Statistical Analysis of Molecular Signal Recording

A molecular device that records time-varying signals would enable new approaches in neuroscience. We have recently proposed such a device, termed a “molecular ticker tape”, in which an engineered DNA polymerase (DNAP) writes time-varying signals into DNA in the form of nucleotide misincorporation patterns. Here, we define a theoretical framework quantifying the expected capabilities of molecular ticker tapes as a function of experimental parameters. We present a decoding algorithm for estimating time-dependent input signals, and DNAP kinetic parameters, directly from misincorporation rates as determined by sequencing. We explore the requirements for accurate signal decoding, particularly the constraints on (1) the polymerase biochemical parameters, and (2) the amplitude, temporal resolution, and duration of the time-varying input signals. Our results suggest that molecular recording devices with kinetic properties similar to natural polymerases could be used to perform experiments in which neural activity is compared across several experimental conditions, and that devices engineered by combining favorable biochemical properties from multiple known polymerases could potentially measure faster phenomena such as slow synchronization of neuronal oscillations. Sophisticated engineering of DNAPs is likely required to achieve molecular recording of neuronal activity with single-spike temporal resolution over experimentally relevant timescales.United States. Defense Advanced Research Projects Agency. Living Foundries ProgramGoogle (Firm)New York Stem Cell Foundation. Robertson Neuroscience Investigator AwardNational Institutes of Health (U.S.) (EUREKA Award 1R01NS075421)National Institutes of Health (U.S.) (Transformative R01 1R01GM104948)National Institutes of Health (U.S.) (Single Cell Grant 1 R01 EY023173)National Institutes of Health (U.S.) (Grant 1R01DA029639)National Institutes of Health (U.S.) (Grant 1R01NS067199)National Science Foundation (U.S.) (CAREER Award CBET 1053233)National Science Foundation (U.S.) (Grant EFRI0835878)National Science Foundation (U.S.) (Grant DMS1042134)Paul G. Allen Family Foundation (Distinguished Investigator in Neuroscience Award

Between-Monitor Differences in Step Counts Are Related to Body Size: Implications for Objective Physical Activity Measurement

The quantification of the relationships between walking and health requires that walking is measured accurately. We correlated different measures of step accumulation to body size, overall physical activity level, and glucose regulation.Participants were 25 men and 25 women American Indians without diabetes (Age: 20-34 years) in Phoenix, Arizona, USA. We assessed steps/day during 7 days of free living, simultaneously with three different monitors (Accusplit-AX120, MTI-ActiGraph, and Dynastream-AMP). We assessed total physical activity during free-living with doubly labeled water combined with resting metabolic rate measured by expired gas indirect calorimetry. Glucose tolerance was determined during an oral glucose tolerance test.Based on observed counts in the laboratory, the AMP was the most accurate device, followed by the MTI and the AX120, respectively. The estimated energy cost of 1000 steps per day was lower in the AX120 than the MTI or AMP. The correlation between AX120-assessed steps/day and waist circumference was significantly higher than the correlation between AMP steps and waist circumference. The difference in steps per day between the AX120 and both the AMP and the MTI were significantly related to waist circumference.Between-monitor differences in step counts influence the observed relationship between walking and obesity-related traits

Proceedings of SPIE - The International Society for Optical Engineering

The display of polarimetric imaging data has been a subject of considerable debate. Display strategies range from direct display of the Stokes vector images (or their derivatives) to false color representations. In many cases, direct interpretation of polarimetric image data using traditional display strategies is not intuitive and can at times result in confusion as to what benefit polarimetric information is actually providing. Here we investigate approaches that attempt to augment the s0 image with polarimetric information, rather than directly display it, as a means of enhancing the baseband s0 image. The benefit is that the polarization-enhanced visible or infrared image maintains a familiar look without the need for complex interpretation of the meaning of the polarimetric data, thus keeping the incorporation of polarimetric information transparent to the end user. The method can be applied to monochromatic or multi-band data, which allows color to be used for representing spectral data in multi-or hyper-spectropolarimetric applications. We take a more subjective approach to image enhancement than current techniques employ by simply seeking to improve contrast and shape information for polarized objects within a scene. We find that such approaches provide clear enhancement to the imagery when polarized objects are contained within the scene without the need for complex interpretation of polarization phenomenology

Adapting the HSV polarization-color mapping for regions with low irradiance and high polarization

Many mappings from polarization into color have been developed so that polarization information can be displayed. One of the most common of these maps the angle of linear polarization into color hue and degree of linear polarization into color saturation, while preserving the irradiance information from the polarization data. While this strategy enjoys wide popularity, there is a large class of polarization images for which it is not ideal. It is common to have images where the strongest polarization signatures (in terms of degree of polarization) occur in regions of relatively low irradiance: either in shadow in reflective bands or in cold regions in emissive bands. Since the irradiance is low, the chromatic properties of the resulting images are generally not apparent. Here we present an alternate mapping that uses the statistics of the angle of polarization as a measure of confidence in the polarization signature, then amplifies the irradiance in regions of high confidence, and leaves it unchanged in regions of low confidence. Results are shown from an LWIR and a visible spectrum imager