Rational tangle surgery and Xer recombination on catenanes

The protein recombinase can change the knot type of circular DNA. The action of a recombinase converting one knot into another knot is normally mathematically modeled by band surgery. Band surgeries on a 2-bridge knot N((4mn-1)/(2m)) yielding a (2,2k)-torus link are characterized. We apply this and other rational tangle surgery results to analyze Xer recombination on DNA catenanes using the tangle model for protein-bound DNA.Comment: 20 pages, 23 figure

'Why Just Go for 51%?' Organizational Structure in the Religious Society of Friends

http://deepblue.lib.umich.edu/bitstream/2027.42/51331/1/567.pd

Neural and Neuroendocrine Processing of a Non-Photic Cue in an Opportunistically Breeding Songbird

Recent studies of the onset of breeding in long-day photoperiodic breeders have focused on the roles of type 2 and 3 iodothyronine deiodinases (DIO2 and DIO3) in the conversion of thyroxine (T4) to triiodothyronine (T3) and subsequent activation of the reproductive axis. It has been hypothesized that an increase in DIO2 and a reciprocal decrease in DIO3 causes the release of gonadotropinreleasing hormone (GnRH) from the hypothalamus, setting off a reproductive cascade, and that this DIO mechanism for GnRH release is conserved across vertebrate taxa. We sought to test whether social cues that are known to stimulate reproductive behaviors can activate the DIO system to initiate reproduction in a non-photoperiodic bird, the zebra finch (Taeniopygia guttata). Isolation of males and subsequent presentation of females did not increase DIO2 or GnRH expression in the hypothalamus, nor did it decrease gonadotropin-inhibitory hormone (GnIH) or DIO3. Males receiving a female stimulus showed significantly higher mRNA expression and immunoreactive cell count of the immediate-early gene early growth response protein 1 (EGR-1) than isolated males, indicating hypothalamic activation in response to a female. Cells immunoreactive for EGR-1 were not co-localized with those immunoreactive for GnRH. Reproductive behaviors (singing, copulation attempts and overall activity) were significantly higher in males receiving a female stimulus. This study presents a social effect on behavior and EGR-1 expression in the hypothalamus of males in response to females, but more research is needed to determine whether the DIO2 system and the GnRH system are responsive to social stimulation in this species

Modeling knotted proteins with tangles

Although rare, an increasing number of proteins have been observed to contain entanglements in their native structures. To gain more insight into the significance of protein knotting, researchers have been investigating protein knot formation using both experimental and theoretical methods. Motivated by the hypothesized folding pathway of $\alpha$-haloacid dehalogenase (DehI) protein, Flapan, He, and Wong proposed a theory of how protein knots form, which includes existing folding pathways described by Taylor and B\"olinger et al. as special cases. In their topological descriptions, two loops in an unknotted open protein chain containing at most two twists each come close together, and one end of the protein eventually passes through the two loops. In this paper, we build on Flapan, He, and Wong's theory where we pay attention to the crossing signs of the threading process and assume that the unknotted protein chain may arrange itself into a more complicated configuration before threading occurs. We then apply tangle calculus, originally developed by Ernst and Sumners to analyze the action of specific proteins on DNA, to give all possible knots or knotoids that may be discovered in the future according to our model and give recipes for engineering specific knots in proteins from simpler pieces. We show why twists knots are the most likely knots to occur in proteins. We use chirality to show that the most likely knots to occur in proteins via Taylor's twisted hairpin model are the knots $+3_1$, $4_1$, and $-5_2$

Design and qualification of an absolute thickness measuring machine

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2004.Includes bibliographical references (leaf 68).The target fabrication group at Lawrence Livermore National Laboratory develops various high energy density physics targets, which are used to study the interaction of materials when shot with high energy lasers. These targets consist of many different types of materials glued together including low density foams, plastics, and metals. To verify models, the physicists need to know the exact thickness of the targets and target components to [plus-minus] 1.0 [mu]m. The target components are typically 3-5 mm in diameter and 200-300 [mu]m thick and may have features such as moguls or two-dimensional sine waves machined onto them. As of yet, no commercial thickness measuring machine exists on the market capable of measuring thicknesses to [plus-minus] 1.0 [mu]m. To solve this problem, an absolute thickness measuring machine was developed that uses a precision air-bearing XY stage to scan a target between two confocal displacement lasers that measure the profile of each side of the target. A NIST traceable gage block of known thickness is used to calculate the thickness of the target. This paper describes the design and qualification of the absolute thickness measuring machine. It focuses on the error budget and tests performed to qualify the machine. Without compensation factors, the absolute thickness measuring machine was able to measure the thickness of a gage block to 0.5 [mu]m.by Darcy K. Kelly.S.M

Populating SAE J2735 Message Confidence Values for Traffic Signal Transitions Along a Signalized Corridor

The communication between connected vehicles and traffic signal controllers is defined in SAE Surface Vehicle Standard J2735. SAE J2735 defines traffic signal status messages and a series of 16 confidence levels for traffic signal transitions. This paper discusses a statistical method for tabulating traffic signal data by phase and time of day and populating the SAE J2735 messages. Graphical representation of the red-green and green-yellow transitions are presented from six intersections along a 4-mile corridor for five different time of day timing plans. The case study provided illustrates the importance of characterizing the stochastic variation of traffic signals to understand locations, phases, and time of day when traffic indications operate with high predictability, and periods when there are large variations in traffic signal change times. Specific cases, such as low vehicle demand and occasional actuation of pedestrian phases are highlighted as situations that may reduce the predictability of traffic signal change intervals. The results from this study also opens up discussion among transportation professionals on the importance of consistent tabulation of confidence values for both beginning and end of green signal states. We believe this paper will initiate dialog on how to consistently tabulate important data elements transmitted in SAE J2735 and perhaps refine those definitions. The paper concludes by highlighting the importance of traffic engineers and connected vehicle developers to work together to develop shared visions on traffic signal change characteristics so that the in-vehicle use cases and human-machine interface (HMI) meet user expectations

Utilization of Dedicated Electric Vehicle Plug-In Charging Stations in a College Campus Environment

As electric mobility is expanding at a rapid pace, the standardized availability of gas stations compared to a scarcity of charging stations continues to be the greatest challenge for electric vehicles. With cities, university campuses and businesses promoting electric vehicle infrastructure and incentives, it is necessary to develop key performance metrics and visualizations that can track the utilization of the charging infrastructure. This study performs a manual data collection at dedicated plug-in charging stations across Purdue University to assess their utilization. Approximately 2,800 observations were conducted over 50 days across seven level 2 plug-in charging stations. Results showed that for large portion of the observations, vehicles were parked at the spots (40%) but not plugged in. Vehicles plugged in to charging stations accounted for 34% of observations. Charging station spots were vacant for 25% of observations indicating that current infrastructure meets the demand. There were 74 unique vehicles that used the spots, of which 27% were plugged in more than 10 times. Illegally parked vehicles accounted for less than 1% with only 4 repeat offenders who used these spots more than once. As electric deployment continues to increase, performance metrics will be an integral tool for agencies and decision makers to help with the maintenance and expansion of electric vehicle infrastructure

Using Crowdsourced Vehicle Braking Data to Identify Roadway Hazards

Modern vehicles know more about the road conditions than transportation agencies. Enhanced vehicle data that provides information on “close calls” such as hard braking events or road conditions during winter such as wheel slips and traction control will be critical for improving safety and traffic operations. This research applied conflict analyses techniques to process approximately 1.5 million hard braking events that occurred in the state of Indiana over a period of one week in August 2019. The study looked at work zones, signalized intersections, interchanges and entry/exit ramps. Qualitative spatial frequency analysis of hard-braking events on the interstate demonstrated the ability to quickly identify temporary and long-term construction zones that warrant further investigation to improve geometry and advance warning signs. The study concludes by recommending the frequency of hard-braking events across different interstate routes to identify roadway locations that have abnormally high numbers of “close calls” for further engineering assessment

Spatial and Temporal Distribution and Habitat Selection of Native Yellowstone Cutthroat Trout and Nonnative Utah Chub

Henrys Lake, Idaho, is a renowned trophy trout fishery that faces an uncertain future following the establishment of Utah Chub (UTC) Gila atraria. Utah Chub were first documented in the lake in 1993 and have become abundant over the past two decades. Little is known about the ecology of UTC, but they typically have negative effects on salmonids in systems where they have been introduced. We sought to fill knowledge gaps in UTC ecology and provide insight on potential interactions with Yellowstone Cutthroat Trout (YCT) Oncorhynchus clarkii bouvieri. Ninety-four YCT and 95 UTC were radio-tagged in spring 2019 and 2020 to better understand potential interactions between YCT and UTC in Henrys Lake. Fish were located via mobile tracking and fixed receivers from June to December 2019 and 2020. In June of both years, YCT and UTC were concentrated in nearshore habitats. As water temperatures increased, UTC were documented in deeper water (mean ± SD = 3.6 ± 1.4 m) and YCT became more concentrated in areas with cold water (e.g., mouths of tributaries, in-lake springs). In July and August, large congregations of UTC were observed. Yellowstone Cutthroat Trout were detected in tributaries from June to August, but no UTC were detected in the tributaries. By late fall (November–December), YCT were located along the shoreline and UTC were detected in the middle of the lake. Both YCT and UTC were observed in areas with dense vegetation. Macrophytes likely provided a food source for UTC and cover from predators for both species. Locations of YCT were negatively related to warm water temperatures, whereas UTC were positively associated with warm water temperatures. Results from this research fill knowledge gaps in UTC and YCT interactions as well as provide valuable insight on the ecology of UTC and adfluvial Cutthroat Trout populations. Furthermore, distribution patterns and habitat selectivity of YCT and UTC in Henrys Lake can be used to inform management decisions for fishery improvement and YCT conservation