gebhart/patrepeval huggingface dataset:
Partial redundancy elimination for access path expressions (2001)

Abstract Pointer traversals pose significant overhead to the execution of object‐oriented programs, since every access to an object's state requires a pointer dereference. Eliminating redundant pointer traversals reduces both instructions executed as well as redundant memory accesses to relieve pressure on the memory subsystem. We describe an approach to elimination of redundant access expressions that combines partial redundancy elimination (PRE) with type‐based alias analysis (TBAA). To explore the potential of this approach we have implemented an optimization framework for Java class files incorporating TBAA‐based PRE over pointer access expressions. The framework is implemented as a class‐file‐to‐class‐file transformer; optimized classes can then be run in any standard Java execution environment. Our experiments demonstrate improvements in the execution of optimized code for several Java benchmarks running in diverse execution environments: the standard interpreted JDK virtual machine, a virtual machine using ‘just‐in‐time’ compilation, and native binaries compiled off‐line (‘way‐ahead‐of‐time’). Overall, however, our experience is of mixed success with the optimizations, mainly because of the isolation between our optimizer and the underlying execution environments which prevents more effective cooperation between them. We isolate the impact of access path PRE using TBAA, and demonstrate that Java's requirement of precise exceptions can noticeably impact code‐motion optimizations like PRE. Copyright © 2001 John Wiley & Sons, Ltd.
Combinatorial analysis of the fault-diameter of the n-cube (1993)

It is shown that the diameter of an n-dimensional hypercube can only increase by an additive constant of 1 when (n-1) faulty processors are present. Based on the concept of forbidden faulty sets, which guarantees the connectivity of the cube in the presence of up to (2n-3) faulty processors. It is shown that the diameter of the n-cube increases to (n-2) as a result of (2n-3) processor failures. It is also shown that only those nodes whose Hamming distance is (n-2) have the potential to be located at two ends of the diameter of the damaged cube. It is proven that all the n-cubes with (2n-3) faulty processors and a fault-diameter of (n+2) are isomorphic. A generalization to the subject study is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Discriminant analysis of lower respiratory tract components associated with cigarette smoking, based on quantitative sputum cytology. (1990)

Cigarette smoking is the major contributor to chronic bronchial irritation, and tobacco smoke is the most common bronchial carcinogen. A newly developed quantitative sputum cytology test was applied to three-day-pooled, spontaneously produced sputa collected from 349 cigarette smokers and 93 patients who had never smoked; the samples were processed by the Saccomanno technique. In addition to identifying malignant and precancerous cells in sputum, this test identifies eight morphologic parameters of bronchial irritation. Cross-sectional analysis of the cytologic data indicated that, within a 99% confidence interval, cigarette smokers had statistically significantly higher levels of all eight components, producing a unique profile. Discriminant analysis revealed that pigmentation of macrophages, alveolar macrophages and mucous spirals (in that order) were the leading components differentiating smokers from nonsmokers. This new quantitative sputum cytology test correlates with the model of lung carcinogenesis. The detection of proliferative cellular alterations, such as benign and early atypical metaplasia, represent the detection of chronic persistent irritation, which is considered to be a reversible change. The ability to monitor individual responses to toxic inhalants (before the development of irreversible disease) by utilizing a noninvasive test represents a unique opportunity to impact the historic course of lung carcinogenesis.
Expanding across time to deliver bandwidth efficiency and low latency (2019)

Datacenters need networks that support both low-latency and high-bandwidth packet delivery to meet the stringent requirements of modern applications. We present Opera, a dynamic network that delivers latency-sensitive traffic quickly by relying on multi-hop forwarding in the same way as expander-graph-based approaches, but provides near-optimal bandwidth for bulk flows through direct forwarding over time-varying source-to-destination circuits. The key to Opera's design is the rapid and deterministic reconfiguration of the network, piece-by-piece, such that at any moment in time the network implements an expander graph, yet, integrated across time, the network provides bandwidth-efficient single-hop paths between all racks. We show that Opera supports low-latency traffic with flow completion times comparable to cost-equivalent static topologies, while delivering up to 4x the bandwidth for all-to-all traffic and supporting 60% higher load for published datacenter workloads.
Isolation and Characterization of Gram-Positive Cyanophycin-Degrading BacteriaKinetic Studies on Cyanophycin Depolymerase Activity in Aerobic Bacteria (2003)

This study is the first report on the extracellular degradation of cyanophycin (CGP) by Gram-positive bacteria. Three different Gram-positive bacteria were isolated from forest soil that were able to utilize CGP as the sole carbon source for growth. The isolates were assigned to species of the genera Bacillus and Micromonospora. From one of the isolates, which was taxonomically affiliated as Bacillus megaterium strain BAC19, the extracellular CGP depolymerase (extracellular CGPase; CphEBm) was purified to electrophoretic homogeneity by fast protein liquid chromatography and affinity binding to an arginine-agarose column. The purified enzyme was specific for hydrolytic cleavage of CGP, and inhibitor studies indicated that CphEBm is a serine-type peptidase. As CGP degradation products, (beta-Asp-Arg)2 tetrapeptides in addition to beta-Asp-Arg dipeptides occurred, which were identified by electrospray ionization mass spectrometry analysis. Furthermore, a novel quantitative enzyme assay was developed for kinetic studies on CGP depolymerases. For CphEBm, as well as for the extracellular CGPase of Pseudomonas anguilliseptica strain BI (CphEPa), KM values of 2.2 and 1.0 microM, respectively, for CGP were determined.
Dynamic AGV-Container Job Deployment Strategy (2002)

Automated Guided Vehicles (AGVs) are now becoming popular in container-handling applications at seaport. Efficacy of the dispatching strategy adopted to deploy AGVs is a prime factor affecting the performance of the entire system. The objective of this project is thus to develop an efficient dispatching strategy to deploy AGVs in a container terminal. The scenario considered was a container terminal where containers are uploaded to and discharged from ships. Discharged containers are stored at specific storage locations in the terminal yard. Containers are moved between dock and yard by a dedicated fleet of AGVs. At any point of time, each AGV carries at most two containers. This two-container load may comprise of any plausible permutation of containers for discharge or upload. To reduce congestion and increase utility level, an efficient dispatching strategy for AGVs is paramount. At present, a variety of heuristic methods for dispatching AGVs are available, but these methods were primarily developed to work in a manufacturing context where the network structure is uncomplicated and only a small number of AGVs are required. The situation under consideration entails greater network complexity and also a large fleet of close to 80 AGVs. In this study, the problem was modeled via network flows with constraints, which describe the disparate instances when the AGV carries one container and when it carries two. Heuristic algorithms based on this model are proposed and their performance investigated.
Disulfide-Intact and -Reduced Lysozyme in the Gas Phase:  Conformations and Pathways of Folding and Unfolding (1997)

The conformations of gaseous lysozyme ions (+5 through +18) produced by electrospray ionization have been studied in the gas phase using ion mobility mass spectrometry techniques. When solutions containing the disulfide-intact and disulfide-reduced lysozyme are electrosprayed, the gas-phase ions that are produced have distinctly different collision cross sections. Disulfide-intact ions favor two conformer types: a highly folded conformer with a cross section near that calculated for the crystal structure and a partially unfolded conformer that is formed when the ions are injected into the drift tube at high injection voltages. Ions formed from the disulfide-reduced solution have collision cross sections that are much larger than any observed for the disulfide-intact protein, showing that these ions are largely unfolded. Gas-phase proton-transfer reactions in the ion source can be used to favor lower charge states for both solutions. When protons are removed from disulfide-intact lysozyme ions, highly folded compact conformations are favored. Exposing the disulfide-reduced lysozyme ions to proton-transfer reagents causes the protein to fold up, and several of the new conformations have cross sections that are indistinguishable from those measured for the disulfide-intact protein. It appears that an array of gas-phase folding intermediates or misfolded metastable states are stable because of the well-defined interplay between attractive−folding and repulsive−Coulombic interactions.
A peptidomimetic inhibitor of matrix metalloproteinases containing a tetherable linker group (2011)

Successful wound repair and normal turnover of the extracellular matrix relies on a balance between matrix metalloproteinases (MMPs) and their natural tissue inhibitor of metalloproteinases (TIMPs). When overexpression of MMPs and abnormally high levels of activation or low expression of TIMPs are encountered, excessive degradation of connective tissue and the formation of chronic ulcers can occur. One strategy to rebalance MMPs and TIMPs is to use inhibitors. We have designed a synthetic pseudopeptide inhibitor with an amine linker group based on a known high-affinity peptidomimetic MMP inhibitor and have demonstrated inhibition of MMP-1, -2, -3, and -9 activity in standard solutions. The inhibitor was also tethered to a polyethylene glycol hydrogel using a facile reaction between the linker unit on the inhibitor and the hydrogel precursors. After tethering, we observed inhibition of the MMPs although there was an increase in the IC₅₀s that was attributed to poor diffusion of the MMPs into the hydrogels, reduced activity of the tethered inhibitor, or incomplete incorporation of the inhibitor into the hydrogels. When the tethered inhibitors were tested against chronic wound fluid, we observed partial inhibition in proteolytic activity suggesting this approach may prove useful in rebalancing MMPs within chronic wounds.
All three acyl moieties of trilinolein are efficiently oxygenated by recombinant His‐tagged lipid body lipoxygenase in vitro (1998)

Recently, we found a 13-lipoxygenase in germinating cucumber cotyledons, which was located at the lipid body membrane. Based on its products formed mobilization of storage lipids seems to be initiated by this 13-lipoxygenase. For biochemical characterization its cDNA was expressed as His-tagged protein. Active recombinant enzyme was obtained from low temperature cultivation of E. coli after affinity purification. It (i) exhibited an unchanged region specificity, and (ii) showed a pH optimum of 7.2 against trilinolein as substrate. We compared its ability to oxygenate trilinolein with the one of another 13-lipoxygenase, soybean lipoxygenase-1. At the pH optimum of soybean lipoxygenase-1 (9.0), trilinolein was oxygenated only to 28% of the amount converted by the lipid body lipoxygenase. Moreover, trilinolein oxygenation by soybean lipoxygenase-1 leads mainly to monohydroperoxy derivatives, whereas oxygenation by lipid body LOX leads to a trihydroperoxy derivative.
The Effectiveness of Tape Playback in Estimating Black Rail Density (1999)

Michael L. Legare, William R. Eddleman, P. A. Buckley, Colleen Kelly, The Effectiveness of Tape Playback in Estimating Black Rail Density, The Journal of Wildlife Management, Vol. 63, No. 1 (Jan., 1999), pp. 116-125
Selectivity and Copper Chemical Vapor Deposition (1992)

The question of selectivity (on metal vs. insulator) in the growth of copper thin films from organometallic precursors is addressed by studying the adsorption of Cu(hfac)(vtms) (where hfac = 1,1,1,5,5,5‐hexafluoroacetylacetonate and vtms = vinyltrimethylsilane) on high surface area silica using transmission infrared spectroscopy. No deposition is observed on dehydrated . In the presence of adsorbed, hydrogen bonded OH (OD) groups (from the dissociative adsorption of either water or ), thin film growth is nucleated and selectivity is lost. In addition, temperature‐programmed desorption is employed to study the bonding of a number of neutral ligands to Cu(100). This information is then used to correlate the activation energy for desorption with the observed selectivity of a series of CuI β‐diketonates.
Identificaiton of Non‐Alcoholic Steatohepatitis (NASH) Using Plasma Metabolome in Humans (2008)

The plasma metabolomic profile of subjects with non‐alcoholic fatty liver disease (NAFLD), hepatic steatosis and steatohepatitis (NASH), was examined to identify specific disease‐related patterns and to identify physiological and biochemical perturbations. Plasma samples were obtained after an overnight fast from histologically confirmed subjects with NASH (N=24) or steatosis (N=11), and compared with healthy age and sex‐matched controls (n=25). Subjects with steatosis and NASH were obese and were insulin resistant, as determined by HOMA. Using GC‐MS and LC‐MS, 345 metabolites were detected in the plasma samples, of which 137 compounds were different amongst the groups (p<0.05, q<0.1). Significant differences between NASH and controls were observed for branched chain amino acids, serine, threonine, glutamine, glutamate and aromatic amino acids. Other changes were related to glutathione, purine and fatty acid metabolism. Plasma concentrations of hexanoylcarnitine, cholate and glycocholate were higher in NAFLD when compared with controls. Random forest analysis and recursive partitioning could separate subjects with NASH from controls with an error rate of ∼13%. A recursive partitioning model using body mass index (BMI) and an unnamed compound had an excellent predictive value for subjects with NASH. We conclude that the plasma metabolome can be used to identify subjects with NASH, generate metabolic pathway related hypotheses, and used to follow response to therapeutic interventions without the need for repeat liver biopsies.
Elicitation, assessment, and pooling of expert judgments using possibility theory (1995)

The problem of modeling expert knowledge about numerical parameters in the field of reliability is reconsidered in the framework of possibility theory. Usually expert opinions about quantities such as failure rates are modeled, assessed, and pooled in the setting of probability theory. This approach does not seem to always be natural since probabilistic information looks too rich to be currently supplied by individuals. Indeed, information supplied by individuals is often incomplete, imprecise rather than tainted with randomness. Moreover, the probabilistic framework looks somewhat restrictive to express the variety of possible pooling modes. In this paper, the authors formulate a model of expert opinion by means of possibility distributions that are thought to better reflect the imprecision pervading expert judgments. They are weak substitutes to unreachable subjective probabilities. Assessment evaluation is carried out in terms of calibration and level of precision, respectively, measured by membership grades and fuzzy cardinality indexes. Finally, drawing from previous works on data fusion using possibility theory, the authors present various pooling modes with their formal model under various assumptions concerning the experts. A comparative experiment between two computerized systems for expert opinion analysis has been carried out, and its results are presented in this paper.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A nuclear form of the heparin-binding epidermal growth factor-like growth factor precursor is a feature of aggressive transitional cell carcinoma. (2003)

Heparin-binding epidermal growth factor-like growth factor (HB-EGF), a member of the ErbB receptor ligand family, exists in distinct molecular forms with disparate biological activities. Previous studies have shown that the HB-EGF precursor, proHB-EGF, localizes to the cytoplasm of transitional cells of the human bladder urothelium and that the soluble form of the growth factor is an autocrine urothelial cell mitogen. In this study, we identify a potential role for proHB-EGF in transitional cell carcinoma (TCC) of the bladder. In an analysis of 33 TCC specimens and 8 normal controls, proHB-EGF, identified using an antibody directed against the cytoplasmic tail domain, localized to cell nuclei in a manner that correlated positively with tumor stage and grade (P < 0.001). The ability of proHB-EGF to localize to the nucleus was independently confirmed in a TCC cell line (TCCSUP), in which approximately 40% of transfected proHB-EGF was found to reside in the nuclear compartment. In Kaplan-Meier survival analysis, TCC patients with >20% proHB-EGF-positive cell nuclei demonstrated markedly reduced survival compared with patients with <20% proHB-EGF-positive nuclei (P < 0.005, log-rank test). In multivariate analysis, nuclear localization of proHB-EGF of >20% was an independent prognostic indicator of disease-specific mortality. This is the first report in any cell type that HB-EGF is capable of translocating to the cell nucleus. In addition, our findings suggest that nuclear proHB-EGF may play a role in disease progression in bladder cancer and possibly other cancers.
Staphylococcus aureus Tolerance and Genomic Response to Photodynamic Inactivation (2021)

<i>Staphylococcus aureus</i> is an opportunistic pathogen with a clinical spectrum ranging from asymptomatic skin colonization to invasive infections. While traditional antibiotic therapies can be effective against <i>S. aureus</i>, the increasing prevalence of antibiotic-resistant strains results in treatment failures and high mortality rates. Photodynamic inactivation (PDI) is an innovative and promising alternative to antibiotics. While progress has been made in our understanding of the bacterial response to PDI, major gaps remain in our knowledge of PDI tolerance, the global cellular response, and adaptive genomic mutations acquired as a result of PDI. To address these gaps, <i>S. aureus</i> HG003 and isogenic mutants with mutations in <i>agr</i>, <i>mutS</i>, <i>mutL</i>, and <i>mutY</i> exposed to single or multiple doses of PDI were assessed for survival and tolerance and examined by global transcriptome and genome analyses to identify regulatory and genetic adaptations that contribute to tolerance. Pathways in inorganic ion transport, oxidative response, DNA replication recombination and repair, and cell wall and membrane biogenesis were identified in a global cellular response to PDI. Tolerance to PDI was associated with superoxide dismutase and the <i>S. aureus</i> global methylhydroquinone (MHQ)-quinone transcriptome network. Genome analysis of PDI-tolerant HG003 identified a nonsynonymous mutation in the quinone binding domain of the transcriptional repressor QsrR, which mediates quinone sensing and oxidant response. Acquisition of a heritable QsrR mutation through repeated PDI treatment demonstrates selective adaption of <i>S. aureus</i> to PDI. PDI tolerance of a <i>qsrR</i> gene deletion in HG003 confirmed that QsrR regulates the <i>S. aureus</i> response to PDI.<b>IMPORTANCE</b><i>Staphylococcus aureus</i> can cause disease at most body sites, with illness ranging from asymptomatic infection to death. The increasing prevalence of antibiotic-resistant strains results in treatment failures and high mortality rates. <i>S. aureus</i> acquires resistance to antibiotics through multiple mechanisms, often by genetic variation that alters antimicrobial targets. Photodynamic inactivation (PDI), which employs a combination of a nontoxic dye and low-intensity visible light, is a promising alternative to antibiotics that effectively eradicates <i>S. aureus</i> in human infections when antibiotics are no longer effective. In this study, we demonstrate that repeated exposure to PDI results in resistance of <i>S. aureus</i> to further PDI treatment and identify the underlying bacterial mechanisms that contribute to resistance. This work supports further analysis of these mechanisms and refinement of this novel technology as an adjunctive treatment for <i>S. aureus</i> infections.
Southern molecular hybridization experiments with parallel complementary DNA probes (1992)

We have detected the specific binding in Southern blot hybridization experiments of both complementary antiparallel and parallel 40 bp synthetic DNA probes, corresponding to a cloned Drosophila DNA fragment. The highly cooperative annealing and melting were observed in solution with these probes, which are complementary in the same direction and possess 17 GC pairs. The binding of ethidium bromide is indicative of formation of a perfect parallel DNA duplex. The specific binding was also detected in both genomic and in plaque hybridization experiments.
Comprehensive management of the chronic pain patient (1991)

Director Pain Management Program Veterans Administration Medical Center Assistant Professor Department of Psychiatry School of Medicine University of California, San Diego Director Chronic Low Back Pain Clinic Veterans Administration Medical Center San Diego, California