Genetic research in a public-private research consortium: prospects for indirect use of Elige breeding germplasm in academic research

The creation of a public¿private research partnership between plant breeding industry and academia can be beneficial for all parties involved. Academic partners benefit from the material contributions by industry and a practically relevant research focus, while industry benefits from increased insights and methodology tailored to a relevant set of data. However, plant breeding industry is highly competitive and there are obvious limits to the data and material partners are willing and able to share. This will usually include current and historic released cultivated materials, but will very often not include the elite germplasm used in-house to create new cultivars. Especially for crops where hybrid cultivars dominate the market, parental lines of hybrid cultivars are considered core assets that are never provided to outside parties. However, this limitation often does not apply to DNA or genetic fingerprints of these parental lines. We developed a procedure to take advantage of elite breeding materials for the creation of new promising research populations, through indirect selection of parents. The procedure starts with the identification of a number of traits for further study based on the presence of marker-trait associations and a priori knowledge within the participating companies about promising traits for quality improvement. Next, regression-based multi-QTL models are fitted to hybrid cultivar data to identify QTLs. Fingerprint data of parental lines of a limited number of specific hybrids are then used to predict parental phenotypes using the multi-QTL model fitted on hybrid data. The specific hybrids spanned the whole of the sensory space adequately. Finally, a choice of parental lines is made based on the QTL model predictions and new promising line combinations are identified. Breeding industry is then asked to create and provide progeny of these line combinations for further research. This approach will be illustrated with a case study in tomato

Economics-Based Optimization of Unstable Flows

As an example for the optimization of unstable flows, we present an economics-based method for deciding the optimal rates at which vehicles are allowed to enter a highway. It exploits the naturally occuring fluctuations of traffic flow and is flexible enough to adapt in real time to the transient flow characteristics of road traffic. Simulations based on realistic parameter values show that this strategy is feasible for naturally occurring traffic, and that even far from optimality, injection policies can improve traffic flow. Moreover, the same method can be applied to the optimization of flows of gases and granular media.Comment: Revised version of ``Optimizing Traffic Flow'' (cond-mat/9809397). For related work see http://www.parc.xerox.com/dynamics/ and http://www.theo2.physik.uni-stuttgart.de/helbing.htm

The Milky Way's circular velocity curve between 4 and 14 kpc from APOGEE data

We measure the Milky Way's rotation curve over the Galactocentric range 4 kpc <~ R <~ 14 kpc from the first year of data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE). We model the line-of-sight velocities of 3,365 stars in fourteen fields with b = 0 deg between 30 deg < l < 210 deg out to distances of 10 kpc using an axisymmetric kinematical model that includes a correction for the asymmetric drift of the warm tracer population (\sigma_R ~ 35 km/s). We determine the local value of the circular velocity to be V_c(R_0) = 218 +/- 6 km/s and find that the rotation curve is approximately flat with a local derivative between -3.0 km/s/kpc and 0.4 km/s/kpc. We also measure the Sun's position and velocity in the Galactocentric rest frame, finding the distance to the Galactic center to be 8 kpc < R_0 < 9 kpc, radial velocity V_{R,sun} = -10 +/- 1 km/s, and rotational velocity V_{\phi,sun} = 242^{+10}_{-3} km/s, in good agreement with local measurements of the Sun's radial velocity and with the observed proper motion of Sgr A*. We investigate various systematic uncertainties and find that these are limited to offsets at the percent level, ~2 km/s in V_c. Marginalizing over all the systematics that we consider, we find that V_c(R_0) 99% confidence. We find an offset between the Sun's rotational velocity and the local circular velocity of 26 +/- 3 km/s, which is larger than the locally-measured solar motion of 12 km/s. This larger offset reconciles our value for V_c with recent claims that V_c >~ 240 km/s. Combining our results with other data, we find that the Milky Way's dark-halo mass within the virial radius is ~8x10^{11} M_sun.Comment: submitted to Ap

A Hot Uranus Orbiting the Super Metal-rich Star HD77338 and the Metallicity - Mass Connection

We announce the discovery of a low-mass planet orbiting the super metal-rich K0V star HD77338 as part of our on-going Calan-Hertfordshire Extrasolar Planet Search. The best fit planet solution has an orbital period of 5.7361\pm0.0015 days and with a radial velocity semi-amplitude of only 5.96\pm1.74 m/s, we find a minimum mass of 15.9+4.7-5.3 Me. The best fit eccentricity from this solution is 0.09+0.25-0.09, and we find agreement for this data set using a Bayesian analysis and a periodogram analysis. We measure a metallicity for the star of +0.35\pm0.06 dex, whereas another recent work (Trevisan et al. 2011) finds +0.47\pm0.05 dex. Thus HD77338b is one of the most metal-rich planet host stars known and the most metal-rich star hosting a sub-Neptune mass planet. We searched for a transit signature of HD77338b but none was detected. We also highlight an emerging trend where metallicity and mass seem to correlate at very low masses, a discovery that would be in agreement with the core accretion model of planet formation. The trend appears to show that for Neptune-mass planets and below, higher masses are preferred when the host star is more metal-rich. Also a lower boundary is apparent in the super metal-rich regime where there are no very low-mass planets yet discovered in comparison to the sub-solar metallicity regime. A Monte Carlo analysis shows that this, low-mass planet desert, is statistically significant with the current sample of 36 planets at around the 4.5\sigma\ level. In addition, results from Kepler strengthen the claim for this paucity of the lowest-mass planets in super metal-rich systems. Finally, this discovery adds to the growing population of low-mass planets around low-mass and metal-rich stars and shows that very low-mass planets can now be discovered with a relatively small number of data points using stable instrumentation.Comment: 25 pages, 15 figures, 5 tables, accepted for publication in Ap

Target Selection for the SDSS-IV APOGEE-2 Survey

APOGEE-2 is a high-resolution, near-infrared spectroscopic survey observing roughly 300,000 stars across the entire sky. It is the successor to APOGEE and is part of the Sloan Digital Sky Survey IV (SDSS-IV). APOGEE-2 is expanding upon APOGEE's goals of addressing critical questions of stellar astrophysics, stellar populations, and Galactic chemodynamical evolution using (1) an enhanced set of target types and (2) a second spectrograph at Las Campanas Observatory in Chile. APOGEE-2 is targeting red giant branch (RGB) and red clump (RC) stars, RR Lyrae, low-mass dwarf stars, young stellar objects, and numerous other Milky Way and Local Group sources across the entire sky from both hemispheres. In this paper, we describe the APOGEE-2 observational design, target selection catalogs and algorithms, and the targeting-related documentation included in the SDSS data releases.Comment: 19 pages, 6 figures. Accepted to A

Chemical Cartography with APOGEE: Large-scale Mean Metallicity Maps of the Milky Way

We present Galactic mean metallicity maps derived from the first year of the SDSS-III APOGEE experiment. Mean abundances in different zones of Galactocentric radius (0 < R < 15 kpc) at a range of heights above the plane (0 < |z| < 3 kpc), are derived from a sample of nearly 20,000 stars with unprecedented coverage, including stars in the Galactic mid-plane at large distances. We also split the sample into subsamples of stars with low and high-[{\alpha}/M] abundance ratios. We assess possible biases in deriving the mean abundances, and find they are likely to be small except in the inner regions of the Galaxy. A negative radial gradient exists over much of the Galaxy; however, the gradient appears to flatten for R < 6 kpc, in particular near the Galactic mid-plane and for low-[{\alpha}/M] stars. At R > 6 kpc, the gradient flattens as one moves off of the plane, and is flatter at all heights for high-[{\alpha}/M] stars than for low-[{\alpha}/M] stars. Alternatively, these gradients can be described as vertical gradients that flatten at larger Galactocentric radius; these vertical gradients are similar for both low and high-[{\alpha}/M] populations. Stars with higher [{\alpha}/M] appear to have a flatter radial gradient than stars with lower [{\alpha}/M]. This could suggest that the metallicity gradient has grown steeper with time or, alternatively, that gradients are washed out over time by migration of stars.Comment: 16 pages, 12 figures, submitted to A

Criterion for traffic phases in single vehicle data and empirical test of a microscopic three-phase traffic theory

A microscopic criterion for distinguishing synchronized flow and wide moving jam phases in single vehicle data measured at a single freeway location is presented. Empirical local congested traffic states in single vehicle data measured on different days are classified into synchronized flow states and states consisting of synchronized flow and wide moving jam(s). Then empirical microscopic characteristics for these different local congested traffic states are studied. Using these characteristics and empirical spatiotemporal macroscopic traffic phenomena, an empirical test of a microscopic three-phase traffic flow theory is performed. Simulations show that the microscopic criterion and macroscopic spatiotemporal objective criteria lead to the same identification of the synchronized flow and wide moving jam phases in congested traffic. It is found that microscopic three-phase traffic models can explain both microscopic and macroscopic empirical congested pattern features. It is obtained that microscopic distributions for vehicle speed difference as well as fundamental diagrams and speed correlation functions can depend on the spatial co-ordinate considerably. It turns out that microscopic optimal velocity (OV) functions and time headway distributions are not necessarily qualitatively different, even if local congested traffic states are qualitatively different. The reason for this is that important spatiotemporal features of congested traffic patterns are it lost in these as well as in many other macroscopic and microscopic traffic characteristics, which are widely used as the empirical basis for a test of traffic flow models, specifically, cellular automata traffic flow models.Comment: 27 pages, 16 figure

Spectrometric Monitoring of Atmospheric Carbon Tetrafluoride (CF4) Above the Jungfraujoch Station Since 1989: Evidence of Continued Increase But at a Slowing Rate

The long-term evolution of the vertical column abundance of carbon tetrafluoride (CF4) above the high-altitude Jungfraujoch station (Swiss Alps, 46.5 ° N, 8.0 ° E, 3580 ma.s.l.) has been derived from the spectrometric analysis of Fourier transform infrared solar spectra recorded at that site between 1989 and 2012. The investigation is based on a multi-microwindow approach, two encompassing pairs of absorption lines belonging to the R-branch of the strong ν3 band of CF4 centered at 1283 cm-1, and two additional ones to optimally account for weak but overlapping HNO3 interferences. The analysis reveals a steady accumulation of the very long-lived CF4 above the Jungfraujoch at mean rates of (1.38 ± 0.11) x 1013 molec cm-2 yr-1 from 1989 to 1997, and (0.98 +/- 0.02) x 1013 molec cm-2 yr-1 from 1998 to 2012, which correspond to linear growth rates of 1.71 ± 0.14 and 1.04 ± 0.02% yr-1 respectively referenced to 1989 and 1998. Related global CF4 anthropogenic emissions required to sustain these mean increases correspond to 15.8 ±1.3 and 11.1 ± 0.2 Gg yr-1 over the above specified time intervals. Findings reported here are compared and discussed with respect to relevant northern mid-latitude results obtained remotely from space and balloons as well as in situ at the ground, including new gas chromatography mass spectrometry measurements performed at the Jungfraujoch since 2010

The Galactic Halo in Mixed Dark Matter Cosmologies

A possible solution to the small scale problems of the cold dark matter (CDM) scenario is that the dark matter consists of two components, a cold and a warm one. We perform a set of high resolution simulations of the Milky Way halo varying the mass of the WDM particle ($m_{\rm WDM}$) and the cosmic dark matter mass fraction in the WDM component ($\bar{f}_{\rm W}$). The scaling ansatz introduced in combined analysis of LHC and astroparticle searches postulates that the relative contribution of each dark matter component is the same locally as on average in the Universe (e.g. $f_{\rm W,\odot} = \bar{f}_{\rm W}$). Here we find however, that the normalised local WDM fraction ($f_{\rm W,\odot}$ / $\bar{f}_{\rm W}$) depends strongly on $m_{\rm WDM}$ for $m_{\rm WDM} <$ 1 keV. Using the scaling ansatz can therefore introduce significant errors into the interpretation of dark matter searches. To correct this issue a simple formula that fits the local dark matter densities of each component is provided.Comment: 19 pages, 10 figures, accepted for publication in JCA