MEMS practice, from the lab to the telescope

Micro-electro-mechanical systems (MEMS) technology can provide for deformable mirrors (DMs) with excellent performance within a favorable economy of scale. Large MEMS-based astronomical adaptive optics (AO) systems such as the Gemini Planet Imager are coming on-line soon. As MEMS DM end-users, we discuss our decade of practice with the micromirrors, from inspecting and characterizing devices to evaluating their performance in the lab. We also show MEMS wavefront correction on-sky with the "Villages" AO system on a 1-m telescope, including open-loop control and visible-light imaging. Our work demonstrates the maturity of MEMS technology for astronomical adaptive optics.Comment: 14 pages, 15 figures, Invited Paper, SPIE Photonics West 201

Characterizing the Adaptive Optics Off-Axis Point-Spread Function - I: A Semi-Empirical Method for Use in Natural-Guide-Star Observations

Even though the technology of adaptive optics (AO) is rapidly maturing, calibration of the resulting images remains a major challenge. The AO point-spread function (PSF) changes quickly both in time and position on the sky. In a typical observation the star used for guiding will be separated from the scientific target by 10" to 30". This is sufficient separation to render images of the guide star by themselves nearly useless in characterizing the PSF at the off-axis target position. A semi-empirical technique is described that improves the determination of the AO off-axis PSF. The method uses calibration images of dense star fields to determine the change in PSF with field position. It then uses this information to correct contemporaneous images of the guide star to produce a PSF that is more accurate for both the target position and the time of a scientific observation. We report on tests of the method using natural-guide-star AO systems on the Canada-France-Hawaii Telescope and Lick Observatory Shane Telescope, augmented by simple atmospheric computer simulations. At 25" off-axis, predicting the PSF full width at half maximum using only information about the guide star results in an error of 60%. Using an image of a dense star field lowers this error to 33%, and our method, which also folds in information about the on-axis PSF, further decreases the error to 19%.Comment: 29 pages, 9 figures, accepted for publication in the PAS

KAPAO: a MEMS-based natural guide star adaptive optics system

We describe KAPAO, our project to develop and deploy a low-cost, remote-access, natural guide star adaptive optics (AO) system for the Pomona College Table Mountain Observatory (TMO) 1-meter telescope. We use a commercially available 140-actuator BMC MEMS deformable mirror and a version of the Robo-AO control software developed by Caltech and IUCAA. We have structured our development around the rapid building and testing of a prototype system, KAPAO-Alpha, while simultaneously designing our more capable final system, KAPAO-Prime. The main differences between these systems are the prototype's reliance on off-the-shelf optics and a single visible-light science camera versus the final design's improved throughput and capabilities due to the use of custom optics and dual-band, visible and near-infrared imaging. In this paper, we present the instrument design and on-sky closed-loop testing of KAPAO-Alpha as well as our plans for KAPAO-Prime. The primarily undergraduate-education nature of our partner institutions, both public (Sonoma State University) and private (Pomona and Harvey Mudd Colleges), has enabled us to engage physics, astronomy, and engineering undergraduates in all phases of this project. This material is based upon work supported by the National Science Foundation under Grant No. 0960343.Comment: 10 pages and 11 figure

Imaginal Discs – A New Source of Chromosomes for Genome Mapping of the Yellow Fever Mosquito Aedes aegypti

Dengue fever is an emerging health threat to as much as half of the human population around the world. No vaccines or drug treatments are currently available. Thus, disease prevention is largely based on efforts to control its major mosquito vector Ae. aegypti. Novel vector control strategies, such as population replacement with pathogen-incompetent transgenic mosquitoes, rely on detailed knowledge of the genome organization for the mosquito. However, the current genome assembly of Ae. aegypti is highly fragmented and requires additional physical mapping onto chromosomes. The absence of readable polytene chromosomes makes genome mapping for this mosquito extremely challenging. In this study, we discovered and investigated a new source of chromosomes useful for the cytogenetic analysis in Ae. aegypti – mitotic chromosomes from imaginal discs of 4th instar larvae. Using natural banding patterns of these chromosomes, we developed a new band-based approach for physical mapping of DNA probes to the precise chromosomal positions. Further application of this approach for genome mapping will greatly enhance the utility of the existing draft genome sequence assembly for Ae. aegypti and thereby facilitate application of advanced genome technologies for investigating and developing novel genetic control strategies for dengue transmission

KAPAO First Light: the design, construction and operation of a low-cost natural guide star adaptive optics system

We present the instrument design and first light observations of KAPAO, a natural guide star adaptive optics (AO) system for the Pomona College Table Mountain Observatory (TMO) 1-meter telescope. The KAPAO system has dual science channels with visible and near-infrared cameras, a Shack-Hartmann wavefront sensor, and a commercially available 140-actuator MEMS deformable mirror. The pupil relays are two pairs of custom off-axis parabolas and the control system is based on a version of the Robo-AO control software. The AO system and telescope are remotely operable, and KAPAO is designed to share the Cassegrain focus with the existing TMO polarimeter. We discuss the extensive integration of undergraduate students in the program including the multiple senior theses/capstones and summer assistantships amongst our partner institutions. This material is based upon work supported by the National Science Foundation under Grant No. 0960343

Which women stop smoking during pregnancy and the effect on breastfeeding duration

BACKGROUND: Cigarette smoking during pregnancy increases the risk of adverse pregnancy outcomes and women who quit smoking at this time are able to reduce the risk of low birth weight, preterm labour, spontaneous abortion and perinatal death. This study investigates the socio-demographic characteristics of pregnant women who stop smoking during pregnancy and the association between stopping smoking and breastfeeding duration. METHODS: A 12 month longitudinal study was conducted in two public maternity hospitals in Perth, Australia between mid-September 2002 and mid-July 2003. While in hospital, participating mothers completed a self-administered baseline questionnaire. Follow up telephone interviews were conducted at 4, 10, 16, 22, 32, 40 and 52 weeks. RESULTS: A total of 587 (55%) mothers participated in the study. Two hundred and twenty six (39%) mothers reported smoking prior to pregnancy and 77 (34%) of these stopped smoking during pregnancy. Women who were pregnant for the first time were twice as likely (OR = 2.05; 95% CI 1.047 – 4.03; p < 0.05) to quit smoking as multiparous women. Women who smoked more than 10 cigarettes per day were significantly less likely to quit smoking during pregnancy (OR = 0.36; 95% CI 0.18 – 0.69; p < 0.05). Women who consumed alcohol before pregnancy were three times more likely to quit smoking (OR = 2.58; 95% CI 1.00 – 6.66; p < 0.05). Quitting smoking during pregnancy was significantly associated with breastfeeding for longer than six months (OR = 3.70; 95% CI 1.55 – 8.83; p < 0.05). CONCLUSION: Pregnancy is a time when many women are motivated to quit smoking and providing targeted smoking cessation interventions at this time, which take into account factors predictive of quitting smoking, are more likely to be successful

Opposing transcriptional programs of KLF5 and AR emerge during therapy for advanced prostate cancer.

Endocrine therapies for prostate cancer inhibit the androgen receptor (AR) transcription factor. In most cases, AR activity resumes during therapy and drives progression to castration-resistant prostate cancer (CRPC). However, therapy can also promote lineage plasticity and select for AR-independent phenotypes that are uniformly lethal. Here, we demonstrate the stem cell transcription factor Krüppel-like factor 5 (KLF5) is low or absent in prostate cancers prior to endocrine therapy, but induced in a subset of CRPC, including CRPC displaying lineage plasticity. KLF5 and AR physically interact on chromatin and drive opposing transcriptional programs, with KLF5 promoting cellular migration, anchorage-independent growth, and basal epithelial cell phenotypes. We identify ERBB2 as a point of transcriptional convergence displaying activation by KLF5 and repression by AR. ERBB2 inhibitors preferentially block KLF5-driven oncogenic phenotypes. These findings implicate KLF5 as an oncogene that can be upregulated in CRPC to oppose AR activities and promote lineage plasticity

VectorBase: a home for invertebrate vectors of human pathogens

VectorBase () is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.All raw sequence data are available through NCBI SRA under project number SRP021923. Sequences containing SSRs and designed primers are attached as supplementary material