Biodefense: Scenarios, Science, and Security

A look at some plausible threats, and what the nation can do to protect us

Hypertemporal Imaging of NYC Grid Dynamics

Hypertemporal visible imaging of an urban lightscape can reveal the phase of the electrical grid granular to individual housing units. In contrast to in-situ monitoring or metering, this method offers broad, persistent, real-time, and non-permissive coverage through a single camera sited at an urban vantage point. Rapid changes in the phase of individual housing units signal changes in load (e.g., appliances turning on and off), while slower building- or neighborhood-level changes can indicate the health of distribution transformers. We demonstrate the concept by observing the 120 Hz flicker of lights across a NYC skyline. A liquid crystal shutter driven at 119.75 Hz down-converts the flicker to 0.25 Hz, which is imaged at a 4 Hz cadence by an inexpensive CCD camera; the grid phase of each source is determined by analysis of its sinusoidal light curve over an imaging "burst" of some 25 seconds. Analysis of bursts taken at ~15 minute cadence over several hours demonstrates both the stability and variation of phases of halogen, incandescent, and some fluorescent lights. Correlation of such results with ground-truth data will validate a method that could be applied to better monitor electricity consumption and distribution in both developed and developing cities.Comment: This paper uses astronomical techniques applied to the study of urban lights. This research is reproducible but the data access is restricted. A Github repository contains all code supporting this research as well as additional material: https://github.com/fedhere/detect12

Complex Langevin Equation and the Many-Fermion Problem

We study the utility of a complex Langevin (CL) equation as an alternative for the Monte Carlo (MC) procedure in the evaluation of expectation values occurring in fermionic many-body problems. We find that a CL approach is natural in cases where non-positive definite probability measures occur, and remains accurate even when the corresponding MC calculation develops a severe ``sign problem''. While the convergence of CL averages cannot be guaranteed in principle, we show how convergent results can be obtained in three examples ranging from simple one-dimensional integrals over quantum mechanical models to a schematic shell model path integral.Comment: 19 pages, 10 PS figures embedded in tex

Dynamics of the urban lightscape

The manifest importance of cities and the advent of novel data about them are stimulating interest in both basic and applied “urban science” (Bettencourt et al., 2007 [4]; Bettencourt, 2013 [3]). A central task in this emerging field is to document and understand the “pulse of the city” in its diverse manifestations (e.g., in mobility, energy use, communications, economics) both to define the normal state against which anomalies can be judged and to understand how macroscopic city observables emerge from the aggregate behavior of many individuals (Louail, 2013 [9]; Ferreira et al., 2013 [6]). Here we quantify the dynamics of an urban lightscape through the novel modality of persistent synoptic observations from an urban vantage point. Established astronomical techniques are applied to visible light images captured at 0.1 Hz to extract and analyze the light curves of 4147 sources in an urban scene over a period of 3 weeks. We find that both residential and commercial sources in our scene exhibit recurring aggregate patterns, while the individual sources decorrelate by an average of one hour after only one night. These highly granular, stand-off observations of aggregate human behavior – which do not require surveys, in situ monitors, or other intrusive methodologies – have a direct relationship to average and dynamic energy usage, lighting technology, and the impacts of light pollution. They may also be used indirectly to address questions in urban operations as well as behavioral and health science. Our methodology can be extended to other remote sensing modalities and, when combined with correlative data, can yield new insights into cities and their inhabitants

Computation in Classical Mechanics

There is a growing consensus that physics majors need to learn computational skills, but many departments are still devoid of computation in their physics curriculum. Some departments may lack the resources or commitment to create a dedicated course or program in computational physics. One way around this difficulty is to include computation in a standard upper-level physics course. An intermediate classical mechanics course is particularly well suited for including computation. We discuss the ways we have used computation in our classical mechanics courses, focusing on how computational work can improve students' understanding of physics as well as their computational skills. We present examples of computational problems that serve these two purposes. In addition, we provide information about resources for instructors who would like to include computation in their courses.Comment: 6 pages, 3 figures, submitted to American Journal of Physic

Evolution of AANAT: expansion of the gene family in the cephalochordate amphioxus

<p>Abstract</p> <p>Background</p> <p>The arylalkylamine <it>N</it>-acetyltransferase (AANAT) family is divided into structurally distinct vertebrate and non-vertebrate groups. Expression of vertebrate AANATs is limited primarily to the pineal gland and retina, where it plays a role in controlling the circadian rhythm in melatonin synthesis. Based on the role melatonin plays in biological timing, AANAT has been given the moniker "the Timezyme". Non-vertebrate AANATs, which occur in fungi and protists, are thought to play a role in detoxification and are not known to be associated with a specific tissue.</p> <p>Results</p> <p>We have found that the amphioxus genome contains seven <it>AANAT</it>s, all having non-vertebrate type features. This and the absence of <it>AANATs </it>from the genomes of Hemichordates and Urochordates support the view that a major transition in the evolution of the <it>AANATs </it>may have occurred at the onset of vertebrate evolution. Analysis of the expression pattern of the two most structurally divergent <it>AANAT</it>s in <it>Branchiostoma lanceolatum </it>(<it>bl</it>) revealed that they are expressed early in development and also in the adult at low levels throughout the body, possibly associated with the neural tube. Expression is clearly not exclusively associated with the proposed analogs of the pineal gland and retina. blAANAT activity is influenced by environmental lighting, but light/dark differences do not persist under constant light or constant dark conditions, indicating they are not circadian in nature. bfAANATα and bfAANATδ' have unusually alkaline (> 9.0) optimal pH, more than two pH units higher than that of vertebrate AANATs.</p> <p>Conclusions</p> <p>The substrate selectivity profiles of bfAANATα and δ' are relatively broad, including alkylamines, arylalkylamines and diamines, in contrast to vertebrate forms, which selectively acetylate serotonin and other arylalkylamines. Based on these features, it appears that amphioxus AANATs could play several roles, including detoxification and biogenic amine inactivation. The presence of seven AANATs in amphioxus genome supports the view that arylalkylamine and polyamine acetylation is important to the biology of this organism and that these genes evolved in response to specific pressures related to requirements for amine acetylation.</p

Genome and Environmental Activity of a Chrysochromulina parva Virus and Its Virophages

Some giant viruses are ecological agents that are predicted to be involved in the top-down control of single-celled eukaryotic algae populations in aquatic ecosystems. Despite an increased interest in giant viruses since the discovery and characterization of Mimivirus and other viral giants, little is known about their physiology and ecology. In this study, we characterized the genome and functional potential of a giant virus that infects the freshwater haptophyte Chrysochromulina parva, originally isolated from Lake Ontario. This virus, CpV-BQ2, is a member of the nucleo-cytoplasmic large DNA virus (NCLDV) group and possesses a 437 kb genome encoding 503 ORFs with a GC content of 25%. Phylogenetic analyses of core NCLDV genes place CpV-BQ2 amongst the emerging group of algae-infecting Mimiviruses informally referred to as the “extended Mimiviridae,” making it the first virus of this group to be isolated from a freshwater ecosystem. During genome analyses, we also captured and described the genomes of three distinct virophages that co-occurred with CpV-BQ2 and likely exploit CpV for their own replication. These virophages belong to the polinton-like viruses (PLV) group and encompass 19–23 predicted genes, including all of the core PLV genes as well as several genes implicated in genome modifications. We used the CpV-BQ2 and virophage reference sequences to recruit reads from available environmental metatranscriptomic data to estimate their activity in fresh waters. We observed moderate recruitment of both virus and virophage transcripts in samples obtained during Microcystis aeruginosa blooms in Lake Erie and Lake Tai, China in 2013, with a spike in activity in one sample. Virophage transcript abundance for two of the three isolates strongly correlated with that of the CpV-BQ2. Together, the results highlight the importance of giant viruses in the environment and establish a foundation for future research on the physiology and ecology CpV-BQ2 as a model system for algal Mimivirus dynamics in freshwaters

Phenotype MicroArray Profiling of Zymomonas mobilis ZM4

In this study, we developed a Phenotype MicroArray™ (PM) protocol to profile cellular phenotypes in Zymomonas mobilis, which included a standard set of nearly 2,000 assays for carbon, nitrogen, phosphorus and sulfur source utilization, nutrient stimulation, pH and osmotic stresses, and chemical sensitivities with 240 inhibitory chemicals. We observed two positive assays for C-source utilization (fructose and glucose) using the PM screen, which uses redox chemistry and cell respiration as a universal reporter to profile growth phenotypes in a high-throughput 96-well plate-based format. For nitrogen metabolism, the bacterium showed a positive test results for ammonia, aspartate, asparagine, glutamate, glutamine, and peptides. Z. mobilis appeared to use a diverse array of P-sources with two exceptions being pyrophosphate and tripolyphosphate. The assays suggested that Z. mobilis uses both inorganic and organic compounds as S-sources. No stimulation by nutrients was detected; however, there was evidence of partial inhibition by purines and pyrimidines, NAD, and deferoxamine. Z. mobilis was relatively resistant to acid pH, tolerating a pH down to about 4.0. It also tolerated phosphate, sulfate, and nitrate, but was rather sensitive to chloride and nitrite. Z. mobilis showed resistance to a large number of diverse chemicals that inhibit most bacteria. The information from PM analysis provides an overview of Z. mobilis physiology and a foundation for future comparisons of other wild-type and mutant Z. mobilis strains