Immersive Visualization for Enhanced Computational Fluid Dynamics Analysis

Modern biomedical computer simulations produce spatiotemporal results that are often viewed at a single point in time on standard 2D displays. An immersive visualization environment (IVE) with 3D stereoscopic capability can mitigate some shortcomings of 2D displays via improved depth cues and active movement to further appreciate the spatial localization of imaging data with temporal computational fluid dynamics (CFD) results. We present a semi-automatic workflow for the import, processing, rendering, and stereoscopic visualization of high resolution, patient-specific imaging data, and CFD results in an IVE. Versatility of the workflow is highlighted with current clinical sequelae known to be influenced by adverse hemodynamics to illustrate potential clinical utility

Inhibition of microbial sulfate reduction in a flow-through column system by (per)chlorate treatment.

Microbial sulfate reduction is a primary cause of oil reservoir souring. Here we show that amendment with chlorate or perchlorate [collectively (per)chlorate] potentially resolves this issue. Triplicate packed columns inoculated with marine sediment were flushed with coastal water amended with yeast extract and one of nitrate, chlorate, or perchlorate. Results showed that although sulfide production was dramatically reduced by all treatments, effluent sulfide was observed in the nitrate (10 mM) treatment after an initial inhibition period. In contrast, no effluent sulfide was observed with (per)chlorate (10 mM). Microbial community analyses indicated temporal community shifts and phylogenetic clustering by treatment. Nitrate addition stimulated Xanthomonadaceae and Rhizobiaceae growth, supporting their role in nitrate metabolism. (Per)chlorate showed distinct effects on microbial community structure compared with nitrate and resulted in a general suppression of the community relative to the untreated control combined with a significant decrease in sulfate reducing species abundance indicating specific toxicity. Furthermore, chlorate stimulated Pseudomonadaceae and Pseudoalteromonadaceae, members of which are known chlorate respirers, suggesting that chlorate may also control sulfidogenesis by biocompetitive exclusion of sulfate-reduction. Perchlorate addition stimulated Desulfobulbaceae and Desulfomonadaceae, which contain sulfide oxidizing and elemental sulfur-reducing species respectively, suggesting that effluent sulfide concentrations may be controlled through sulfur redox cycling in addition to toxicity and biocompetitive exclusion. Sulfur isotope analyses further support sulfur cycling in the columns, even when sulfide is not detected. This study indicates that (per)chlorate show great promise as inhibitors of sulfidogenesis in natural communities and provides insight into which organisms and respiratory processes are involved

On-stack replacement, distilled

On-stack replacement (OSR) is essential technology for adaptive optimization, allowing changes to code actively executing in a managed runtime. The engineering aspects of OSR are well-known among VM architects, with several implementations available to date. However, OSR is yet to be explored as a general means to transfer execution between related program versions, which can pave the road to unprecedented applications that stretch beyond VMs. We aim at filling this gap with a constructive and provably correct OSR framework, allowing a class of general-purpose transformation functions to yield a special-purpose replacement. We describe and evaluate an implementation of our technique in LLVM. As a novel application of OSR, we present a feasibility study on debugging of optimized code, showing how our techniques can be used to fix variables holding incorrect values at breakpoints due to optimizations

Probability of acoustic transmitter detections by receiver lines in Lake Huron: Results of multi-year field tests and simulations

Background: Advances in acoustic telemetry technology have led to an improved understanding of the spatial ecology of many freshwater and marine fish species. Understanding the performance of acoustic receivers is necessary to distinguish between tagged fish that may have been present but not detected and from those fish that were absent from the area. In this study, two stationary acoustic transmitters were deployed 250 m apart within each of four acoustic receiver lines each containing at least 10 receivers (i.e., eight acoustic transmitters) located in Saginaw Bay and central Lake Huron for nearly 2 years to determine whether the probability of detecting an acoustic transmission varied as a function of time (i.e., season), location, and distance between acoustic transmitter and receiver. Distances between acoustic transmitters and receivers ranged f

Federal Research, Additional Actions Needed to Improve Public Access to Research Results: Report to Congressional Requesters [with Responses from Federal Agencies]

Why GAO Did This Study Research and development helps catalyze breakthroughs that improve the overall health and wellbeing of our society. Federal research and development expenditures averaged about $135 billion annually for fiscal years 2015 to 2017. According to OSTP, providing free public access to federally funded research results can improve both the impact and accountability of this important federal investment. In February 2013, OSTP directed federal agencies with more than$100 million in annual research and development expenditures to develop a plan to support increased public access to the results of federally funded research. GAO was asked to examine public access to federally funded research results. This report examines the extent of agencies’ (1) progress implementing plans to increase public access to federally funded research results and (2) coordination on public access plan implementation. GAO administered a questionnaire to 19 federal agencies selected based on annual research and development expenditure amounts, among other criteria; reviewed agency documents; and interviewed officials from 11 agencies, OSTP, and 21 stakeholder organizations. What GAO Found The 19 agencies that GAO reviewed have made progress implementing their plans to increase public access to federally funded research results (publications and data), as called for in a 2013 Office of Science and Technology Policy (OSTP) memorandum. However, some agencies have not fully implemented some aspects of their plans, in particular those related to data access and mechanisms to ensure researchers comply with public access requirements. Agencies are coordinating with each other and with nonfederal stakeholders to implement public access plans, including through an interagency group led by OSTP and five other agencies. However, the group has not fully implemented selected leading practices identified by GAO that can enhance and sustain interagency collaboration, such as defining and articulating common outcomes. For example, according to OSTP staff, key outcomes have not yet been decided upon. Agency officials and stakeholders identified several challenges to implementing public access plans that interagency coordination might help them address, such as • Absence of common standards in several areas; • Measuring effectiveness of public access plan implementation; and • Balancing providing public access with safeguarding sensitive information. By taking steps to fully implement relevant leading collaboration practices, the interagency group could help agencies better marshal their collective efforts to address common challenges to public access plan implementation. What GAO Recommends GAO is making 37 recommendations to 16 agencies to promote full and effective implementation of agency public access plans. For example, GAO recommends that OSTP and 5 agencies leading a public access interagency group take steps to fully implement selected leading collaboration practices. Of the 16 agencies, 15 agreed with GAO’s recommendations while 1 (OSTP) disagreed. GAO continues to believe the recommendation to OSTP is warranted

A subset of myofibroblastic cancer-associated fibroblasts regulate collagen fiber elongation, which is prognostic in multiple cancers

Collagen structure has been shown to influence tumor cell invasion, metastasis and clinical outcome in breast cancer. However, it remains unclear how it affects other solid cancers. Here we utilized multi-photon laser scanning microscopy and Second Harmonic Generation to identify alterations to collagen fiber structure within the tumor stroma of head & neck, esophageal and colorectal cancers. Image segmentation algorithms were then applied to quantitatively characterize these morphological changes, showing that elongated collagen fibers significantly correlated with poor clinical outcome (Log Rank p < 0.05). We used TGF-? treatment to model fibroblast conversion to smooth muscle actin SMA-positive cancer associated fibroblasts (CAFs) and found that these cells induce the formation of elongated collagen fibers in vivo. However, proteomic/transcriptomic analysis of SMA-positive CAFs cultured ex-vivo showed significant heterogeneity in the expression of genes with collagen fibril organizing gene ontology. Notably, stratifying patients according to stromal SMA-positivity and collagen fiber elongation was found to provide a highly significant correlation with poor survival in all 3 cancer types (Log Rank p ? 0.003). In summary, we show that increased collagen fiber length correlates with poor patient survival in multiple tumor types and that only a sub-set of SMA-positive CAFs can mediate the formation of this collagen structure

The Massive and Distant Clusters of WISE Survey: MOO J1142+1527, a 10^(15) M_⊙ Galaxy Cluster at z = 1.19

We present confirmation of the cluster MOO J1142+1527, a massive galaxy cluster discovered as part of the Massive and Distant Clusters of WISE Survey. The cluster is confirmed to lie at z = 1.19, and using the Combined Array for Research in Millimeter-wave Astronomy we robustly detect the Sunyaev–Zel'dovich (SZ) decrement at 13.2σ. The SZ data imply a mass of M_(200m) = (1.1 ± 0.2) × 10^(15)M_⊙, making MOO J1142+1527 the most massive galaxy cluster known at z > 1.15 and the second most massive cluster known at z > 1. For a standard ΛCDM cosmology it is further expected to be one of the ~5 most massive clusters expected to exist at z ≥ 1.19 over the entire sky. Our ongoing Spitzer program targeting ~1750 additional candidate clusters will identify comparably rich galaxy clusters over the full extragalactic sky

Medication adherence: A call for action

Poor adherence to efficacious cardiovascular related medications has led to considerable morbidity, mortality, and avoidable health care costs. This paper provides results of a recent think tank meeting in which various stakeholder groups representing key experts from consumers, community health providers, the academic community, decision-making government officials (FDA, NIH, etc), and industry scientists met to evaluate the current status of medication adherence and provide recommendations for improving outcomes. Below, we review the magnitude of the problem of medication adherence, prevalence, impact, and cost. We then summarize proven effective approaches and conclude with a discussion of recommendations to address this growing and significant public health issue of medication non adherence