Security Data Warehouse Application

The Security Data Warehouse (SDW) is used to aggregate and correlate all JSC IT security data. This includes IT asset inventory such as operating systems and patch levels, users, user logins, remote access dial-in and VPN, and vulnerability tracking and reporting. The correlation of this data allows for an integrated understanding of current security issues and systems by providing this data in a format that associates it to an individual host. The cornerstone of the SDW is its unique host-mapping algorithm that has undergone extensive field tests, and provides a high degree of accuracy. The algorithm comprises two parts. The first part employs fuzzy logic to derive a best-guess host assignment using incomplete sensor data. The second part is logic to identify and correct errors in the database, based on subsequent, more complete data. Host records are automatically split or merged, as appropriate. The process had to be refined and thoroughly tested before the SDW deployment was feasible. Complexity was increased by adding the dimension of time. The SDW correlates all data with its relationship to time. This lends support to forensic investigations, audits, and overall situational awareness. Another important feature of the SDW architecture is that all of the underlying complexities of the data model and host-mapping algorithm are encapsulated in an easy-to-use and understandable Perl language Application Programming Interface (API). This allows the SDW to be quickly augmented with additional sensors using minimal coding and testing. It also supports rapid generation of ad hoc reports and integration with other information systems

Geometrical analysis of the inland topography to assess the likely response of wave-dominated coastline to sea level: application to Great Britain

The need for quantitative assessments at a large spatial scale (103 km) and over time horizons of the order 101 to 102 years have been reinforced by the 2019 Special Report on the Ocean and Cryosphere in a Changing Climate, which concluded that adaptation to a sea-level rise will be needed no matter what emission scenario is followed. Here, we used a simple geometrical analysis of the backshore topography to assess the likely response of any wave-dominated coastline to a sea-level rise, and we applied it along the entire Great Britain (GB) coastline, which is ca. 17,820 km long. We illustrated how the backshore geometry can be linked to the shoreline response (rate of change and net response: erosion or accretion) to a sea-level rise by using a generalized shoreline Exner equation, which includes the effect of the backshore slope and differences in sediment fractions within the nearshore. To apply this to the whole of GB, we developed an automated delineation approach to extract the main geometrical attributes. Our analysis suggests that 71% of the coast of GB is best described as gentle coast, including estuarine coastline or open coasts where back-barrier beaches can form. The remaining 39% is best described as cliff-type coastlines, for which the majority (57%) of the backshore slope values are negative, suggesting that a non-equilibrium trajectory will most likely be followed as a response to a rise in sea level. For the remaining 43% of the cliffed coast, we have provided regional statistics showing where the potential sinks and sources of sediment are likely to be

Pulmonary metastasectomy in colorectal cancer: health utility scores by EQ-5D-3L in a randomized controlled trial show no benefit from lung metastasectomy.

AIM: The aim was to assess the health utility of lung metastasectomy in the treatment of patients with colorectal cancer (CRC) using the EQ-5D-3L questionnaire. METHODS: Multidisciplinary CRC teams at 14 sites recruited patients to a two-arm randomized controlled trial-Pulmonary Metastasectomy in Colorectal Cancer (PulMiCC). Remote randomization was used, stratified by site and with minimization for seven known confounders. Participants completed the EQ-5D-3L questionnaire together with other patient reported outcome measures at randomization and then again at 3, 6, 12 and 24 months. These were returned by post to the coordinating centre. RESULTS: Between December 2010 and December 2016, 93 participants were randomized, 91 of whom returned questionnaires. Survival and patient reported quality of life have been published previously, revealing no significant differences between the trial arms. Described here are patient reported data from the five dimensions of the EQ-5D-3L and the visual analogue scale (VAS) health state. No significant difference was seen at any time point. The estimated difference between control and metastasectomy patients was -0.23 (95% CI -0.113, 0.066) for the composite 0 to 1 index scale based on the descriptive system and 0.123 (95% CI -7.24, 7.49) for the 0 to 100 VAS scale. CONCLUSIONS: Following lung metastasectomy for CRC, no benefit was demonstrated for health utility, which alongside a lack of a survival or quality of life benefit calls into question the widespread use of the procedure

Long-term Hydro-economic Analysis Tool for Evaluating Global Groundwater Cost and Supply: Superwell v1.0

Groundwater plays a key role in meeting water demands, supplying over 40 % of irrigation water globally, with this role likely to grow as water demands and surface water variability increase. A better understanding of the future role of groundwater in meeting sectoral demands requires an integrated hydro-economic evaluation of its cost and availability. Yet substantial gaps remain in our knowledge and modeling capabilities related to groundwater availability, feasible locations for extraction, extractable volumes, and associated extraction costs, which are essential for large-scale analyses of integrated human-water systems scenarios, particularly at the global scale. To address these needs, we developed Superwell, a physics-based groundwater extraction and cost accounting model that operates at 0.5° (≈50x50 km) gridded spatial resolution with global coverage. The model produces location-specific groundwater supply-cost curves that provide the levelized cost to access different quantities of available groundwater. The inputs to Superwell include recent high-resolution hydrogeologic datasets of permeability, porosity, aquifer thickness, depth to water table, and hydrogeological complexity zones. It also accounts for well capital and maintenance costs, and the energy costs required to lift water to the surface. The model employs a Theis-based scheme coupled with an amortization-based cost accounting formulation to simulate groundwater extraction and quantify the cost of groundwater pumping. The result is a spatiotemporally flexible, physically-realistic, economics-based model that produces groundwater supply-cost curves. We show examples of these supply-cost curves and the insights that can be derived from them across a set of scenarios designed to explore model outcomes. The supply-cost curves produced by the model show that most nonrenewable groundwater in storage globally is extractable at costs lower than 0.23 USD/m3, while half of the volume remains extractable at under 0.138 USD/m3. We also demonstrate and discuss examples of how these cost curves could be used by linking Superwell’s outputs with other models to explore coupled human-environmental systems challenges, such as water resources planning and management, or broader analyses of multi-sectoral feedbacks

A Global Hydrologic Framework to Accelerate Scientific Discovery

With the ability to simulate historical and future global water availability on a monthly time step at a spatial resolution of 0.5 geographic degree, the Python package Xanthos version 1 provided a solid foundation for continuing advancements in global water dynamics science. The goal of Xanthos version 2 was to build upon previous investments by creating a Python framework where core components of the model (potential evapotranspiration (PET), runoff generation, and river routing) could be interchanged or extended without having to start from scratch. Xanthos 2 utilizes a component-style architecture which enables researchers to quickly incorporate and test cutting-edge research in a stable modeling environment prebuilt with diagnostics. Major advancements for Xanthos 2 were also achieved by the creation of a robust default configuration with a calibration module, hydropower modules, and new PET modules, which are now available to the scientific community. Funding statement: This research was supported by the U.S. Department of Energy, Office of Science, as part of research in Multi-Sector Dynamics, Earth and Environmental System Modeling Program. The Pacific Northwest National Laboratory is operated for DOE by Battelle Memorial Institute under contract DE-AC05-76RL01830. The views and opinions expressed in this paper are those of the authors alone

Associations with photoreceptor thickness measures in the UK Biobank.

Spectral-domain OCT (SD-OCT) provides high resolution images enabling identification of individual retinal layers. We included 32,923 participants aged 40-69 years old from UK Biobank. Questionnaires, physical examination, and eye examination including SD-OCT imaging were performed. SD OCT measured photoreceptor layer thickness includes photoreceptor layer thickness: inner nuclear layer-retinal pigment epithelium (INL-RPE) and the specific sublayers of the photoreceptor: inner nuclear layer-external limiting membrane (INL-ELM); external limiting membrane-inner segment outer segment (ELM-ISOS); and inner segment outer segment-retinal pigment epithelium (ISOS-RPE). In multivariate regression models, the total average INL-RPE was observed to be thinner in older aged, females, Black ethnicity, smokers, participants with higher systolic blood pressure, more negative refractive error, lower IOPcc and lower corneal hysteresis. The overall INL-ELM, ELM-ISOS and ISOS-RPE thickness was significantly associated with sex and race. Total average of INL-ELM thickness was additionally associated with age and refractive error, while ELM-ISOS was additionally associated with age, smoking status, SBP and refractive error; and ISOS-RPE was additionally associated with smoking status, IOPcc and corneal hysteresis. Hence, we found novel associations of ethnicity, smoking, systolic blood pressure, refraction, IOPcc and corneal hysteresis with photoreceptor thickness

The pulmonary metastasectomy in colorectal cancer (PulMiCC) burden of care study: analysis of local treatments for lung metastases and systemic chemotherapy in 220 patients in the PulMiCC cohort

Aim The aim of this work was to examine the burden of further treatments in patients with colorectal cancer following a decision about lung metastasectomy. Method Five teams participating in the Pulmonary Metastasectomy in Colorectal Cancer (PulMiCC) study provided details on subsequent local treatments for lung metastases, including the use of chemotherapy. For patients in three groups (no metastasectomy, one metastasectomy or multiple local interventions), baseline factors and selection criteria for additional treatments were examined. Results The five teams recruited 220 patients between October 2010 and January 2017. No lung metastasectomy was performed in 51 patients, 114 patients had one metastasectomy and 55 patients had multiple local interventions. Selection for initial metastasectomy was associated with nonelevated carcinoembryonic antigen, fewer metastases and no prior liver metastasectomy. These patients also had better Eastern Cooperative Oncology Group scores and lung function at baseline. Four sites provided information on chemotherapy in 139 patients: 79 (57%) had one to five courses of chemotherapy, to a total of 179 courses. The patterns of survival after one or multiple metastasectomy interventions showed evidence of guarantee-time bias contributing to an impression of benefit over no metastasectomy. After repeated metastasectomy, a significantly higher risk of death was observed, with no apparent reduction in chemotherapy usage. Conclusion Repeated metastasectomy is associated with a higher risk of death without reducing the use of chemotherapy. Continued monitoring without surgery might reassure patients with indolent disease or allow response assessment during systemic treatment. Overall, the carefully collected information from the PulMICC study provides no indication of an important survival benefit from metastasectomy

Automated retinal image quality assessment on the UK Biobank dataset for epidemiological studies.

Morphological changes in the retinal vascular network are associated with future risk of many systemic and vascular diseases. However, uncertainty over the presence and nature of some of these associations exists. Analysis of data from large population based studies will help to resolve these uncertainties. The QUARTZ (QUantitative Analysis of Retinal vessel Topology and siZe) retinal image analysis system allows automated processing of large numbers of retinal images. However, an image quality assessment module is needed to achieve full automation. In this paper, we propose such an algorithm, which uses the segmented vessel map to determine the suitability of retinal images for use in the creation of vessel morphometric data suitable for epidemiological studies. This includes an effective 3-dimensional feature set and support vector machine classification. A random subset of 800 retinal images from UK Biobank (a large prospective study of 500,000 middle aged adults; where 68,151 underwent retinal imaging) was used to examine the performance of the image quality algorithm. The algorithm achieved a sensitivity of 95.33% and a specificity of 91.13% for the detection of inadequate images. The strong performance of this image quality algorithm will make rapid automated analysis of vascular morphometry feasible on the entire UK Biobank dataset (and other large retinal datasets), with minimal operator involvement, and at low cost

Suitability of UK biobank retinal images for automatic analysis of morphometric properties of the vasculature

To assess the suitability of retinal images held in the UK Biobank--the largest retinal data repository in a prospective population-based cohort--for computer assisted vascular morphometry, generating measures that are commonly investigated as candidate biomarkers of systemic disease.Non-mydriatic fundus images from both eyes of 2,690 participants--people with a self-reported history of myocardial infarction (n=1,345) and a matched control group (n=1,345)--were analysed using VAMPIRE software. These images were drawn from those of 68,554 UK Biobank participants who underwent retinal imaging at recruitment. Four operators were trained in the use of the software to measure retinal vascular tortuosity and bifurcation geometry.Total operator time was approximately 360 hours (4 minutes per image). 2,252 (84%) of participants had at least one image of sufficient quality for the software to process, i.e. there was sufficient detection of retinal vessels in the image by the software to attempt the measurement of the target parameters. 1,604 (60%) of participants had an image of at least one eye that was adequately analysed by the software, i.e. the measurement protocol was successfully completed. Increasing age was associated with a reduced proportion of images that could be processed (p=0.0004) and analysed (p<0.0001). Cases exhibited more acute arteriolar branching angles (p=0.02) as well as lower arteriolar and venular tortuosity (p<0.0001).A proportion of the retinal images in UK Biobank are of insufficient quality for automated analysis. However, the large size of the UK Biobank means that tens of thousands of images are available and suitable for computational analysis. Parametric information measured from the retinas of participants with suspected cardiovascular disease was significantly different to that measured from a matched control group

The Relationship Between Ambient Atmospheric Fine Particulate Matter (PM2.5) and Glaucoma in a Large Community Cohort.

Purpose: Glaucoma is more common in urban populations than in others. Ninety percent of the world's population are exposed to air pollution above World Health Organization (WHO) recommended limits. Few studies have examined the association between air pollution and glaucoma. Methods: Questionnaire data, ophthalmic measures, and ambient residential area air quality data for 111,370 UK Biobank participants were analyzed. Particulate matter with an aerodynamic diameter < 2.5 μm (PM2.5) was selected as the air quality exposure of interest. Eye measures included self-reported glaucoma, intraocular pressure (IOP), and average thickness of macular ganglion cell-inner plexiform layer (GCIPL) across nine Early Treatment Diabetic Retinopathy Study (ETDRS) retinal subfields as obtained from spectral-domain optical coherence tomography. We examined the associations of PM2.5 concentration with self-reported glaucoma, IOP, and GCIPL. Results: Participants resident in areas with higher PM2.5 concentration were more likely to report a diagnosis of glaucoma (odds ratio = 1.06, 95% confidence interval [CI] = 1.01-1.12, per interquartile range [IQR] increase P = 0.02). Higher PM2.5 concentration was also associated with thinner GCIPL (β = -0.56 μm, 95% CI = -0.63 to -0.49, per IQR increase, P = 1.2 × 10-53). A dose-response relationship was observed between higher levels of PM2.5 and thinner GCIPL (P < 0.001). There was no clinically relevant relationship between PM2.5 concentration and IOP. Conclusions: Greater exposure to PM2.5 is associated with both self-reported glaucoma and adverse structural characteristics of the disease. The absence of an association between PM2.5 and IOP suggests the relationship may occur through a non-pressure-dependent mechanism, possibly neurotoxic and/or vascular effects