Stochastic Parameter Estimation of Poroelastic Processes Using Geomechanical Measurements

Understanding the structure and material properties of hydrologic systems is important for a number of applications, including carbon dioxide injection for geological carbon storage or enhanced oil recovery, monitoring of hydraulic fracturing projects, mine dewatering, environmental remediation and managing geothermal reservoirs. These applications require a detailed knowledge of the geologic systems being impacted, in order to optimize their operation and safety. In order to evaluate, monitor and manage such hydrologic systems, a stochastic estimation framework was developed which is capable of characterizing the structure and physical parameters of the subsurface. This software framework uses a set of stochastic optimization algorithms to calibrate a heterogeneous subsurface flow model to available field data, and to construct an ensemble of models which represent the range of system states that would explain this data. Many of these systems, such as oil reservoirs, are deep and hydraulically isolted from the shallow subsurface making near-surface fluid pressure measurements uninformative. Near-surface strainmeter, tiltmeter and extensometer signals were therefore evaluated in terms of their potential information content for calibrating poroelastic flow models. Such geomechanical signals are caused by mechanical deformation, and therefore travel through hydraulically impermeable rock much more quickly. A numerical geomechanics model was therefore developed using Geocentric, which couples subsurface flow and elastic deformation equations to simulate geomechanical signals (e.g. pressure, strain, tilt and displacement) given a set of model parameters. A high-performance cluster computer performs this computationally expensive simulation for each set of parameters, and compares the simulation results to measured data in order to evaluate the likelihood of each model. The set of data-model comparisons are then used to estimate each unknown parameter, as well as the uncertainty of each parameter estimate. This uncertainty can be inuenced by limitations in the measured dataset such as random noise, instrument drift, and the number and location of sensors, as well as by conceptual model errors and false underlying assumptions. In this study we find that strain measurements taken from the shallow subsurface can be used to estimate the structure and material parameters of geologic layers much deeper in the subsurface. This can signicantly mitigate drilling and installation costs of monitoring wells, as well as reduce the risk of puncturing or fracturing a target reservoir. These parameter estimates were also used to develop an ensemble of calibrated hydromechanical models which can predict the range of system behavior and inform decision-making on the management of an aquifer or reservoir

Multi-Messenger Astronomy with Extremely Large Telescopes

The field of time-domain astrophysics has entered the era of Multi-messenger Astronomy (MMA). One key science goal for the next decade (and beyond) will be to characterize gravitational wave (GW) and neutrino sources using the next generation of Extremely Large Telescopes (ELTs). These studies will have a broad impact across astrophysics, informing our knowledge of the production and enrichment history of the heaviest chemical elements, constrain the dense matter equation of state, provide independent constraints on cosmology, increase our understanding of particle acceleration in shocks and jets, and study the lives of black holes in the universe. Future GW detectors will greatly improve their sensitivity during the coming decade, as will near-infrared telescopes capable of independently finding kilonovae from neutron star mergers. However, the electromagnetic counterparts to high-frequency (LIGO/Virgo band) GW sources will be distant and faint and thus demand ELT capabilities for characterization. ELTs will be important and necessary contributors to an advanced and complete multi-messenger network.Comment: White paper submitted to the Astro2020 Decadal Surve

A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles : Implications for the Exploration of Mars

A major objective in the exploration of Mars is to test the hypothesis that the planet hosted life. Even in the absence of life, the mapping of habitable and uninhabitable environments is an essential task in developing a complete understanding of the geological and aqueous history of Mars and, as a consequence, understanding what factors caused Earth to take a different trajectory of biological potential. We carried out the aseptic collection of samples and comparison of the bacterial and archaeal communities associated with basaltic fumaroles and rocks of varying weathering states in Hawai'i to test four hypotheses concerning the diversity of life in these environments. Using high-throughput sequencing, we found that all these materials are inhabited by a low-diversity biota. Multivariate analyses of bacterial community data showed a clear separation between sites that have active fumaroles and other sites that comprised relict fumaroles, unaltered, and syn-emplacement basalts. Contrary to our hypothesis that high water flow environments, such as fumaroles with active mineral leaching, would be sites of high biological diversity, alpha diversity was lower in active fumaroles compared to relict or nonfumarolic sites, potentially due to high-temperature constraints on microbial diversity in fumarolic sites. A comparison of these data with communities inhabiting unaltered and weathered basaltic rocks in Idaho suggests that bacterial taxon composition of basaltic materials varies between sites, although the archaeal communities were similar in Hawai'i and Idaho. The taxa present in both sites suggest that most of them obtain organic carbon compounds from the atmosphere and from phototrophs and that some of them, including archaeal taxa, cycle fixed nitrogen. The low diversity shows that, on Earth, extreme basaltic terrains are environments on the edge of sustaining life with implications for the biological potential of similar environments on Mars and their exploration by robots and humans.Peer reviewe

Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples

Background: Detection of critical cancer gene mutations in clinical tumor specimens may predict patient outcomes and inform treatment options; however, high-throughput mutation profiling remains underdeveloped as a diagnostic approach. We report the implementation of a genotyping and validation algorithm that enables robust tumor mutation profiling in the clinical setting. Methodology: We developed and implemented an optimized mutation profiling platform (“OncoMap”) to interrogate ∼400 mutations in 33 known oncogenes and tumor suppressors, many of which are known to predict response or resistance to targeted therapies. The performance of OncoMap was analyzed using DNA derived from both frozen and FFPE clinical material in a diverse set of cancer types. A subsequent in-depth analysis was conducted on histologically and clinically annotated pediatric gliomas. The sensitivity and specificity of OncoMap were 93.8% and 100% in fresh frozen tissue; and 89.3% and 99.4% in FFPE-derived DNA. We detected known mutations at the expected frequencies in common cancers, as well as novel mutations in adult and pediatric cancers that are likely to predict heightened response or resistance to existing or developmental cancer therapies. OncoMap profiles also support a new molecular stratification of pediatric low-grade gliomas based on BRAF mutations that may have immediate clinical impact. Conclusions: Our results demonstrate the clinical feasibility of high-throughput mutation profiling to query a large panel of “actionable” cancer gene mutations. In the future, this type of approach may be incorporated into both cancer epidemiologic studies and clinical decision making to specify the use of many targeted anticancer agents

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes

Do público e do privado: uma perspectiva de género sobre uma dicotomia moderna

Neste texto propomos uma interpretação crítica da dicotomia histórica entre público e privado como dinâmica fundamental da modernidade. A partir de uma perspectiva de género, discutimos as fronteiras construídas entre espaço coletivo de cidadania e de sociabilidade e espaço individual de intimidade e desigualdade. Argumentamos a favor de uma relação de cumplicidade, ainda que tensa, entre as duas esferas, observando que a vida privada foi, em grande medida, moldada pelas mudanças operadas na vida pública. Recorrendo a diferentes definições de "público", notamos que, à medida que as sociabilidades tradicionais, essencialmente masculinas, estudadas entre outros por Ariès ou Sennett, sofriam uma erosão, crescia o sentimento de intimidade, aumentando igualmente a inclusão do privado no público através do alargamento da cidadania, em consequência das lutas travadas na esfera pública por vários movimentos de emancipação, como o operário ou o feminista. À medida que a pessoa era retirada da comunidade, do clã, do grupo de parentesco, em que eram "naturais" as desigualdades, no sentido aristotélico do termo, ia-se reencontrando progressivamente como indivíduo portador de cidadania. Se o espaço privado se tornou central na definição de uma identidade, ele é também crescentemente atravessado por mecanismos públicos de regulação. Nesse sentido, o movimento de ascensão do privado, que nas últimas décadas tem ocupado espaço de debate, deve ser cuidadosamente reinterpretado

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Funder: Bundesministerium für Bildung und ForschungFunder: Bundesministerium für Bildung und Forschung (BMBF)We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective

Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer

Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research communities. We evaluated sources of variability in sTIL assessment by pathologists in three previous sTIL ring studies. We identify common challenges and evaluate impact of discrepancies on outcome estimates in early TNBC using a newly-developed prognostic tool. Discordant sTIL assessment is driven by heterogeneity in lymphocyte distribution. Additional factors include: technical slide-related issues; scoring outside the tumor boundary; tumors with minimal assessable stroma; including lymphocytes associated with other structures; and including other inflammatory cells. Small variations in sTIL assessment modestly alter risk estimation in early TNBC but have the potential to affect treatment selection if cutpoints are employed. Scoring and averaging multiple areas, as well as use of reference images, improve consistency of sTIL evaluation. Moreover, to assist in avoiding the pitfalls identified in this analysis, we developed an educational resource available at www.tilsinbreastcancer.org/pitfalls.Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research communities. We evaluated sources of variability in sTIL assessment by pathologists in three previous sTIL ring studies. We identify common challenges and evaluate impact of discrepancies on outcome estimates in early TNBC using a newly-developed prognostic tool. Discordant sTIL assessment is driven by heterogeneity in lymphocyte distribution. Additional factors include: technical slide-related issues; scoring outside the tumor boundary; tumors with minimal assessable stroma; including lymphocytes associated with other structures; and including other inflammatory cells. Small variations in sTIL assessment modestly alter risk estimation in early TNBC but have the potential to affect treatment selection if cutpoints are employed. Scoring and averaging multiple areas, as well as use of reference images, improve consistency of sTIL evaluation. Moreover, to assist in avoiding the pitfalls identified in this analysis, we developed an educational resource available at www.tilsinbreastcancer.org/pitfalls.Peer reviewe

American Gut: an Open Platform for Citizen Science Microbiome Research

McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3):e00031-18