FMRI Clustering and False Positive Rates

Recently, Eklund et al. (2016) analyzed clustering methods in standard FMRI packages: AFNI (which we maintain), FSL, and SPM [1]. They claimed: 1) false positive rates (FPRs) in traditional approaches are greatly inflated, questioning the validity of "countless published fMRI studies"; 2) nonparametric methods produce valid, but slightly conservative, FPRs; 3) a common flawed assumption is that the spatial autocorrelation function (ACF) of FMRI noise is Gaussian-shaped; and 4) a 15-year-old bug in AFNI's 3dClustSim significantly contributed to producing "particularly high" FPRs compared to other software. We repeated simulations from [1] (Beijing-Zang data [2], see [3]), and comment on each point briefly.Comment: 3 pages, 1 figure. A Letter accepted in PNA

Estimating oil concentration and flow rate with calibrated vessel-mounted acoustic echo sounders

As part of a larger program aimed at evaluating acoustic techniques for mapping the distribution of subsurface oil and gas associated with the Deepwater Horizon-Macondo oil spill, observations were made on June 24 and 25, 2010 using vessel-mounted calibrated single-beam echo sounders on the National Oceanic and Atmospheric Administration ship Thomas Jefferson. Coincident with visual observations of oil at the sea surface, the 200-kHz echo sounder showed anomalously high-volume scattering strength in the upper 200 m on the western side of the wellhead, more than 100 times higher than the surrounding waters at 1,800-m distance from the wellhead, and weakening with increasing distance out to 5,000 m. Similar high-volume scattering anomalies were not observed at 12 or 38 kHz, although observations of anomalously low-volume scattering strength were made in the deep scattering layer at these frequencies at approximately the same locations. Together with observations of ocean currents, the acoustic observations are consistent with a rising plume of small (\u3c 1-mm radius) oil droplets. Using simplistic but reasonable assumptions about the properties of the oil droplets, an estimate of the flow rate was made that is remarkably consistent with those made at the wellhead by other means. The uncertainty in this acoustically derived estimate is high due to lack of knowledge of the size distribution and rise speed of the oil droplets. If properly constrained, these types of acoustic measurements can be used to rapidly estimate the flow rate of oil reaching the surface over large temporal and spatial scales

GaAs solar cells for laser power beaming

Efforts to develop GaAs solar cells for coupling to laser beams in the wavelength range of 800 to 840 nm are described. This work was motivated primarily by interests in space-tp-space power beaming applications. In particular, the Battelle Pacific Northwest Laboratories is conducting studies of the utilization of power beaming for several future space missions. Modeling calculations of GaAs cell performance were carried out using PC-1D to determine an appropriate design for a p/n cell structure. Epitaxial wafers were grown by MOCVD and cells fabricated at WSU Tri-Cities. Under simulated conditions, an efficiency of 53 percent was achieved for a cell coupled to 806 nm light at 400 mW/sq cm

Essential operating principles for tumor spheroid growth

<p>Abstract</p> <p>Background</p> <p>Our objective was to discover in silico axioms that are plausible representations of the operating principles realized during characteristic growth of EMT6/Ro mouse mammary tumor spheroids in culture. To reach that objective we engineered and iteratively falsified an agent-based analogue of EMT6 spheroid growth. EMT6 spheroids display consistent and predictable growth characteristics, implying that individual cell behaviors are tightly controlled and regulated. An approach to understanding how individual cell behaviors contribute to system behaviors is to discover a set of principles that enable abstract agents to exhibit closely analogous behaviors using only information available in an agent's immediate environment. We listed key attributes of EMT6 spheroid growth, which became our behavioral targets. Included were the development of a necrotic core surrounded by quiescent and proliferating cells, and growth data at two distinct levels of nutrient.</p> <p>Results</p> <p>We then created an analogue made up of quasi-autonomous software agents and an abstract environment in which they could operate. The system was designed so that upon execution it could mimic EMT6 cells forming spheroids in culture. Each agent used an identical set of axiomatic operating principles. In sequence, we used the list of targeted attributes to falsify and revise these axioms, until the analogue exhibited behaviors and attributes that were within prespecified ranges of those targeted, thereby achieving a level of validation.</p> <p>Conclusion</p> <p>The finalized analogue required nine axioms. We posit that the validated analogue's operating principles are reasonable representations of those utilized by EMT6/Ro cells during tumor spheroid development.</p

A semantic Grid for molecular science

Proceedings of the 2003 UK e-Science All Hands Meeting, 31st August - 3rd September, Nottingham UKThe properties of molecules have very well defined semantics and allow the creation of a semantic GRID. Markup languages (CML - Chemical Markup Language) and dictionary-based ontologies have been designed to support a wide range of applications, including chemical supply, publication and the safety of compounds. Many properties can be computed by Quantum Mechanical (QM) programs and we have developed a "black-box" system based on XML wrappers for all components. This is installed on a Condor system on which we have computed properties for 250, 000 compounds. The results of this will be available in an OpenData/OpenSource peer-to-peer (P2P) system (WorldWide Molecular Matrix - WWMM)

The Role of the Community Health Delivery System in the Health and Well-Being of Justice-Involved Women: A Narrative Review

Background: Over seven million imprisoned and jailed women are released into the community each year and many are ill-equipped to meet the challenges of re-integration. Upon release into their community, women are faced with uncertain barriers and challenges using community services to improve their health and well-being and reuniting with families. Few studies have identified and described the barriers of the community health delivery system (CHDS)- a complex set of social, justice, and healthcare organizations that provide community services aimed to improve the health and well-being (i.e. safety, health, the success of integration, and life satisfaction) of justice-involved women. We conducted a narrative review of peer-reviewed and gray literature to identify and describe the CHDS and the CHDS service delivery. Results: Peer-reviewed and gray literature (n = 82) describing the CHDS organizations’ missions, incentives, goals, and services were coded in three domains, justice, social, and healthcare, to examine their service delivery to justice-involved women and their efforts to improve the health and well-being of justice-involved women. Conclusions: We found that the CHDS is fragmented, identified gaps in knowledge about the CHDS that serves justice-involved women, and offer recommendations to reduce fragmentation and integrate service delivery aimed to improve the health and well-being of justice-involved women

Human GUCY2C-Targeted Chimeric Antigen Receptor (CAR)-Expressing T Cells Eliminate Colorectal Cancer Metastases.

One major hurdle to the success of adoptive T-cell therapy is the identification of antigens that permit effective targeting of tumors in the absence of toxicities to essential organs. Previous work has demonstrated that T cells engineered to express chimeric antigen receptors (CAR-T cells) targeting the murine homolog of the colorectal cancer antigen GUCY2C treat established colorectal cancer metastases, without toxicity to the normal GUCY2C-expressing intestinal epithelium, reflecting structural compartmentalization of endogenous GUCY2C to apical membranes comprising the intestinal lumen. Here, we examined the utility of a human-specific, GUCY2C-directed single-chain variable fragment as the basis for a CAR construct targeting human GUCY2C-expressing metastases. Human GUCY2C-targeted murine CAR-T cells promoted antigen-dependent T-cell activation quantified by activation marker upregulation, cytokine production, and killing of GUCY2C-expressing, but not GUCY2C-deficient, cancer cells in vitro. GUCY2C CAR-T cells provided long-term protection against lung metastases of murine colorectal cancer cells engineered to express human GUCY2C in a syngeneic mouse model. GUCY2C murine CAR-T cells recognized and killed human colorectal cancer cells endogenously expressing GUCY2C, providing durable survival in a human xenograft model in immunodeficient mice. Thus, we have identified a human GUCY2C-specific CAR-T cell therapy approach that may be developed for the treatment of GUCY2C-expressing metastatic colorectal cancer

Epithelial Cell Coculture Models for Studying Infectious Diseases: Benefits and Limitations

Countless in vitro cell culture models based on the use of epithelial cell types of single lineages have been characterized and have provided insight into the mechanisms of infection for various microbial pathogens. Diverse culture models based on disease-relevant mucosal epithelial cell types derived from gastrointestinal, genitourinary, and pulmonary organ systems have delineated many key host-pathogen interactions that underlie viral, parasitic, and bacterial disease pathogenesis. An alternative to single lineage epithelial cell monoculture, which offers more flexibility and can overcome some of the limitations of epithelial cell culture models based on only single cell types, is coculture of epithelial cells with other host cell types. Various coculture models have been described, which incorporate epithelial cell types in culture combination with a wide range of other cell types including neutrophils, eosinophils, monocytes, and lymphocytes. This paper will summarize current models of epithelial cell coculture and will discuss the benefits and limitations of epithelial cell coculture for studying host-pathogen dynamics in infectious diseases