Refining Finite-Time Lyapunov Exponent Ridges and the Challenges of Classifying Them

While more rigorous and sophisticated methods for identifying Lagrangian based coherent structures exist, the finite-time Lyapunov exponent (FTLE) field remains a straightforward and popular method for gaining some insight into transport by complex, time-dependent two-dimensional flows. In light of its enduring appeal, and in support of good practice, we begin by investigating the effects of discretization and noise on two numerical approaches for calculating the FTLE field. A practical method to extract and refine FTLE ridges in two-dimensional flows, which builds on previous methods, is then presented. Seeking to better ascertain the role of a FTLE ridge in flow transport, we adapt an existing classification scheme and provide a thorough treatment of the challenges of classifying the types of deformation represented by a FTLE ridge. As a practical demonstration, the methods are applied to an ocean surface velocity field data set generated by a numerical model. (C) 2015 AIP Publishing LLC.ONR N000141210665Center for Nonlinear Dynamic

Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual microbial taxa, microbial communities, and metagenomic assemblages. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of indices of published genetic data deriving from ancient microbial samples that provides basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These collections are community-curated and span multiple sub-disciplines in order to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks to facilitate compatibility with established sequence-read archives and term-ontologies ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.Competing Interest StatementThe authors have declared no competing interest.Background & Summary Methods - Repository Structure - Data Acquisition - Data Validation Data Records Technical Validation Usage Note

Using non-parametric Bayes shrinkage to assess relationships between multiple environmental and social stressors and neonatal size and body composition in the Healthy Start cohort

Background: Both environmental and social factors have been linked to birth weight and adiposity at birth, but few studies consider the effects of exposure mixtures. Our objective was to identify which components of a mixture of neighborhood-level environmental and social exposures were driving associations with birth weight and adiposity at birth in the Healthy Start cohort. Methods: Exposures were assessed at the census tract level and included air pollution, built environment characteristics, and socioeconomic status. Prenatal exposures were assigned based on address at enrollment. Birth weight was measured at delivery and adiposity was measured using air displacement plethysmography within three days. We used non-parametric Bayes shrinkage (NPB) to identify exposures that were associated with our outcomes of interest. NPB models were compared to single-predictor linear regression. We also included generalized additive models (GAM) to assess nonlinear relationships. All regression models were adjusted for individual-level covariates, including maternal age, pre-pregnancy BMI, and smoking. Results: Results from NPB models showed most exposures were negatively associated with birth weight, though credible intervals were wide and generally contained zero. However, the NPB model identified an interaction between ozone and temperature on birth weight, and the GAM suggested potential non-linear relationships. For associations between ozone or temperature with birth weight, we observed effect modification by maternal race/ethnicity, where effects were stronger for mothers who identified as a race or ethnicity other than non-Hispanic White. No associations with adiposity at birth were observed. Conclusions: NPB identified prenatal exposures to ozone and temperature as predictors of birth weight, and mothers who identify as a race or ethnicity other than non-Hispanic White might be disproportionately impacted. However, NPB models may have limited applicability when non-linear effects are present. Future work should consider a two-stage approach where NPB is used to reduce dimensionality and alternative approaches examine non-linear effects

Geomasking sensitive health data and privacy protection: an evaluation using an E911 database

Geomasking is used to provide privacy protection for individual address information while maintaining spatial resolution for mapping purposes. Donut geomasking and other random perturbation geomasking algorithms rely on the assumption of a homogeneously distributed population to calculate displacement distances, leading to possible under-protection of individuals when this condition is not met. Using household data from 2007, we evaluated the performance of donut geomasking in Orange County, North Carolina. We calculated the estimated k-anonymity for every household based on the assumption of uniform household distribution. We then determined the actual k-anonymity by revealing household locations contained in the county E911 database. Census block groups in mixed-use areas with high population distribution heterogeneity were the most likely to have privacy protection below selected criteria. For heterogeneous populations, we suggest tripling the minimum displacement area in the donut to protect privacy with a less than 1% error rate

Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies

Data base for the analysis of compositional characteristics of coal seams and macerals. Part 7. Petrographic variation due to depositional setting of the lower Kittanning seam, western Pennsylvania. Final report

Detailed megascopic and microscopic petrographic analyses were conducted on samples of the Lower Kittanning seam from western Pennsylvania. Relationships were sought between the paleoenvironmental setting of the coal swamp and the vertical and lateral variability of lithotypes, maceral composition and vitrinite types. Megascopically, the four samples collected from the freshwater facies of the seam are similar in appearance and relative lithotype composition, and display no distinct vertical zonations. The sample from the marine-influenced central portion of the basin (PSOC-1340) possesses a marked vertical zonation into a bright lower zone and a dull upper zone. The lower zone is similar in appearance to the freswater samples. Detailed microscopic analyses revealed that the vertical zonation of PSOC-1340 is apparent in both the maceral and vitrinite type composition. No similar zonation is apparent in the microscopic analysis of the four freshwater facies samples. Similarities between the lower zone of PSOC-1340 and the whole seam of the freshwater samples are most apparent in the vitrinite-type analysis. The lower zone of PSOC-1340 and the whole seam from the freshwater facies are considered to be laterally equivalent coal types. The dull upper zone of PSOC-1340 is considered to have formed in response to a major change in the paleoenvironment of the swamp, probably a marine transgression. 49 references, 25 figures, 15 tables

Design and performance of the Z magnetically-insulated transmission lines

The 36-module Z accelerator was designed to drive z-pinch loads for weapon-physics and inertial-confinement-fusion experiments, and to serve as a testing facility for pulsed-power research required to develop higher-current drivers. The authors have designed and tested a 10-nH 1.5-m-radius vacuum section for the Z accelerator. The vacuum section consists of four vacuum flares, four conical 1.3-m-radius magnetically-insulated transmission lines, a 7.6-cm-radius 12-post double-post-hole convolute which connects the four outer MITLs in parallel, and a 5-cm-long inner MITL which connects the output of the convolute to a z-pinch load. IVORY and ELECTRO calculations were performed to minimize the inductance of the vacuum flares with the constraint that there be no significant electron emission from the insulator-stack grading rings. Iterative TLCODE calculations were performed to minimize the inductance of the outer MITLs with the constraint that the MITL electron-flow-current fraction be {le} 7% at peak current. The TLCODE simulations assume a 2.5 cm/{micro}s MITL-cathode-plasma expansion velocity. The design limits the electron dose to the outer-MITL anodes to 50 J/g to prevent the formation of an anode plasma. The TLCODE results were confirmed by SCREAMER, TRIFL, TWOQUICK, IVORY, and LASNEX simulations. For the TLCODE, SCREAMER, and TRIFL calculations, the authors assume that after magnetic insulation is established, the electron-flow current launched in the outer MITLs is lost at the convolute. This assumption has been validated by 3-D QUICKSILVER simulations for load impedances {le} 0.36 ohms. LASNEX calculations suggest that ohmic resistance of the pinch and conduction-current-induced energy loss to the MITL electrodes can be neglected in Z power-flow modeling that is accurate to first order. To date, the Z vacuum section has been tested on 100 shots. They have demonstrated they can deliver a 100-ns rise-time 20-MA current pulse to the baseline z-pinch load