Thinking Outside the Box: Using Computer Science Skills to Make Sense of the Biology of Life

While I liked coding and the logical aspects of computer programming, my gut was telling me I hadn\u27t quite found my niche yet. In what field could my computer science skills make a difference while also providing me with challenging problems to solve? As these questions percolated through my subconscious, I came across a brief article about a field called “bioinformatics.

Optical interferometer in space

The present design concepts for a Laser Gravitational Wave Observatory in Space are described. Laser heterodyne distance measurements are made between test masses located in three spacecraft separated by roughly 10(exp 6) km. The major technology issues are: the reduction of spurious acceleration noise for the test masses to below 2 x 10(exp -15) cm/sq sec/Hz(0.5) from 10(exp -5) to 10(exp -3) Hz; and the measurement of changes in the difference of the antenna arm lengths to 5 x 10(exp -11) cm/Hz(0.5) from 10(exp -3) to 1 Hz with high reliability. The science objectives are: to measure discrete sinusoidal gravitational wave signals from individual sources with periods of 1 second to 1 day; to measure the stochastic background due to unresolved binaries; and to search for gravitational wave pulses with periods longer than 1 sec from possible exotic sources such as gravitational collapse of very massive objects

COMPLIANCE TESTING OF IOWA’S SKID-MOUNTED SIGN DEVICE

A wide variety of traffic control devices are used in work zones, some of which are nont ormally found on the roadside or in the traveled way outsideofthe work zones. These devices are used to enhance the safety of the work zones by controlling the traffic through these areas. Due to the placement of the traffic control devices, the devices themselves may be potentially hazardous to both workers and errant vehicles. The impact performance of many work zone traffic control devices is mainly unknown and to date limited crash testing has been conducted under the criteria of National Cooperative Highway Research Program (NCHRP) Report No. 350, Recommended Procedures for the Safety Performance Evaluation of Highway Features. The objective of the study was to evaluatethe safety performance of existing skid-mounted sign supports through full- scale crash testing. Two full-scale crash tests were conducted on skid-mounted sign supports to determine their safety performance according to the Test Level 3 (TL-3) criteria set forth in the NCHRP Report No. 350. The safety performancevaluations indicate that these skid-mounted sign supports did not perform satisfactorily in the full-scale crash tests. The results of the crash tests were documented, and conclusions and recommendations pertaining tothe safety performance of the existing work zone traffic control devices were made

Functional analysis of a missense mutation in the serine protease inhibitor SPINT2 associated with congenital sodium diarrhea.

Membrane-bound serine proteases play important roles in different biological processes. Their regulation by endogenous inhibitors is poorly understood. A Y163C mutation in the SPINT2 gene encoding the serine protease inhibitor Hepatocyte Growth Factor Inhibitor HAI-2 is associated with a congenital sodium diarrhea. The functional consequences of this mutation on HAI-2 activity and its physiological targets are unknown. We established a cellular assay in Xenopus laevis oocytes to study functional interactions between HAI-2 and candidate membrane-bound serine proteases expressed in the gastro-intestinal tract. We found that the wild-type form of HAI-2 is a potent inhibitor of nine gastro-intestinal serine proteases. The Y163C mutation in the second Kunitz domain of HAI-2 resulted in a complete loss of inhibitory activity on two intestinal proteases, prostasin and tmprss13. The effect of the mutation of the homologous Y68C in the first Kunitz domain of HAI-2 is consistent with a differential contribution of the two Kunitz domains of HAI-2 in the inhibition of serine proteases. By contrast to the Tyr to Cys, the Tyr to Ser substitution did not change the inhibitory potency of HAI-2, indicating that the thiol-group of the cysteine rather than the Tyr deletion is responsible for the HAI-2 loss of function. Our functional assay allowed us to identify membrane-bound serine proteases as cellular target for inhibition by HAI-2 wild type and mutants, and to better define the role of the Tyr in the second Kunitz domain in the inhibitory activity of HAI-2

On two intrinsic length scales in polymer physics: topological constraints vs. entanglement length

The interplay of topological constraints, excluded volume interactions, persistence length and dynamical entanglement length in solutions and melts of linear chains and ring polymers is investigated by means of kinetic Monte Carlo simulations of a three dimensional lattice model. In unknotted and unconcatenated rings, topological constraints manifest themselves in the static properties above a typical length scale $dt \sim 1/\sqrt{l\phi}$ ($\phi$ being the volume fraction, $l$ the mean bond length). Although one might expect that the same topological length will play a role in the dynamics of entangled polymers, we show that this is not the case. Instead, a different intrinsic length de, which scales like excluded volume blob size $\xi$, governs the scaling of the dynamical properties of both linear chains and rings.Comment: 7 pages. 4 figure

A YY1-dependent increase in aerobic metabolism is indispensable for intestinal organogenesis

During late gestation, villi extend into the intestinal lumen to dramatically increase the surface area of the intestinal epithelium, preparing the gut for the neonatal diet. Incomplete development of the intestine is the most common gastrointestinal complication in neonates, but the causes are unclear. We provide evidence in mice that Yin Yang 1 (Yy1) is crucial for intestinal villus development. YY1 loss in the developing endoderm had no apparent consequences until late gestation, after which the intestine differentiated poorly and exhibited severely stunted villi. Transcriptome analysis revealed that YY1 is required for mitochondrial gene expression, and ultrastructural analysis confirmed compromised mitochondrial integrity in the mutant intestine. We found increased oxidative phosphorylation gene expression at the onset of villus elongation, suggesting that aerobic respiration might function as a regulator of villus growth. Mitochondrial inhibitors blocked villus growth in a fashion similar to Yy1 loss, thus further linking oxidative phosphorylation with late-gestation intestinal development. Interestingly, we find that necrotizing enterocolitis patients also exhibit decreased expression of oxidative phosphorylation genes. Our study highlights the still unappreciated role of metabolic regulation during organogenesis, and suggests that it might contribute to neonatal gastrointestinal disorders

Exploring Spirituality in Teaching Within a Christian School Context Through Collaborative Action Research

This article reports on a collaborative action research project conducted in New Zealand, during 2012, exploring spirituality in teaching within a Christian school context. The experienced primary school teacher participant chose to take action around the issue of personal fear and insecurity which were believed to be hindering professional growth and relationships. Through self-directed inquiry, critical reflective journaling, Bible study, fellowship and prayer with trusted friends, the teacher experienced a renewed sense of peace and freedom in Christ. This personal transformation was believed to be influential on subsequent professional practice, assisting the teacher to become more relational, responsive and compassionate. The findings provide a rich description of the participant’s spirituality, the lived reality of a person’s spiritual life. This report will be of interest to teachers, teacher-leaders and teacher-educators who desire to explore Christian spirituality through practitioner-led inquiry

Acoustic Calibration of the Exterior Effects Room at the NASA Langley Research Center

The Exterior Effects Room (EER) at the NASA Langley Research Center is a 39-seat auditorium built for psychoacoustic studies of aircraft community noise. The original reproduction system employed monaural playback and hence lacked sound localization capability. In an effort to more closely recreate field test conditions, a significant upgrade was undertaken to allow simulation of a three-dimensional audio and visual environment. The 3D audio system consists of 27 mid and high frequency satellite speakers and 4 subwoofers, driven by a real-time audio server running an implementation of Vector Base Amplitude Panning. The audio server is part of a larger simulation system, which controls the audio and visual presentation of recorded and synthesized aircraft flyovers. The focus of this work is on the calibration of the 3D audio system, including gains used in the amplitude panning algorithm, speaker equalization, and absolute gain control. Because the speakers are installed in an irregularly shaped room, the speaker equalization includes time delay and gain compensation due to different mounting distances from the focal point, filtering for color compensation due to different installations (half space, corner, baffled/unbaffled), and cross-over filtering

Detection, Measurement and Gravitational Radiation

Here I examine how to determine the sensitivity of the LIGO, VIRGO, and LAGOS gravitational wave detectors to sources of gravitational radiation by considering the process by which data are analyzed in a noisy detector. By constructing the probability that the detector output is consistent with the presence of a signal, I show how to (1) quantify the uncertainty that the output contains a signal and is not simply noise, and (2) construct the probability distribution that the signal parameterization has a certain value. From the distribution and its mode I determine volumes $V(P)$ in parameter space such that actual signal parameters are in $V(P)$ with probability $P$. If we are {\em designing} a detector, or determining the suitability of an existing detector for observing a new source, then we don't have detector output to analyze but are interested in the ``most likely'' response of the detector to a signal. I exploit the techniques just described to determine the ``most likely'' volumes $V(P)$ for detector output corresponding to the source. Finally, as an example, I apply these techniques to anticipate the sensitivity of the LIGO and LAGOS detectors to the gravitational radiation from a perturbed Kerr black hole.Comment: 37 pages (plus 6 figures), LaTeX/REVTE

Stratified spatiotemporal chaos in anisotropic reaction-diffusion systems

Numerical simulations of two dimensional pattern formation in an anisotropic bistable reaction-diffusion medium reveal a new dynamical state, stratified spatiotemporal chaos, characterized by strong correlations along one of the principal axes. Equations that describe the dependence of front motion on the angle illustrate the mechanism leading to stratified chaos