Arrayed synthetic aperture radar

In this thesis, the use of array processing techniques applied to Single Input Multiple Output (SIMO) SAR systems with enhanced capabilities is investigated. In Single Input Single Output (SISO) SAR systems there is a high resolution, wide swath contradiction, whereby it is not possible to increase both cross-range resolution and the imaged swath width simultaneously. To overcome this, a novel beamformer for SAR systems in the cross-range direction is proposed. In particular, this beamformer is a superresolution beamformer capable of forming wide nulls using subspace based approaches. SIMO SAR systems also give rise to additional sets of received data, which includes geometrical information about the SAR and target environment, and can be used for enhanced target parameter estimation. In particular, this thesis looks at round trip delay, joint azimuth and elevation angle, and relative target power estimation. For round trip delay estimation, the use of the traditional matched filter with subspace partitioning is proposed. Then by using a joint 2D Multiple Signal Classification (MUSIC) algorithm, joint Direction of Arrival (DOA) estimation can be achieved. Both the use of range lines of raw SAR data and the use of a Region of Interest (ROI) of a SAR image are investigated. However in terms of imaging, MUSIC is not well-suited for SAR, due to its target response not corresponding to the target's true power return. Therefore a joint DOA and target power estimation algorithm is proposed to overcome this limitation. These algorithms provide the framework for the development of three processing techniques. These allow sidelobe suppression in the slant range direction, along with the reconstruction of undersampled data and region enhancement using MUSIC with power preservation.Open Acces

Detecting Small Vessel Pathology in Cocaine Use Disorder

BackgroundCocaine use is associated with an increased risk of cerebrovascular accidents. Small vessel pathology has been linked to the risk of stroke in cocaine users, but can be challenging to detect on conventional magnetic resonance (MR) scans. Fluid-attenuated inversion recovery (FLAIR) scans permit better resolution of small vessel lesions.ObjectivesFLAIR scans are currently only acquired based on the subjective judgement of abnormalities on MR scans at face value. We sought to evaluate this practice and the added value of FLAIR scans for patients with cocaine use disorder (CUD), by comparing microbleeds detected by MR and FLAIR scans. We hypothesised that microbleeds are more pronounced in CUD patients, particularly so in participants who had been selected for a FLAIR scan by radiographers.MethodsSixty-four patients with CUD and 60 control participants underwent a brain scan. The MR of 20 CUD patients and 16 control participants showed indicators of cerebral infarction at face value and were followed up by a FLAIR scan. We determined the volume of microbleeds in both MR and FLAIR scans and examined associations with various risk factors.ResultsWhile MR lesion volumes were significantly increased in CUD patients, no significant differences in lesion volume were found in the subgroup of individuals who received a FLAIR.ConclusionThe current practice of subjectively evaluating MR scans as a basis for the follow-up FLAIR scans to detect vascular pathology may miss vulnerable individuals. Hence, FLAIR scans should be included as a routine part of research studies.</jats:sec

Inequalities in the incidence of cervical cancer in South East England 2001–2005: an investigation of population risk factors

BACKGROUND: The incidence of cervical cancer varies dramatically, both globally and within individual countries. The age-standardised incidence of cervical cancer was compared across primary care trusts (PCTs) in South East England, taking into account the prevalence of known behavioural risk factors, screening coverage and the deprivation of the area. METHODS: Data on 2,231 cases diagnosed between 2001 and 2005 were extracted from the Thames Cancer Registry, and data on risk factors and screening coverage were collated from publicly available sources. Age-standardised incidence rates were calculated for each PCT using cases of squamous cell carcinoma in the screening age group (25-64 years). RESULTS: The age-standardised incidence rate for cervical cancer in South East England was 6.7 per 100,000 population (European standard) but varied 3.1 fold between individual PCTs. Correlations between the age-standardised incidence rate and smoking prevalence, teenage conception rates, and deprivation were highly significant at the PCT level (p < 0.001). However, screening coverage was not associated with the incidence of cervical cancer at the PCT level. Poisson regression indicated that these variables were all highly correlated and could not determine the level of independent contribution at a population level. CONCLUSION: There is excess disease burden within South East England. Significant public health gains can be made by reducing exposure to known risk factors at a population level

Three patients with homozygous familial hypercholesterolemia: Genomic sequencing and kindred analysis.

BackgroundHomozygous Familial Hypercholesterolemia (HoFH) is an inherited recessive condition associated with extremely high levels of low-density lipoprotein (LDL) cholesterol in affected individuals. It is usually caused by homozygous or compound heterozygous functional mutations in the LDL receptor (LDLR). A number of mutations causing FH have been reported in literature and such genetic heterogeneity presents great challenges for disease diagnosis.ObjectiveWe aim to determine the likely genetic defects responsible for three cases of pediatric HoFH in two kindreds.MethodsWe applied whole exome sequencing (WES) on the two probands to determine the likely functional variants among candidate FH genes. We additionally applied 10x Genomics (10xG) Linked-Reads whole genome sequencing (WGS) on one of the kindreds to identify potentially deleterious structural variants (SVs) underlying HoFH. A PCR-based screening assay was also established to detect the LDLR structural variant in a cohort of 641 patients with elevated LDL.ResultsIn the Caucasian kindred, the FH homozygosity can be attributed to two compound heterozygous&nbsp;LDLR damaging variants, an exon 12 p.G592E missense mutation and a novel 3kb exon 1 deletion. By analyzing the 10xG phased data, we ascertained that this deletion allele was most likely to have originated from a Russian ancestor. In the Mexican kindred, the strikingly elevated LDL cholesterol level can be attributed to a homozygous frameshift LDLR variant p.E113fs.ConclusionsWhile the application of WES can provide a cost-effective way of identifying the genetic causes of FH, it often lacks sensitivity for detecting structural variants. Our finding of the LDLR exon 1 deletion highlights the broader utility of Linked-Read WGS in detecting SVs in the clinical setting, especially when HoFH patients remain undiagnosed after WES

Capturing Provenance of Data Curation at BCO-DMO

Presented at Data Curation Network, May 15, 2020At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easer for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.NSF #192461

Capturing Provenance of Data Curation at BCO-DMO

Presented at USGS Data Management Working Group, 9, November 2020At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easier for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.NSF #192461

The Angola Gyre is a hotspot of dinitrogen fixation in the South Atlantic Ocean

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marshall, T., Granger, J., Casciotti, K. L., Dahnke, K., Emeis, K.-C., Marconi, D., McIlvin, M. R., Noble, A. E., Saito, M. A., Sigman, D. M., & Fawcett, S. E. The Angola Gyre is a hotspot of dinitrogen fixation in the South Atlantic Ocean. Communications Earth & Environment, 3(1), (2022): 151, https://doi.org/10.1038/s43247-022-00474-x.Biological dinitrogen fixation is the major source of new nitrogen to marine systems and thus essential to the ocean’s biological pump. Constraining the distribution and global rate of dinitrogen fixation has proven challenging owing largely to uncertainty surrounding the controls thereon. Existing South Atlantic dinitrogen fixation rate estimates vary five-fold, with models attributing most dinitrogen fixation to the western basin. From hydrographic properties and nitrate isotope ratios, we show that the Angola Gyre in the eastern tropical South Atlantic supports the fixation of 1.4–5.4 Tg N.a−1, 28-108% of the existing (highly uncertain) estimates for the basin. Our observations contradict model diagnoses, revealing a substantial input of newly-fixed nitrogen to the tropical eastern basin and no dinitrogen fixation west of 7.5˚W. We propose that dinitrogen fixation in the South Atlantic occurs in hotspots controlled by the overlapping biogeography of excess phosphorus relative to nitrogen and bioavailable iron from margin sediments. Similar conditions may promote dinitrogen fixation in analogous ocean regions. Our analysis suggests that local iron availability causes the phosphorus-driven coupling of oceanic dinitrogen fixation to nitrogen loss to vary on a regional basis.This work was supported by the South African National Research Foundation (114673 and 130826 to T.M., 115335, 116142 and 129320 to S.E.F.); the US National Science Foundation (CAREER award, OCE-1554474 to J.G., OCE-1736652 to D.M.S. and K.L.C., OCE-05-26277 to K.L.C.); the German Federal Agency for Education and Research (DAAD-SPACES 57371082 to T.M.); the Royal Society (FLAIR fellowship to S.E.F.); and the University of Cape Town (T.M., J.G., S.E.F.). The authors also recognize the support of the South African Department of Science and Innovation’s Biogeochemistry Research Infrastructure Platform (BIOGRIP)

Is 'oil pulling' a 'snake oil'? : a clinical trial

The traditional Ayurveda practice of ‘oil pulling’ has become a recent phenomenon and concerns about its efficacy have been raised. Objectives: (1) to determine awareness about the practice of ‘oil pulling’ among a group of young adults, and to determine variations in awareness with respect to socio-demographic factors, oral health behaviours (oral hygiene and dental attendance) and use of natural health products; (2) to determine the effectiveness of ‘oil pulling’ and conventional oral hygiene practice compared to the use of conventional oral hygiene practice alone in terms of oral hygiene and (3) to determine the effectiveness of ‘oil pulling’ and conventional oral hygiene practice compared to the use of conventional oral hygiene practice alone in terms of gingival health. Methods: Group members recruited seventy-four young adults to participate in a clinical trial over a two-month period comparing the effectiveness of (a) ‘oil pulling’ and conventional oral hygiene methods (toothbrush and toothpaste) versus (b) conventional oral hygiene methods alone. Oral hygiene was assessed using the Plaque Index - PI (Silness and Löe, 1964) and the proportion of sites with visible plaque (PVP). Gingival health was assessed using the Gingival Index – GI (Silness and Löe,1963) and the proportion of sites with gingival bleeding (PGB). Participants were block randomized in groups of four to a cross over clinical trial and assessments were conducted at one-month and two-months. Results: Approximately a quarter (28.4%, 21) of participants was aware of the practice of ‘oil pulling’. Awareness of the practice was associated with reported use of natural dental/oral health products (p0.05). There were observed significant differences in gingival health among both the test and control groups from baseline to one-month (p0.05). No significant differences were observed in oral health parameters from one-month to two-month among neither the test nor control groups (p>0.05). Conclusion: Awareness of the practice of ‘oil pulling’ is relatively common and is associated with use of natural dental/oral health products. Findings from the clinical trial failed to support the adjunct use of ‘oil pulling’ in addition to conventional oral hygiene practices.published_or_final_versio

Basin-scale inputs of cobalt, iron, and manganese from the Benguela-Angola front to the South Atlantic Ocean

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2012. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 57 (2012): 989-1010, doi:10.4319/lo.2012.57.4.0989.We present full-depth zonal sections of total dissolved cobalt, iron, manganese, and labile cobalt from the South Atlantic Ocean. A basin-scale plume from the African coast appeared to be a major source of dissolved metals to this region, with high cobalt concentrations in the oxygen minimum zone of the Angola Dome and extending 2500 km into the subtropical gyre. Metal concentrations were elevated along the coastal shelf, likely due to reductive dissolution and resuspension of particulate matter. Linear relationships between cobalt, N2O, and O2, as well as low surface aluminum supported a coastal rather than atmospheric cobalt source. Lateral advection coupled with upwelling, biological uptake, and remineralization delivered these metals to the basin, as evident in two zonal transects with distinct physical processes that exhibited different metal distributions. Scavenging rates within the coastal plume differed for the three metals; iron was removed fastest, manganese removal was 2.5 times slower, and cobalt scavenging could not be discerned from water mass mixing. Because scavenging, biological utilization, and export constantly deplete the oceanic inventories of these three hybrid-type metals, point sources of the scale observed here likely serve as vital drivers of their oceanic cycles. Manganese concentrations were elevated in surface waters across the basin, likely due to coupled redox processes acting to concentrate the dissolved species there. These observations of basin-scale hybrid metal plumes combined with the recent projections of expanding oxygen minimum zones suggest a potential mechanism for effects on ocean primary production and nitrogen fixation via increases in trace metal source inputs.This research was supported US National Science Foundation Chemical Oceanography (Division of Ocean Sciences OCE-0452883, OCE-0752291, OCE-0928414, OCE-1031271), the Center for Microbial Research and Education, the Gordon and Betty Moore Foundation, the WHOI Coastal Ocean Institute, and the WHOI Ocean Life Institute