Polarization Ray Tracing and Polarization Aberration Compensation in Reflective Astronomical Telescopes

Assessing and optimizing polarization performance in the context of ray-based optical design can be challenging. We describe an approach to this problem that decouples polarization effects from optical system geometry for reflective systems. Each surface's polarization properties are parameterized in terms of their impact on retardance and diattenuation in the small angle-of-incidence limit, separating polarization assessment from the task of coating design. A low-resolution ray trace of the system is adequate to determine ray geometry at each interface, which can then be interpolated to rapidly evaluate net Jones Matrix pupil functions. Coating behavior can be easily varied using the ellipsometric parameters to investigate impacts and compensation. Desired values of these parameters can then be specified as constraints in coating design. Investigation with candidate telescope optical designs for LUVOIR show baseline root-mean-square wavefront errors in the nm range for the on-diagonal Jones matrix component, and throughputs of tens of parts per million. Promising possibilities for compensation using a purpose-designed coating on the secondary mirror are discussed, which reduce the on-diagonal wavefront error by a factor 20, with accompanying but more modest reductions in coupling into off-diagonal terms

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

BackgroundFungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child.ResultsWe applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non-phylogenetic methods for larger effect sizes.ConclusionsThe Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees.Availabilityghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree

Geography and Location Are the Primary Drivers of Office Microbiome Composition.

In the United States, humans spend the majority of their time indoors, where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices. Our data elucidate several important features of microbial communities in BEs. First, under normal office environmental conditions, bacterial communities do not differ on the basis of surface material (e.g., ceiling tile or carpet) but do differ on the basis of the location in a room (e.g., ceiling or floor), two features that are often conflated but that we are able to separate here. We suspect that previous work showing differences in bacterial composition with surface material was likely detecting differences based on different usage patterns. Next, we find that offices have city-specific bacterial communities, such that we can accurately predict which city an office microbiome sample is derived from, but office-specific bacterial communities are less apparent. This differs from previous work, which has suggested office-specific compositions of bacterial communities. We again suspect that the difference from prior work arises from different usage patterns. As has been previously shown, we observe that human skin contributes heavily to the composition of BE surfaces. IMPORTANCE Our study highlights several points that should impact the design of future studies of the microbiology of BEs. First, projects tracking changes in BE bacterial communities should focus sampling efforts on surveying different locations in offices and in different cities but not necessarily different materials or different offices in the same city. Next, disturbance due to repeated sampling, though detectable, is small compared to that due to other variables, opening up a range of longitudinal study designs in the BE. Next, studies requiring more samples than can be sequenced on a single sequencing run (which is increasingly common) must control for run effects by including some of the same samples in all of the sequencing runs as technical replicates. Finally, detailed tracking of indoor and material environment covariates is likely not essential for BE microbiome studies, as the normal range of indoor environmental conditions is likely not large enough to impact bacterial communities

Alignment Test Results of the JWST Pathfinder Telescope Mirrors in the Cryogenic Environment

After integration of the Optical Telescope Element (OTE) to the Integrated Science Instrument Module (ISIM) to become the OTIS, the James Webb Space Telescope OTIS is tested at NASAs Johnson Space Center (JSC) in the cryogenic vacuum Chamber A for alignment and optical performance. The alignment of the mirrors comprises a sequence of steps as follows: The mirrors are coarsely aligned using photogrammetry cameras with reflective targets attached to the sides of the mirrors. Then a multi-wavelength interferometer is aligned to the 18-segment primary mirror using cameras at the center of curvature to align reflected light from the segments and using fiducials at the edge of the primary mirror. Once the interferometer is aligned, the 18 primary mirror segments are then adjusted to optimize wavefront error of the aggregate mirror. This process phases the piston and tilt positions of all the mirror segments. An optical fiber placed at the Cassegrain focus of the telescope then emits light towards the secondary mirror to create a collimated beam emitting from the primary mirror. Portions of the collimated beam are retro-reflected from flat mirrors at the top of the chamber to pass through the telescope to the SI detector. The image on the detector is used for fine alignment of the secondary mirror and a check of the primary mirror alignment using many of the same analysis techniques used in the on-orbit alignment. The entire process was practiced and evaluated in 2015 at cryogenic temperature with the Pathfinder telescope

Characterization and calibration of the James Webb space telescope mirror actuators fine stage motion

The James Webb Space Telescope’s (Webb’s) deployable primary and secondary mirrors are actively controlled to achieve and maintain precise optical alignment on-orbit. Each of the 18 primary mirror segment assemblies (PMSAs) and the secondary mirror assembly (SMA) are controlled in six degrees of freedom by using six linear actuators in a hexapod arrangement. In addition, each PMSA contains a seventh actuator that adjusts radius of curvature (RoC). The actuators are of a novel stepper motor-based cryogenic two-stage design that is capable of sub-10 nm motion accuracy over a 20 mm range. The nm-level motion of the 132 actuators were carefully tested and characterized before integration into the mirror assemblies. Using these test results as an initial condition, knowledge of each actuator’s length (and therefore mirror position) has relied on software bookkeeping and configuration control to keep an accurate motor step count from which actuator position can be calculated. These operations have been carefully performed through years of Webb test operations using both ground support actuator control software as well as the flight Mirror Control Software (MCS). While the actuator’s coarse stage length is cross-checked using a linear variable differential transformer (LVDT), no on-board cross-check exists for the nm-level length changes of the actuators’ fine stage. To ensure that the software bookkeeping of motor step count is still accurate after years of testing and to test that the actuator position knowledge was properly handed off from the ground software to the flight MCS, a series of optical tests were devised and performed through the Center of Curvature (CoC) ambient optical test campaigns at the Goddard Space Flight Center (GSFC) and during the thermal-vacuum tests of the entire optical payload that were conducted in Chamber A at Johnson Space Center (JSC). In each test, the actuator Fine Step Count (FSC) value is compared to an external measurement provided by an optical metrology tool with the goal of either confirming the MCS database value, or providing a recommendation for an updated calibration if the measured FSC differs significantly from the MCS-based expectation. During ambient testing of the PMSA hexapods, the nm-level actuator length changes were measured with a custom laser deflectometer by measuring tilts of the PMSA. The PMSA RoC fine stage characterization was performed at JSC using multi-wave interferometric measurements with the CoC Optical Assembly (COCOA). Finally, the SMA hexapod fine stage characterization test was performed at JSC using the NIRCam instrument in the “pass-and-a-half” test configuration using a test source from the Aft-Optics System Source Plate Assembly (ASPA). In this paper, each of these three tests, subsequent data analyses, and uncertainty estimations will be presented. Additionally, a summary of the ensemble state of Webb’s actuator fine stages is provided, along with a comparison to a Wavefront Sensing and Control (WFSC)-based requirement for FSC errors as they relate to the optical alignment convergence of the telescope on-orbit

Diffusion as mixing mechanism in granular materials

We present several numerical results on granular mixtures. In particular, we examine the efficiency of diffusion as a mixing mechanism in these systems. The collisions are inelastic and to compensate the energy loss, we thermalize the grains by adding a random force. Starting with a segregated system, we show that uniform agitation (heating) leads to a uniform mixture of grains of different sizes. We define a characteristic mixing time, $\tau_{mix}$, and study theoretically and numerically its dependence on other parameters like the density. We examine a model for bidisperse systems for which we can calculate some physical quantities. We also examine the effect of a temperature gradient and demonstrate the appearance of an expected segregation.Comment: 15 eps figures, include

Spectrum of antibacterial activity and mode of action of a novel tris-stilbene bacteriostatic compound

The spectrum of activity and mode of action of a novel antibacterial agent, 135C, was investigated using a range of microbiological and genomic approaches. Compound 135C was active against Gram-positive bacteria with MICs for Staphylococcus aureus ranging from 0.12-0.5 μg/ml. It was largely inactive against Gram-negative bacteria. The compound showed bacteriostatic activity in time-kill studies and did not elicit bacterial cell leakage or cell lysis. Checkerboard assays showed no synergy or antagonism when 135C was combined with a range of other antibacterials. Multi-step serial passage of four S. aureus isolates with increasing concentrations of 135C showed that resistance developed rapidly and was stable after drug-free passages. Minor differences in the fitness of 135C-resistant strains and parent wildtypes were evident by growth curves, but 135C-resistant strains did not show cross-resistance to other antibacterial agents. Genomic comparison of resistant and wildtype parent strains showed changes in genes encoding cell wall teichoic acids. 135C shows promising activity against Gram-positive bacteria but is currently limited by the rapid resistance development. Further studies are required to investigate the effects on cell wall teichoic acids and to determine whether the issue of resistance development can be overcome

Advancing the Microbiome Research Community

The human microbiome has become a recognized factor in promoting and maintaining health. We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. Advances in these aspects of the research community may in turn advance our understanding of human microbiome biology. It is now widely recognized that disturbances in our normal microbial populations may be linked to acute infections such as Clostridium difficile and to chronic diseases such as heart disease, cancer, obesity, and autoimmune disorders (Clemente et al., 2012). This has prompted substantial interest in the microbiome from both basic and clinical perspectives. Although our genome is relatively static throughout life, each of our microbial communities changes profoundly from infancy through adulthood, continuing to adapt through ongoing exposures to diet, drugs and environment. Understanding the microbiome and its dynamic nature may be critical for diagnostics and, eventually, interventions based on the microbiome itself. However, several important challenges limit the ability of researchers to enter the microbiome field and/or conduct research most effectively

Optical Budgeting for LUVOIR

Future large astronomical telescopes in space will have architectures that will have complex and demanding requirements to meet the science goals. The Large UV/Optical/IR Surveyor (LUVOIR) mission concept being assessed by the NASA/Goddard Space Flight Center is expected to be 8 to 16 meters in diameter, have a segmented primary mirror, active control, and be diffraction limited at a wavelength of 500 nanometers. The optical stability is expected to be in the picometer range for minutes to hours. Architecture studies to support the NASA Science and Technology Definition teams (STDTs) are underway to evaluate systems performance. A wave front error budget has been developed to help define the technology needs and assess performance. The budget includes both spatial and temporal domain aspects for the active, adaptive and passive elements in the optical design

Antimicrobial Microwebs of DNA–Histone Inspired from Neutrophil Extracellular Traps

Neutrophil extracellular traps (NETs) are decondensed chromatin networks released by neutrophils that can trap and kill pathogens but can also paradoxically promote biofilms. The mechanism of NET functions remains ambiguous, at least in part, due to their complex and variable compositions. To unravel the antimicrobial performance of NETs, a minimalistic NET‐like synthetic structure, termed “microwebs,” is produced by the sonochemical complexation of DNA and histone. The prepared microwebs have structural similarity to NETs at the nanometer to micrometer dimensions but with well‐defined molecular compositions. Microwebs prepared with different DNA to histone ratios show that microwebs trap pathogenic Escherichia coli in a manner similar to NETs when the zeta potential of the microwebs is positive. The DNA nanofiber networks and the bactericidal histone constituting the microwebs inhibit the growth of E. coli. Moreover, microwebs work synergistically with colistin sulfate, a common and a last‐resort antibiotic, by targeting the cell envelope of pathogenic bacteria. The synthesis of microwebs enables mechanistic studies not possible with NETs, and it opens new possibilities for constructing biomimetic bacterial microenvironments to better understand and predict physiological pathogen responses.Microwebs with bacteria trapping and killing functions are designed to mimic neutrophil extracellular traps—an immune defense weapon to fight against invading pathogens. The composition–structure–function relationship of the synthetic structure is discussed, and the collaborative action between microwebs and antibiotics allows better elimination of pathogenic bacteria, Escherichia coli.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149216/1/adma201807436-sup-0001-S1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149216/2/adma201807436_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149216/3/adma201807436.pd