Concurrent Image Processing Executive (CIPE)

The design and implementation of a Concurrent Image Processing Executive (CIPE), which is intended to become the support system software for a prototype high performance science analysis workstation are discussed. The target machine for this software is a JPL/Caltech Mark IIIfp Hypercube hosted by either a MASSCOMP 5600 or a Sun-3, Sun-4 workstation; however, the design will accommodate other concurrent machines of similar architecture, i.e., local memory, multiple-instruction-multiple-data (MIMD) machines. The CIPE system provides both a multimode user interface and an applications programmer interface, and has been designed around four loosely coupled modules; (1) user interface, (2) host-resident executive, (3) hypercube-resident executive, and (4) application functions. The loose coupling between modules allows modification of a particular module without significantly affecting the other modules in the system. In order to enhance hypercube memory utilization and to allow expansion of image processing capabilities, a specialized program management method, incremental loading, was devised. To minimize data transfer between host and hypercube a data management method which distributes, redistributes, and tracks data set information was implemented

Tiamulin-Resistant Mutants of the Thermophilic Bacterium \u3cem\u3eThermus thermophilus\u3c/em\u3e

Tiamulin is a semisynthetic pleuromutilin antibiotic that binds to the 50S ribosomal subunit A site and whose (((2-diethylamino)ethyl)thio)-acetic acid tail extends into the P site to interfere with peptide bond formation. We have isolated spontaneous tiamulin-resistant mutants of the thermophilic bacterium Thermus thermophilus, containing either single amino acid substitutions in ribosomal protein uL3 or single base substitutions in the peptidyltransferase active site of 23S rRNA. These mutations are consistent with those found in other organisms and are in close proximity to the crystallographically determined tiamulin binding site. We also conducted a cross-resistance analysis of nine other single-base substitutions in or near the peptidyltransferase active site, previously selected for resistance to structurally unrelated antibiotics. While some of the base substitutions in 23S rRNA are positioned to directly affect tiamulin-ribosome contacts, others are some distance from the tiamulin binding site, indicating an indirect mechanism of resistance. Similarly, amino acid substitutions in uL3 are predicted to act indirectly by destabilizing rRNA conformation in the active site. We interpret these observations in light of the available ribosome X-ray crystal structures. These results provide a more comprehensive profile of tiamulin resistance caused by mutations in the bacterial ribosome

Alterations in the ribosomal protein bL12 of E. coli affecting the initiation, elongation and termination of protein synthesis

In bacteria, ribosomal protein bL12 forms the prominent stalk structure on the ribosome and binds to multiple, distinct translational GTPase factors during the sequential steps of translation. Using a genetic selection in E. coli for altered readthrough of UGA stop codons, we have isolated seven different mutations affecting the C-terminal domain of the protein that forms the interaction surface with translation factors. Analysis of these altered proteins, along with four additional alterations previously shown to affect IF2-ribosome interactions, indicates that multiple steps of translation are affected, consistent with bL12’s interaction with multiple factors. Surprisingly, deletion of the release factor GTPase, RF3, has relatively little effect on bL12-promoted stop codon readthrough, suggesting that other steps in termination are also influenced by bL12

Fault-Tolerant Quantum Memory using Low-Depth Random Circuit Codes

Low-depth random circuit codes possess many desirable properties for quantum error correction but have so far only been analyzed in the code capacity setting where it is assumed that encoding gates and syndrome measurements are noiseless. In this work, we design a fault-tolerant distillation protocol for preparing encoded states of one-dimensional random circuit codes even when all gates and measurements are subject to noise. This is sufficient for fault-tolerant quantum memory since these encoded states can then be used as ancillas for Steane error correction. We show through numerical simulations that our protocol can correct erasure errors up to an error rate of $2\%$. In addition, we also extend results in the code capacity setting by developing a maximum likelihood decoder for depolarizing noise similar to work by Darmawan et al. As in their work, we formulate the decoding problem as a tensor network contraction and show how to contract the network efficiently by exploiting the low-depth structure. Replacing the tensor network with a so-called ''tropical'' tensor network, we also show how to perform minimum weight decoding. With these decoders, we are able to numerically estimate the depolarizing error threshold of finite-rate random circuit codes and show that this threshold closely matches the hashing bound even when the decoding is sub-optimal

Status and Relative Abundance of Alabama Shad, \u3ci\u3eAlosa alabamae\u3c/i\u3e, in Alabama

Alabama Shad, Alosa alabamae, an anadromous fish found historically from the Mississippi River basin eastward to the Suwanee River, has experienced population declines and even extirpation in some States. In Alabama, A. alabamae have been found in rivers of the Mobile River basin and Conecuh, Yellow, and Choctawhatchee rivers in the coastal Gulf Plain. We report on our directed and targeted efforts to assess the current status and relative abundance of A. alabamae in Alabama and compare our results to past A. alabamae surveys in Alabama. We completed 52 sampling trips and expended 129.5 hours of boat-electrofishing effort targeting A. alabamae. Sampling was conducted during the spring to coincide with the spring-spawning migration at historical sites and sites conducive for the collection of A. alabamae. No A. alabamae was collected from the Mobile River basin (i.e., Alabama and Tombigbee rivers) and only one A. alabamae was collected from the Conecuh River. We collected seven A. alabamae in 2011 and three in 2018 from the Choctawhatchee River. For the Choctawhatchee River population, our results indicated a precipitous decline in abundance by 71% and 98% from 1999/2000 to 2011 and 2018, respectively. In addition, our results support the extirpation of A. alabamae from the Mobile River basin and a severely depressed population in the Conecuh River. Although A. alabamae was recently denied listing under the Endangered Species Act by the National Marine Fisheries Service due to lack of apparent range-wide extinction, our results indicate what was once considered the second largest population of A. alabamae from the Choctawhatchee River is on the verge of extirpation. Alosa alabamae could become extirpated from Alabama in the near future, which is a significant portion of its range

Light hadron properties with improved staggered quarks

Preliminary results from simulations with 2+1 dynamical quark flavors at a lattice spacing of 0.09 fm are combined with earlier results at a=0.13 fm. We examine the approach to the continuum limit and investigate the dependence of the pseudoscalar masses and decay constants as the sea and valence quark masses are separately varied.Comment: Lattice2002(spectrum

The Phase Diagram of High Temperature QCD with Three Flavors of Improved Staggered Quarks

We report on progress in our study of high temperature QCD with three flavors of improved staggered quarks. Simulations are being carried out with three degenerate quarks with masses less than or equal to the strange quark mass, $m_s$, and with degenerate up and down quarks with masses in the range $0.1 m_s \leq m_{u,d}\leq 0.6 m_s$, and the strange quark mass fixed near its physical value. For the quark masses studied to date we find rapid crossovers, which sharpen as the quark mass is reduced, rather than bona fide phase transitions.Comment: Lattice 2003 (Nonzero temperature and density

A Survey of Spontaneous Antibiotic-Resistant Mutants of the Halophilic, Thermophilic Bacterium Rhodothermus marinus

Rhodothermus marinus is a halophilic extreme thermophile, with potential as a model organism for studies of the structural basis of antibiotic resistance. In order to facilitate genetic studies of this organism, we have surveyed the antibiotic sensitivity spectrum of R. marinus and identified spontaneous antibiotic-resistant mutants. R. marinus is naturally insensitive to aminoglycosides, aminocylitols and tuberactinomycins that target the 30S ribosomal subunit, but is sensitive to all 50S ribosomal subunit-targeting antibiotics examined, including macrolides, lincosamides, streptogramin B, chloramphenicol, and thiostrepton. It is also sensitive to kirromycin and fusidic acid, which target protein synthesis factors. It is sensitive to rifampicin (RNA polymerase inhibitor) and to the fluoroquinolones ofloxacin and ciprofloxacin (DNA gyrase inhibitors), but insensitive to nalidixic acid. Drug-resistant mutants were identified using rifampicin, thiostrepton, erythromycin, spiramycin, tylosin, lincomycin, and chloramphenicol. The majority of these were found to have mutations that are similar or identical to those previously found in other species, while several novel mutations were identified. This study provides potential selectable markers for genetic manipulations and demonstrates the feasibility of using R. marinus as a model system for studies of ribosome and RNA polymerase structure, function, and evolution

Heavy-light meson decay constants with N_f=3

During the past year the MILC Collaboration has continued its study of heavy-light meson decay constants with three dynamical quarks. Calculations have been extended to a second lattice spacing of about 0.09 fm. At this lattice spacing, there are results in the quenched approximation and for three sets of dynamical quark mass: m_l=m_s; m_l=0.4 m_s and m_l=0.2 m_s, where m_l is the light mass for the u and d quarks and m_s is the strange quark mass. At the coarser lattice spacing, for which results were presented at Lattice 2001, statistics have been increased for two sets of quark masses and three additional sets of quark masses have been studied, giving a total of eight combinations used to interpolate between the quenched and chiral limits. When these calculations are completed, we can study the decay constants taking into account both chiral and continuum extrapolations.Comment: Lattice2002(heavyquark), 3 pages, 3 color figures, to appear in the proceedings of Lattice 200