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The Gulf of Mexico is the largest offshore fossil fuel production basin in the United States. Decisions on expanding production in the region legally depend on assessments of the climate impact of new growth. Here, we collect airborne observations and combine them with previous surveys and inventories to estimate the climate impact of current field operations. We evaluate all major on-site greenhouse gas emissions, carbon dioxide (CO 2 ) from combustion, and methane from losses and venting. Using these findings, we estimate the climate impact per unit of energy of produced oil and gas (the carbon intensity). We find high methane emissions (0.60 Tg/y [0.41 to 0.81, 95% confidence interval]) exceeding inventories. This elevates the average CI of the basin to 5.3 g CO 2 e/MJ [4.1 to 6.7] (100-y horizon) over twice the inventories. The CI across the Gulf varies, with deep water production exhibiting a low CI dominated by combustion emissions (1.1 g CO 2 e/MJ), while shallow federal and state waters exhibit an extraordinarily high CI (16 and 43 g CO 2 e/MJ) primarily driven by methane emissions from central hub facilities (intermediaries for gathering and processing). This shows that production in shallow waters, as currently operated, has outsized climate impact. To mitigate these climate impacts, methane emissions in shallow waters must be addressed through efficient flaring instead of venting and repair, refurbishment, or abandonment of poorly maintained infrastructure. We demonstrate an approach to evaluate the CI of fossil fuel production using observations, considering all direct production emissions while allocating to all fossil products.

Supplementary Data Figure 1 from Two Distinct Types of Blood Vessels in Clear Cell Renal Cell Carcinoma Have Contrasting Prognostic Implications

Purpose: Intratumoral microvascular density (MVD) has been controversial as an indicator of prognosis in clear cell renal cell carcinoma (CCRCC). Classification of the intratumoral blood vessels based on differential expressions of blood vessel markers has not been correlated with patient prognosis in CCRCC. In this study, we aimed to evaluate the association of different categories of blood vessels with the patients' outcomes.Experimental Design: Seventy-eight CCRCC patients who underwent nephrectomy alone were enrolled. Paraffin-embedded CCRCC tissues, together with 16 nonmalignant kidney cortex tissues, were used in tissue microarray analyses and conventional section analyses. The characteristics of intratumoral blood vessels were identified by multiple blood vessel markers and pericyte markers. A computerized image analysis program was used to quantitatively calculate the vascular density.Results: Two distinct types of microvessels were identified in CCRCC: undifferentiated (CD31+/CD34−) and differentiated (CD34+) vessels. A higher undifferentiated MVD significantly correlated with higher tumor grades and shorter patient survival. In contrast, a higher differentiated MVD significantly correlated with lower tumor grade and longer survival. Multivariate analyses showed that undifferentiated MVD was an independent prognostic factor for patient survival. An inverse correlation between undifferentiated MVD and differentiated MVD was also identified in CCRCC.Conclusions: This is the first report showing distinct types of vasculature in CCRCC correlated with contrasting prognoses. A refined classification of CCRCC based on vasculature is therefore important for evaluating prognosis, and it may also have therapeutic implications.

Supplementary Data Figure 2 from Two Distinct Types of Blood Vessels in Clear Cell Renal Cell Carcinoma Have Contrasting Prognostic Implications

Renal cell carcinoma (RCC) is a heterogeneous disease that includes several histologically distinct subtypes. The most common RCC subtypes are clear cell, papillary, and chromophobe, and recent gene expression profiling studies suggest that classification of RCC based on transcriptional signatures could be beneficial. Traditionally, however, patterns of chromosomal alterations have been used to assist in the molecular classification of RCC. The purpose of this study was to determine whether it was possible to develop a classification model for the three major RCC subtypes that utilizes gene expression profiles as the bases for both molecular genetic and cytogenetic classification. Gene expression profiles were first used to build an expression-based RCC classifier. The RCC gene expression profiles were then examined for the presence of regional gene expression biases. Regional expression biases are genetic intervals that contain a disproportionate number of genes that are coordinately up- or down-regulated. The presence of a regional gene expression bias often indicates the presence of a chromosomal abnormality. In this study, we demonstrate an expression-based classifier can distinguish between the three most common RCC subtypes in 99% of cases (n = 73). We also demonstrate that detection of regional expression biases accurately identifies cytogenetic features common to RCC. Additionally, the in silico-derived cytogenetic profiles could be used to classify 81% of cases. Taken together, these data demonstrate that it is possible to construct a robust classification model for RCC using both transcriptional and cytogenetic features derived from a gene expression profile.

Urothelial carcinoma of the renal pelvis is a deadly disease with an unclear tumorigenic mechanism. We conducted gene expression profiling on a set of human tumors of this type and identified a phosphatidylinositol 3-kinase (PI3K)/AKT activation expression signature in 76.9% (n = 13) of our samples. Sequence analysis found both activating mutations of PIK3CA (13.6%, n = 22) and loss of heterozygosity at the PTEN locus (25%, n = 8). In contrast, none of the other subtypes of kidney neoplasms (e.g., clear-cell renal cell carcinoma) harbored PIK3CA mutations (n = 87; P < 0.001). Immunohistochemical analysis of urothelial carcinoma samples found loss of PTEN protein expression (36.4%, n = 11) and elevation of phosphorylated mammalian target of rapamycin (mTOR; 63.6%, n = 11). To confirm the role of the PI3K/AKT pathway in urothelial carcinoma, we generated mice containing biallelic inactivation of Pten in the urogenital epithelia. These mice developed typical renal pelvic urothelial carcinomas, with an incidence of 57.1% in mice older than 1 year. Laser capture microdissection followed by PCR confirmed the deletion of Pten exons 4 and 5 in the animal tumor cells. Immunohistochemical analyses showed increased phospho-mTOR and phospho-S6K levels in the animal tumors. Renal lymph node metastases were found in 15.8% of the animals with urothelial carcinoma. In conclusion, we identified and confirmed an important role for the PI3K/AKT pathway in the development of urothelial carcinoma and suggested that inhibitors of this pathway (e.g., mTOR inhibitor) may serve as effective therapeutic agents. [Cancer Res 2009;69(21):8256–64]

Supplementary Figure 1 from Activation of the PI3K/AKT Pathway Induces Urothelial Carcinoma of the Renal Pelvis: Identification in Human Tumors and Confirmation in Animal Models

Supplementary Table 1 from Activation of the PI3K/AKT Pathway Induces Urothelial Carcinoma of the Renal Pelvis: Identification in Human Tumors and Confirmation in Animal Models

Supplementary Figures C1-C2 from A Molecular Classification of Papillary Renal Cell Carcinoma

Supplementary Table 1 from A Molecular Classification of Papillary Renal Cell Carcinoma

Supplementary Figure Legend from Activation of the PI3K/AKT Pathway Induces Urothelial Carcinoma of the Renal Pelvis: Identification in Human Tumors and Confirmation in Animal Models

Supplementary Figures 1-6 from The Decline in U.S. Cancer Mortality in People Born since 1925

Sentinel lymph node (SLN) metastasis is the first step in the spreading of cancer in many malignancies. Tumor-reactive lymphadenopathy in SLNs has been observed for decades, but alterations of the lymphatic channels and vasculature in these nodes before the arrival of metastatic tumor cells remain unexplored. Using animal models, we show here that, before the establishment of metastasis in the SLN, there are reorganizations of the lymphatic channels and the vasculature. The node becomes a functional blood vessel–enriched and lymph vessel/sinus-enriched organ before metastasis. The enlargement of the lymph sinuses is correlated with the primary tumor weight. The newly emerged functional blood vessels develop from high endothelial venules (HEV), in which the proliferation rate of the endothelial cells is also significantly increased. Similar alterations of the HEVs are also characterized in the axillary lymph nodes from human breast cancer patients without the evidence of metastasis. These findings support the hypothesis that modification of the microenvironment for a secondary tumor (i.e., vasculature reorganization in the SLN) can be initiated by a primary tumor before and independent of the physical presence of metastatic cancer cells. (Cancer Res 2006; 66(21): 10365-76)

Supplementary Table 2 from Activation of the PI3K/AKT Pathway Induces Urothelial Carcinoma of the Renal Pelvis: Identification in Human Tumors and Confirmation in Animal Models

Supplementary Figure 1 from Robust Classification of Renal Cell Carcinoma Based on Gene Expression Data and Predicted Cytogenetic Profiles

Supplementary Figure 1 from Preparing the “Soil”: The Primary Tumor Induces Vasculature Reorganization in the Sentinel Lymph Node before the Arrival of Metastatic Cancer Cells

Supplementary Figure 2 from Preparing the “Soil”: The Primary Tumor Induces Vasculature Reorganization in the Sentinel Lymph Node before the Arrival of Metastatic Cancer Cells

Despite the moderate incidence of papillary renal cell carcinoma (PRCC), there is a disproportionately limited understanding of its underlying genetic programs. There is no effective therapy for metastatic PRCC, and patients are often excluded from kidney cancer trials. A morphologic classification of PRCC into type 1 and 2 tumors has been recently proposed, but its biological relevance remains uncertain. We studied the gene expression profiles of 34 cases of PRCC using Affymetrix HGU133 Plus 2.0 arrays (54,675 probe sets) using both unsupervised and supervised analyses. Comparative genomic microarray analysis was used to infer cytogenetic aberrations, and pathways were ranked with a curated database. Expression of selected genes was validated by immunohistochemistry in 34 samples with 15 independent tumors. We identified two highly distinct molecular PRCC subclasses with morphologic correlation. The first class, with excellent survival, corresponded to three histologic subtypes: type 1, low-grade type 2, and mixed type 1/low-grade type 2 tumors. The second class, with poor survival, corresponded to high-grade type 2 tumors (n = 11). Dysregulation of G1-S and G2-M checkpoint genes were found in class 1 and 2 tumors, respectively, alongside characteristic chromosomal aberrations. We identified a seven-transcript predictor that classified samples on cross-validation with 97% accuracy. Immunohistochemistry confirmed high expression of cytokeratin 7 in class 1 tumors and of topoisomerase IIα in class 2 tumors. We report two molecular subclasses of PRCC, which are biologically and clinically distinct and may be readily distinguished in a clinical setting.

Supplementary Table 1 from Robust Classification of Renal Cell Carcinoma Based on Gene Expression Data and Predicted Cytogenetic Profiles

Endothelial dysfunction and impaired vasodilation are linked with adverse cardiovascular events. T lymphocytes expressing choline acetyltransferase (ChAT), the enzyme catalyzing biosynthesis of the vasorelaxant acetylcholine (ACh), regulate vasodilation and are integral to the cholinergic antiinflammatory pathway in an inflammatory reflex in mice. Here, we found that human T cell ChAT mRNA expression was induced by T cell activation involving the PI3K signaling cascade. Mechanistically, we identified that ChAT mRNA expression was induced following the attenuation of RE-1 Silencing Transcription factor REST-mediated methylation of the ChAT promoter, and that ChAT mRNA expression levels were up-regulated by GATA3 in human T cells. In functional experiments, T cell-derived ACh increased endothelial nitric oxide-synthase activity, promoted vasorelaxation, and reduced vascular endothelial activation and promoted barrier integrity by a cholinergic mechanism. Further, we observed that survival in a cohort of patients with severe circulatory failure correlated with their relative frequency of ChAT + CD4 + T cells in blood. These findings on ChAT + human T cells provide a mechanism for cholinergic immune regulation of vascular endothelial function in human inflammation.

Limiting emissions of climate-warming methane from oil and gas (OG) is a major opportunity for short-term climate benefits. We deploy a basin-wide airborne survey of OG extraction and transportation activities in the New Mexico Permian Basin, spanning 35 923 km

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–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 ± 9.7) kg h-1 deviates by a factor 0.7 (0.35–12) 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.

Flaring is widely used by the fossil fuel industry to dispose of natural gas. Industry and governments generally assume that flares remain lit and destroy methane, the predominant component of natural gas, with 98% efficiency. Neither assumption, however, is based on real-world observations. We calculate flare efficiency using airborne sampling across three basins responsible for >80% of US flaring and combine these observations with unlit flare prevalence surveys. We find that both unlit flares and inefficient combustion contribute comparably to ineffective methane destruction, with flares effectively destroying only 91.1% (90.2, 91.8; 95% confidence interval) of methane. This represents a fivefold increase in methane emissions above present assumptions and constitutes 4 to 10% of total US oil and gas methane emissions, highlighting a previously underappreciated methane source and mitigation opportunity.

When estimating fossil fuel carbon dioxide (FFCO2) emissions from observed CO2 concentrations, the accuracy can be hampered by biogenic carbon exchanges during the growing season, even for urban areas where strong fossil fuel emissions are found. While biogenic carbon fluxes have been studied extensively across natural vegetation types, biogenic carbon fluxes within an urban area have been challenging to quantify due to limited observations and differences between urban and rural regions. Here we developed a simple model representation, i.e., Solar-Induced Fluorescence (SIF) for Modeling Urban biogenic Fluxes (“SMUrF”), that estimates the gross primary production (GPP) and ecosystem respiration (Reco) over cities around the globe. Specifically, we leveraged space-based SIF, machine learning, eddy-covariance (EC) flux data, and ancillary remote-sensing-based products, and we developed algorithms to gap-fill fluxes for urban areas. Grid-level hourly mean net ecosystem exchange (NEE) fluxes are extracted from SMUrF and evaluated against (1) non-gap-filled measurements at 67 EC sites from FLUXNET during 2010–2014 (r>0.7 for most data-rich biomes), (2) independent observations at two urban vegetation and two crop EC sites over Indianapolis from August 2017 to December 2018 (r=0.75), and (3) an urban biospheric model based on fine-grained land cover classification in Los Angeles (r=0.83). Moreover, we compared SMUrF-based NEE with inventory-based FFCO2 emissions over 40 cities and addressed the urban–rural contrast in both the magnitude and timing of CO2 fluxes. To illustrate the application of SMUrF, we used it to interpret a few summertime satellite tracks over four cities and compared the urban–rural gradient in column CO2 (XCO2) anomalies due to NEE against XCO2 enhancements due to FFCO2 emissions. With rapid advances in space-based measurements and increased sampling of SIF and CO2 measurements over urban areas, SMUrF can be useful to inform the biogenic CO2 fluxes over highly vegetated regions during the growing season.

Viral infections affecting the lower respiratory tract place enormous burdens on hospitals. As neither vaccines nor antiviral agents exist for many viruses, understanding risk factors and outcomes in each patient using minimally invasive analysis, such as blood, can lead to improved health care delivery. A cohort of PAXgene RNA sequencing of infants admitted with moderate or severe acute bronchiolitis and respiratory syncytial virus were compared with case-control statistical analysis and cohort-based outlier mapping for precision transcriptomics. Patients with severe bronchiolitis had signatures connected to the immune system, interferon signaling, and cytokine signaling, with marked sex differences in XIST, RPS4Y1, KDM5D, and LINC00278 for severity. Several patients had unique secondary infections, cytokine activation, immune responses, biological pathways, and immune cell activation, highlighting the need for defining patient-level transcriptomic signatures. Balancing relative contributions of cohort-based biomarker discoveries with patient’s biological responses is needed to understand the totality of mechanisms of adverse outcomes in viral bronchiolitis.