metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella

The metabolic SearcH And Reconstruction Kit (metaSHARK) is a new fully automated software package for the detection of enzyme-encoding genes within unannotated genome data and their visualization in the context of the surrounding metabolic network. The gene detection package (SHARKhunt) runs on a Linux systemand requires only a set of raw DNA sequences (genomic, expressed sequence tag and/ or genome survey sequence) as input. Its output may be uploaded to our web-based visualization tool (SHARKview) for exploring and comparing data from different organisms. We first demonstrate the utility of the software by comparing its results for the raw Plasmodium falciparum genome with the manual annotations available at the PlasmoDB and PlasmoCyc websites. We then apply SHARKhunt to the unannotated genome sequences of the coccidian parasite Eimeria tenella and observe that, at an E-value cut-off of 10(-20), our software makes 142 additional assertions of enzymatic function compared with a recent annotation package working with translated open reading frame sequences. The ability of the software to cope with low levels of sequence coverage is investigated by analyzing assemblies of the E.tenella genome at estimated coverages from 0.5x to 7.5x. Lastly, as an example of how metaSHARK can be used to evaluate the genomic evidence for specific metabolic pathways, we present a study of coenzyme A biosynthesis in P.falciparum and E.tenella

Detection of neutral metastable fragments from electron-impact on argon clusters

We have studied the production of neutral metastable fragments in electron collisions with neutral argon clusters. The fragments are detected using a time-of-flight technique. The time-of-flight spectra show that the metastable fragments appear in two velocity ranges. Kinetic energy distributions are obtained, showing that the faster fragments are ejected with energies from 0.2 to 1.5 eV and that the slower fragments have energies less than 0.2 eV. It is argued that the fragmentation of the clusters involves the excitation and decay of excitons in the clusters.The faster fragments are produced by n52 excitons, which localize on an excimer or an excited trimer within the cluster and upon dissociation cause the ejection of a metastable atom. The slower fragments are produced by n51 excitons, which tend to localize on the periphery of the cluster, leading to the ejection of a metastable atom due to weak repulsive forces with neighboring atoms. Four different production mechanisms for neutral metastable fragments are observed

Detection of neutral metastable fragments from electron-impact on argon clusters

We have studied the production of neutral metastable fragments in electron collisions with neutral argon clusters. The fragments are detected using a time-of-flight technique. The time-of-flight spectra show that the metastable fragments appear in two velocity ranges. Kinetic energy distributions are obtained, showing that the faster fragments are ejected with energies from 0.2 to 1.5 eV and that the slower fragments have energies less than 0.2 eV. It is argued that the fragmentation of the clusters involves the excitation and decay of excitons in the clusters.The faster fragments are produced by n52 excitons, which localize on an excimer or an excited trimer within the cluster and upon dissociation cause the ejection of a metastable atom. The slower fragments are produced by n51 excitons, which tend to localize on the periphery of the cluster, leading to the ejection of a metastable atom due to weak repulsive forces with neighboring atoms. Four different production mechanisms for neutral metastable fragments are observed

Volume I. Introduction to DUNE

The preponderance of matter over antimatter in the early universe, the dynamics of the supernovae that produced the heavy elements necessary for life, and whether protons eventually decay—these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our universe, its current state, and its eventual fate. The Deep Underground Neutrino Experiment (DUNE) is an international world-class experiment dedicated to addressing these questions as it searches for leptonic charge-parity symmetry violation, stands ready to capture supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector technical design report (TDR) describes the DUNE physics program and the technical designs of the single- and dual-phase DUNE liquid argon TPC far detector modules. This TDR is intended to justify the technical choices for the far detector that flow down from the high-level physics goals through requirements at all levels of the Project. Volume I contains an executive summary that introduces the DUNE science program, the far detector and the strategy for its modular designs, and the organization and management of the Project. The remainder of Volume I provides more detail on the science program that drives the choice of detector technologies and on the technologies themselves. It also introduces the designs for the DUNE near detector and the DUNE computing model, for which DUNE is planning design reports. Volume II of this TDR describes DUNE\u27s physics program in detail. Volume III describes the technical coordination required for the far detector design, construction, installation, and integration, and its organizational structure. Volume IV describes the single-phase far detector technology. A planned Volume V will describe the dual-phase technology

Deep Underground Neutrino Experiment (DUNE), far detector technical design report, volume III: DUNE far detector technical coordination

The preponderance of matter over antimatter in the early universe, the dynamics of the supernovae that produced the heavy elements necessary for life, and whether protons eventually decay—these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our universe, its current state, and its eventual fate. The Deep Underground Neutrino Experiment (DUNE) is an international world-class experiment dedicated to addressing these questions as it searches for leptonic charge-parity symmetry violation, stands ready to capture supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector technical design report (TDR) describes the DUNE physics program and the technical designs of the single- and dual-phase DUNE liquid argon TPC far detector modules. Volume III of this TDR describes how the activities required to design, construct, fabricate, install, and commission the DUNE far detector modules are organized and managed. This volume details the organizational structures that will carry out and/or oversee the planned far detector activities safely, successfully, on time, and on budget. It presents overviews of the facilities, supporting infrastructure, and detectors for context, and it outlines the project-related functions and methodologies used by the DUNE technical coordination organization, focusing on the areas of integration engineering, technical reviews, quality assurance and control, and safety oversight. Because of its more advanced stage of development, functional examples presented in this volume focus primarily on the single-phase (SP) detector module

Metastable fragment production by electron-impact dissociation of CF4

Time-of-flight detection of neutral metastable fragments has been applied to the study of electron-impact dissociation of CF4 molecules. The time-of-flight distributions indicate that a number of distinct processes are involved in the production of metastable fragments. Excitation functions for these processes have been measured up to 400 eV. The results presented are compared with other studies of fragmentation of CF4 and indicate that fragmentation into an excited CF3+ ion and an excited F atom is a prominent process

Detection of neutral metastable fragments from electron-impact on argon clusters

We have studied the production of neutral metastable fragments in electron collisions with neutral argon clusters. The fragments are detected using a time-of-flight technique. The time-of-flight spectra show that the metastable fragments appear in two velocity ranges. Kinetic energy distributions are obtained, showing that the faster fragments are ejected with energies from 0.2 to 1.5 eV and that the slower fragments have energies less than 0.2 eV. It is argued that the fragmentation of the clusters involves the excitation and decay of excitons in the clusters.The faster fragments are produced by n52 excitons, which localize on an excimer or an excited trimer within the cluster and upon dissociation cause the ejection of a metastable atom. The slower fragments are produced by n51 excitons, which tend to localize on the periphery of the cluster, leading to the ejection of a metastable atom due to weak repulsive forces with neighboring atoms. Four different production mechanisms for neutral metastable fragments are observed

Detection of neutral metastable fragments from electron-impact on argon clusters

We have studied the production of neutral metastable fragments in electron collisions with neutral argon clusters. The fragments are detected using a time-of-flight technique. The time-of-flight spectra show that the metastable fragments appear in two velocity ranges. Kinetic energy distributions are obtained, showing that the faster fragments are ejected with energies from 0.2 to 1.5 eV and that the slower fragments have energies less than 0.2 eV. It is argued that the fragmentation of the clusters involves the excitation and decay of excitons in the clusters.The faster fragments are produced by n52 excitons, which localize on an excimer or an excited trimer within the cluster and upon dissociation cause the ejection of a metastable atom. The slower fragments are produced by n51 excitons, which tend to localize on the periphery of the cluster, leading to the ejection of a metastable atom due to weak repulsive forces with neighboring atoms. Four different production mechanisms for neutral metastable fragments are observed