The Trick Simulation Toolkit: A NASA/Open source Framework for Running Time Based Physics Models

This paper describes the design and use at of the Trick Simulation Toolkit, a simulation development environment for creating high fidelity training and engineering simulations at the NASA Johnson Space Center and many other NASA facilities. It describes Trick's design goals and how the development environment attempts to achieve those goals. It describes how Trick is used in some of the many training and engineering simulations at NASA. Finally it describes the Trick NASA/Open source project on Github

Trick Simulation Environment 07

The Trick Simulation Environment is a generic simulation toolkit used for constructing and running simulations. This release includes a Monte Carlo analysis simulation framework and a data analysis package. It produces all auto documentation in XML. Also, the software is capable of inserting a malfunction at any point during the simulation. Trick 07 adds variable server output options and error messaging and is capable of using and manipulating wide characters for international support. Wide character strings are available as a fundamental type for variables processed by Trick. A Trick Monte Carlo simulation uses a statistically generated, or predetermined, set of inputs to iteratively drive the simulation. Also, there is a framework in place for optimization and solution finding where developers may iteratively modify the inputs per run based on some analysis of the outputs. The data analysis package is capable of reading data from external simulation packages such as MATLAB and Octave, as well as the common comma-separated values (CSV) format used by Excel, without the use of external converters. The file formats for MATLAB and Octave were obtained from their documentation sets, and Trick maintains generic file readers for each format. XML tags store the fields in the Trick header comments. For header files, XML tags for structures and enumerations, and the members within are stored in the auto documentation. For source code files, XML tags for each function and the calling arguments are stored in the auto documentation. When a simulation is built, a top level XML file, which includes all of the header and source code XML auto documentation files, is created in the simulation directory. Trick 07 provides an XML to TeX converter. The converter reads in header and source code XML documentation files and converts the data to TeX labels and tables suitable for inclusion in TeX documents. A malfunction insertion capability allows users to override the value of any simulation variable, or call a malfunction job, at any time during the simulation. Users may specify conditions, use the return value of a malfunction trigger job, or manually activate a malfunction. The malfunction action may consist of executing a block of input file statements in an action block, setting simulation variable values, call a malfunction job, or turn on/off simulation jobs

Role for Extracellular Signal-Responsive Kinase-1 and -2 in Retinal Angiogenesis

PURPOSE. Vascular endothelial growth factor (VEGF) is a potent mitogen for micro-and macrovascular endothelial cells (ECs). Evidence points to a possible role for two mitogen-activated protein (MAP) kinases, the extracellular-signal responsive kinases (ERK)-1 and -2, in VEGF signaling in ECs. This study was undertaken to begin to define the precise role of MAP kinases in VEGF signal transduction related to angiogenesis. METHODS. Bovine retinal microvascular endothelial cells (BRMECs) and a well-established rat model of retinopathy of prematurity (ROP) were used to investigate the role of ERK-1/2 in EC proliferation and tube formation and in retinal angiogenesis in vivo. RESULTS. Administration of VEGF to BRMEC cultures increased ERK-1/2 phosphorylation, cell proliferation, and tube formation in a dose-dependent manner. Phosphorylation of retinal ERK-1/2 also was increased in the ROP model. An inhibitor of ERK, AG126, and an inhibitor of ERK kinase (MEK), PD98059, exhibited a dose-dependent reduction of ERK phosphorylation and EC proliferation, but not tube formation, in VEGF-stimulated BRMECs. In the ROP model, intravitreous injection of 10 M AG126 or PD98059 reduced the retinal neovascular area by 71% and 48%, respectfully. No effect was seen on intraretinal blood vessel growth. CONCLUSIONS. These experiments point to a critical role for ERK and MEK in proliferation of ECs, but not in tube formation. Furthermore, inhibition of either of these two signal intermediates can significantly retard retinal neovascularization. This suggests that the MAPK pathway may provide rational targets for therapeutic intervention in ocular and other diseases with an angiogenic component. (Invest Ophthalmol Vis Sci

Facilitating treatment engagement for early psychosis through peer-delivered decision support : Intervention development and protocol for pilot evaluation

Background: Emerging adults with early psychosis demonstrate high rates of service disengagement from critical early intervention services. Decision support interventions and peer support have both been shown to enhance service engagement but are understudied in this population. The purposes of this article are to describe the development of a novel peer-delivered decision coaching intervention for this population and to report plans for a pilot study designed to gather preliminary data about its feasibility, acceptability, and potential impact. Methods: The intervention was developed based on formative qualitative data and in collaboration with a diverse team of researchers, key stakeholders, and expert consultants. The pilot trial will utilize a single-group (N = 20), pre-post, convergent mixed-methods design to explore whether and how the intervention addresses decision-making needs (the primary intervention target). The impact of the intervention on secondary outcomes (e.g., engagement in the program) will also be assessed. Additionally, through observation and feedback from the peer decision coach and study participants, we will evaluate the feasibility of research and intervention procedures, and the acceptability of information and support from the peer decision coach. Discussion: The peer-delivered decision coaching intervention holds promise for assisting young people with making informed and values-consistent decisions about their care, and potentially enhancing service engagement within this traditionally difficult-to-engage population. If the intervention demonstrates feasibility and acceptability, and pilot data show its potential for improving treatment decision-making, our work will also lay the foundation for a new evidence base regarding roles for peer specialists on early intervention teams

Akt kinase C-terminal modifications control activation loop dephosphorylation and enhance insulin response.

The Akt protein kinase, also known as protein kinase B, plays key roles in insulin receptor signalling and regulates cell growth, survival and metabolism. Recently, we described a mechanism to enhance Akt phosphorylation that restricts access of cellular phosphatases to the Akt activation loop (Thr(308) in Akt1 or protein kinase B isoform alpha) in an ATP-dependent manner. In the present paper, we describe a distinct mechanism to control Thr(308) dephosphorylation and thus Akt deactivation that depends on intramolecular interactions of Akt C-terminal sequences with its kinase domain. Modifications of amino acids surrounding the Akt1 C-terminal mTORC2 (mammalian target of rapamycin complex 2) phosphorylation site (Ser(473)) increased phosphatase resistance of the phosphorylated activation loop (pThr(308)) and amplified Akt phosphorylation. Furthermore, the phosphatase-resistant Akt was refractory to ceramide-dependent dephosphorylation and amplified insulin-dependent Thr(308) phosphorylation in a regulated fashion. Collectively, these results suggest that the Akt C-terminal hydrophobic groove is a target for the development of agents that enhance Akt phosphorylation by insulin

Prevention of type 2 diabetes in adults with impaired glucose tolerance: the European Diabetes Prevention RCT in Newcastle upon Tyne, UK

<p>Abstract</p> <p>Background</p> <p>Diabetes prevalence is increasing. The Finnish Diabetes Prevention Study (DPS) showed a 58% reduction in Type 2 Diabetes (T2D) incidence in adults with impaired glucose tolerance (IGT). The European Diabetes Prevention Study (EDIPS) extends the DPS to different European populations, using the same study design. In the Newcastle arm of this study (EDIPS-Newcastle), we tested the hypothesis that T2D can be prevented by lifestyle intervention and explored secondary outcomes in relation to diabetes incidence.</p> <p>Methods</p> <p>We recruited 102 participants (42 men and 60 women, mean age 57 years, mean BMI 34 kgm^-2) with IGT to EDIPS-Newcastle and randomised to Intervention and usual care Control groups. The intervention included individual motivational interviewing aimed at: weight reduction, increase in physical activity, fibre and carbohydrate intake and reduction of fat intake (secondary outcomes). The primary outcome was diagnosis of T2D.</p> <p>Results</p> <p>Mean duration of follow-up was 3.1 years. T2D was diagnosed in 16 participants (I = 5, C = 11). Absolute incidence of T2D was 32.7 per 1000 person-years in the Intervention-group and 67.1 per 1000 person-years in the Control-group. The overall incidence of diabetes was reduced by 55% in the Intervention-group, compared with the Control-group: RR 0.45 (95%CI 0.2 to 1.2).</p> <p>Explanatory survival analysis of secondary outcomes showed that those who sustained beneficial changes for two or more years reduced their risk of developing T2D.</p> <p>Conclusion</p> <p>Our results are consistent with other diabetes prevention trials. This study was designed as part of a larger study and although the sample size limits statistical significance, the results contribute to the evidence that T2D can be prevented by lifestyle changes in adults with IGT. In explanatory analysis small sustained beneficial changes in weight, physical activity or dietary factors were associated with reduction in T2D incidence.</p> <p>Trial Registration</p> <p>International Standard Randomised Controlled Trial Number registry (ISRCTN)</p> <p>Registry number: ISRCTN 15670600</p> <p><url>http://www.controlled-trials.com/isrctn/search.html?srch=15670600&sort=3&dir=desc&max=10</url></p

Pharmacologic and Genetic Manipulation of MMP-2 and -9 Affects Retinal Neovascularization in Rodent Models of OIR

PURPOSE. The efficacy of three matrix metalloproteinase (MMP) inhibitors with various selectivities (Ro-31-9790, AG3340, and DPC-A37668) was investigated in a rat model of retinopathy of prematurity, to examine the roles of MMP-2 and -9 in retinal neovascularization. The susceptibilities of MMP-2 Ϫ/Ϫ and -9 Ϫ/Ϫ mice to preretinal neovascularization were investigated in a mouse model of oxygen-induced retinopathy. METHODS. Sprague-Dawley newborn rats were exposed to alternating episodes of 50% and 10% oxygen (variable oxygen exposure) to induce retinal neovascularization. Three MMP inhibitors with various selectivity profiles were administered to variable oxygen-exposed rats via local or systemic routes. Antineovascular efficacy was determined in drug-treated versus vehicle-treated rat pups by computerized imaging of adenosine diphosphatase (ADPase)-stained retinal flatmounts. Wild-type C57BL/6J and isogenic MMP-2 Ϫ/Ϫ and -9 Ϫ/Ϫ mice were exposed to 75% oxygen followed by normoxia. The mice were killed immediately before or after the normoxic exposure, and eyes were either harvested for retinal dissection and flatmounting or were paraffin embedded and sectioned. Retinal vascular area and retinal neovascularization were assessed by adenosine diphosphatase staining of retinal flatmounts and by counting preretinal nuclei of hematoxylin and eosin-stained retinal sections, respectively. RESULTS. Ro-31-9790, AG3340, and DPC-A37668 had no effect on normal development of the rat retinal vasculature, regardless of dose or route of administration. Intravitreal injection of Ro-31-9790 (broad-spectrum) immediately after variable-oxygen exposure and 2 days after exposure resulted in 78% and 82% inhibition of retinal neovascularization, respectively. AG3340 (MMP-2-and -9-selective inhibitor) and DPC-A37668 (MMP-2-selective inhibitor) resulted in 65% and 52% inhibition, respectively, when administered by intravitreal injection immediately after variable-oxygen exposure. Intraperitoneal injection of 5, 15, and 50 mg/mL AG3340 or DPC-A37668 for 6 days after variable oxygen exposure resulted in 22% to 39% and 0% to 31% inhibition of neovascularization, respectively. AG3340 and DPC-A37668 administered by oral gavage at doses of 3, 10, or 30 mg/mL provided up to 42% and 86% inhibition of neovascularization, respectively. The average vascular areas of retinas from MMP-2 Ϫ/Ϫ or -9 Ϫ/Ϫ mice at postnatal day 12 were not significantly different from the wild-type control. There was a 75% (P Ͻ 0.001) and 44% (P Ͻ 0.01) reduction in preretinal neovascularization in oxygen-exposed MMP-2 Ϫ/Ϫ and -9 Ϫ/Ϫ mice at postnatal day 19, respectively, compared with wild-type control mice. CONCLUSIONS. The results of this study suggest that MMP-2 plays a predominant role in retinal angiogenesis in both the mouse and rat models of oxygen-induced retinopathy. Furthermore, MMP-2 inhibition may be a viable therapeutic approach for ocular diseases characterized by retinal neovascularization. (Invest Ophthalmol Vis Sci. 2007;48:907-915) DOI:10.1167/ iovs.06-0082 T he term angiogenesis refers to the growth of new capillaries from preexisting blood vessels. The initial events of angiogenesis involve proteolytic basement membrane degradation; extracellular matrix remodeling; and endothelial cell (EC) proliferation, migration, and differentiation. The integration of these events in physiologic angiogenesis involves complex interactions among cells, growth factors, cytokines, and extracellular matrix components. 1 Matrix metalloproteinases (MMPs) comprise a family of proteolytic enzymes of more than 20 members that are zinc and calcium dependent. Most MMPs are secreted in the inactive proenzyme form, some of them by endothelial cells of the angiogenic phenotype. 2 MMP proenzymes are activated, in part, by the plasminogen activator (PA) system, giving rise to active forms that digest and remodel the basement membrane and extracellular matrix. 6 Although tPA is secreted by established vessels, 7 studies in a guinea pig corneal neovascularization (NV) model demonstrated that endothelial cells in new vessel sprouts secrete uPA exclusively (Jerdan JA et al. IOVS 1988;29:ARVO Abstract 109). uPA and tPA activities are rigidly controlled by plasminogen activator inhibitor (PAI)-1. MMP-2 and -9 degrade gelatin; elastin; and collagens IV (a major basement membrane component), V, VII, and X. 2 MMP-2 and -9 are most likely involved in tumor angiogenesis, 9 -11 and recent studies indicate that MMP-2 and -9 are critical for NV in the posterior segment of the eye. For example, experiments From th

Does supplementation of oocytes with additional mtDNA influence developmental outcome?

Introducing extra mitochondrial DNA (mtDNA) into oocytes at fertilization can rescue poor quality oocytes. However, supplementation alters DNA methylation and gene expression profiles of preimplantation embryos. To determine if these alterations impacted offspring, we introduced mtDNA from failed-tomature sister (autologous) or third party (heterologous) oocytes into mature oocytes and transferred zygotes into surrogates. Founders exhibited significantly greater daily weight gain (heterologous) and growth rates (heterologous and autologous) to controls. In weaners, cholesterol, bilirubin (heterologous and autologous), anion gap, and lymphocyte count (autologous) were elevated. In mature pigs, potassium (heterologous) and bicarbonate (autologous) were altered. mtDNA and imprinted gene analyses did not reveal aberrant profiles. Neither group exhibited gross anatomical, morphological, or histopathological differences that would lead to clinically significant lesions. Female founders were fertile and their offspring exhibited modified weight and height gain, biochemical, and hematological profiles. mtDNA supplementation induced minor differences that did not affect health and well-being.Stephen McIlfatrick, Sean O, Leary, Takashi Okada, Alexander Penn, Vy Hoang Thao Nguyen, Lisa McKenny, Shang-Yu Huang, Eryk Andreas, John Finnie, Roy Kirkwood, and Justin C. St. Joh

Retinal Angiogenesis Suppression through Small Molecule Activation of p53

Neovascular age-related macular degeneration is a leading cause of irreversible vision loss in the Western world. Cytokine-targeted therapies (such as anti-vascular endothelial growth factor) are effective in treating pathologic ocular angiogenesis, but have not led to a durable effect and often require indefinite treatment. Here, we show that Nutlin-3, a small molecule antagonist of the E3 ubiquitin protein ligase MDM2, inhibited angiogenesis in several model systems. We found that a functional p53 pathway was essential for Nutlin-3-mediated retinal antiangiogenesis and disruption of the p53 transcriptional network abolished the antiangiogenic activity of Nutlin-3. Nutlin-3 did not inhibit established, mature blood vessels in the adult mouse retina, suggesting that only proliferating retinal vessels are sensitive to Nutlin-3. Furthermore, Nutlin-3 inhibited angiogenesis in nonretinal models such as the hind limb ischemia model. Our work demonstrates that Nutlin-3 functions through an antiproliferative pathway with conceivable advantages over existing cytokine-targeted antiangiogenesis therapies

Search for gravitational wave bursts in LIGO's third science run

We report on a search for gravitational wave bursts in data from the three LIGO interferometric detectors during their third science run. The search targets subsecond bursts in the frequency range 100-1100 Hz for which no waveform model is assumed, and has a sensitivity in terms of the root-sum-square (rss) strain amplitude of hrss ~ 10^{-20} / sqrt(Hz). No gravitational wave signals were detected in the 8 days of analyzed data.Comment: 12 pages, 6 figures. Amaldi-6 conference proceedings to be published in Classical and Quantum Gravit