4), a novel stable isotope tracer for phosphorus, offers new opportunities to understand the importance of phosphorus derived from sources such as drinking water. We report the first assessment of δ18OPO4 within drinking water supplies. A total of 40 samples from phosphate-dosed distribution networks were analyzed from across England and Wales. In addition, samples of the source orthophosphoric acid used for dosing were also analyzed. Two distinct isotopic signatures for drinking water were identified (average = +13.2 or +19.7‰), primarily determined by δ18OPO4 of the source acid (average = +12.4 or +19.7‰). Dependent upon the source acid used, drinking water δ18OPO4 appears isotopically distinct from a number of other phosphorus sources. Isotopic offsets from the source acid ranging from −0.9 to +2.8‰ were observed. There was little evidence that equilibrium isotope fractionation dominated within the networks, with offsets from temperature-dependent equilibrium ranging from −4.8 to +4.2‰. While partial equilibrium fractionation may have occurred, kinetic effects associated with microbial uptake of phosphorus or abiotic sorption and dissolution reactions may also contribute to δ18OPO4 within drinking water supplies

Imaging biomarkers of lung ventilation in interstitial lung disease from ¹²⁹Xe and oxygen enhanced ¹H MRI

PURPOSE: To compare imaging biomarkers from hyperpolarised 129Xe ventilation MRI and dynamic oxygen-enhanced MRI (OE-MRI) with standard pulmonary function tests (PFT) in interstitial lung disease (ILD) patients. To evaluate if biomarkers can separate ILD subtypes and detect early signs of disease resolution or progression. STUDY TYPE: Prospective longitudinal. POPULATION: Forty-one ILD (fourteen idiopathic pulmonary fibrosis (IPF), eleven hypersensitivity pneumonitis (HP), eleven drug-induced ILD (DI-ILD), five connective tissue disease related-ILD (CTD-ILD)) patients and ten healthy volunteers imaged at visit 1. Thirty-four ILD patients completed visit 2 (eleven IPF, eight HP, ten DIILD, five CTD-ILD) after 6 or 26 weeks. FIELD STRENGTH/SEQUENCE: MRI performed at 1.5 T. Inversion recovery T1 mapping, dynamic MRI acquisition with varying oxygen levels, and hyperpolarised 129Xe ventilation MRI. Subjects underwent standard spirometry and gas transfer testing. ASSESSMENT: Five 1H MRI and two 129Xe MRI ventilation metrics were compared with spirometry and gas transfer measurements. STATISTICAL TEST: To evaluate differences at visit 1 among subgroups: ANOVA or Kruskal-Wallis rank tests with correction for multiple comparisons. To assess the relationships between imaging biomarkers, PFT, age and gender, at visit 1 and for the change between visit 1 and 2: Pearson correlations and multilinear regression models. RESULTS: The global PFT tests could not distinguish ILD subtypes. Ventilated volumes were lower in ILD patients than in HVs when measured with 129Xe MRI (HV 97.4 ± 2.6, CTD-ILD: 91.0 ± 4.8 p = 0.017, DI-ILD 90.1 ± 7.4 p = 0.003, HP 92.6 ± 4.0 p = 0.013, IPF 88.1 ± 6.5 p < 0.001), but not with OE-MRI. 129Xe reported more heterogeneous ventilation in DI-ILD and IPF than in HV, and OE-MRI reported more heterogeneous ventilation in DI-ILD and IPF than in HP or CTD-ILD. The longitudinal changes reported by the imaging biomarkers did not correlate with the PFT changes between visits. DATA CONCLUSION: Neither 129Xe ventilation nor OE-MRI biomarkers investigated in this study were able to differentiate between ILD subtypes, suggesting that ventilation-only biomarkers are not indicated for this task. Limited but progressive loss of ventilated volume as measured by 129Xe-MRI may be present as the biomarker of focal disease progresses. OE-MRI biomarkers are feasible in ILD patients and do not correlate strongly with PFT. Both OE-MRI and 129Xe MRI revealed more spatially heterogeneous ventilation in DI-ILD and IPF

The Malaria Cell Atlas: single parasite transcriptomes across the complete Plasmodium life cycle

Malaria parasites adopt a remarkable variety of morphological life stages as they transition through multiple mammalian host and mosquito vector environments. We profiled the single-cell transcriptomes of thousands of individual parasites, deriving the first high-resolution transcriptional atlas of the entire life cycle. We then used our atlas to precisely define developmental stages of single cells from three different human malaria parasite species, including parasites isolated directly from infected individuals. The Malaria Cell Atlas provides both a comprehensive view of gene usage in a eukaryotic parasite and an open-access reference dataset for the study of malaria parasites

Toward Return to Duty Decision-Making After Military Mild Traumatic Brain Injury: Preliminary Validation of the Charge of Quarters Duty Test

Determining duty-readiness after mild traumatic brain injury (mTBI) remains a priority of the United States Department of Defense as warfighters in both deployed and non-deployed settings continue to sustain these injuries in relatively large numbers. Warfighters with mTBI may experience unresolved sensorimotor, emotional, cognitive sequelae including problems with executive functions, a category of higher order cognitive processes that enable people to regulate goal-directed behavior. Persistent mTBI sequelae interfere with warfighters’ proficiency in performing military duties and signal the need for graded return to activity and possibly rehabilitative services. Although significant strides have been carried out in recent years to enhance the identification and management of mTBI in garrison (EXORD 165–13) and deployed settings (EXORD 242–11; DoDI 6,490.11), the Department of Defense still lacks reliable, valid, and clinically feasible functional assessments to help inform duty-readiness decisions. Traditional functional assessments lack face validity for warfighters and may have ceiling effects, especially as related to executive functions. Performance-based multitasking assessments have been shown to be sensitive to executive dysfunction after acquired brain injury but no multitasking assessments have been validated in adults with mTBI. Existing multitasking assessments are not ecologically valid relative to military contexts. A multidisciplinary military–civilian team of researchers developed and evaluated a performance-based assessment called the Assessment of Military Multitasking Performance. One of the Assessment of Military Multitasking Performance multitasks, the Charge of Quarters Duty Test (CQDT), was designed to challenge the divided attention, foresight, and planning dimensions of executive functions. Here, we report on the preliminary validation results of the CQDT

Correction: Mutations in LRRK2 linked to Parkinson disease sequester Rab8a to damaged lysosomes and regulate transferrin-mediated iron uptake in microglia

[This corrects the article DOI: 10.1371/journal.pbio.3001480.]

Bridging Alone: Religious Conservatism, Marital Homogamy, and Voluntary Association Membership

This study characterizes social insularity of religiously conservative American married couples by examining patterns of voluntary associationmembership. Constructing a dataset of 3938 marital dyads from the second wave of the National Survey of Families and Households, the author investigates whether conservative religious homogamy encourages membership in religious voluntary groups and discourages membership in secular voluntary groups. Results indicate that couples’ shared affiliation with conservative denominations, paired with beliefs in biblical authority and inerrancy, increases the likelihood of religious group membership for husbands and wives and reduces the likelihood of secular group membership for wives, but not for husbands. The social insularity of conservative religious groups appears to be reinforced by homogamy—particularly by wives who share faith with husbands

A Case Study Competition among Methods for Analyzing Large Spatial Data

The Gaussian process is an indispensable tool for spatial data analysts. The onset of the "big data" era, however, has lead to the traditional Gaussian process being computationally infeasible for modern spatial data. As such, various alternatives to the full Gaussian process that are more amenable to handling big spatial data have been proposed. These modern methods often exploit low rank structures and/or multi-core and multi-threaded computing environments to facilitate computation. This study provides, first, an introductory overview of several methods for analyzing large spatial data. Second, this study describes the results of a predictive competition among the described methods as implemented by different groups with strong expertise in the methodology. Specifically, each research group was provided with two training datasets (one simulated and one observed) along with a set of prediction locations. Each group then wrote their own implementation of their method to produce predictions at the given location and each which was subsequently run on a common computing environment. The methods were then compared in terms of various predictive diagnostics. Supplementary materials regarding implementation details of the methods and code are available for this article online