Estuarine clay mineral distribution:Modern analogue for ancient sandstone reservoir quality prediction

The spatial distribution of clay minerals in sandstones, which may both enhance or degrade reservoir quality, is poorly understood. To address this, clay mineral distribution patterns and host‐sediment properties (grain size, sorting, clay fraction abundance and bioturbation intensity) have, for the first time, been determined and mapped at an unprecedentedly high‐resolution in a modern estuarine setting (Ravenglass Estuary, UK). Results show that the estuary sediment is dominated by illite with subordinate chlorite and kaolinite, although the rivers supply sediment with less illite and significantly more chlorite than found in the estuary. Fluvial‐supplied sediment has been locally diluted by sediment derived from glaciogenic drift deposits on the margins of the estuary. Detailed clay mineral maps and statistical analyses reveal that the estuary has a heterogeneous distribution of illite, chlorite and kaolinite. Chlorite is relatively most abundant on the northern foreshore and backshore and is concentrated in coarse‐grained inner estuary dunes and tidal bars. Illite is relatively most abundant (as well as most crystalline and most Fe–Mg‐rich) in fine‐grained inner estuary and central basin mud and mixed flats. Kaolinite has the highest abundance in fluvial sediment and is relatively homogenous in tidally‐influenced environments. Clay mineral distribution patterns in the Ravenglass Estuary have been strongly influenced by sediment supply (residence time) and subsequently modified by hydrodynamic processes. There is no relationship between macro‐faunal bioturbation intensity and the abundance of chlorite, illite or kaolinite. Based on this modern‐analogue study, outer estuarine sediments are likely to be heavily quartz cemented in deeply‐buried (burial temperatures exceeding 80 to 100°C) sandstone reservoirs due to a paucity of clay grade material (<0·5%) to form complete grain coats. In contrast, chlorite‐enriched tidal bars and dunes in the inner estuary, with their well‐developed detrital clay coats, are likely to have quartz cement inhibiting authigenic clay coats in deeply‐buried sandstones

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

A Historiometric Examination of Machiavellianism and a New Taxonomy of Leadership

Although researchers have extensively examined the relationship between charismatic leadership and Machiavellianism (Deluga, 2001; Gardner & Avolio, 1995; House & Howell, 1992), there has been a lack of investigation of Machiavellianism in relation to alternative forms of outstanding leadership. Thus, the purpose of this investigation was to examine the relationship between Machiavellianism and a new taxonomy of outstanding leadership comprised of charismatic, ideological, and pragmatic leaders. Using an historiometric approach, raters assessed Machiavellianism via the communications of 120 outstanding leaders in organizations across the domains of business, political, military, and religious institutions. Academic biographies were used to assess twelve general performance measures as well as twelve general controls and five communication specific controls. The results indicated that differing levels of Machiavellianism is evidenced across the differing leader types as well as differing leader orientation. Additionally, Machiavellianism appears negatively related to performance, though less so when type and orientation are taken into account.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the molecular processes governing oncogenesis. We illustrate our insights into cancer through synthesis of the findings of the TCGA PanCancer Atlas project on three facets of oncogenesis: (1) somatic driver mutations, germline pathogenic variants, and their interactions in the tumor; (2) the influence of the tumor genome and epigenome on transcriptome and proteome; and (3) the relationship between tumor and the microenvironment, including implications for drugs targeting driver events and immunotherapies. These results will anchor future characterization of rare and common tumor types, primary and relapsed tumors, and cancers across ancestry groups and will guide the deployment of clinical genomic sequencing

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a comprehensive encyclopedia of somatic mutation calls for the TCGA data to enable robust cross-tumor-type analyses. Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybridization-capture, sequencing, and analysis methods over time. We present best practices for applying an ensemble of seven mutation-calling algorithms with scoring and artifact filtering. The dataset created by this analysis includes 3.5 million somatic variants and forms the basis for PanCan Atlas papers. The results have been made available to the research community along with the methods used to generate them. This project is the result of collaboration from a number of institutes and demonstrates how team science drives extremely large genomics projects