NOUS: Construction and Querying of Dynamic Knowledge Graphs

The ability to construct domain specific knowledge graphs (KG) and perform question-answering or hypothesis generation is a transformative capability. Despite their value, automated construction of knowledge graphs remains an expensive technical challenge that is beyond the reach for most enterprises and academic institutions. We propose an end-to-end framework for developing custom knowledge graph driven analytics for arbitrary application domains. The uniqueness of our system lies A) in its combination of curated KGs along with knowledge extracted from unstructured text, B) support for advanced trending and explanatory questions on a dynamic KG, and C) the ability to answer queries where the answer is embedded across multiple data sources.Comment: Codebase: https://github.com/streaming-graphs/NOU

Does living by the coast improve health and wellbeing?

This is the author’s version of a work that was accepted for publication in Health and Place. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Health and Place,vol. 18 (5)(2012) DOI:0.1016/j.healthplace.2012.06.015It is often assumed that spending time by the coast leads to better health and wellbeing, but there is strikingly little evidence regarding specific effects or mechanisms to support such a view. We analysed small-area census data for the population of England, which indicate that good health is more prevalent the closer one lives to the coast. We also found that, consistent with similar analyses of greenspace accessibility, the positive effects of coastal proximity may be greater amongst more socio-economically deprived communities. We hypothesise that these effects may be due to opportunities for stress reduction and increased physical activity

Optimizing automatic morphological classification of galaxies with machine learning and deep learning using Dark Energy Survey imaging

There are several supervised machine learning methods used for the application of automated morphological classification of galaxies; however, there has not yet been a clear comparison of these different methods using imaging data, or a investigation for maximising their effectiveness.We carry out a comparison between several common machine learning methods for galaxy classification (Convolutional Neural Network (CNN), K-nearest neighbour, LogisticRegression, Support Vector Machine, Random Forest, and Neural Networks) by using DarkEnergy Survey (DES) data combined with visual classifications from the Galaxy Zoo 1 project(GZ1). Our goal is to determine the optimal machine learning methods when using imaging data for galaxy classification. We show that CNN is the most successful method of these ten methods in our study. Using a sample of _2,800 galaxies with visual classification from GZ1, we reach an accuracy of _0.99 for the morphological classification of Ellipticals and Spirals. The further investigation of the galaxies that have a different ML and visual classification but with high predicted probabilities in our CNN usually reveals an the incorrect classification provided by GZ1. We further find the galaxies having a low probability of being either spirals or ellipticals are visually Lenticulars (S0), demonstrating that supervised learning is able to rediscover that this class of galaxy is distinct from both Es and Spirals.We confirm that _2.5% galaxies are misclassified by GZ1 in our study. After correcting these galaxies’ labels, we improve our CNN performance to an average accuracy of over 0.99 (accuracy of 0.994 is our best result)

Gender Differences in Compensation, Job Satisfaction and Other Practice Patterns in Urology

The proportion of women in urology has increased from <0.5% in 1981 to 10% today. Furthermore, 33% of students matching in urology are now female. This analysis sought to characterize the female workforce in urology in comparison to men with regard to income, workload, and job satisfaction

Cosmological constraints from the cross-correlation of DESI Luminous Red Galaxies with CMB lensing from Planck PR4 and ACT DR6

We infer the growth of large scale structure over the redshift range $0.4\lesssim z \lesssim 1$ from the cross-correlation of spectroscopically calibrated Luminous Red Galaxies (LRGs) selected from the Dark Energy Spectroscopic Instrument (DESI) legacy imaging survey with CMB lensing maps reconstructed from the latest Planck and ACT data. We adopt a hybrid effective field theory (HEFT) model that robustly regulates the cosmological information obtainable from smaller scales, such that our cosmological constraints are reliably derived from the (predominantly) linear regime. We perform an extensive set of bandpower- and parameter-level systematics checks to ensure the robustness of our results and to characterize the uniformity of the LRG sample. We demonstrate that our results are stable to a wide range of modeling assumptions, finding excellent agreement with a linear theory analysis performed on a restricted range of scales. From a tomographic analysis of the four LRG photometric redshift bins we find that the rate of structure growth is consistent with $\Lambda$CDM with an overall amplitude that is $\simeq5-7\%$ lower than predicted by primary CMB measurements with modest $(\sim2\sigma)$ statistical significance. From the combined analysis of all four bins and their cross-correlations with Planck we obtain $S_8 = 0.765\pm0.023$, which is less discrepant with primary CMB measurements than previous DESI LRG cross Planck CMB lensing results. From the cross-correlation with ACT we obtain $S_8 = 0.790^{+0.024}_{-0.027}$, while when jointly analyzing Planck and ACT we find $S_8 = 0.775^{+0.019}_{-0.022}$ from our data alone and $\sigma_8 = 0.772^{+0.020}_{-0.023}$ with the addition of BAO data. These constraints are consistent with the latest Planck primary CMB analyses at the $\simeq 1.6-2.2\sigma$ level, and are in excellent agreement with galaxy lensing surveys.Comment: 60 pages, 26 figures, comments welcom

Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets

The NIAID (National Institute for Allergy and Infectious Diseases) Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents. The Biodefense Resource Center (www.proteomicsresource.org) has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and heterogeneous data. Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases. Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case studies presented here. (1) The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells) infected by different bacterial (Bacillus anthracis and Salmonella typhimurium) and viral (orthopox) pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. (2) The analysis of a vaccinia-human protein interaction network supplemented with protein accumulation levels led to the identification of human Keratin, type II cytoskeletal 4 protein as a potential therapeutic target. (3) Comparison of complete genomes from pathogenic variants coupled with experimental information on complete proteomes allowed the identification and prioritization of ten potential diagnostic targets from Bacillus anthracis. The integrative analysis across data sets from multiple centers can reveal potential functional significance and hidden relationships between pathogen and host proteins, thereby providing a systems approach to basic understanding of pathogenicity and target identification

The Atacama Cosmology Telescope DR6 and DESI: Structure formation over cosmic time with a measurement of the cross-correlation of CMB Lensing and Luminous Red Galaxies

We present a high-significance cross-correlation of CMB lensing maps from the Atacama Cosmology Telescope (ACT) Data Release 6 (DR6) with spectroscopically calibrated luminous red galaxies (LRGs) from the Dark Energy Spectroscopic Instrument (DESI). We detect this cross-correlation at a significance of 38$\sigma$; combining our measurement with the Planck Public Release 4 (PR4) lensing map, we detect the cross-correlation at 50$\sigma$. Fitting this jointly with the galaxy auto-correlation power spectrum to break the galaxy bias degeneracy with $\sigma_8$, we perform a tomographic analysis in four LRG redshift bins spanning $0.4 \le z \le 1.0$ to constrain the amplitude of matter density fluctuations through the parameter combination $S_8^\times = \sigma_8 \left(\Omega_m / 0.3\right)^{0.4}$. Prior to unblinding, we confirm with extragalactic simulations that foreground biases are negligible and carry out a comprehensive suite of null and consistency tests. Using a hybrid effective field theory (HEFT) model that allows scales as small as $k_{\rm max}=0.6$ $h/{\rm Mpc}$, we obtain a 3.3% constraint on $S_8^\times = \sigma_8 \left(\Omega_m / 0.3\right)^{0.4} = 0.792^{+0.024}_{-0.028}$ from ACT data, as well as constraints on $S_8^\times(z)$ that probe structure formation over cosmic time. Our result is consistent with the early-universe extrapolation from primary CMB anisotropies measured by Planck PR4 within 1.2$\sigma$. Jointly fitting ACT and Planck lensing cross-correlations we obtain a 2.7% constraint of $S_8^\times = 0.776^{+0.019}_{-0.021}$, which is consistent with the Planck early-universe extrapolation within 2.1$\sigma$, with the lowest redshift bin showing the largest difference in mean. The latter may motivate further CMB lensing tomography analyses at $z<0.6$ to assess the impact of potential systematics or the consistency of the $\Lambda$CDM model over cosmic time.Comment: Prepared for submission to JCAP (47 pages, 13 figures

1-year health outcomes associated with systemic corticosteroids for COVID-19:a longitudinal cohort study

BACKGROUND: In patients with coronavirus disease 2019 (COVID-19) requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) 1 year after discharge.METHODS: Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies (Post-hospitalisation COVID-19 and the International Severe Acute Respiratory and emerging Infection Consortium). HRQoL, assessed by the EuroQol-Five Dimensions-Five Levels utility index (EQ-5D-5L UI), pre-hospital and 1 year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient-reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias.FINDINGS: Of the 1888 participants included in the primary analysis, 1149 received corticosteroids. There was no between-group difference in EQ-5D-5L UI at 1 year (mean difference 0.004, 95% CI -0.026-0.034). A similar reduction in EQ-5D-5L UI was seen at 1 year between corticosteroid exposed and nonexposed groups (mean±sd change -0.12±0.22 versus -0.11±0.22). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a cohort of 109 318 patients admitted to hospital with COVID-19, EQ-5D-5L UI at 1 year remained similar between the two groups.INTERPRETATION: Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL 1 year after hospital discharge. Treatments to address the persistent reduction in HRQoL are urgently needed.</p

Increased Incidence of Vestibular Disorders in Patients With SARS-CoV-2

OBJECTIVE: Determine the incidence of vestibular disorders in patients with SARS-CoV-2 compared to the control population. STUDY DESIGN: Retrospective. SETTING: Clinical data in the National COVID Cohort Collaborative database (N3C). METHODS: Deidentified patient data from the National COVID Cohort Collaborative database (N3C) were queried based on variant peak prevalence (untyped, alpha, delta, omicron 21K, and omicron 23A) from covariants.org to retrospectively analyze the incidence of vestibular disorders in patients with SARS-CoV-2 compared to control population, consisting of patients without documented evidence of COVID infection during the same period. RESULTS: Patients testing positive for COVID-19 were significantly more likely to have a vestibular disorder compared to the control population. Compared to control patients, the odds ratio of vestibular disorders was significantly elevated in patients with untyped (odds ratio [OR], 2.39; confidence intervals [CI], 2.29-2.50; CONCLUSIONS: The incidence of vestibular disorders differed between COVID-19 variants and was significantly elevated in COVID-19-positive patients compared to the control population. These findings have implications for patient counseling and further research is needed to discern the long-term effects of these findings