gebhart/patrepeval huggingface dataset:
Feature Identification: An Epidemiological Metaphor (2006)

Feature identification is a technique to identify the source code constructs activated when exercising one of the features of a program. We propose new statistical analyses of static and dynamic data to accurately identify features in large multithreaded object-oriented programs. We draw inspiration from epidemiology to improve previous approaches to feature identification and develop an epidemiological metaphor. We build our metaphor on our previous approach to feature identification, in which we use processor emulation, knowledge-based filtering, probabilistic ranking, and metamodeling. We carry out three case studies to assess the usefulness of our metaphor, using the "save a bookmark" feature of Web browsers as an illustration. In the first case study, we compare our approach with three previous approaches (a naive approach, a concept analysis-based approach, and our previous probabilistic approach) in identifying the feature in MOZILLA, a large, real-life, multithreaded object-oriented program. In the second case study, we compare the implementation of the feature in the FIREFOX and MOZILLA Web browsers. In the third case study, we identify the same feature in two more Web browsers, Chimera (in C) and ICEBrowser (in Java), and another feature in JHOTDRAW and XFIG, to highlight the generalizability of our metaphor
Les historiens belgiques au XVIIIe siècle: entre particularismes et conscience nationale (1999)

info:eu-repo/semantics/published
Molecular ion and metastable atom formations and their effects on the electron temperature in medium-pressure rare-gas positive-column plasmas (1980)

A theoretical study has been made of the medium-pressure rare-gas positive-column plasma by taking into account the effects of molecular ion formation, volume recombination and ionisation due to metastable atoms, simultaneously. Calculated values of the electron temperature and the densities of metastable atoms, molecular and atomic ions, at various gas pressures for both He and Ne gases are presented. Numerical results show that in a rare-gas positive-column plasma, molecular ions become dominant in the discharge as the gas pressure increases above approximately 10 Torr. Theoretical values are compared with the experimental data and discussed. A new method to determine the three-body conversion rate coefficient is also proposed.
Stabilizer Codes and Quantum Error Correction (1997)

Controlling operational errors and decoherence is one of the major challenges facing the field of quantum computation and other attempts to create specified many-particle entangled states. The field of quantum error correction has developed to meet this challenge. A group-theoretical structure and associated subclass of quantum codes, the stabilizer codes, has proved particularly fruitful in producing codes and in understanding the structure of both specific codes and classes of codes. I will give an overview of the field of quantum error correction and the formalism of stabilizer codes. In the context of stabilizer codes, I will discuss a number of known codes, the capacity of a quantum channel, bounds on quantum codes, and fault-tolerant quantum computation
Safety and Immunogenicity from a Phase I Trial of Inactivated Severe Acute Respiratory Syndrome Coronavirus Vaccine (2007)

The inactivated vaccine was safe and well tolerated and can elicit SARS-CoV-specific neutralizing antibodies.
Optical response of linear chains of metal nanospheres and nanospheroids (2008)

A semi-analytical method for computing the electric field surrounding a finite linear chain of metal nanospheres and nanospheroids is described. In treating chains or clusters of spheres, a common approach is to use the spherical-harmonic addition theorem to relate the multipole expansion coefficients between different spheres. A method is described here that avoids the use of spherical-harmonic addition theorems, which are not applicable to spheroidal chains. Simulations are given that illustrate the large field enhancements that can occur in the gaps between silver nanoparticles arising from plasmon resonances.
In Silico Prediction of Scaffold/Matrix Attachment Regions in Large Genomic Sequences (2002)

Scaffold/matrix attachment regions (S/MARs) are essential regulatory DNA elements of eukaryotic cells. They are major determinants of locus control of gene expression and can shield gene expression from position effects. Experimental detection of S/MARs requires substantial effort and is not suitable for large-scale screening of genomic sequences. In silico prediction of S/MARs can provide a crucial first selection step to reduce the number of candidates. We used experimentally defined S/MAR sequences as the training set and generated a library of new S/MAR-associated, AT-rich patterns described as weight matrices. A new tool called SMARTest was developed that identifies potential S/MARs by performing a density analysis based on the S/MAR matrix library (http://www.genomatix.de/cgi-bin/smartest_pd/smartest.pl). S/MAR predictions were evaluated by using six genomic sequences from animal and plant for which S/MARs and non-S/MARs were experimentally mapped. SMARTest reached a sensitivity of 38% and a specificity of 68%. In contrast to previous algorithms, the SMARTest approach does not depend on the sequence context and is suitable to analyze long genomic sequences up to the size of whole chromosomes. To demonstrate the feasibility of large-scale S/MAR prediction, we analyzed the recently published chromosome 22 sequence and found 1198 S/MAR candidates.
Numerical study of wavelength-swept semiconductor ring lasers: the role of refractive-index nonlinearities in semiconductor optical amplifiers and implications for biomedical imaging applications (2006)

Recent results have demonstrated unprecedented wavelength-tuning speed and repetition rate performance of semiconductor ring lasers incorporating scanning filters. However, several unique operational characteristics of these lasers have not been adequately explained, and the lack of an accurate model has hindered optimization. We numerically investigated the characteristics of these sources, using a semiconductor optical amplifier (SOA) traveling-wave Langevin model, and found good agreement with experimental measurements. In particular, we explored the role of the SOA refractive-index nonlinearities in determining the intracavity frequency-shift-broadening and the emitted power dependence on scan speed and direction. Our model predicts both continuous-wave and pulse operation and shows a universal relationship between the output power of lasers that have different cavity lengths and the filter peak frequency shift per round trip, therefore revealing the advantage of short cavities for high-speed biomedical imaging.
Solution structural studies of the A and Z forms of DNA. (1981)

We report transient electric dichroism studies of short double-helical DNA and poly[d(G-C)] fragments in alcohol/water mixtures. The limiting reduced dichroism and the rotational correlation time changed abruptly in the alcohol concentration range expected for the DNA B-to-A and poly[d(G-C)] B-to-Z transitions. The Z form of poly[d(G-C)] was also induced by mitomycin C crosslinking in aqueous solution. The rotational correlation times observed for A- and Z-DNA were approximately consistent with dimensions determined by crystallographic and fiber diffraction analysis: the estimated rise per base pair was 2.8 A for A-DNA and 3.7 A for Z-DNA in solution. In addition, the observed limiting reduced dichroism values for A- and Z-DNA were close to the theoretical limit of -1.5, requiring a structure in which the base transition moments are effectively perpendicular to the double-helix axis. This is the result expected for any DNA double helix having dyad symmetry in which the base pairs are flat and the base transition moments lie predominantly in the short axis of the base pair and therefore close to a helix dyad axis. Only B-DNA deviates from this rule, strongly reinforcing our earlier conclusion that the base pairs in B-DNA are not flat but are propeller twisted, either statically or as a dynamic average.
Discovering Cross-Ontology Subsumption Relationships by Using Ontological Annotations on Biomedical Literature. (2012)

Cross-ontology concept subsumption relationships facilitate the integration of ontologies by explicitly defining the generalization of a concept over other concepts in different ontologies. However, existing methods for discovering these relationships show poor performances and one of the problems is the lack of instance data in ontologies that can be used to identify cross-ontology subsumptions reliably. To address the problem, we present a novel method, SURD (SUbsumption Relation Discovery), which uses annotations on biomedical text corpora for populating ontologies with instances. Subsumption relationships between pairs of concepts are then determined based on their shared instances. SURD shows good performance when applied to biomedical ontologies, achieving precision values of 0.786 and 0.729 for cross-ontology subsumptions between the ontology pairs GRO-UMLS Metathesaurus and GENIA-UMLS Metathesaurus respectively. As a practical application, we used SURD’s subsumptions for automated ontological corpus annotation and achieved F-measures of 0.693 and 0.783 on the GRO and GENIA corpora respectively. These results are superior to the results of using subsumption relations inferred from equivalence relations (F-measures of 0.569 and 0.645) and subsumption relations identified with Hearst patterns (F-measures of 0.002 and 0.096). 1
Characterization of plasminogen binding to human capillary and arterial endothelial cells (1991)

Phenotypic diversity of endothelial cells that line the various vascular spaces has been well established. However, it is not known if biochemical differences also exist, particularly in the numbers of receptors for plasma proteins. Equilibrium binding techniques were used to assess potential differences in the binding of 125I-labelled plasminogen to cultured human umbilical arterial endothelial cells and capillary endothelium, as compared with umbilical venous cells. The kinetic behaviour of plasminogen binding to all three types of cells was similar, with optimal binding occurring between 20 and 30 min of incubation. Binding of plasminogen to arterial, capillary, and venous cells was concentration dependent and reversible upon addition to excess unlabelled plasminogen. Scatchard analyses showed that artery, capillary, and venous endothelial cells all possess low affinity sites for plasminogen with Kd values of 0.30 +/- 0.07, 0.40 +/- 0.06, and 0.40 +/- 0.08 microM, respectively. Vein cells also possess an additional higher affinity binding site with a Kd of 0.07 +/- 0.01 microM, exhibiting a 6-fold greater affinity for plasminogen than the lower affinity sites on capillary and arterial endothelial cells. Assuming a stoichiometry of 1:1 for binding, the data indicate that arterial and capillary endothelial cells contain approximately 4.2 (+/- 0.9) x 10(6) and 4.1 (+/- 0.6) x 10(6) plasminogen receptors per cell. Venous cells contain both low and high density binding sites with 6.2 (+/- 0.8) x 10(6) and 12.4 (+/- 2.4) x 10(6) sites per endothelial cell. The presence of a higher affinity site on vein cells, but not on artery or capillary cells, may signal functional differences relating to fibrinolytic activity on the surface of these cells.(ABSTRACT TRUNCATED AT 250 WORDS)
Chromogranin A in Cerebrospinal Fluid: A Biochemical Marker for Synaptic Degeneration in Alzheimer’s Disease? (1995)

Biochemical markers for AD would be of great value both to improve the clinical diagnostic accuracy in scientific studies and to increase the knowledge of the pathogenesis of the disorder. One of the main features of AD is a degeneration of synapses. Therefore, we examined if chromogranin A (CrA), the major protein of large dense-core synaptic vesicles, in cerebrospinal fluid (CSF) may be of value as a biochemical marker for the synaptic function in AD. The mean concentration of CrA in CSF was about 7.5 times higher than its concentration in serum, and there was no significant correlation between CSF-CrA and the blood-brain barrier function (measured as the CSF/serum albumin ratio), nor between CSF-CrA and serum-CrA. These findings suggest that the major portion of CSF-CrA is locally produced within the CNS. There were no significant differences in CSF-CrA between the AD (n = 29), vascular dementia (n = 13), and age-matched control (n = 9) groups (99.9 +/- 58.9 ng/ml, 108.0 +/- 69.4 ng/ml, and 115.1 +/- 44.4 ng/ml, respectively). However, when the AD group was subdivided into AD type I (n = 12) and AD type II (n = 17), a lower concentration of CSF-CrA was found in AD type I (72.8 +/- 28.9 ng/ml) compared with controls (115.1 +/- 44.4 ng/ml), p < 0.02, and compared with AD type II (119.1 +/- 67.5 ng/ml), p < 0.05, while CSF-CrA did not significantly differ between AD type II and controls. These findings suggest that CSF-CrA has a potential as a biochemical marker for the synaptic degeneration in AD type I, and gives further support for the relevance of identifying the AD type I (pure AD) subgroup in scientific studies.
Physical Limits and Design Principles for Plant and Fungal Movements (2005)

The typical scales for plant and fungal movements vary over many orders of magnitude in time and length, but they are ultimately based on hydraulics and mechanics. We show that quantification of the length and time scales involved in plant and fungal motions leads to a natural classification, whose physical basis can be understood through an analysis of the mechanics of water transport through an elastic tissue. Our study also suggests a design principle for nonmuscular hydraulically actuated structures: Rapid actuation requires either small size or the enhancement of motion on large scales via elastic instabilities.
The Use of Shape Memory Polymers for MEMS Assembly (2015)

The advantages of utilizing the polymeric shape memory effect for deterministic assembly of microscale objects are explored in this paper. Assembly of building blocks, referred to as inks, by transfer printing is performed using a polymeric stamp with reversible adhesion as a manipulator. The dynamic rigidity control of a shape memory polymer (SMP) stamp afforded by heating or cooling it across its glass transition temperature allows for a dramatic increase in adhesion during ink retrieval. Furthermore, the shape-fixing and recovery property of the SMP material enables substantial freedom in stamp design, such as more complex surface patterning and heterogeneous surface features, to further reduce adhesion during release, not otherwise available. The mechanics of the stamp adhesion, including the effect of the material's viscoelasticity and dynamic rigidity on performance, is discussed. Example structures, including a micro-motor structure with a movable rotor, are assembled in order to highlight the benefits afforded using the SMP material over existing alternatives.
Targeted cleavage of mRNA by human RNase P. (1992)

Ribonuclease P from Escherichia coli can cleave RNAs in simple, hydrogen-bonded complexes of two oligoribonucleotides that resemble the aminoacyl stem and 5' leader sequence of tRNA precursors. RNase P from human (HeLa) cells cannot catalyze the cleavage in vitro of the 5'-proximal oligoribonucleotide that contains the leader sequence in such simple complexes but can do so when the 3'-proximal oligoribonucleotide (external guide sequence) is altered to resemble three-quarters of a tRNA molecule. In such a complex, the efficiency of cleavage of the mRNA for chloramphenicol acetyltransferase, as the 5'-proximal oligoribonucleotide, depends on the structural details of the external guide sequence and on the choice of target site within the mRNA. The presence of the appropriately designed external guide sequence in cells in tissue culture reduces chloramphenicol acetyltransferase activity and the level of the corresponding intact mRNA in the cells. Thus, it appears that the use of such external guide sequences may provide a general technique for gene inactivation.
Prostaglandins in the pathogenesis of food intolerance. (1983)

Prostaglandins appear to have cytoprotective effects in the upper bowel and are released in increased amounts in patients with abnormal peristalsis and diarrhea. Drugs which interfere with prostaglandin (PG) synthesis often prevent the symptoms of food intolerance and have been reported as improving food-related symptoms in the irritable bowel syndrome.
Increasing the Acetyl-CoA Pool in the Presence of Overexpressed Phosphoenolpyruvate Carboxylase or Pyruvate Carboxylase Enhances Succinate Production in Escherichia coli (2004)

An in vivo strategy to apply the activation effect of acetyl-CoA on phosphoenolpyruvate carboxylase (PEPC) and pyruvate carboxylase (PYC) to increase succinate production in Escherichia coli was studied. This approach relies on the increased intracellular acetyl-CoA and CoA levels by overexpressing E. coli pantothenate kinase (PANK). The results showed that coexpression of PANK and PEPC, and PANK and PYC, did improve succinate production compared to the individual expression of PEPC and PYC, respectively. The intracellular acetyl-CoA and CoA levels were also measured, and each showed a significant increase when the PANK was overexpressed. Another effect observed was a decrease in lactate production. The least amount of lactate was produced when PANK and PEPC, and PANK and PYC, were coexpressed. This result showed increased competitiveness of the succinate pathway at the phosphoenolpyruvate and pyruvate nodes for the carbon flux, as a result reducing the carbon flux toward the lactate pathway. The study also demonstrates a feasible method for metabolic engineering to modulate enzyme activity in vivo through specific activators and inhibitors.
Impact of Sequence Variation in the UL128 Locus on Production of Human Cytomegalovirus in Fibroblast and Epithelial Cells (2013)

The human cytomegalovirus (HCMV) virion envelope contains a complex consisting of glycoproteins gH and gL plus proteins encoded by the UL128 locus (UL128L): pUL128, pUL130, and pUL131A. UL128L is necessary for efficient infection of myeloid, epithelial, and endothelial cells but limits replication in fibroblasts. Consequently, disrupting mutations in UL128L are rapidly selected when clinical isolates are cultured in fibroblasts. In contrast, bacterial artificial chromosome (BAC)-cloned strains TB40-BAC4, FIX, and TR do not contain overt disruptions in UL128L, yet no virus reconstituted from them has been reported to acquire mutations in UL128L in vitro. We performed BAC mutagenesis and reconstitution experiments to test the hypothesis that these strains contain subtle mutations in UL128L that were acquired during passage prior to BAC cloning. Compared to strain Merlin containing wild-type UL128L, all three strains produced higher yields of cell-free virus. Moreover, TB40-BAC4 and FIX spread cell to cell more rapidly than wild-type Merlin in fibroblasts but more slowly in epithelial cells. The differential growth properties of TB40-BAC4 and FIX (but not TR) were mapped to single-nucleotide substitutions in UL128L. The substitution in TB40-BAC4 reduced the splicing efficiency of UL128, and that in FIX resulted in an amino acid substitution in UL130. Introduction of these substitutions into Merlin dramatically increased yields of cell-free virus and increased cell-to-cell spread in fibroblasts but reduced the abundance of pUL128 in the virion and the efficiency of epithelial cell infection. These substitutions appear to represent mutations in UL128L that permit virus to be propagated in fibroblasts while retaining epithelial cell tropism.
Nanoparticle Assembly of Mesoporous AlOOH (Boehmite) (2002)

The first examples of a new mesoporous form of crystalline AlOOH (boehmite) were prepared using aluminum sec-butoxide as the alumina precursor and an amine surfactant as a hierarchical structure director. The hydrolysis of the alkoxide in the presence of various amine surfactants at ambient temperature afforded boehmite−surfactant nanocomposites, denoted MSU−S/B. TEM images of the as-made nanocomposites indicated the presence of a scaffold-like structure formed through the aggregation and intergrowth of boehmite nanofibers. Thermal treatment of the nanocomposite at 325 °C topochemically removed the surfactant component and afforded a surfactant-free boehmite phase, denoted MSU−B, with retention of the scaffold structure. The surface areas of the MSU−B products prepared at AlOOH:surfactant mass ratios of 1:1 were 1.27−1.43 times as large as the surface area obtained for boehmite prepared under equivalent hydrolysis conditions in the absence of an amine structure modifier. No correlation was found between the mesostructure pore size and the size of the structure-directing surfactant, which is consistent with a hierarchical scaffold structure formed through the assembly of nanoparticles of more or less uniform size. Both the surfactant−boehmite MSU−S/B nanocomposite and the surfactant-free MSU−B boehmite phase could be converted to mesostructured γ-Al2O3 through calcination at 500 °C. Substantially higher surface areas and pore volumes were obtained for the γ-Al2O3 phases derived from the nanocomposite, indicating that the surfactant mediates nanoparticle assembly even during the topochemical transformation of mesostructured boehmite to γ-Al2O3.
Transfectant Influenza A Viruses with Long Deletions in the NS1 Protein Grow Efficiently in Vero Cells (1998)

We established a reverse genetics system for the nonstructural (NS) gene segment of influenza A virus. This system is based on the use of the temperature-sensitive (ts) reassortant virus 25A-1. The 25A-1 virus contains the NS gene from influenza A/Leningrad/134/57 virus and the remaining gene segments from A/Puerto Rico (PR)/8/34 virus. This particular gene constellation was found to be responsible for the ts phenotype. For reverse genetics of the NS gene, a plasmid-derived NS gene from influenza A/PR/8/34 virus was ribonucleoprotein transfected into cells that were previously infected with the 25A-1 virus. Two subsequent passages of the transfection supernatant at 40 degreesC selected viruses containing the transfected NS gene derived from A/PR/8/34 virus. The high efficiency of the selection process permitted the rescue of transfectant viruses with large deletions of the C-terminal part of the NS1 protein. Viable transfectant viruses containing the N-terminal 124, 80, or 38 amino acids of the NS1 protein were obtained. Whereas all deletion mutants grew to high titers in Vero cells, growth on Madin-Darby canine kidney (MDCK) cells and replication in mice decreased with increasing length of the deletions. In Vero cells expression levels of viral proteins of the deletion mutants were similar to those of the wild type. In contrast, in MDCK cells the level of the M1 protein was significantly reduced for the deletion mutants.
Identification of Yeast Rho1p GTPase as a Regulatory Subunit of 1,3-β-Glucan Synthase (1996)

1,3-beta-D-glucan synthase [also known as beta(1-->3) glucan synthase] is a multi-enzyme complex that catalyzes the synthesis of 1,3-beta-linked glucan, a major structural component of the yeast cell wall. Temperature-sensitive mutants in the essential Rho-type guanosine triphosphatase (GTPase), Rho1p, displayed thermolabile glucan synthase activity, which was restored by the addition of recombinant Rho1p. Glucan synthase from mutants expressing constitutively active Rho1p did not require exogenous guanosine triphosphate for activity. Rho1p copurified with beta(1-->3)glucan synthase and associated with the Fks1p subunit of this complex in vivo. Both proteins were localized predominantly at sites of cell wall remodeling. Therefore, it appears that Rho1p is a regulatory subunit of beta(1-->3)glucan synthase.