Resolving deep relationships of PACMAD grasses : a phylogenomic approach

Advisors: Melvin R. Duvall.Committee members: Nicholas A. Barber; Thomas L. Sims.The phylogenetically recognized PACMAD (Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) clade of grasses has been the subject of numerous phylogenetic studies that have made an attempt at determining subfamilial relationships of the clade (Clark et al., 1995, GPWGI, 2001, Duvall et al., 2007, GPWGII, 2012). The purpose of this thesis was to examine chloroplast genome sequences for 18 PACMAD species, and analyze them phylogenomically. These analyses were conducted to provide resolution of deep subfamilial relationships within the clade. Divergence estimates were assessed to determine potential factors that led to the rapid radiation of this lineage and its dominance of open habitats. This was accomplished via Next Generation Sequencing methods to provide complete plastome sequence for 12 species. Sanger Sequencing was performed on one species, Hakonechloa macra, to provide a reference. Phylogenomic analyses and divergence estimates were conducted on these plastomes in conjunction with six other previously banked plastomes. The results presented here support Panicoideae as the earliest diverging PACMAD lineage. The initial diversification of PACMAD subfamilies was estimated to occur 32.4 mya. Phylogenomic analyses of complete plastome sequences provide strong support for deep relationships of PACMAD grasses. The divergence estimate of 32.4 mya at the crown node of the PACMAD clade coincides with the Eocene-Oligocene Transition (EOT). Throughout the Eocene, prior to the EOT, was a period of global cooling and drying, which led to forest fragmentation and the expansion of open habitats now dominated by these grasses.M.S. (Master of Science

Supporting registration of child-focused clinical trials in Africa: The Child Strategy Project

Editorial abstract not applicabl

The appropriation of endogenously provided common-pool resources

Abstract Because game theory suggests that the origin of a common-pool resource should not affect appropriation behavior, experimental studies of appropriation from common-pool resources generally presume resources are exogenously provided. However, behavioral economic research indicates that the origin of a resource may affect the use of that resource. We investigate the potential role of resource origin by considering the appropriation of a common-pool resource after users have determined its productive capacity through contributions. Results indicate that resource origin does not significantly influence aggregate appropriation levels but that endogenous resource provision leads to individual strategic behavior

Advanced Processing of Food Waste Based Digestate for Mitigating Nitrogen Losses in a Winter Wheat Crop

The anaerobic digestion of food waste converts waste products into ‘green’ energy. Additionally, the secondary product from this process is a nutrient-rich digestate, which could provide a viable alternative to synthetically-produced fertilisers. However, like fertilisers, digestate applied to agricultural land can be susceptible to both ammonia (NH3) and nitrous oxide (N2O) losses, having negative environmental impacts, and reducing the amount of N available for crop uptake. Our main aim was to assess potential methods for mitigating N losses from digestate applied to a winter wheat crop and subsequent impact on yield. Plot trials were conducted at two UK sites, England (North Wyke-NW) and Wales (Henfaes-HF), to assess NH3 and N2O losses, yield and N offtake following a single band-spread digestate application. Treatments examined were digestate (D), acidified-digestate (AD), digestate with the nitrification inhibitor DMPP (D+NI), AD with DMPP (AD+NI), and a zero-N control (C). Determination of N losses was conducted using wind tunnels for NH3, and static manual and automatic chambers for N2O. The N offtake in both grain and straw was also measured. Ammonium nitrate (NH4NO3) fertiliser N response plots (from 75 to 300 kg N ha−1) were included to compare yields with the organic N source. Cumulative NH3-N losses were 27.6 % from D and D+NI plots and 1.5 % for AD and AD+NI of the total N applied, a significant reduction of 95 % with acidification. Cumulative N2O losses varied between 0.13 and 0.35 % of the total N applied and were reduced by 50 % with the use of DMPP. Grain yields for the digestate treatments were 7.52 – 9.21 and 7.23 – 9.23 t DM ha−1 at HF and NW, respectively. Yields were greater from the plots receiving acidified‐digestate relative to the non-acidified treatments but the differences were not significant. The yields (as a function of the N applied with each treatment) obtained for the digestate treatments ranged between 84.2 % (D+NI) and 103.6 % (D) of the yields produced by the same N rate from an inorganic source at HF. Advanced processing of digestate reduced N losses providing an environmentally sound option for N-management

Measuring and Correcting Wind-Induced Pointing Errors of the Green Bank Telescope Using an Optical Quadrant Detector

Wind-induced pointing errors are a serious concern for large-aperture high-frequency radio telescopes. In this paper, we describe the implementation of an optical quadrant detector instrument that can detect and provide a correction signal for wind-induced pointing errors on the 100m diameter Green Bank Telescope (GBT). The instrument was calibrated using a combination of astronomical measurements and metrology. We find that the main wind-induced pointing errors on time scales of minutes are caused by the feedarm being blown along the direction of the wind vector. We also find that wind-induced structural excitation is virtually non-existent. We have implemented offline software to apply pointing corrections to the data from imaging instruments such as the MUSTANG 3.3 mm bolometer array, which can recover ~70% of sensitivity lost due to wind-induced pointing errors. We have also performed preliminary tests that show great promise for correcting these pointing errors in real-time using the telescope's subreflector servo system in combination with the quadrant detector signal.Comment: 17 pages, 11 figures; accepted for publication in PAS

Resolving deep relationships of PACMAD grasses: a phylogenomic approach

Background Plastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation sequencing methods were used to provide complete plastome sequences for 12 species. Sanger sequencing was performed to determine the plastome of one species, Hakonechloa macra, to provide a reference for annotation. These analyses were conducted to resolve deep subfamilial relationships within the clade. Divergence estimates were assessed to determine potential factors that led to the rapid radiation of this lineage and its dominance of warmer open habitats. Results New plastomes were completely sequenced and characterized for 13 PACMAD species. An autapomorphic ~1140 bp deletion was found in Hakonechloa macra putatively pseudogenizing rpl14 and eliminating rpl16 from this plastome. Phylogenomic analyses support Panicoideae as the sister group to the ACMAD clade. Complete plastome sequences provide greater support at deep nodes within the PACMAD clade. The initial diversification of PACMAD subfamilies was estimated to occur at 32.4 mya. Conclusions Phylogenomic analyses of complete plastomes provides resolution for deep relationships of PACMAD grasses. The divergence estimate of 32.4 mya at the crown node of the PACMAD clade coincides with the Eocene-Oligocene Transition (EOT). The Eocene was a period of global cooling and drying, which led to forest fragmentation and the expansion of open habitats now dominated by these grasses. Understanding how these grasses are related and determining a cause for their rapid radiation allows for future predictions of grassland distribution in the face of a changing global climate.This work was supported in part by the Plant Molecular Biology Center, the Department of Biological Sciences at Northern Illinois University and the National Science Foundation under Grant Numbers DEB-1120750 to LGC, DEB-1120856 to SAK and DEB-1120761 to MRD.This article is made openly accessible in part by an award from the Northern Illinois University Libraries’ Open Access Publishing Fund

The 74MHz System on the Very Large Array

The Naval Research Laboratory and the National Radio Astronomy Observatory completed implementation of a low frequency capability on the VLA at 73.8 MHz in 1998. This frequency band offers unprecedented sensitivity (~25 mJy/beam) and resolution (~25 arcsec) for low-frequency observations. We review the hardware, the calibration and imaging strategies, comparing them to those at higher frequencies, including aspects of interference excision and wide-field imaging. Ionospheric phase fluctuations pose the major difficulty in calibrating the array. Over restricted fields of view or at times of extremely quiescent ionospheric ``weather'', an angle-invariant calibration strategy can be used. In this approach a single phase correction is devised for each antenna, typically via self-calibration. Over larger fields of view or at times of more normal ionospheric ``weather'' when the ionospheric isoplanatic patch size is smaller than the field of view, we adopt a field-based strategy in which the phase correction depends upon location within the field of view. This second calibration strategy was implemented by modeling the ionosphere above the array using Zernike polynomials. Images of 3C sources of moderate strength are provided as examples of routine, angle-invariant calibration and imaging. Flux density measurements indicate that the 74 MHz flux scale at the VLA is stable to a few percent, and tied to the Baars et al. value of Cygnus A at the 5 percent level. We also present an example of a wide-field image, devoid of bright objects and containing hundreds of weaker sources, constructed from the field-based calibration. We close with a summary of lessons the 74 MHz system offers as a model for new and developing low-frequency telescopes. (Abridged)Comment: 73 pages, 46 jpeg figures, to appear in ApJ

Whole Blood Resuscitation and Association with Survival in Injured Patients with an Elevated Probability of Mortality.

BACKGROUND: Low-titer group O whole blood (LTOWB) resuscitation is becoming common in both military and civilian settings and may represent the ideal resuscitation intervention. We sought to characterize the safety and efficacy of LTOWB resuscitation relative to blood component resuscitation. STUDY DESIGN: A prospective, multicenter, observational cohort study was performed using 7 trauma centers. Injured patients at risk of massive transfusion who required both blood transfusion and hemorrhage control procedures were enrolled. The primary outcome was 4-hour mortality. Secondary outcomes included 24-hour and 28-day mortality, achievement of hemostasis, death from exsanguination, and the incidence of unexpected survivors. RESULTS: A total of 1,051 patients in hemorrhagic shock met all enrollment criteria. The cohort was severely injured with \u3e70% of patients requiring massive transfusion. After propensity adjustment, no significant 4-hour mortality difference across LTOWB and component patients was found (relative risk [RR] 0.90, 95% CI 0.59 to 1.39, p = 0.64). Similarly, no adjusted mortality differences were demonstrated at 24 hours or 28 days for the enrolled cohort. When patients with an elevated prehospital probability of mortality were analyzed, LTOWB resuscitation was independently associated with a 48% lower risk of 4-hour mortality (relative risk [RR] 0.52, 95% CI 0.32 to 0.87, p = 0.01) and a 30% lower risk of 28-day mortality (RR 0.70, 95% CI 0.51 to 0.96, p = 0.03). CONCLUSIONS: Early LTOWB resuscitation is safe but not independently associated with survival for the overall enrolled population. When patients were selected with an elevated probability of mortality based on prehospital injury characteristics, LTOWB was independently associated with a lower risk of mortality starting at 4 hours after arrival through 28 days after injury

Early Cold Stored Platelet Transfusion Following Severe Injury: A Randomized Clinical Trial

OBJECTIVE: To determine the feasibility, efficacy, and safety of early cold stored platelet transfusion compared with standard care resuscitation in patients with hemorrhagic shock. BACKGROUND: Data demonstrating the safety and efficacy of early cold stored platelet transfusion are lacking following severe injury. METHODS: A phase 2, multicenter, randomized, open label, clinical trial was performed at 5 US trauma centers. Injured patients at risk of large volume blood transfusion and the need for hemorrhage control procedures were enrolled and randomized. The intervention was the early transfusion of a single apheresis cold stored platelet unit, stored for up to 14 days versus standard care resuscitation. The primary outcome was feasibility and the principal clinical outcome for efficacy and safety was 24-hour mortality. RESULTS: Mortality at 24 hours was 5.9% in patients who were randomized to early cold stored platelet transfusion compared with 10.2% in the standard care arm (difference, -4.3%; 95% CI, -12.8% to 3.5%; P =0.26). No significant differences were found for any of the prespecified ancillary outcomes. Rates of arterial and/or venous thromboembolism and adverse events did not differ across treatment groups. CONCLUSIONS AND RELEVANCE: In severely injured patients, early cold stored platelet transfusion is feasible, safe and did not result in a significant lower rate of 24-hour mortality. Early cold stored platelet transfusion did not result in a higher incidence of arterial and/or venous thrombotic complications or adverse events. The storage age of the cold stored platelet product was not associated with significant outcome differences