gebhart/patrepeval huggingface dataset:
Static Analysis of Shape in TensorFlow Programs (2016)

Machine learning has been widely adopted in diverse science and engineering domains, aided by reusable libraries and quick development patterns. The TensorFlow library is probably the best-known representative of this trend and most users employ the Python API to its powerful back-end. TensorFlow programs are susceptible to several systematic errors, especially in the dynamic typing setting of Python. We present Pythia, a static analysis that tracks the shapes of tensors across Python library calls and warns of several possible mismatches. The key technical aspects are a close modeling of library semantics with respect to tensor shape, and an identification of violations and error-prone patterns. Pythia is powerful enough to statically detect (with 84.62% precision) 11 of the 14 shape-related TensorFlow bugs in the recent Zhang et al. empirical study - an independent slice of real-world bugs.
Sulfide dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus: a new multifunctional enzyme involved in the reduction of elemental sulfur (1994)

Pyrococcus furiosus is an anaerobic archaeon that grows optimally at 100 degrees C by the fermentation of carbohydrates yielding acetate, CO2, and H2 as the primary products. If elemental sulfur (S0) or polysulfide is added to the growth medium, H2S is also produced. The cytoplasmic hydrogenase of P. furiosus, which is responsible for H2 production with ferredoxin as the electron donor, has been shown to also catalyze the reduction of polysulfide to H2S (K. Ma, R. N. Schicho, R. M. Kelly, and M. W. W. Adams, Proc. Natl. Acad. Sci. USA 90:5341-5344, 1993). From the cytoplasm of this organism, we have now purified an enzyme, sulfide dehydrogenase (SuDH), which catalyzes the reduction of polysulfide to H2S with NADPH as the electron donor. SuDH is a heterodimer with subunits of 52,000 and 29,000 Da. SuDH contains flavin and approximately 11 iron and 6 acid-labile sulfide atoms per mol, but no other metals were detected. Analysis of the enzyme by electron paramagnetic resonance spectroscopy indicated the presence of four iron-sulfur centers, one of which was specifically reduced by NADPH. SuDH has a half-life at 95 degrees C of about 12 h and shows a 50% increase in activity after 12 h at 82 degrees C. The pure enzyme has a specific activity of 7 mumol of H2S produced.min-1.mg of protein-1 at 80 degrees C with polysulfide (1.2 mM) and NADPH (0.4 mM) as substrates. The apparent Km values were 1.25 mM and 11 microM, respectively. NADH was not utilized as an electron donor for polysulfide reduction. P. furiosus rubredoxin (K(m) = 1.6 microM) also functioned as an electron acceptor for SuDH, and SuDH catalyzed the reduction of NADP with reduced P. furiosus ferredoxin (K(m) = 0.7 microM) as an electron donor. The multiple activities of SuDH and its proposed role in the metabolism of S(o) and polysulfide are discussed.
Physiological function of the Pseudomonas putida PpG6 (Pseudomonas oleovorans) alkane hydroxylase: monoterminal oxidation of alkanes and fatty acids (1975)

Pseudomonas putida PpG6 is able to utilize purified n-alkanes of six to ten carbon atoms for growth. It can also grow on the primary terminal oxidation products of these alkanes and on 1-dodecanol but not on the corresponding 2-ketones or 1,6-hexanediol, adipic acid, or pimelic acid. Revertible point mutants can be isolated which have simultaneously lost the ability to grow on all five n-alkane growth substrates but which can still grow on octanol or nonanol. An acetate-negative mutant defective in isocitrate lysase activity is unable to grow on even-numbered alkanes and fatty acids. Analysis of double mutants defective in acetate and propionate or in acetate and glutarate metabolism shows that alkane carbon is assimilated only via acetyl-coenzyme A and propionyl-coenzyme A. These results support the following conclusions: (i) The n-alkane growth specificity of P. putida PpG6 is due to the substrate specificity of whole-cell alkane hydroxylation; (ii) there is a single alkane hydroxylase enzyme complex; (iii) the physiological role of this complex is to initiate the monoterminal oxidation of alkane chains; and (iv) straight-chain fatty acids from butyric through nonanoic are degraded exclusively by beta-oxidation from the carboxyl end of the molecule.
Anti-Human Immunodeficiency Virus Type 1 Activity, Intracellular Metabolism, and Pharmacokinetic Evaluation of 2′-Deoxy-3′-Oxa-4′-Thiocytidine (1999)

The racemic nucleoside analogue 2'-deoxy-3'-oxa-4'-thiocytidine (dOTC) is in clinical development for the treatment of human immunodeficiency virus (HIV) type 1 (HIV-1) infection. dOTC is structurally related to lamivudine (3TC), but the oxygen and sulfur in the furanosyl ring are transposed. Intracellular metabolism studies showed that dOTC is phosphorylated within cells via the deoxycytidine kinase pathway and that approximately 2 to 5% of dOTC is converted into the racemic triphosphate derivatives, which had measurable half-lives (2 to 3 hours) within cells. Both 5'-triphosphate (TP) derivatives of dOTC were more potent than 3TC-TP at inhibiting HIV-1 reverse transcriptase (RT) in vitro. The K(i) values for dOTC-TP obtained against human DNA polymerases alpha, beta, and gamma were 5,000-, 78-, and 571-fold greater, respectively, than those for HIV RT (28 nM), indicating a good selectivity for the viral enzyme. In culture experiments, dOTC is a potent inhibitor of primary isolates of HIV-1, which were obtained from antiretroviral drug-naive patients as well as from nucleoside therapy-experienced (3TC- and/or zidovudine [AZT]-treated) patients. The mean 50% inhibitory concentration of dOTC for drug-naive isolates was 1.76 microM, rising to only 2.53 and 2.5 microM for viruses resistant to 3TC and viruses resistant to 3TC and AZT, respectively. This minimal change in activity is in contrast to the more dramatic changes observed when 3TC or AZT was evaluated against these same viral isolates. In tissue culture studies, the 50% toxicity levels for dOTC, which were determined by using [(3)H]thymidine uptake as a measure of logarithmic-phase cell proliferation, was greater than 100 microM for all cell lines tested. In addition, after 14 days of continuous culture, at concentrations up to 10 microM, no measurable toxic effect on HepG2 cells or mitochondrial DNA replication within these cells was observed. When administered orally to rats, dOTC was well absorbed, with a bioavailability of approximately 77%, with a high proportion (approximately 16.5% of the levels in serum) found in the cerebrospinal fluid.
Human Monoclonal Antibodies againstPseudomonas aeruginosaLipopolysaccharide Derived from Transgenic Mice Containing Megabase Human Immunoglobulin Loci Are Opsonic and Protective against Fatal Pseudomonas Sepsis (2001)

Pseudomonas aeruginosa is a significant human pathogen, and no vaccine is commercially available. Passive antibody prophylaxis using monoclonal antibodies (MAb) against protective P. aeruginosa epitopes is an alternative strategy for preventing P. aeruginosa infection, but mouse MAb are not suitable for use in humans. Polyclonal human antibodies from multiple donors have variable antibody titers, and human MAb are difficult to make. We used immunoglobulin-inactivated transgenic mice reconstituted with megabase-size human immunoglobulin loci to generate a human MAb against the polysaccharide (PS) portion of the lipopolysaccharide O side chain of a common pathogenic serogroup of P. aeruginosa, 06ad. The anti-PS human immunoglobulin G2 MAb made from mice immunized with heat-killed P. aeruginosa was specific for serogroup 06ad pseudomonas. The MAb was highly opsonic for the uptake and killing of P. aeruginosa by human polymorphonuclear leukocytes in the presence of human complement. In addition, 25 microg of the MAb protected 100% of neutropenic mice from fatal P. aeruginosa sepsis. DNA sequence analysis of the genes encoding the MAb revealed V(H)3 and Vkappa2/A2 variable-region genes, similar to variable-region genes in humans immunized with bacterial PS and associated with high-avidity anti-PS antibodies. We conclude that human MAb to P. aeruginosa made in these transgenic mice are highly protective and that these mice mimic the antibody response seen in humans immunized with T-cell-independent antigens such as bacterial PS.
Application-driven sequential designs for simulation experiments: Kriging metamodelling (2004)

This paper proposes a novel method to select an experimental design for interpolation in simulation. Although the paper focuses on Kriging in deterministic simulation, the method also applies to other types of metamodels (besides Kriging), and to stochastic simulation. The paper focuses on simulations that require much computer time, so it is important to select a design with a small number of observations. The proposed method is therefore sequential. The novelty of the method is that it accounts for the specific input/output function of the particular simulation model at hand; that is, the method is application-driven or customized. This customization is achieved through cross-validation and jackknifing. The new method is tested through two academic applications, which demonstrate that the method indeed gives better results than either sequential designs based on an approximate Kriging prediction variance formula or designs with prefixed sample sizes.
Low incidence and high titers of antibodies to hepatitis B virus X‐Protein in sera of chinese patients with hepatocellular carcinoma (1988)

Sera of patients from China with hepatocellular carcinoma (HCC) were tested for the presence of HBc/HBe- and HBx antibodies by immunoblotting using recombinant MS2 or beta gal fusion proteins as substrate. Antibodies against HBx were detected in four out of 68 HBsAg positive and in one out of three HBsAg negative sera, antibodies against HBc/HBe in 52 and two serum samples, respectively. Competition experiments in which sera were preincubated with individual viral proteins synthesized in E. coli were carried out to demonstrate the specificity of signals obtained in immunoblot analyses. In the five anti-HBx positive sera, the antibody titer against X fusion protein was higher than against core fusion protein and in one of these sera anti-x activity could be demonstrated even at a serum dilution of 1:50,000. These data indicate that X antibodies occur rarely in Chinese patients and are not serodiagnostic for HCC. The high titer of X antibodies in some patients shows that the X protein can be highly immunogenic in vivo. Induction of antibody formation may be triggered by X protein expressed from integrated viral DNA.
Selective hydrogen gas nanosensor using individual ZnO nanowire with fast response at room temperature (2009)

In this work, we report on a single ZnO nanowire-based nanoscale sensor fabricated using focused ion beam (FIB/SEM) instrument. We studied the diameter dependence of the gas response and selectivity of ZnO nanowires (NWs) synthesized by chemical vapor phase growth method. The photoluminescence (PL) measurements were used to determine the deep levels related to defects which are presented in the ZnO nanomaterial as well as to evaluate the effect of thermal treatment in H2 atmosphere on the emission from ZnO nanowires. We show that sample annealed in hydrogen leads to passivation of recombination centers thus modifying the NWs properties. We studied the gas response and selectivity of these ZnO nanowires to H2, NH3, i-Butane, CH4 gases at room temperature. Our results indicated that zinc oxide NWs hold a high promise for nanoscale sensor applications due to its capability to operate at room-temperature and its ability to tune the gas response and selectivity by the defect concentration and the diameter of ZnO nanowire. A method is proposed to reduce the nanosensor's recovery time through the irradiation with an ultraviolet radiation pulse. The sensing mechanisms of ZnO nanowires will be discussed.
Immunofluorescence of Dopamine-Beta-Hydroxylase in Small Intensely Fluorescent Cells of Human Sympathetic Ganglia (1981)

Thoracic and lumbar sympathetic ganglia of human males were investigated using a method for the consecutive demonstration of catecholamines and catecholamine synthesizing enzymes in fluorescence microscopy. In the thoracic ganglion, a minor population of small intensely fluorescent (SIF) cells, identified by glyoxylic-acid-induced fluorescence, exhibited positive indirect immunofluorescence after incubation with antibody to dopamine-beta-hydroxylase (DBH). SIF cells in the lumbar ganglion exclusively stained DBH-negative. The findings indicate the presence of two SIF cell populations in the thoracic ganglia of the human sympathetic trunk, one containing dopamine and the other containing norepinephrine and/or epinephrine. In lumbar ganglia, only dopamine-storing SIF cells appear to be present.
Multiwalled carbon nanotube polymer composites: Synthesis and characterization of thin films (2002)

Abstract The aim of this article was to elucidate the basic relationships between processing conditions and the mechanical and electrical properties of multiwalled carbon nanotube reinforced polymer composites. In conventional chopped fiber reinforced polymer composites, uniform distributions of fibers throughout the matrix are critical to producing materials with superior physical properties. Previous methods have dispersed carbon nanotubes by aggressive chemical modification of the nanotubes or by the use of a surfactant prior to dispersion. 1 , 2 Here, ultrasonic energy was used to uniformly disperse multiwalled nanotubes (MWNTs) in solutions and to incorporate them into composites without chemical pretreatment. Polystyrene (PS) solutions containing MWNTs were cast and spun to yield thin film MWNT composites. The rheology of PS/MWNT suspensions was modeled using the Carreau equation. MWNTs were found to align at the shear rates generated by the spin casting process. The tensile modulus and strain to failure of samples compared well to classical micromechanical models, increasing with MWNT loading. The composite films showed lower strains at the yield stress than neat PS films. The presence of MWNTs at 2.5 vol % fraction approximately doubles the tensile modulus, and transforms the film from insulating to conductive (surface resistivity, ρ, approaching 10 3 Ω/□). © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 84: 2660–2669, 2002
11.GHz GaAs Power MESFET Load-Pull Measurements Utilizing a New Method of Determining Tuner Y Parameters (1979)

A Ioad-pull technique utilizing a new method of determining tuner Y parameters is proposed for huge-signal characterization of microwave power transistors. Large-signal input-output transfer characteristics of an active circuit containing a GaAs FET and an input matching circuit are measured by inserting a microstrip tuner between the active circuit output drain terminal and the 50-Omega load. The microstrip-tuner Y parameters are determined by comparing the dc bias-dependent small-signal S parameter S/sub 22/ of the active circuit and that of the circuit which contains the active circuit and microstrip tuner. The reflection coefficient presented to the active circuit output drain terminal is derived from tuner Y parameters. Optimal load impedances for output power, obtained with this new Ioad-pull technique, are used to design X-band GaAs FET power amplifiers. An 11-GHz power amplifier with a 3000-mu m gate-width FET chip delivers 1-W microwave power output with 4-dB gain in the 500-MHz band.
Enhancement of the activity of phenoxodiol by cisplatin in prostate cancer cells (2009)

Phenoxodiol is a novel isoflav-3-ene, currently undergoing clinical trials, that has a broad in vitro activity against a number of human cancer cell lines. Phenoxodiol alone inhibited DU145 and PC3 in a dose- and time-dependent manner with IC(50) values of 8+/-1 and 38+/-9 microM, respectively. The combination of phenoxodiol and cisplatin was synergistic in DU145, and additive in PC3, as assessed by the Chou-Talalay method. Carboplatin was also synergistic in combination with phenoxodiol in DU145 cells. The activity of the phenoxodiol and cisplatin combination was confirmed in vivo using a DU145 xenograft model in nude mice. Pharmacokinetic data from these mice suggest that the mechanism of synergy may occur through a pharmacodynamic mechanism. An intracellular cisplatin accumulation assay showed a 35% (P<0.05) increase in the uptake of cisplatin when it was combined in a ratio of 1 microM:5 microM phenoxodiol, resulting in a 300% (P<0.05) increase in DNA adducts. Taken together, our results suggest that phenoxodiol has interesting properties that make combination therapy with cisplatin or carboplatin appealing.
MuProp: Unbiased Backpropagation for Stochastic Neural Networks (2015)

Deep neural networks are powerful parametric models that can be trained efficiently using the backpropagation algorithm. Stochastic neural networks combine the power of large parametric functions with that of graphical models, which makes it possible to learn very complex distributions. However, as backpropagation is not directly applicable to stochastic networks that include discrete sampling operations within their computational graph, training such networks remains difficult. We present MuProp, an unbiased gradient estimator for stochastic networks, designed to make this task easier. MuProp improves on the likelihood-ratio estimator by reducing its variance using a control variate based on the first-order Taylor expansion of a mean-field network. Crucially, unlike prior attempts at using backpropagation for training stochastic networks, the resulting estimator is unbiased and well behaved. Our experiments on structured output prediction and discrete latent variable modeling demonstrate that MuProp yields consistently good performance across a range of difficult tasks.
In-vitro activity of lomefloxacin against pathogenic and environmental mycobacteria (1992)

Journal Article In-vitro activity of lomefloxacin against pathogenic and environmental mycobacteria Get access D. K. BANERJEE, D. K. BANERJEE aDepartment of Medical Microbiology, St George's Hospital Medical SchoolLondon SW17 ORE Search for other works by this author on: Oxford Academic PubMed Google Scholar J. FORD, J. FORD aDepartment of Medical Microbiology, St George's Hospital Medical SchoolLondon SW17 ORE Search for other works by this author on: Oxford Academic PubMed Google Scholar S. MARKANDAY S. MARKANDAY bMedical Department, G. D. SearleLane End Road, High Wycombe, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Antimicrobial Chemotherapy, Volume 30, Issue 2, August 1992, Pages 236–238, https://doi.org/10.1093/jac/30.2.236 Published: 01 August 1992
The ErbB2 and ErbB3 receptors and their ligand, neuregulin-1, are essential for development of the sympathetic nervous system (1998)

Neuregulins (NDF, heregulin, GGF ARIA, or SMDF) are EGF-like growth and differentiation factors that signal through tyrosine kinase receptors of the ErbB family. Here, we report a novel phenotype in mice with targeted mutations in the erbB2, erbB3, or neuregulin-1 genes. These three mutations cause a severe hypoplasia of the primary sympathetic ganglion chain. We provide evidence that migration of neural crest cells to the mesenchyme lateral of the dorsal aorta, in which they differentiate into sympathetic neurons, depends on neuregulin-1 and its receptors. Neuregulin-1 is expressed at the origin of neural crest cells. Moreover, a tight link between neuregulin-1 expression, the migratory path, and the target site of sympathogenic neural crest cells is observed. Sympathetic ganglia synthesize catecholamines in the embryo and the adult. Accordingly, catecholamine levels in mutant embryos are severely decreased, and we suggest that the lack of catecholamines contributes to the embryonal lethality of the erbB3 mutant mice. Thus, neuregulin-1, erbB2, and erbB3 are required for the formation of the sympathetic nervous system; the block in development observed in mutant mice is caused by a lack of neural crest precursor cells in the anlage of the primary sympathetic ganglion chain. Together with previous observations, these findings establish the neuregulin signaling system as a key regulator in the development of neural crest cells.
Disulfide structures of highly bridged peptides: A new strategy for analysis (1993)

A new approach is described for analyzing disulfide linkage patterns in peptides containing tightly clustered cystines. Such peptides are very difficult to analyze with traditional strategies, which require that the peptide chain be split between close or adjacent Cys residues. The water-soluble tris-(2-carboxyethyl)-phosphine (TCEP) reduced disulfides at pH 3, and partially reduced peptides were purified by high performance liquid chromatography with minimal thiol-disulfide exchange. Alkylation of free thiols, followed by sequencer analysis, provided explicit assignment of disulfides that had been reduced. Thiol-disulfide exchange occurred during alkylation of some peptides, but correct deductions were still possible. Alkylation competed best with exchange when peptide solution was added with rapid mixing to 2.2 M iodoacetamide. Variants were developed in which up to three alkylating agents were used to label different pairs of thiols, allowing a full assignment in one sequencer analysis. Model peptides used included insulin (three bridges, intra- and interchain disulfides; -Cys.Cys- pair), endothelin and apamin (two disulfides; -Cys.x.Cys- pair), conotoxin GI and isomers (two disulfides; -Cys.Cys- pair), and bacterial enterotoxin (three bridges within 13 residues; two -Cys.Cys- pairs). With insulin, all intermediates in the reduction pathway were identified; with conotoxin GI, analysis was carried out successfully for all three disulfide isomers. In addition to these known structures, the method has been applied successfully to the analysis of several previously unsolved structures of similar complexity. Rates of reduction of disulfide bonds varied widely, but most peptides did not show a strongly preferred route for reduction.
Molecular cloning and tissue expression of porcine β‐defensin‐1 (1998)

Beta-defensins constitute an emerging family of cysteine-rich antimicrobial peptides, which are particularly prominent at mucosal epithelial sites in mammals. Here we report the identification of a novel beta-defensin from porcine tissues, porcine beta-defensin-1 (pBD-1). The cDNA sequence of pBD-1 encoded a 64 amino acid prepro-peptide, which contained the beta-defensin consensus sequence of six invariantly spaced cysteine residues. Northern blot analysis showed that pBD-1 was expressed abundantly in tongue epithelia and that the expression was regulated developmentally. Using RT-PCR, pBD-1 mRNA was detected throughout the respiratory and digestive tracts and also in thymus, spleen, lymph node, brain, liver, kidney, urinary bladder, testis, skin, heart, muscle, bone marrow, peripheral blood neutrophils, alveolar macrophages, and umbilical cord. The wide expression of pBD-1 suggests that this endogenous peptide antibiotic may contribute to both mucosal and systemic host defenses in pigs, which may have implications for the use of porcine tissues and organs in xenotransplantation.
Practical Considerations in Design of Internal Amplification Controls for Diagnostic PCR Assays (2004)

The explosive increase since the beginning of 1990s in the number of publications reporting PCR-based methods for detection or molecular typing of food-borne pathogens has attracted the attention of end-user laboratories.

However, the well recognized difficulties in reproducing published tests due