PROPHECY—a database for high-resolution phenomics

The rapid recent evolution of the field phenomics—the genome-wide study of gene dispensability by quantitative analysis of phenotypes—has resulted in an increasing demand for new data analysis and visualization tools. Following the introduction of a novel approach for precise, genome-wide quantification of gene dispensability in Saccharomyces cerevisiae we here announce a public resource for mining, filtering and visualizing phenotypic data—the PROPHECY database. PROPHECY is designed to allow easy and flexible access to physiologically relevant quantitative data for the growth behaviour of mutant strains in the yeast deletion collection during conditions of environmental challenges. PROPHECY is publicly accessible at http://prophecy.lundberg.gu.se

Runoff Losses of Atrazine, Metribuzin, and Nutrients as Affected by Management Practices for Sugarcane (Bulletin #875)

A primary objective of this investigation was to evaluate the effectiveness of selected pesticide management practices on the movement of atrazine and metribuzin in surface runoff from sugarcane fields in south Louisiana.https://digitalcommons.lsu.edu/agcenter_bulletins/1026/thumbnail.jp

Effect of Application Frequency on the Fate of Azinphosmethyl in a Sugercane Field (Bulletin #863)

Reducing the amounts of dissolved substances in surface and ground water is of major concern nationally and within the agricultural community. The primary focus of this study was to investigate the fate of azinphosmethyl (Guthion®) in sugarcane canopy, soil and runoff water.https://digitalcommons.lsu.edu/agcenter_bulletins/1014/thumbnail.jp

A linear CO chemistry parameterization in a chemistry-transport model: evaluation and application to data assimilation

This paper presents an evaluation of a new linear parameterization valid for the troposphere and the stratosphere, based on a first order approximation of the carbon monoxide (CO) continuity equation. This linear scheme (hereinafter noted LINCO) has been implemented in the 3-D Chemical Transport Model (CTM) MOCAGE (MOdèle de Chimie Atmospherique Grande Echelle). First, a one and a half years of LINCO simulation has been compared to output obtained from a detailed chemical scheme output. The mean differences between both schemes are about ±25 ppbv (part per billion by volume) or 15% in the troposphere and ±10 ppbv or 100% in the stratosphere. Second, LINCO has been compared to diverse observations from satellite instruments covering the troposphere (Measurements Of Pollution In The Troposphere: MOPITT) and the stratosphere (Microwave Limb Sounder: MLS) and also from aircraft (Measurements of ozone and water vapour by Airbus in-service aircraft: MOZAIC programme) mostly flying in the upper troposphere and lower stratosphere (UTLS). In the troposphere, the LINCO seasonal variations as well as the vertical and horizontal distributions are quite close to MOPITT CO observations. However, a bias of ~−40 ppbv is observed at 700 Pa between LINCO and MOPITT. In the stratosphere, MLS and LINCO present similar large-scale patterns, except over the poles where the CO concentration is underestimated by the model. In the UTLS, LINCO presents small biases less than 2% compared to independent MOZAIC profiles. Third, we assimilated MOPITT CO using a variational 3D-FGAT (First Guess at Appropriate Time) method in conjunction with MOCAGE for a long run of one and a half years. The data assimilation greatly improves the vertical CO distribution in the troposphere from 700 to 350 hPa compared to independent MOZAIC profiles. At 146 hPa, the assimilated CO distribution is also improved compared to MLS observations by reducing the bias up to a factor of 2 in the tropics. This study confirms that the linear scheme is able to simulate reasonably well the CO distribution in the troposphere and in the lower stratosphere. Therefore, the low computing cost of the linear scheme opens new perspectives to make free runs and CO data assimilation runs at high resolution and over periods of several years

An optimally concentrated Gabor transform for localized time-frequency components

Gabor analysis is one of the most common instances of time-frequency signal analysis. Choosing a suitable window for the Gabor transform of a signal is often a challenge for practical applications, in particular in audio signal processing. Many time-frequency (TF) patterns of different shapes may be present in a signal and they can not all be sparsely represented in the same spectrogram. We propose several algorithms, which provide optimal windows for a user-selected TF pattern with respect to different concentration criteria. We base our optimization algorithm on $l^p$-norms as measure of TF spreading. For a given number of sampling points in the TF plane we also propose optimal lattices to be used with the obtained windows. We illustrate the potentiality of the method on selected numerical examples

Supercooled liquid water cloud observed, analysed, and modelled at the top of the planetary boundary layer above Dome C, Antarctica

Abstract. A comprehensive analysis of the water budget over the Dome C (Concordia, Antarctica) station has been performed during the austral summer 2018–2019 as part of the Year of Polar Prediction (YOPP) international campaign. Thin (∼100 m deep) supercooled liquid water (SLW) clouds have been detected and analysed using remotely sensed observations at the station (tropospheric depolarization lidar, the H2O Antarctica Microwave Stratospheric and Tropospheric Radiometer (HAMSTRAD), net surface radiation from the Baseline Surface Radiation Network (BSRN)), radiosondes, and satellite observations (CALIOP, Cloud-Aerosol LIdar with Orthogonal Polarization/CALIPSO, Cloud Aerosol Lidar and Infrared Pathfinder Satellite Observations) combined with a specific configuration of the numerical weather prediction model: ARPEGE-SH (Action de Recherche Petite Echelle Grande Echelle – Southern Hemisphere). The analysis shows that SLW clouds were present from November to March, with the greatest frequency occurring in December and January when ∼50 % of the days in summer time exhibited SLW clouds for at least 1 h. Two case studies are used to illustrate this phenomenon. On 24 December 2018, the atmospheric planetary boundary layer (PBL) evolved following a typical diurnal variation, which is to say with a warm and dry mixing layer at local noon thicker than the cold and dry stable layer at local midnight. Our study showed that the SLW clouds were observed at Dome C within the entrainment and the capping inversion zones at the top of the PBL. ARPEGE-SH was not able to correctly estimate the ratio between liquid and solid water inside the clouds with the liquid water path (LWP) strongly underestimated by a factor of 1000 compared to observations. The lack of simulated SLW in the model impacted the net surface radiation that was 20–30 W m−2 higher in the BSRN observations than in the ARPEGE-SH calculations, mainly attributable to the BSRN longwave downward surface radiation being 50 W m−2 greater than that of ARPEGE-SH. The second case study took place on 20 December 2018, when a warm and wet episode impacted the PBL with no clear diurnal cycle of the PBL top. SLW cloud appearance within the entrainment and capping inversion zones coincided with the warm and wet event. The amount of liquid water measured by HAMSTRAD was ∼20 times greater in this perturbed PBL than in the typical PBL. Since ARPEGE-SH was not able to accurately reproduce these SLW clouds, the discrepancy between the observed and calculated net surface radiation was even greater than in the typical PBL case, reaching +50 W m−2, mainly attributable to the downwelling longwave surface radiation from BSRN being 100 W m−2 greater than that of ARPEGE-SH. The model was then run with a new partition function favouring liquid water for temperatures below −20 down to −40 ∘C. In this test mode, ARPEGE-SH has been able to generate SLW clouds with modelled LWP and net surface radiation consistent with observations during the typical case, whereas, during the perturbed case, the modelled LWP was 10 times less than the observations and the modelled net surface radiation remained lower than the observations by ∼50 W m−2. Accurately modelling the presence of SLW clouds appears crucial to correctly simulate the surface energy budget over the Antarctic Plateau

PROPHECY—a yeast phenome database, update 2006

Connecting genotype to phenotype is fundamental in biomedical research and in our understanding of disease. Phenomics—the large-scale quantitative phenotypic analysis of genotypes on a genome-wide scale—connects automated data generation with the development of novel tools for phenotype data integration, mining and visualization. Our yeast phenomics database PROPHECY is available at . Via phenotyping of 984 heterozygous diploids for all essential genes the genotypes analysed and presented in PROPHECY have been extended and now include all genes in the yeast genome. Further, phenotypic data from gene overexpression of 574 membrane spanning proteins has recently been included. To facilitate the interpretation of quantitative phenotypic data we have developed a new phenotype display option, the Comparative Growth Curve Display, where growth curve differences for a large number of mutants compared with the wild type are easily revealed. In addition, PROPHECY now offers a more informative and intuitive first-sight display of its phenotypic data via its new summary page. We have also extended the arsenal of data analysis tools to include dynamic visualization of phenotypes along individual chromosomes. PROPHECY is an initiative to enhance the growing field of phenome bioinformatics

Midlatitude stratosphere - troposphere exchange as diagnosed by MLS O3 and MOPITT CO assimilated fields

International audienceThis paper presents a comprehensive characterization of a very deep stratospheric intrusion which occurred over the British Isles on 15 August 2007. The signature of this event is diagnosed using ozonesonde measurements over Lerwick, UK (60.14 N, 1.19 W) and is also well characterized using meteorological analyses from the global operational weather prediction model of Météo-France, ARPEGE. Modelled as well as assimilated fields of both ozone (O3) and carbon monoxide (CO) have been used in order to better document this event. O3 and CO from Aura/MLS and Terra/MOPITT instruments, respectively, are assimilated into the three-dimensional chemical transport model MOCAGE of Météo-France using a variational 3-DFGAT (First Guess at Appropriate Time) method. The validation of O3 and CO assimilated fields is done using selfconsistency diagnostics and by comparison with independent observations such as MOZAIC (O3 and CO), AIRS (CO) and OMI (O3). It particularly shows in the upper troposphere and lower stratosphere region that the assimilated fields are closer to MOZAIC than the free model run. The O3 bias between MOZAIC and the analyses is −11.5 ppbv with a RMS of 22.4 ppbv and a correlation coefficient of 0.93, whereas between MOZAIC and the free model run, the corresponding values are 33 ppbv, 38.5 ppbv and 0.83, respectively. In the same way, for CO, the bias, RMS and correlation coefficient between MOZAIC and the analyses are −3.16 ppbv, 13 ppbv and 0.79, respectively, whereas between MOZAIC and the free model run, the corresponding values are 33 ppbv, 38.5 ppbv and 0.83, respectively. In the same way, for CO, the bias, RMS and correlation coefficient between MOZAIC and the analyses are −3.16 ppbv, 13 ppbv and 0.79, respectively, whereas between MOZAIC and the free model they are 6.3 ppbv, 16.6 ppbv and 0.71, respectively. The paper also presents a demonstration of the capability of O3 and CO assimilated fields to better describe a stratosphere-troposphere exchange (STE) event in comparison with the free run modelled O3 and CO fields. Although the assimilation of MLS data improves the distribution of O3 above the tropopause compared to the free model run, it is not sufficient to reproduce the STE event well. Assimilated MOPITT CO allows a better qualitative description of the stratospheric intrusion event. The MOPITT CO analyses appear more promising than the MLS O3 analyses in terms of their ability to capture a deep STE event. Therefore, the results of this study open the perspectives for using MOPITT CO in the STE studies