A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria.

To broadly explore mitochondrial structure and function as well as the communication of mitochondria with other cellular pathways, we constructed a quantitative, high-density genetic interaction map (the MITO-MAP) in Saccharomyces cerevisiae. The MITO-MAP provides a comprehensive view of mitochondrial function including insights into the activity of uncharacterized mitochondrial proteins and the functional connection between mitochondria and the ER. The MITO-MAP also reveals a large inner membrane-associated complex, which we term MitOS for mitochondrial organizing structure, comprised of Fcj1/Mitofilin, a conserved inner membrane protein, and five additional components. MitOS physically and functionally interacts with both outer and inner membrane components and localizes to extended structures that wrap around the inner membrane. We show that MitOS acts in concert with ATP synthase dimers to organize the inner membrane and promote normal mitochondrial morphology. We propose that MitOS acts as a conserved mitochondrial skeletal structure that differentiates regions of the inner membrane to establish the normal internal architecture of mitochondria

Double Sampling Auxiliary Information Chart And Exponentially Weighted Moving Average Auxiliary Information Chart, Both Based On Variable Sampling Interval, And Measurement Errors Based Triple Sampling Chart

The concept of using auxiliary information (AI) in control charts is growing in popularity among researchers. Control charts using the AI technique have been found to be more effective than control charts without the AI technique. The first objective of this thesis is to develop a variable sampling interval (VSI) double sampling (DS) chart using the AI technique (called VSI DS-AI chart) for monitoring the process mean. The charting statistics, optimal designs and implementation of the VSI DS-AI chart are discussed. The steady-state average time to signal (ssATS) and steady-state expected average time to signal (ssEATS) criteria are used as the performance measures of the proposed VSI DS-AI chart. The ssATS and ssEATS results of the VSI DS-AI chart are compared with those of the double sampling AI, variable sample size and sampling interval AI, exponentially weighted moving average AI (EWMA-AI) and run sum AI (RS-AI) charts. The comparison reveals that the VSI DS-AI chart performs better than the competing charts for all shift sizes, except the EWMA-AI and RS-AI charts for small shifts

Massively parallel implicit equal-weights particle filter for ocean drift trajectory forecasting

Forecasting of ocean drift trajectories are important for many applications, including search and rescue operations, oil spill cleanup and iceberg risk mitigation. In an operational setting, forecasts of drift trajectories are produced based on computationally demanding forecasts of three-dimensional ocean currents. Herein, we investigate a complementary approach for shorter time scales by using the recently proposed two-stage implicit equal-weights particle filter applied to a simplified ocean model. To achieve this, we present a new algorithmic design for a data-assimilation system in which all components – including the model, model errors, and particle filter – take advantage of massively parallel compute architectures, such as graphical processing units. Faster computations can enable in-situ and ad-hoc model runs for emergency management, and larger ensembles for better uncertainty quantification. Using a challenging test case with near-realistic chaotic instabilities, we run data-assimilation experiments based on synthetic observations from drifting and moored buoys, and analyze the trajectory forecasts for the drifters. Our results show that even sparse drifter observations are sufficient to significantly improve short-term drift forecasts up to twelve hours. With equidistant moored buoys observing only 0.1% of the state space, the ensemble gives an accurate description of the true state after data assimilation followed by a high-quality probabilistic forecast

Design of side-sensitive double sampling control schemes for monitoring the location parameter

Double sampling procedure is adapted from a statistical branch called acceptance sampling. The first Shewhart-type double sampling monitoring scheme was introduced in the statistical process monitoring (SPM) field in 1974. The double sampling monitoring scheme has been proven to effectively decrease the sampling effort and, at the same time, to decrease the time to detect potential out-of-control situations when monitoring the location, variability, joint location and variability using univariate or multivariate techniques. Consequently, an overview is conducted to give a full account of all 76 publications on double sampling monitoring schemes that exist in the SPM literature. Moreover, in the review conducted here, these are categorized and summarized so that any research gaps in the SPM literature can easily be identified. Next, based on the knowledge gained from the literature review about the existing designs for monitoring the process mean, a new type of double sampling design is proposed. The new charting region design lead to a class of a control charts called a side-sensitive double sampling (SSDS) monitoring schemes. In this study, the SSDS scheme is implemented to monitor the process mean when the underlying process parameters are known as well as when they are unknown. A variety of run-length properties (i.e., the 5th, 25th, 50th, 75th, 95th percentiles, the average run-length (), standard deviation of the run-length (), the average sample size () and the average extra quadratic loss () metrics) are used to design and implement the new SSDS scheme. Comparisons with other established monitoring schemes (when parameters are known and unknown) indicate that the proposed SSDS scheme has a better overall performance. Illustrative examples are also given to facilitate the real-life implementation of the proposed SSDS schemes. Finally, a list of possible future research ideas is given with hope that this will stimulate more future research on simple as well as complex double sampling schemes (especially using the newly proposed SSDS design) for monitoring a variety of quality characteristics in the future.StatisticsM. Sc. (Statistics

Dynare: Reference Manual Version 4

Dynare is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium (DSGE) and overlapping generations (OLG) models. The models solved by Dynare include those relying on the rational expectations hypothesis, wherein agents form their expectations about the future in a way consistent with the model. But Dynare is also able to handle models where expectations are formed differently: on one extreme, models where agents perfectly anticipate the future; on the other extreme, models where agents have limited rationality or imperfect knowledge of the state of the economy and, hence, form their expectations through a learning process. Dynare offers a user-friendly and intuitive way of describing these models. It is able to perform simulations of the model given a calibration of the model parameters and is also able to estimate these parameters given a dataset. Dynare is a free software, which means that it can be downloaded free of charge, that its source code is freely available, and that it can be used for both non-profit and for-profit purposes.Dynare; Numerical methods; Perturbation; Rational expectations

Aqueous solvent-gel cleaning of poly (methyl methacrylate) surfaces in museum collections

This research explores the use of aqueous solvent-gel systems for cleaning transparent and highly polished poly(methyl methacrylate) (PMMA) surfaces found in historical, technological, art and design museum collections. Surface transparency and glossiness were identified as conservators’ priorities when cleaning plastics, in a survey conducted for the purposes of this research. The absence of established conservation cleaning treatments for plastics has led to the inappropriate use of methods employed on other materials. Gels are used here as solvent carriers for their potential to optimise cleaning with their purported abilities to control solvent diffusion and limit mechanical stresses. Factors affecting cleaning are investigated through a series of statistically designed laboratory-based experiments on unaged and accelerated light-aged PMMA samples. A range of polar and nonpolar solvents, and natural as well as synthetic polymeric matrices are tested independently and in combination. Artificial oily dirt and pressure-sensitive adhesive are applied to surfaces to respectively simulate human fingerprints and labels/packaging tape remains. PMMA is mechanically and chemically characterised with Dynamic Mechanical Analysis, tensile testing and pyrolysis-Gas Chromatography/Mass Spectrometry. Macroscopic observation, stereomicroscopy and Scanning Electron Microscopy imaging are used to evaluate visual change. Weight and gloss measurements offer quantitative evidence of post-treatment changes. Surface chemical modifications are detected with Attenuated Total Reflection Fourier Transform Infrared spectroscopy and bulk mechanical changes are monitored with Nuclear Magnetic Resonance Mobile Universal Surface Explorer. Finally, three PMMA museum objects with a user life are treated with the successful gels to test the validity of lab-based results. The research has shown that direct application of deionised water, ethanol, isopropanol and petroleum ether with cotton swabs causes dissolution of PMMA components and is to be avoided. Solvents dispersed in Agar, Gellan, Pemulen TR2/triethanolamine and 80 % Poly(vinyl acetate)/borax gels regulate the damaging solvent effect and reduce visual damage. Carbopol EZ2/Ethomeen C-25 is unsuitable due to inducing numerous scratches and leaving gel residues. Pemulen performed the best; with isopropanol being the most efficient at oily dirt removal and petroleum ether at adhesive removal. Repeated gel applications are recommended for improved results. This research recommends the use of Poly(vinyl acetate)/borax ethanol and Pemulen TR2/triethanolamine gels/emulsions with isopropanol or petroleum ether for cleaning transparent and glossy PMMA in museum collections

Spontaneous Reaction Silencing in Metabolic Optimization

Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated with this behavior remain very poorly understood. Here we predict computationally and analytically that any organism evolving to maximize growth rate, ATP production, or any other linear function of metabolic fluxes tends to significantly reduce the number of active metabolic reactions compared to typical non-optimal states. The reduced number appears to be constant across the microbial species studied and just slightly larger than the minimum number required for the organism to grow at all. We show that this massive spontaneous reaction silencing is triggered by the irreversibility of a large fraction of the metabolic reactions and propagates through the network as a cascade of inactivity. Our results help explain existing experimental data on intracellular flux measurements and the usage of latent pathways, shedding new light on microbial evolution, robustness, and versatility for the execution of specific biochemical tasks. In particular, the identification of optimal reaction activity provides rigorous ground for an intriguing knockout-based method recently proposed for the synthetic recovery of metabolic function.Comment: 34 pages, 6 figure

Jet Mixing Enhancement by High Amplitude Pulse Fluidic Actuation

Turbulent mixing enhancement has received a great deal of attention in the fluid mechanics community in the last few decades. Generally speaking, mixing enhancement involves the increased dispersion of the fluid that makes up a flow. The current work focuses on mixing enhancement of an axisymmetric jet via high amplitude fluidic pulses applied at the nozzle exit with high aspect ratio actuator nozzles. The work consists of small scale clean jet experiments, small scale micro-turbine engine experiments, and full scale laboratory simulated core exhaust experiments using actuators designed to fit within the engine nacelle of a full scale aircraft. The small scale clean jet experiments show that mixing enhancement compared to the unforced case is likely due to a combination of mechanisms. The first mechanism is the growth of shear layer instabilities, similar to that which occurs with an acoustically excited jet except that, in this case, the forcing is highly nonlinear. The result of the instability is a frequency bucket with an optimal forcing frequency. The second mechanism is the generation of counter rotating vortex pairs similar to those generated by mechanical tabs. The penetration depth determines the extent to which this mechanism acts. The importance of this mechanism is therefore a function of the pulsing amplitude. The key mixing parameters were found to be the actuator to jet momentum ratio (amplitude) and the pulsing frequency, where the optimal frequency depends on the amplitude. The importance of phase, offset, duty cycle, and geometric configuration were also explored. The experiments on the jet engine and full scale simulated core nozzle demonstrated that pulse fluidic mixing enhancement was effective on realistic flows. The same parameters that were important for the cleaner small scale experiments were found to be important for the more realistic cases as well. This suggests that the same mixing mechanisms are at work. Additional work was done to optimize, in real time, mixing on the small jet engine using an evolution strategy.Ph.D.Committee Chair: David Parekh; Committee Member: Ari Glezer; Committee Member: Jeff Jagoda; Committee Member: Richard Gaeta; Committee Member: Samuel Shelto

Remote sensing in the coastal and marine environment. Proceedings of the US North Atlantic Regional Workshop

Presentations were grouped in the following categories: (1) a technical orientation of Earth resources remote sensing including data sources and processing; (2) a review of the present status of remote sensing technology applicable to the coastal and marine environment; (3) a description of data and information needs of selected coastal and marine activities; and (4) an outline of plans for marine monitoring systems for the east coast and a concept for an east coast remote sensing facility. Also discussed were user needs and remote sensing potentials in the areas of coastal processes and management, commercial and recreational fisheries, and marine physical processes