Structural Study of the Complex Between DNA Polymerase Iota and Ub-PCNA

DNA polymerase iota (polι) is a member of the Y-family, polymerases which are key components in translesion synthesis (TLS). As part of the DNA damage response, TLS allows cells to bypass damaged template DNA. Each member of the Y-family is capable of accurately replicating across from certain lesions. All Y-family polymerases are recruited by ubiquitination of the DNA sliding clamp, PCNA, by direct interaction with PCNA and ubiquitin. The mechanism of polymerase choice is not well understood, nor are the interactions between Ub-PCNA and the TLS polymerases. We studied the structure of the complex between the interacting region of polι and Ub-PCNA. Polι appears to be unable to bind all three monomers of homotrimeric Ub-PCNA simultaneously, even in a heavily truncated form. The maximum complex ratio observed was two polymerases per Ub-PCNA ring. This assembly ratio limit may give insight into switching of multiple polymerases at the PCNA platform in DNA damage response

A proposed psychological model of driving automation

This paper considers psychological variables pertinent to driver automation. It is anticipated that driving with automated systems is likely to have a major impact on the drivers and a multiplicity of factors needs to be taken into account. A systems analysis of the driver, vehicle and automation served as the basis for eliciting psychological factors. The main variables to be considered were: feed-back, locus of control, mental workload, driver stress, situational awareness and mental representations. It is expected that anticipating the effects on the driver brought about by vehicle automation could lead to improved design strategies. Based on research evidence in the literature, the psychological factors were assembled into a model for further investigation

The Creation of a low-cost, reliable platform for mobile robotics research

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, June 2011."June 2011." Cataloged from PDF version of thesis.Includes bibliographical references (p. 29).This work documents the planning process, design, fabrication, and integration of a low-cost robot designed for research on the problem of life-long robot mapping. The robotics platform used is the iRobot Create. This robot also employs the PrimeSensor, a sensor with the ability to provide a pixel-matched, colored depth field in real time. This sensor was later purchased by Microsoft and leveraged in their popular gaming device, the Microsoft Kinect. The robot has a powerful Acer Aspire 1830T-6651 laptop with an Intel Core i5 to perform processor-intensive, real-time image processing. The actual construction of the robot consisted of two phases: the physical integration of the components on a chassis and the software integration through the computer. The physical integration is mainly a central chassis made from laser-cut acrylic. This chassis is capable of securely holding the laptop computer in place and provides an elevated mount for the PrimeSensor. This mount has the ability to change the viewing angle of the sensor and lock that angle at 5' increments using a pin. The software integration was completed using open-source packages for the Robot Operating System (ROS) developed by Brown University and a not-for-profit company called OpenNI. These packages were installed on the onboard laptop and the ROS core functions running on the laptop provide the foundation to run new code on this testing platform. This robot is low in cost and provides a reliable, robust, and versatile platform for visionbased artificial intelligence research. The mapping software and vision algorithms developed on this platform will contribute to the development of more intelligent and meaningful vision capabilities for tomorrow's robots.by Taylor Harrison Gilbert.S.B

Test cell set-up to enable drive-cycle testing of a variable valve actuation enabled camless diesel engine

The previous facility which was used for engine testing at Purdue\u27s Ray W. Herrick Laboratories utilized an eddy current dynamometer which is only suited for steady-state testing and throttle snaps. To better utilize a pre-existing camless diesel engine, which is is enabled via variable valve actuation, it was desired to perform transient drive-cycle tests. To accomplish this goal, a variable frequency drive AC dynamometer was required. Given that a brand new facility was constructed, the team was presented with an opportunity for ground up design of a test cell. The new test cell\u27s operation was proved out using a cammed diesel engine before moving the vairable valve actuation (VVA) enabled camless engine over. The research group\u27s best practice is to only utilize the VVA engine when collecting novel or experimental data as additional run time on this engine increases the risk of damage due to valve-to-piston interference. The goal of proving out the test cell with the cammed engine was to validate that engine operation and data collection was \u27\u27as good as or better than the previous test facility, and to solve any issues preventing the group from reaching that goal. Data acquisition results from the new test cell had noise issues which were worked out before moving over the VVA engine from the previous test cell. Fuel metering with a Cybermetrix fuel metering unit (FMU) proved to be more difficult than just plug and play, with fully functional and reliable operation taking place after the move. While the test cell\u27s room ventilation proved fully functional, additional research and work was required to hook up the conditioned combustion air system. Transient drive-cycle testing was performed with the cammed engine, and statistical analysis was performed which confirmed that the feedback speed and torque matched the reference speed and torque within EPA guidelines. This same analysis was later performed with the VVA engine and also showed capability of the VVA engine to perform repeatable drive-cycle tests. The new test cell continues to see new additions, with future work including the installation and validation of a full diesel after-treatment system which will allow for research into improving not only engine-out emissions but also tailpipe emissions through studies of the dynamic interactions between the individual exhaust components. The scope of VVA enabled diesel engine research in the Cummins Power Lab has increased from steady-state testing to transient drive-cycle testing which is more representative of how the engine is used by the end-customers

The relationship between plasma osmolarity and feed efficiency in beef cattle and effect of feeding cows medicated feed through mineral containing AltosidRTM IGR on the growth of beef calves

Dietary cation-anion modification in cattle has effects on productivity through various means. Alterations of dietary cation-anion balances has been shown to affect plasma osmolarity. Plasma osmolarity is directly related to renal function and metabolism in all animals. In a feeding operation with a single diet fed to a similar population of animals, plasma osmolarity should fall within a somewhat normal range (approximately 270-310 mOsm). However, subtle, yet very distinguishable differences will exist between animals. In theory, variances in osmolarity may reflect differences in metabolism and as such, efficiency of feed utilization. Many researchers believe that utilizing residual feed intake (RFI) expressed in a population as a selection tool will lead to improved production efficiency in beef cattle. Residual feed intake is normally distributed. Like osmolarity, RFI will have subtle, yet very distinguishable differences existing between animals. The objective of this study is to determine if there are any detectable relationships between plasma osmolarity measurements and RFI within a controlled test population and to further determine how this information may be used in improving the utility of RFI measurements. In this study (77d), intake, BW, and ultrasound measurements of yearling heifers were observed. Frozen (-60oC) plasma samples were thawed at room temperature and osmolarity determined. Plasma samples (n=67, n=70) were analyzed to determine osmolarity. All data were analyzed using the CORR procedures of SAS. Plasma osmolarity measured on day 70 demonstrated a weak relationship to RFI (r = 0.226; P = 0.0); no other correlations existed ( P \u3e 0.10) in this data set. There were little to no relationships between osmolarity and ultrasound rump fat (P \u3e 0.90), rib fat (P \u3e 0.98) and intramuscular fat (P \u3e 0.13). Only days 21 and 35 had relationships between ribeye area and osmolarity. (P = 0.04; P = 0.0002). There were also minimal detectable relationships of osmolarity with metabolic body size ( P \u3e 0.06) or intake (P \u3e 0.08). However, osmolarity values fluctuated over the nine (year 1) or ten (year 2) different time points, thus plasma osmolarity measurements taken during or shortly after dietary adaptation may not directly correlate to an animal\u27s RFI value. However, analysis of how animals establish a cation-anion balance may have some relationship to the animals RFI phenotype

Investigation of Unnatural Amino Acids as a Means to Modulate Protein Function

In order to elucidate the biological processes that occur in everyday life, chemical biologists have developed technologies that allow the study of a various biological systems. Bioorthogonal chemistry is an ever-growing technology that involves performing chemical reactions with biological systems that do not rely on existing biological chemistries. In this work we attempt to develop and characterize novel bioorthognal chemistries that further expand the utility of this field. Additionally, we explore the utility of fluorescent probes in labeling applications. Finally, we attempt to create novel methods of control for a gene-editing protein using light as a mechanism of regulation

A new development in railway equipment financing: the Equitable plan

Thesis (M.N.A.)--Boston Universit

Optimal control of a Brownian storage system

AbstractConsider a storage system (such as an inventory or bank account) whose content fluctuates as a Brownian Motion X = {X(t), t ⩾ 0} in the absence of any control. Let Y = {Y(t), t ⩾ 0} and Z = {Z(t), t ⩾ 0} be non-decreasing, non-anticipating functionals representing the cumulative input to the system and cumulative output from the system respectively. Theproblem is to choose Y and Z so as to minimize expected discounted cost subject to the requirement that X(t) + Y(t) - Z(t) ⩾ 0 for all t ⩾ 0 almost surely. In our first formulation, we assume a proportional input cost, a linear holding cost, and a proportional output reward (or cost). We explicitly compute an optimal policy involving a single critical number. In our second formulation, the cumulative input Y is required to be a step function, and an additional fixed charge is incurred each time that an input jump occurs. We explicitly compute an optimal policy involving two critical numbers. Applications to inventory/production control and stochastic cash management are discussed