SoyBase, the USDA-ARS soybean genetics and genomics database

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the well-annotated ‘Williams 82’ genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies. SoyBase can be accessed at http://soybase.org

Overview of the Nordic Seas CARINA data and salinity measurements

Water column data of carbon and carbon relevant hydrographic and hydrochemical parameters from 188 previously non-publicly available cruises in the Arctic, Atlantic, and Southern Ocean have been retrieved and merged into a new database: CARINA (CARbon IN the Atlantic). The data have been subject to rigorous quality control (QC) in order to ensure highest possible quality and consistency. The data for most of the parameters included were examined in order to quantify systematic biases in the reported values, i.e. secondary quality control. Significant biases have been corrected for in the data products, i.e. the three merged files with measured, calculated and interpolated values for each of the three CARINA regions; the Arctic Mediterranean Seas (AMS), the Atlantic (ATL) and the Southern Ocean (SO). With the adjustments the CARINA database is consistent both internally as well as with GLODAP (Key et al., 2004) and is suitable for accurate assessments of, for example, oceanic carbon inventories and uptake rates and for model validation. The Arctic Mediterranean Seas include the Arctic Ocean and the Nordic Seas, and the quality control was carried out separately in these two areas. This contribution provides an overview of the CARINA data from the Nordic Seas and summarises the findings of the QC of the salinity data. One cruise had salinity data that were of questionable quality, and these have been removed from the data product. An evaluation of the consistency of the quality controlled salinity data suggests that they are consistent to at least ±0.005

Near Real Time Data Processing In ICOS RI

This paper describes the implementation of (near) real-time (NRT) data processing in the recently launched European environmental research infrastructure ICOS. NRT applications include handling of raw sensor data (including safe storage and quality control), processing and evaluation of greenhouse gas mixing ratios and exchange fluxes, and the provision of data to the RI’s user communities

Online measurements of the emissions of intermediate-volatility and semi-volatile organic compounds from aircraft

A detailed understanding of the climate and air quality impacts of aviation requires measurements of the emissions of intermediate-volatility and semi-volatile organic compounds (I/SVOCs) from aircraft. Currently both the amount and chemical composition of aircraft I/SVOC emissions remain poorly characterized. Here we characterize I/SVOC emissions from aircraft, using a novel instrument for the online, quantitative measurement of the mass loading and composition of low-volatility organic vapors. Emissions from the NASA DC8 aircraft were sampled on the ground 143 m downwind of the engines and characterized as a function of engine power from idle (4% maximum rated thrust) through 85% power. Results show that I/SVOC emissions are highest during engine idle operating conditions, with decreasing but non-zero I/SVOC emissions at higher engine powers. Comparison of I/SVOC emissions with total hydrocarbon (THC) measurements, VOC measurements, and an established emissions profile indicates that I/SVOCs comprise 10–20% of the total organic gas-phase emissions at idle, and an increasing fraction of the total gas-phase organic emissions at higher powers. Positive matrix factorization of online mass spectra is used to identify three distinct types of I/SVOC emissions: aliphatic, aromatic and oxygenated. The volatility and chemical composition of the emissions suggest that unburned fuel is the dominant source of I/SVOCs at idle, while pyrolysis products make up an increasing fraction of the I/SVOCs at higher powers. Oxygenated I/SVOC emissions were detected at lower engine powers (≤30%) and may be linked to cracked, partially oxidized or unburned fuel components.United States. Dept. of Energy. Office of Science (Small Business Innovation Research Program Grant DE-SC0001666)United States. Environmental Protection Agency (National Center for Environmental Research Grant RD834560

Dispersion Effects in Nucleon Polarisabilities

We present a formalism to extract the dynamical nucleon polarisabilities defined via a multipole expansion of the structure amplitudes in nucleon Compton scattering. In contradistinction to the static polarisabilities, dynamical polarisabilities gauge the response of the internal degrees of freedom of a composed object to an external, real photon field of arbitrary energy. Being energy dependent, they therefore contain additional information about dispersive effects induced by internal relaxation mechanisms, baryonic resonances and meson production thresholds of the nucleon. We give explicit formulae to extract the dynamical electric and magnetic dipole as well as quadrupole polarisabilities from low energy nucleon Compton scattering up to the one pion production threshold and discuss the connection to the definition of static nucleon polarisabilities. As a concrete example, we examine the results of leading order Heavy Baryon Chiral Perturbation Theory for the four leading spin independent iso-scalar polarisabilities of the nucleon. Finally, we consider the possible r{\^o}le of energy dependent effects in low energy extractions of the iso-scalar dipole polarisabilities from Compton scattering on the deuteron.Comment: 17 pages LaTeX2e with 2 figures, using includegraphicx (5 .eps files). Minor corrections, references updated. Contents identical to version to appear in Phys. Rev. C 65, spelling differen

Effective decrease of photoelectric emission threshold from gold plated surfaces

Many applications require charge neutralisation of isolated test bodies and this has been successfully done using photoelectric emission from surfaces which are electrically benign(gold) or superconducting (niobium). Gold surfaces nominally have a high work function ($\sim 5.1$\,eV)which should require deep UV photons for photoemission. In practice it has been found that it can be achieved with somewhat lower energy photons with indicative work functions of ($4.1-4.3$\,eV). A detailed working understanding of the process is lacking and this work reports on a study of the photoelectric emission properties of 4.6x4.6 cm^2 gold plated surfaces, representative of those used in typical satellite applications with a film thickness of 800 nm, and measured surface roughnesses between 7 and 340 nm. Various UV sources with photon energies from 4.8 to 6.2 eV and power outputs from 1 nW to 1000 nW, illuminated a ~0.3 cm^2 of the central surface region at angles of incidence from 0 to 60 degrees. Final extrinsic quantum yields in the range 10 ppm to 44 ppm were reliably obtained during 8 campaigns, covering a ~3 year period, but with intermediate long-term variations lasting several weeks and, in some cases, bake-out procedures at up to 200 C. Experimental results were obtained in a vacuum system with a baseline pressure of ~10^{-7} mbar at room temperature. A working model, designed to allow accurate simulation of any experimental configuration, is proposed.Comment: 35 pages, 12 figure

Colo-Colonic Intussusception Caused by a Submucosal Lipoma: Case Report and Review of the Literature

Adult intussusception is a rare clinical presentation and often not considered clinically in the differential diagnosis of adult patients with vague abdominal complaints. A 44-year-old woman visited our emergency department with sudden onset of intermittent abdominal pain. Diagnostic imaging revealed an intussusception caused by a submucosal lipoma of the sigmoid. A laparotomy was performed and the diagnosis was proven by histological examination. Submucosal lipomas are usually asymptomatic but may cause bleeding, obstruction, intussusception, or abdominal pain and thus mimic a malignancy. Surgical excision is indicated for symptomatic cases

Restriction of AID activity and somatic hypermutation by PARP-1

Affinity maturation of the humoral immune response depends on somatic hypermutation (SHM) of immunoglobulin (Ig) genes, which is initiated by targeted lesion introduction by activation-induced deaminase (AID), followed by error-prone DNA repair. Stringent regulation of this process is essential to prevent genetic instability, but no negative feedback control has been identified to date. Here we show that poly(ADP-ribose) polymerase-1 (PARP-1) is a key factor restricting AID activity during somatic hypermutation. Poly(ADP-ribose) (PAR) chains formed at DNA breaks trigger AID-PAR association, thus preventing excessive DNA damage induction at sites of AID action. Accordingly, AID activity and somatic hypermutation at the Ig variable region is decreased by PARP-1 activity. In addition, PARP-1 regulates DNA lesion processing by affecting strand biased A:T mutagenesis. Our study establishes a novel function of the ancestral genome maintenance factor PARP-1 as a critical local feedback regulator of both AID activity and DNA repair during Ig gene diversification

Automatic radiographic quantification of hand osteoarthritis; accuracy and sensitivity to change in joint space width in a phantom and cadaver study

This is the final version of the article. Available from Springer Verlag via the DOI in this record.OBJECTIVE: To validate a newly developed quantification method that automatically detects and quantifies the joint space width (JSW) in hand radiographs. Repeatability, accuracy and sensitivity to changes in JSW were determined. The influence of joint location and joint shape on the measurements was tested. METHODS: A mechanical micrometer set-up was developed to define and adjust the true JSW in an acrylic phantom joint and in human cadaver-derived phalangeal joints. Radiographic measurements of the JSW were compared to the true JSW. Repeatability, systematic error (accuracy) and sensitivity (defined as the smallest detectable difference (SDD)) were determined. The influence of joint position on the JSW measurement was assessed by varying the location of the acrylic phantom on the X-ray detector with respect to the X-ray beam and the influence of joint shape was determined by using morphologically different human cadaver joints. RESULTS: The mean systematic error was 0.052 mm in the phantom joint and 0.210 mm in the cadaver experiment. In the phantom experiments, the repeatability was high (SDD = 0.028 mm), but differed slightly between joint locations (p = 0.046), and a change in JSW of 0.037 mm could be detected. Dependent of the joint shape in the cadaver hand, a change in JSW between 0.018 and 0.047 mm could be detected. CONCLUSIONS: The automatic quantification method is sensitive to small changes in JSW. Considering the published data of JSW decline in the normal and osteoarthritic population, the first signs of OA progression with this method can be detected within 1 or 2 years.This work was funded by the Dutch Arthritis Association (Reumafonds). The study sponsor had no involvement in study design, data collection, data analysis, or interpretation of the results