gebhart/patrepeval huggingface dataset:
Issues in Testing Dependable Event-Based Systems at a Systems Integration Company (2007)

Testing of dependable event-based systems is very important to ensure that all requirements (including nonfunctional requirements such as reliability, availability, safety and security) are met and the relevant standards are considered. Siemens Program and Systems Engineering is a company that builds dependable event-based systems in multiple domains. A special unit at PSE, the Support Center Test, focuses on testing issues. In this paper we provide an overview of the state-of-the-practice in testing dependable event-based systems and identify the challenges that have to be addressed in the future. We illustrate our findings by two case studies, one for a transportation system and one for telecommunications. The top three topics for improvement are: testability and requirements tracing, generation of test cases, and verification and validation
The Mechanism of Enzyme-catalyzed Reduced Nicotinamide Adenine Dinucleotide-dependent Reductions (1972)

Abstract Yeast alcohol dehydrogenase has been found to catalyze the reduction of a series of para-substituted benzaldehydes at markedly different rates. By steady state kinetic analysis, values of kh and kd have been obtained for yeast alcohol dehydrogenase reduction of p-Br-, p-Cl-, H-, p-CH3, p-CH3O-benzaldehyde by reduced nicotinamide adenine dinucleotide (NADH) and reduced nicotinamide adenine dinucleotide with deuterium in the nicotinamide 4-A position (NADD). Hammett plots of log kh and log kd versus σ+ are linear with p = 2.17 and 2.24, respectively. Since the p values are almost the same for both NADH and NADD reduction, the difference in the intercept of the two Hammett plots gives the value of the kinetic isotope effect, kh:kd = 3.6. The significance of the sign and magnitude of these p values is discussed and shown to be consistent with a direct hydride transfer. The p value for the equilibrium conversion of para-substituted benzaldehydes to their corresponding alcohols was determined to be p = 1.5. The difference between the kinetically determined p and the p for Keq may reflect an enhanced polarization of the carbonyl of the substrate in forming the ternary complex. Consistent with this hypothesis, the association constants of substituted benzaldehydes for binary complex, calculated from the observed isotope effects on the limiting Michaelis constants, were found to increase with electron-donating group (p = -0.85).
Characterization of <i>hapR</i>, a positive regulator of the <i>Vibrio cholerae</i> HA/protease gene <i>hap</i>, and its identification as a functional homologue of the <i>Vibrio harveyi luxR</i> gene (1997)

The Vibrio cholerae HA/protease gene (hap) promoter is inactive in Escherichia coli. We cloned and sequenced the 0.7kb hap promoter fragment from strain 3083-2 and showed that hap is located immediately 3' of ompW, encoding a minor outer membrane protein. A clone from a genomic library of strain 3083-2 was isolated, which was required for activation of the hap promoter in E. coli. Expression from the hap promoter only occurred late in the growth phase. A single complete open reading frame (ORF) designated HapR was identified on a 1.7 kb DNA fragment that was required for activation. Allelic replacements showed that hapR was also essential for hap expression in V. cholerae. In El Tor, but not in classical biotypes of V. cholerae, hapR mutations also produced a rugose colonial phenotype. HapR was shown to encode a 203-amino-acid polypeptide with 71% identity to LuxR of V. harveyi, an essential positive regulator of the lux operon that has no previously identified homologues. The amino-terminal domain (residues 21-68) showed significant homology to the TetR family of helix-turn-helix DNA-binding domains and was 95% identical to the same domain of LuxR. HapR and LuxR activated both the hap and the lux promoters at near wild-type levels, despite only limited homology in the promoter sequences (46% identity with 12 gaps over 420bp). DNA sequences and ORFs 5' (but not 3') of the hapR and luxR loci were homologous, suggesting a common origin for these loci, and hapR-hybridizing sequences were found in other vibrios. We conclude that HapR is absolutely required for hap expression and that HapR and LuxR form a new family of transcriptional activator proteins.
Thermal expansion, normalized thermo-optic coefficients, and condition for second harmonic generation of a Nd:YAG laser with wide temperature bandwidth in RbTiOPO_4 (2011)

Interferometric determination of thermal expansion and of normalized thermo-optic coefficients of RbTiOPO4 at four laser wavelengths are performed as a function of temperature. A suitable vectorial formalism applied to obtained data allows the establishment of the temperature dependence of refractive indices, and subsequent theoretical analysis enables one to predict that an extremum in the evolution of the phase-matching direction in the (X,Y) plane should occur near 100 °C for type II second harmonic generation of Nd:YAG lasers, with a temperature bandwidth that can be as large as 117 °C for a crystal of 10 mm in length. Such unusual behavior is observed experimentally by recording the conversion efficiency from 20 °C up to 220 °C for various propagation angles of light in the (X,Y) plane. Slight quadratic temperature dependence of the effective nonlinear coefficient is also observed.
Double-stage, integrated, acousto-optical add-drop multiplexers with improved crosstalk performance (1997)

A new type of integrated acousto-optical add-drop multiplexer in LiNbO 3 has been developed combining four acousto-optical mode converters and four polarization splitters. The pigtailed device yields high extinction (>25 dB) and neglectable crosstalk between add- and drop signals.
Novel candidate targets of beta-catenin/T-cell factor signaling identified by gene expression profiling of ovarian endometrioid adenocarcinomas. (2003)

The activity of beta-catenin (beta-cat), a key component of the Wnt signaling pathway, is deregulated in about 40% of ovarian endometrioid adenocarcinomas (OEAs), usually as a result of CTNNB1 gene mutations. The function of beta-cat in neoplastic transformation is dependent on T-cell factor (TCF) transcription factors, but specific genes activated by the interaction of beta-cat with TCFs in OEAs and other cancers with Wnt pathway defects are largely unclear. As a strategy to identify beta-cat/TCF transcriptional targets likely to contribute to OEA pathogenesis, we used oligonucleotide microarrays to compare gene expression in primary OEAs with mutational defects in beta-cat regulation (n = 11) to OEAs with intact regulation of beta-cat activity (n = 17). Both hierarchical clustering and principal component analysis based on global gene expression distinguished beta-cat-defective tumors from those with intact beta-cat regulation. We identified 81 potential beta-cat/TCF targets by selecting genes with at least 2-fold increased expression in beta-cat-defective versus beta-cat regulation-intact tumors and significance in a t test (P < 0.05). Seven of the 81 genes have been previously reported as Wnt/beta-cat pathway targets (i.e., BMP4, CCND1, CD44, FGF9, EPHB3, MMP7, and MSX2). Differential expression of several known and candidate target genes in the OEAs was confirmed. For the candidate target genes CST1 and EDN3, reporter and chromatin immunoprecipitation assays directly implicated beta-cat and TCF in their regulation. Analysis of presumptive regulatory elements in 67 of the 81 candidate genes for which complete genomic sequence data were available revealed an apparent difference in the location and abundance of consensus TCF-binding sites compared with the patterns seen in control genes. Our findings imply that analysis of gene expression profiling data from primary tumor samples annotated with detailed molecular information may be a powerful approach to identify key downstream targets of signaling pathways defective in cancer cells.
Probability of Error and Capacity of Multipolarization Antenna Systems for Downlink Mobile Communications (2006)

A theoretical channel model is proposed to study the probability of error and channel capacity of multipolarization antenna systems for downlink mobile communications. The effect of scattering on polarization is first studied based on Fresnel reflection law. Expressions for correlation between antennas at both sides are derived for different polarizations. To simplify the analysis, it is assumed that there is only a single reflection and the path angular spread at the base station is approximately zero. Next, the probability of error and channel capacity are studied numerically for different antenna configurations. The impact of scattering environment on performance is also investigated. It is found that when a three-branch orthogonal structure is used for diversity at the mobile station, the error probability is invariant to receiver orientations, and the improvement is insignificant for more receive antennas. At the base station, both probability of error and channel capacity are substantially improved by using two transmit antennas that produce orthogonal polarizations in the direction of the mobile station, and the performance is invariant to rotations of the two transmit antennas. In addition, for almost all configurations, the performance becomes better in general for larger angular spread of reflectors.
Multistage continuous cultivation of blue‐green alga spirulina maxima in the flat tank photobioreactors with recycle (1985)

Abstract Spirulina maxima was continuously cultivated in four 64‐liter flat tank photobioreactors in cascade, under continuous 30 klx fluorescent light and nonaseptic condition, in an industrial grade synthetic medium which bubbled with atmospheric air. The increase in the number of stages resulted in the higher biomass concentration and allowed operation with a dilution rate D higher than the alga specific growth rate μ. However, multistage operation does not permit a significant increase in productivity. The recycling of the all culture medium with biomass increased the net productivity of the first two stages of the multistage system. The flat tank design offered great advantages over other geometrical configurations by occupying less space for indoor cultivation, minimizing the water loss by evaporation, and permitting a greater flexibility in construction, installation, and operation. This system was operating continuously for two years in our laboratory for indoor mass production of S. maxima biomass. The flat tank configuration gave the highest areal productivity Pa = 60.5 g/m 2 ·d and highest volumetric productivity Pv = 1.17 g/L·d when operated as a single stage continuous cultivation with high solid recycle. These values are the highest ever reported for any indoor or outdoor mass production system for S. maxima.
Manipulation of nanoscale V-pits to optimize internal quantum efficiency of InGaN multiple quantum wells (2015)

We systematically investigated the influence of nanoscale V-pits on the internal quantum efficiency (IQE) of InGaN multiple quantum wells (MQWs) by adjusting the underlying superlattices (SLS). The analysis indicated that high barrier energy of sidewall MQWs on V-pits and long diffusion distance between the threading dislocation (TD) center and V-pit boundary were crucial to effectively passivate the non-radiative centers of TDs. For a larger V-pit, the thicker sidewall MQW on V-pit would decrease the barrier energy. On the contrary, a shorter distance between the TD center and V-pit boundary would be observed in a smaller V-pit, which could increase the carrier capturing capability of TDs. An optimized V-pit size of approximately 200–250 nm in our experiment could be concluded for MQWs with 15 pairs SLS, which exhibited an IQE value of 70%.
Modified MPEG-2 video coders with efficient multi-layer scalability (2002)

The paper describes a multi-layer video coder based on spatiotemporal scalability and data partitioning. The coder consists of two parts: a low-resolution coder and full-resolution coder. The first one encodes pictures with reduced spatial and temporal resolution. The data are partitioned into some base layers with fine granularity. The full-resolution encoder exploits interpolated images from the base layers. Here, again the output data can be partitioned into some layers. For the two-layer system, the bitrate overhead measured relative to the single layer MPEG-2 bitstream varies about 10% - 25% for progressive television test sequences. Further layers are related to bitrate overheads of about 3% per layer. The coder structure exhibits high level of compatibility with individual building blocks of MPEG-2 coders.
Enkephalin systems in diencephalon and brainstem of the rat (1983)

The immunocytochemical distribution of [Leu]enkephalin and an adrenal enkephalin precursor fragment (BAM-22P) immunoreactivity was investigated in the diencephalon and brainstem of rats pretreated with relatively high doses of colchicine (300-400 micrograms/10 microliters intracerebroventricularly). The higher ranges of colchicine pretreatment allowed the visualization of extensive enkephalin-containing systems in these brain regions, some of which are reported for the first time. Immunoreactive perikarya were found in many hypothalamic and thalamic nuclei, interpeduncular nucleus, substantia nigra, the colliculi, periaqueductal gray, parabrachial nuclei, trigeminal motor and spinal nuclei, nucleus raphe magnus and other raphe nuclei, nucleus reticularis paragigantocellularis, vestibular nuclei, several noradrenergic cell groups, nucleus tractus solitarius, as well as in the spinal cord dorsal horn. In addition to the above regions, immunoreactive fibers were also noted in the habenular nuclei, trigeminal sensory nuclei, locus coeruleus, motor facial nucleus, cochlear nuclei, dorsal motor nucleus of the vagus, and hypoglossal nucleus. When adjacent sections of those stained for [Leu]enkephalin were processed for BAM-22P immunoreactivity, it was found that these two immunoreactivities were distributed identically at almost all anatomical locations. BAM-22P immunoreactivity was generally less pronounced and ws preferentially localized to neuronal perikarya. The results of the present as well as the preceding studies (Khachaturian et al., '83) strongly suggest substantial structural similarity between the adrenal proenkephalin precursor and that which occurs in the brain. Also discussed are some differences and parallels between the distribution of [Leu]enkephalin and dynorphin immunoreactivities.
The base dopant out diffusion and the optimized setback layers in SiGe HBT (2002)

The influences of the base dopant out-diffusion on SiGe HBT electrical characteristics are simulated numerically by ISE-TCAD software; at the some time, the action of the setback layers and difference between SiGe and Si setback layers are also simulated numerically. The simulation results indicated that the optimized width of SiGe and Si intrinsic setback layers are equal to and less than the length of the base dopant out-diffusion respectively. Finally, the model are confirmed by the experiment.
Transcriptome-wide distribution and function of RNA hydroxymethylcytosine (2016)

Hydroxymethylcytosine, well described in DNA, occurs also in RNA. Here, we show that hydroxymethylcytosine preferentially marks polyadenylated RNAs and is deposited by Tet in Drosophila. We map the transcriptome-wide hydroxymethylation landscape, revealing hydroxymethylcytosine in the transcripts of many genes, notably in coding sequences, and identify consensus sites for hydroxymethylation. We found that RNA hydroxymethylation can favor mRNA translation. Tet and hydroxymethylated RNA are found to be most abundant in the Drosophila brain, and Tet-deficient fruitflies suffer impaired brain development, accompanied by decreased RNA hydroxymethylation. This study highlights the distribution, localization, and function of cytosine hydroxymethylation and identifies central roles for this modification in Drosophila.
Novel 4′-Substituted Stavudine Analog with Improved Anti-Human Immunodeficiency Virus Activity and Decreased Cytotoxicity (2004)

The antiviral drug 2',3'-didehydro-3'-deoxythymidine (D4T; also know as stavudine and Zerit), which is used against human immunodeficiency virus (HIV), causes delayed toxicity (peripheral neuropathy) in long-term use. After examining a series of 2',3'-didehydro-3'-deoxy-4'-substituted thymidine (4'-substituted D4T) analogs, 4'-ethynyl D4T was found to have a fivefold-better antiviral effect and to cause less cellular and mitochondrial toxicity than D4T. The antiviral activity of this compound can be reversed by dThd but not by dCyd. The compound acted synergistically with beta-L-2',3'-deoxy-3'-thiacytidine (also known as lamivudine) and beta-L-2',3'-dideoxy-2',3'-didehydro-5-fluorocytidine (also known as elvucitabine) and additively with 2',3'-dideoxyinosine (also known as didanosine and Videx) and 3'-azido-3'-deoxythymidine (also known as Retovir and zidovudine) against HIV. 4'-Ethynyl D4T is phosphorylated by purified human thymidine kinase 1 (TK-1) from CEM cells with a faster relative V(max) and a lower K(m) value than D4T. The efficiency of TK-1 in the phosphorylation of 4'-ethynyl D4T is fourfold better than that of D4T. While D4T is broken down by the catabolic enzyme thymidine phosphorylase, the level of breakdown of 4'-ethynyl D4T was below detection. Since 4'-ethynyl D4T has increased anti-HIV activity and decreased toxicity and interacts favorably with other currently used anti-HIV drugs, it should be considered for further development as an anti-HIV drug.
Flurbiprofen axetil promotes neuroprotection by activation of cerebral peroxisome proliferator-activated receptor gamma after focal cerebral ischemia in rats. (2012)

FA confers the neuroprotective effect on tMCAO in rats and the selective PPAR-γ antagonist GW9662 attenuates the effect of FA. FA could promote a neuroprotective effect by, or in part, activation of PPAR-γ after focal cerebral ischemia in rats.
Low-Cost Spark Plug-Integrated Fiber Optic Sensor for Combustion Pressure Monitoring (1993)

<div class="htmlview paragraph">A fiber optic in-cylinder combustion pressure sensor system design is presented that exhibits the necessary operation and cost characteristics required for combustion pressure-based engine control applications. The sensor system consists of a small, spark plug-integrated, rugged, and high temperature operable sensor head; a low cost optoelectronic transceiver including LEDs, photodiodes, and simple optical couplers; and a DSP-based signal processing circuitry intended for future ASIC integration. A theoretical approach is developed to predict sensor response and signal-to-noise performance. The agreement between theoretical analysis and experimental results demonstrates that the present low cost system design results in required signal-to-noise performance and provides pressure measurement accuracies better than 5%. Engine tests performed with the fiber optic sensors demonstrate signal-to-noise performance comparable to instrumentation grade piezoelectric combustion pressure transducers as well as better temperature stability. The fiber optic pressure sensor can readily detect engine misfire and mis-timing of spark advance.</div>
An Efficient Localization Scheme for a Differential-Driving Mobile Robot Based on RFID System (2007)

This paper presents an efficient localization scheme for an indoors mobile robot using Radio-Frequency IDentification (RFID) systems. The mobile robot carries an RFID reader at the bottom of the chassis, which reads the RFID tags on the floor to localize the mobile robot. Each of the RFID tags stores its own absolute position, which is used to calculate the position, orientation, and velocity of the mobile robot. However, a localization system based on RFID technology inevitably suffers from an estimation error. In this paper, a new triangular pattern of arranging the RFID tags on the floor has been proposed to reduce the estimation error of the conventional square pattern. In addition, the motion-continuity property of the differential-driving mobile robot has been utilized to improve the localization accuracy of the mobile robot. According to the conventional approach, two readers are necessary to identify the orientation of the mobile robot. Therefore, this new approach, based on the motion-continuity property of the differential-driving mobile robot, provides a cheap and fast estimation of the orientation. The proposed algorithms used to raise the accuracy of the robot localization are successfully verified through experiments.
Cloning gibberellin dioxygenase genes from pumpkin endosperm by heterologous expression of enzyme activities in <i>Escherichia coli</i> (1997)

Gibberellin (GA) plant hormones are biosynthesized via complex pathways, the final steps of which are catalyzed by 2-oxoglutarate-dependent dioxygenases. Here, the cloning of two such enzymes, the GA 7-oxidase and the GA 20-oxidase, is reported using a novel approach, namely, by screening for GA dioxygenase activities expressed as T7 gene 10 fusion proteins in recombinant Escherichia coli. In vitro translation products of mRNA from endosperm of immature pumpkin seeds contained three GA dioxygenase activities, including 7-oxidase, 20-oxidase, and 3beta-hydroxylase. A cDNA expression library was prepared from the endosperm mRNA in lambdaMOSElox. An aliquot of the amplified library was converted to plasmids in vivo and used for transformation of E. coli BL21(DE3), which thereafter expressed recombinant fusion proteins containing 7-oxidase, 20-oxidase, and 3beta-hydroxylase activities. By screening for specific GA dioxygenase expression, clones harboring 7-oxidase and 20-oxidase cDNA were isolated. The ORF of the 7-oxidase cDNA is 945 bp long, encoding for 314 amino acid residues with a calculated Mr of 35,712 and pI of 5.7. Recombinant GA 7-oxidase oxidizes GA12-aldehyde to GA12 and GA14-aldehyde to GA14. Evidence was obtained for further metabolism of GA12 by the 7-oxidase to four products, two of which are monohydroxylated GA12. The ORF of the 20-oxidase is-apart from seven changes, resulting in four amino acid substitutions-identical to the 20-oxidase cDNA previously cloned from pumpkin cotyledon mRNA; both 20-oxidases have the same catalytic properties.
Micro-nanopores Fabricated by High-Energy Electron Beam Irradiation: Suitable Structure for Controlling Pesticide Loss (2013)

Pesticide sprayed onto crop leaves tends to be washed off by rainwater and discharge into the environment through leaching and runoff, resulting in severe pollution to both soil and water. Here, to control pesticide loss, we developed a loss-control pesticide (LCP) by adding modified natural nanoclay (diatomite) through high-energy electron beam (HEEB) to traditional pesticide. After HEEB treatment, the originally clogged pores in diatomite opened, resulting in plenty of micro-nanopores in diatomite, which are beneficial for the pesticide molecules to access and be adsorbed. This pesticide-diatomite complex tended to be retained by the rough surface of crop leaves, displaying a high adhesion performance onto the leaves, so that the pesticide loss reduced, sufficient pesticide for crops was supplied, and the pollution risk of the pesticide could be substantially lowered.