Source Code Repositories * Github (http://github.com): A web-based hosting service for software development projects that use the Git revision control system, including many open-source projects. * ...Git (http://git-scm.com): A free and open-source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. * Mercurial (http://mercurial.selenic.com): A free, distributed source control management tool. Systems to Package, Access, and Execute Data and Code * IPython Notebook (http://ipython.org/notebook.html): A web-based interactive computational environment where you can combine code execution, text, mathematics, plots, and rich media into a single document. * ROpenSci (http://ropensci.org): A suite of packages that allow access to data repositories through the R statistical programming environment. * Authorea (https://authorea.com): A collaborative online word processor for scholarly papers that allows the writing of web-native, living, dynamic, "executable" articles that include text, mathematical notation, images, and data.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Careful preservation of experimental data, simulations, analysis products, and theoretical work maximizes their long-term scientific return on investment by enabling new analyses and reinterpretation ...of the results in the future. Key infrastructure and technical developments needed for some high-value science targets are not in scope for the operations program of the large experiments and are often not effectively funded. Increasingly, the science goals of our projects require contributions that span the boundaries between individual experiments and surveys, and between the theoretical and experimental communities. Furthermore, the computational requirements and technical sophistication of this work is increasing. As a result, it is imperative that the funding agencies create programs that can devote significant resources to these efforts outside of the context of the operations of individual major experiments, including smaller experiments and theory/simulation work. In this Snowmass 2021 Computational Frontier topical group report (CompF7: Reinterpretation and long-term preservation of data and code), we summarize the current state of the field and make recommendations for the future.
We present a search at the Jefferson Laboratory for new forces mediated by sub-GeV vector bosons with weak coupling α' to electrons. Such a particle A' can be produced in electron-nucleus ...fixed-target scattering and then decay to an e + e- pair, producing a narrow resonance in the QED trident spectrum. Using APEX test run data, we searched in the mass range 175-250 MeV, found no evidence for an A'→ e+ e- reaction, and set an upper limit of α'/α ~/= 10(-6). Our findings demonstrate that fixed-target searches can explore a new, wide, and important range of masses and couplings for sub-GeV forces.
Atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) is one of the most commonly used herbicides in North America and is frequently detected in ground and surface waters. This research ...investigated possible covalent modifications of hemoglobin following in vivo exposures to atrazine in Sprague Dawley (SD) rats and in vitro incubations with diaminochlorotriazine. SD rats were exposed to 0, 10, 30, 100, and 300 (mg atrazine/kg)/day for 3 days via oral gavages, and blood was drawn at 0 h, 24 h, 72 h, 20 days, 1 month, and 2 months for globin analysis. Globin was purified from red blood cells, separated with high-performance liquid chromatography, and analyzed with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). An additional β globin peak was seen in exposed animals during the HPLC and MALDI-TOF MS analysis with a mass 110 Da greater than the normal β subunits. Tryptic digests of this β peak contained a peptide of 1449.9 m/z that corresponded to a modified peptide of amino acids 121−132. Mass spectrometry sequencing of this peptide indicated a 110 Da addition to Cys-125 of the major β globin chain, which corresponds to a nucleophilic substitution reaction with a diaminochlorotriazine. In vitro incubations of SD globin and diaminochlorotriazine also resulted in a peptide of 1449.6 m/z that was identical in sequence to the modified peptide seen in the in vivo digest, confirming the nucleophilic substitution mechanism of adduct formation. Exposures of SD rats to atrazine results in formation of an adduct that is easily detected and provides an analytical model for detection of triazine adducts in other macromolecules with sulfhydryl functional groups.
The objective of this study was to develop an analytical method to detect and quantitate the chlorotriazine herbicide atrazine (ATRA), and its chlorinated metabolites desethylatrazine (DE-ATRA), ...desisopropylatrazine (DI-ATRA), and diaminochlorotriazine (DACT) in plasma. Control plasma separated from whole rat blood was fortified with known concentrations of ATRA, DE-ATRA, DI-ATRA, and DACT. These compounds were extracted from the plasma using a liquid-liquid extraction technique, and the resulting extracts were derivatized with tetrabutyl ammonium hydroxide and methyl iodide to produce methylated derivatives of ATRA and its chlorinated metabolites. Derivatized samples and standards were analyzed using gas chromatography-mass spectrometry with selected ion monitoring. Recoveries of fortified plasma samples ranged from 84% to 97% and were validated to 100 ng/mL. This analytical method was subsequently verified in a small-scale animal study to determine time course concentrations of chlorotriazines in plasma following a single oral gavage dose of ATRA to female Sprague Dawley rats.
A physiological pharmacokinetic (PPK) model, with blood, body, and brain compartments, was developed to estimate total plasma chlorotriazine (CI-TRI) time courses (i.e., atrazine ATRA and its three ...chlorinated metabolites) after oral dosing with ATRA. The model, based on disposition data for 14 C-ATRA, tracked two pools of compounds: (1) ATRA and chlorinated metabolites (i.e., the CI-TRIs) and (2) glutathione conjugates. The PPK model developed from total radioactivity was valuable for assessing total plasma CI-TRI concentrations, estimating blood protein binding rates of CI-TRIs, and inferring relationships between tissue exposures of CI-TRIs and administered dose. Absorption of radioactivity into plasma was slow with a rate constant of 0.2 h m 1 . 14 C-disposition data indicated that CI-TRIs react with red blood cells (presumably hemoglobin) and plasma proteins. Second-order rates of reaction of CI-TRIs with hemoglobin and plasma protein were estimated to be 0.008 L/mmol/h and 1.14 2 10 m 7 L/mg/h, respectively. A time-course study, conducted as part of this study, evaluated the absorption, disposition, and elimination characteristics of individual CI-TRIs in plasma after a single oral dose of 90 mg ATRA/kg and indicated (1) that slow uptake into blood reflected both absorption and slow dissolution of the ATRA slurry and (2) that diaminochloro-s-triazine (DACT) was the major, persistent plasma CI-TRI after oral dosing. Optimally, PK model development for pesticide compounds like atrazine should include a combination of radiolabeled studies for residues and speciation studies of important metabolites.
The Parallel ROOT Facility – PROOF is a distributed analysis system which allows to exploit inherent event level parallelism of high energy physics data. PROOF can be configured to work with ...centralized storage systems, but it is especially effective together with distributed local storage systems – like Xrootd, when data are distributed over computing nodes. It works efficiently on different types of hardware and scales well from a multi-core laptop to large computing farms. From that point of view it is well suited for both large central analysis facilities and Tier 3 type analysis farms. PROOF can be used in interactive or batch like regimes. The interactive regime allows the user to work with typically distributed data from the ROOT command prompt and get a real time feedback on analysis progress and intermediate results. We will discuss our experience with PROOF in the context of ATLAS Collaboration distributed analysis. In particular we will discuss PROOF performance in various analysis scenarios and in multi-user, multi-session environments. We will also describe PROOF integration with the ATLAS distributed data management system and prospects of running PROOF on geographically distributed analysis farms.
ATLAS is one of the four major LHC experiments, designed to cover a wide range of physics topics. In order to cope with a rate of 40MHz and 25 interactions per bunch crossing, the ATLAS trigger ...system is divided in three different levels. The jet selection starts at first level with dedicated processors that search for high ET hadronic energy depositions. At the LVL2, the jet signatures are verified with the execution of a dedicated, fast jet reconstruction algorithm, followed by a calibration algorithm. Three possible granularities have been proposed and are being evaluated: cell based (standard), energy sums calculated at each Front-End Board and the use of the LVL1 Trigger Towers. In this presentation, the design and implementation of the jet trigger of ATLAS will be discussed in detail, emphasazing the major difficulties of each selection step. The performance of the jet algorithm, including timing, efficiencies and rates will also be shown, with detailed comparisons of the different unpacking modes.
Hydrolysis and adsorption of the sulfonylurea herbicides rimsulfuron and primisulfuron were investigated under laboratory conditions. Degradation in aqueous solutions was determined between pH 3 and ...8 and between 5 and 35 C. Rimsulfuron degraded faster than primisulfuron. Half-lives at different temperatures at pH 4 ranged from 0.16 to 5.8 d for rimsulfuron and from 0.47 to 16.1 d for primisulfuron. Primisulfuron hydrolysis at 30 C decreased with increasing pH, but rimsulfuron decreased up to pH 7, then increased, suggesting rapid degradation in alkaline conditions. Adsorption, measured in six Colorado soils, was complete within 2 h in all soils. Adsorption isotherms were determined by batch equilibration of 75 to 600 μg L−1. Rimsulfuron was adsorbed in amounts 3.7 to 7 times higher than primisulfuron, with adsorption distribution coefficients (Kd) ranging from 0.1 to to 1.18 for primisulfuron and from 0.71 to 5.1 for rimsulfuron. Adsorption of both herbicides was slightly correlated with soil clay content, and primisulfuron adsorption was also correlated with organic matter content.
Metsulfuron sorption, dissipation, and leaching were studied in six Colorado soils. Sorption was studied in the laboratory by batch equilibration of soil horizons from the surface to 1 m deep found ...in each study area. Kd was correlated to several soil parameters with pH (-0.773) and percent organic matter (OM) (0.666) the strongest, although low. Kd generally decreased with depth at each site and ranged from 0.10 to 0.83 among surface soils. The lowest Kd was in the soil with the highest pH. Leaching and dissipation were studied by high-performance liquid chromatography/ultraviolet analysis of field samples collected 1 m deep. Bromide ion as conservative tracer was applied concurrently with metsulfuron at the four dryland and two irrigated sites. In most cases, metsulfuron was found only in upper horizons, and the half-life ranged from 11.8 to 27.7 d, the shortest being in the soil with highest percent OM and lowest pH. Very little leaching below the surface horizon was detected in any soil.
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