Swift: primary data analysis for the Illumina Solexa sequencing platform

Motivation: Primary data analysis methods are of critical importance in second generation DNA sequencing. Improved methods have the potential to increase yield and reduce the error rates. Openly documented analysis tools enable the user to understand the primary data, this is important for the optimization and validity of their scientific work

Aircraft-based mass balance estimate of methane emissions from offshore gas facilities in the Southern North Sea

Atmospheric methane (CH4) concentrations have more than doubled since the beginning of the industrial age, making CH4 the second most important anthropogenic greenhouse gas after carbon dioxide (CO2). The oil and gas sector represent one of the major anthropogenic CH4 emitters as it is estimated to account for 22 % of global anthropogenic CH4 emissions. An airborne field campaign was conducted in April&ndash;May 2019 to study CH4 emissions from offshore gas facilities in the Southern North Sea with the aim to derive emission estimates using a top-down (measurement-led) approach. We present CH4 fluxes for six UK and five Dutch offshore platforms/platform complexes using the well-established mass balance flux method. We identify specific gas production emissions and emission processes (venting/fugitive or flaring/combustion) using observations of co-emitted ethane (C2H6) and CO2. We compare our top-down estimated fluxes with a ship-based top-down study in the Dutch sector and with bottom-up estimates from a globally gridded annual inventory, UK national annual point-source inventories, and with operator-based reporting for individual Dutch facilities. In this study, we find that all inventories, except for the operator-based facility-level reporting, underestimate measured emissions, with the largest discrepancy observed with the globally gridded inventory. Individual facility reporting, as available for Dutch sites for the specific survey date, shows better agreement with our measurement-based estimates. For all sampled Dutch installations together, we find that our estimated flux of (122.7 &plusmn; 9.7) kg h-1 deviates by a factor 0.7 (0.35&ndash;12) from reported values (183.1 kg h-1). Comparisons with aircraft observations in two other offshore regions (Norwegian Sea and Gulf of Mexico) show that measured, absolute facility-level emission rates agree with the general distribution found in other offshore basins despite different production types (oil, gas) and gas production rates, which vary by two orders of magnitude. Therefore, mitigation is warranted equally across geographies.</p

Facility level measurement of offshore oil and gas installations from a medium-sized airborne platform : method development for quantification and source identification of methane emissions

Emissions of methane (CH4) from offshore oil and gas installations are poorly ground-truthed, and quantification relies heavily on the use of emission factors and activity data. As part of the United Nations Climate & Clean Air Coalition (UN CCAC) objective to study and reduce short-lived climate pollutants (SLCPs), a Twin Otter aircraft was used to survey CH4 emissions from UK and Dutch offshore oil and gas installations. The aims of the surveys were to (i) identify installations that are significant CH4 emitters, (ii) separate installation emissions from other emissions using carbon-isotopic fingerprinting and other chemical proxies, (iii) estimate CH4 emission rates, and (iv) improve flux estimation (and sampling) methodologies for rapid quantification of major gas leaks. In this paper, we detail the instrument and aircraft set-up for two campaigns flown in the springs of 2018 and 2019 over the southern North Sea and describe the developments made in both the planning and sampling methodology to maximise the quality and value of the data collected. We present example data collected from both campaigns to demonstrate the challenges encountered during offshore surveys, focussing on the complex meteorology of the marine boundary layer and sampling discrete plumes from an airborne platform. The uncertainties of CH4 flux calculations from measurements under varying boundary layer conditions are considered, as well as recommendations for attribution of sources through either spot sampling for volatile organic compounds (VOCs) /δ 13CCH4 or using in situ instrumental data to determine C2H6-CH4 ratios. A series of recommendations for both planning and measurement techniques for future offshore work within marine boundary layers is provided

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Quantification and assessment of methane emissions from offshore oil and gas facilities on the Norwegian continental shelf

The oil and gas (O&G) sector is a significant source of methane (CH4) emissions. Quantifying these emissions remains challenging, with many studies highlighting discrepancies between measurements and inventory-based estimates. In this study, we present CH4 emission fluxes from 21 offshore O&G facilities collected in 10 O&G fields over two regions of the Norwegian continental shelf in 2019. Emissions of CH4 derived from measurements during 13 aircraft surveys were found to range from 2.6 to 1200 t yr−1 (with a mean of 211 t yr−1 across all 21 facilities). Comparing this with aggregated operator-reported facility emissions for 2019, we found excellent agreement (within 1σ uncertainty), with mean aircraft-measured fluxes only 16 % lower than those reported by operators. We also compared aircraft-derived fluxes with facility fluxes extracted from a global gridded fossil fuel CH4 emission inventory compiled for 2016. We found that the measured emissions were 42 % larger than the inventory for the area covered by this study, for the 21 facilities surveyed (in aggregate). We interpret this large discrepancy not to reflect a systematic error in the operator-reported emissions, which agree with measurements, but rather the representativity of the global inventory due to the methodology used to construct it and the fact that the inventory was compiled for 2016 (and thus not representative of emissions in 2019). This highlights the need for timely and up-to-date inventories for use in research and policy. The variable nature of CH4 emissions from individual facilities requires knowledge of facility operational status during measurements for data to be useful in prioritising targeted emission mitigation solutions. Future surveys of individual facilities would benefit from knowledge of facility operational status over time. Field-specific aggregated emissions (and uncertainty statistics), as presented here for the Norwegian Sea, can be meaningfully estimated from intensive aircraft surveys. However, field-specific estimates cannot be reliably extrapolated to other production fields without their own tailored surveys, which would need to capture a range of facility designs, oil and gas production volumes, and facility ages. For year-on-year comparison to annually updated inventories and regulatory emission reporting, analogous annual surveys would be needed for meaningful top-down validation. In summary, this study demonstrates the importance and accuracy of detailed, facility-level emission accounting and reporting by operators and the use of airborne measurement approaches to validate bottom-up accounting

Rheumatoid arthritis - clinical aspects: 134. Predictors of Joint Damage in South Africans with Rheumatoid Arthritis

Background: Rheumatoid arthritis (RA) causes progressive joint damage and functional disability. Studies on factors affecting joint damage as clinical outcome are lacking in Africa. The aim of the present study was to identify predictors of joint damage in adult South Africans with established RA. Methods: A cross-sectional study of 100 black patients with RA of >5 years were assessed for joint damage using a validated clinical method, the RA articular damage (RAAD) score. Potential predictors of joint damage that were documented included socio-demographics, smoking, body mass index (BMI), disease duration, delay in disease modifying antirheumatic drug (DMARD) initiation, global disease activity as measured by the disease activity score (DAS28), erythrocyte sedimentation rate (ESR), C reactive protein (CRP), and autoantibody status. The predictive value of variables was assessed by univariate and stepwise multivariate regression analyses. A p value <0.05 was considered significant. Results: The mean (SD) age was 56 (9.8) years, disease duration 17.5 (8.5) years, educational level 7.5 (3.5) years and DMARD lag was 9 (8.8) years. Female to male ratio was 10:1. The mean (SD) DAS28 was 4.9 (1.5) and total RAAD score was 28.3 (12.8). The mean (SD) BMI was 27.2 kg/m2 (6.2) and 93% of patients were rheumatoid factor (RF) positive. More than 90% of patients received between 2 to 3 DMARDs. Significant univariate predictors of a poor RAAD score were increasing age (p = 0.001), lower education level (p = 0.019), longer disease duration (p < 0.001), longer DMARD lag (p = 0.014), lower BMI (p = 0.025), high RF titre (p < 0.001) and high ESR (p = 0.008). The multivariate regression analysis showed that the only independent significant predictors of a higher mean RAAD score were older age at disease onset (p = 0.04), disease duration (p < 0.001) and RF titre (p < 0.001). There was also a negative association between BMI and the mean total RAAD score (p = 0.049). Conclusions: Patients with longstanding established RA have more severe irreversible joint damage as measured by the clinical RAAD score, contrary to other studies in Africa. This is largely reflected by a delay in the initiation of early effective treatment. Independent of disease duration, older age at disease onset and a higher RF titre are strongly associated with more joint damage. The inverse association between BMI and articular damage in RA has been observed in several studies using radiographic damage scores. The mechanisms underlying this paradoxical association are still widely unknown but adipokines have recently been suggested to play a role. Disclosure statement: C.I. has received a research grant from the Connective Tissue Diseases Research Fund, University of the Witwatersrand. All other authors have declared no conflicts of interes

Case Reports1. A Late Presentation of Loeys-Dietz Syndrome: Beware of TGFβ Receptor Mutations in Benign Joint Hypermobility

Background: Thoracic aortic aneurysms (TAA) and dissections are not uncommon causes of sudden death in young adults. Loeys-Dietz syndrome (LDS) is a rare, recently described, autosomal dominant, connective tissue disease characterized by aggressive arterial aneurysms, resulting from mutations in the transforming growth factor beta (TGFβ) receptor genes TGFBR1 and TGFBR2. Mean age at death is 26.1 years, most often due to aortic dissection. We report an unusually late presentation of LDS, diagnosed following elective surgery in a female with a long history of joint hypermobility. Methods: A 51-year-old Caucasian lady complained of chest pain and headache following a dural leak from spinal anaesthesia for an elective ankle arthroscopy. CT scan and echocardiography demonstrated a dilated aortic root and significant aortic regurgitation. MRA demonstrated aortic tortuosity, an infrarenal aortic aneurysm and aneurysms in the left renal and right internal mammary arteries. She underwent aortic root repair and aortic valve replacement. She had a background of long-standing joint pains secondary to hypermobility, easy bruising, unusual fracture susceptibility and mild bronchiectasis. She had one healthy child age 32, after which she suffered a uterine prolapse. Examination revealed mild Marfanoid features. Uvula, skin and ophthalmological examination was normal. Results: Fibrillin-1 testing for Marfan syndrome (MFS) was negative. Detection of a c.1270G > C (p.Gly424Arg) TGFBR2 mutation confirmed the diagnosis of LDS. Losartan was started for vascular protection. Conclusions: LDS is a severe inherited vasculopathy that usually presents in childhood. It is characterized by aortic root dilatation and ascending aneurysms. There is a higher risk of aortic dissection compared with MFS. Clinical features overlap with MFS and Ehlers Danlos syndrome Type IV, but differentiating dysmorphogenic features include ocular hypertelorism, bifid uvula and cleft palate. Echocardiography and MRA or CT scanning from head to pelvis is recommended to establish the extent of vascular involvement. Management involves early surgical intervention, including early valve-sparing aortic root replacement, genetic counselling and close monitoring in pregnancy. Despite being caused by loss of function mutations in either TGFβ receptor, paradoxical activation of TGFβ signalling is seen, suggesting that TGFβ antagonism may confer disease modifying effects similar to those observed in MFS. TGFβ antagonism can be achieved with angiotensin antagonists, such as Losartan, which is able to delay aortic aneurysm development in preclinical models and in patients with MFS. Our case emphasizes the importance of timely recognition of vasculopathy syndromes in patients with hypermobility and the need for early surgical intervention. It also highlights their heterogeneity and the potential for late presentation. Disclosures: The authors have declared no conflicts of interes