gebhart/patrepeval huggingface dataset:
Poliovirus RNA-dependent RNA Polymerase (3Dpol) (1999)

We have analyzed the divalent cation specificity of poliovirus RNA-dependent RNA polymerase, 3D(pol). The following preference was observed: Mn(2+) > Co(2+) > Ni(2+) > Fe(2+) > Mg(2+) > Ca(2+) > Cu(2+), and Zn(2+) was incapable of supporting 3D(pol)-catalyzed nucleotide incorporation. In the presence of Mn(2+), 3D(pol) activity was increased by greater than 10-fold relative to that in the presence of Mg(2+). Steady-state kinetic analysis revealed that the increased activity observed in the presence of Mn(2+) was due, primarily, to a reduction in the K(M) value for 3D(pol) binding to primer/template, without any significant effect on the K(M) value for nucleotide. The ability of 3D(pol) to catalyze RNA synthesis de novo was also stimulated approximately 10-fold by using Mn(2+), and the enzyme was now capable of also utilizing a DNA template for primer-independent RNA synthesis. Interestingly, the use of Mn(2+) as divalent cation permitted 3D(pol) activity to be monitored by following extension of 5'-(32)P-end-labeled, heteropolymeric RNA primer/templates. The kinetics of primer extension were biphasic because of the enzyme binding to primer/template in both possible orientations. When bound in the incorrect orientation, 3D(pol) was capable of efficient addition of nucleotides to the blunt-ended duplex; this activity was also apparent in the presence of Mg(2+). In the presence of Mn(2+), 3D(pol) efficiently utilized dNTPs, ddNTPs, and incorrect NTPs. On average, three incorrect nucleotides could be incorporated by 3D(pol). The ability of 3D(pol) to incorporate the correct dNTP, but not the correct ddNTP, was also observed in the presence of Mg(2+). Taken together, these results provide the first glimpse into the nucleotide specificity and fidelity of the poliovirus polymerase and suggest novel alternatives for the design of primer/templates to study the mechanism of 3D(pol)-catalyzed nucleotide incorporation.
Search for ribosomal mutants in<i>Podospora anserina</i>: genetic analysis of cold-sensitive mutants (1980)

SUMMARY Twenty-four cold-sensitive (prototrophic) mutants were isolated after UV mutagenesis of protoplasts of the fungus Podospora anserina . Genetic analysis of these mutants was performed in order to detect those among them which were most likely to be impaired in translational fidelity. The 24 mutations belonged to 24 different genes. One half of the mutants were pleiotropic and displayed an altered phenotype: growth rate at the permissive temperature, germination of the spores, fertility and/or sporulation. Nine mutants differed from wild-type in their resistance levels to cycloheximide, trichodermin and/or paromomycin. Several mutations were linked to known ribosomal loci. Two mutations behaved like informational antisuppressors: one is allelic to the previously described As 3 gene and the other one defines a new antisuppressor gene, AS 6 .
A new approach in insulation systems for rotating machines (2005)

The possibility to increase operating performance and efficiency of an electric machine can be achieved through the improvement or modification of the components of the primary insulating material. Relevant variables in the construction of a machine can be found in the components of the insulating materials and their overall thickness. These components can influence the electric strength and overall service life. In addition, the electrical insulation system dictates the thermal classification and therefore the construction of a machine.
Methods and tools for aerospace operations modeling and simulation: new perspectives towards modeling depot MRO (2002)

There are subtle, and yet critical and unique differences that distinguish the depot maintenance, repair, and overhaul (MRO) domain from production manufacturing. These differences motivate the need for more efficient ways to capture the essence of the depot MRO domain dynamics. The authors provide an informal characterization of the depot MRO by highlighting some of the major differences. Along with this characterization, they propose a set of principles governing the physics of depot MRO operation. Finally, they describe the nature of idealizations needed to model and simulate this domain and a vision for future technologies that could more adequately and directly address these needs.
Central Angiotensin Partially Mediates the Pressor Action of Relaxin in Anesthetized Rats* (1991)

Experiments were conducted to investigate the role of the brain angiotensin system in mediating the pressor effects of porcine relaxin in anesthetized female rats. Continuous intracerebroventricular infusion of a specific angiotensin II receptor antagonist (Sar1-Ala8-angiotensin II) completely negated the pressor response to centrally administered relaxin, but only partially suppressed the increase in blood pressure observed after iv injection of the hormone. These results indicate that the pressor effects of relaxin may be mediated, at least in part, by brain angiotensin. Rats with a compromised central angiotensin system were then treated in combination with a peripheral vasopressin (V1) receptor antagonist. Only after both treatments were the pressor effects of iv relaxin completely negated. These data imply that there is also a significant pressor action of relaxin which is independent of the brain angiotensin system. The most likely alternative is a direct action of relaxin on the neural lobe of the pituitary, to provoke the release of vasopressin.
High power violet laser diodes with crack‐free layers on GaN substrates (2007)

Abstract Nitride based violet laser diodes grown on GaN substrates have been investigated. A grooved substrate, having a striped pattern with a pitch of 400 μm, has been prepared and epitaxial growth has been performed. No cracks have been observed in the epi‐layers. The violet laser device has been fabricated and characterised. At a pulsed output power of 210 mW, the operating current and the voltage have been 164 mA and 6.6 V, respectively. The mean‐time‐to‐failure has been estimated to be over 3000 h under pulsed condition with an output power of 210 mW at 80 °C. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Convolutional neural networks with low-rank regularization (2016)

Abstract: Large CNNs have delivered impressive performance in various computer vision applications. But the storage and computation requirements make it problematic for deploying these models on mobile devices. Recently, tensor decompositions have been used for speeding up CNNs. In this paper, we further develop the tensor decomposition technique. We propose a new algorithm for computing the low-rank tensor decomposition for removing the redundancy in the convolution kernels. The algorithm finds the exact global optimizer of the decomposition and is more effective than iterative methods. Based on the decomposition, we further propose a new method for training low-rank constrained CNNs from scratch. Interestingly, while achieving a significant speedup, sometimes the low-rank constrained CNNs delivers significantly better performance than their non-constrained counterparts. On the CIFAR-10 dataset, the proposed low-rank NIN model achieves $91.31\%$ accuracy (without data augmentation), which also improves upon state-of-the-art result. We evaluated the proposed method on CIFAR-10 and ILSVRC12 datasets for a variety of modern CNNs, including AlexNet, NIN, VGG and GoogleNet with success. For example, the forward time of VGG-16 is reduced by half while the performance is still comparable. Empirical success suggests that low-rank tensor decompositions can be a very useful tool for speeding up large CNNs.
Complete Lipopolysaccharide of <i>Plesiomonas shigelloides</i> O74:H5 (Strain CNCTC 144/92). 2. Lipid A, Its Structural Variability, the Linkage to the Core Oligosaccharide, and the Biological Activity of the Lipopolysaccharide<sup>,</sup> (2006)

Plesiomonas shigelloides is a Gram-negative bacterium associated with waterborne infections, which is common in tropical and subtropical habitats. Contrary to the unified antigenic classification of P. shigelloides, data concerning the structure and activity of their lipopolysaccharides (LPS and endotoxin) are limited. This study completes the structural investigation of phenol- and water-soluble fractions of P. shigelloides O74 (strain CNCTC 144/92) LPS with the emphasis on lipid A heterogeneity, describing the entire molecule and some of its biological in vitro activities. Structures of the lipid A and the affinity-purified decasaccharide obtained by de-N,O-acylation of P. shigelloides O74 LPS were elucidated by chemical analysis combined with electrospray ionization multiple-stage mass spectrometry (ESI-MS(n)), MALDI-TOF MS, and NMR spectroscopy. Lipid A of P. shigelloides O74 is heterogeneous, and three major forms have been identified. They all were asymmetric, phosphorylated, and hexaacylated, showing different acylation patterns. The beta-GlcpN4P-(1-->6)-alpha-GlcpN1P disaccharide was substituted with the primary fatty acids: (R)-3-hydroxytetradecanoic acid [14:0(3-OH)] at N-2 and N-2' and (R)-3-hydroxydodecanoic acid [12:0(3-OH)] at O-3 and O-3'. The heterogeneity among the three forms (I-III) of P. shigelloides O74 lipid A was attributed to the substitution of the acyl residues at N-2' and O-3' with the secondary acyls: (I) cis-9-hexadecenoic acid (9c-16:1) at N-2' and 12:0 at O-3', (II) 14:0 at N-2' and 12:0 at O-3', and (III) 12:0 at N-2' and 12:0 at O-3'. The pro-inflammatory cytokine-inducing activities of P. shigelloides O74 LPS were similar to those of Escherichia coli O55 LPS.
Hallmark Clinical Trials (2014)

Results that dictate a reduction in end points observed in a few hallmark and other recent randomized clinical trials (RCTs) are given. The appropriate reference source is given so that the reader can explore the details of the RCT if required. Because of the constraints of available space, only a brief comment is given in the text regarding the results and their implications.
Crystal Structures of Yeast β-Alanine Synthase Complexes Reveal the Mode of Substrate Binding and Large Scale Domain Closure Movements (2007)

Beta-alanine synthase is the final enzyme of the reductive pyrimidine catabolic pathway, which is responsible for the breakdown of uracil and thymine in higher organisms. The fold of the homodimeric enzyme from the yeast Saccharomyces kluyveri identifies it as a member of the AcyI/M20 family of metallopeptidases. Its subunit consists of a catalytic domain harboring a di-zinc center and a smaller dimerization domain. The present site-directed mutagenesis studies identify Glu(159) and Arg(322) as crucial for catalysis and His(262) and His(397) as functionally important but not essential. We determined the crystal structures of wild-type beta-alanine synthase in complex with the reaction product beta-alanine, and of the mutant E159A with the substrate N-carbamyl-beta-alanine, revealing the closed state of a dimeric AcyI/M20 metallopeptidase-like enzyme. Subunit closure is achieved by a approximately 30 degrees rigid body domain rotation, which completes the active site by integration of substrate binding residues that belong to the dimerization domain of the same or the partner subunit. Substrate binding is achieved via a salt bridge, a number of hydrogen bonds, and coordination to one of the zinc ions of the di-metal center.
TUBERCULOSIS OF THE STOMACH. A CLINICAL AND PATHOLOGIC STUDY (1940)

Sullivan, Ralph C. M.D.; Francona, Nicholas T. M.D.; Kirshbaum, Jack D. M.D., M.S. Author Information
Modification and Application of a Plant Gum as Eco-Friendly Drilling Fluid Additive (2015)

To enhance solubility and the performance of a plant gum (from south peach tree of China, SP gum) as a drilling fluid additive, we explored the potential of Modified SP (MSP) gum by modifying it with epichlorohydrin. The modification conditions, such as the mass ratio of the crosslinking agent, pH and temperature, were optimized and the results show that 56.40 g/100g mass ratio of the crosslinking agent to SP gum with pH=10 at the temperature of 50°C lead to the Modified SP (MSP) gum showed the well performance in the water based drilling fluids.It was discovered that drilling fluids modified with 0.5%wt MSP demonstrated more excellent rheology and lower filtration than that of SP treated drilling fluids, which should be contributed to the good clay inhibition obtained from swelling experiment and high inhibitive to the hydration and swell of the mud supported by mud ball immersing experiments .
Formal Executable Models for Automatic Detection of Timing Anomalies (2018)

A timing anomaly is a counterintuitive timing behavior in the sense that a local fast execution slows down an overall global execution. The presence of such behaviors is inconvenient for the WCET analysis which requires, via abstractions, a certain monotony property to compute safe bounds. In this paper we explore how to systematically execute a previously proposed formal definition of timing anomalies. We ground our work on formal designs of architecture models upon which we employ guided model checking techniques. Our goal is towards the automatic detection of timing anomalies in given computer architecture designs.
DNA-mediated Gene Transfer into Human Diploid Fibroblasts Derived from Normal and Ataxia-telangiectasia Donors: Parameters for DNA Transfer and Properties of DNA Transformants (1984)

We investigate the feasibility of DNA-mediated gene transfer into human diploid fibroblasts derived from patients with the radiation sensitive syndrome ataxia-telangiectasia (A-T) and from a normal donor. Although they are markedly different in their growth characteristics, both normal and A-T strains give similar frequencies for DNA transfer in a model system using the recombinant plasmid pSV2 -gpt. pSV2 -gpt DNA transformants arise with a frequency between 10(-5) and 10(-4) per viable cell. Analysis of such transformants, although possible, is severely handicapped by the limited clonal life span of diploid human cells. Despite these problems it may be concluded that diploid human fibroblasts are competent recipients for DNA-mediated gene transfer and the putative repair deficiency of A-T does not markedly effect the efficiency of this process.
Design and Synthesis of Macromonocyclic Polyamines Composed of Natural Methylene Arrays (1989)

Abstract A general synthetic method applicable to acyclic and cyclic polyamines was developed. The methodology was exemplified by systematical synthesis of twelve macromonocyclic polyamines, 1 ([17]N4) through 12 ([35]N8), composed of the combination of four natural polyamine segments, spermidine, spermine, thermine, and thermospermine. These twelve designed macrocycles are exhausted numbers of possible structures defined by three arbitrarily chosen criteria concerning with methylene chain arrays and nitrogen content (four to eight). The common elements of the structural characteristics were analyzed and were found to be reduced to readily available three classes of simple N,N′-ditosylalkanediamines derived from diamines and triamine. Nitrogen content was increased systematically through the reaction of N,N′-ditosylalkanediamine with one of three ω-phthalimidated electrophiles followed by regeneration of the same functionality at symmetrical both terminals as the starting materials via a series of transformation reaction, in excellent yields. Tractable formamide intermediate profits the facile synthesis of acyclic polyamines with long chains. Cyclization was achieved, under high dilution conditions, through the reaction of α,ω-bis(tosylamide) with α,ω-ditosylates in DMF in the presence of cesium carbonate. The cyclization occurred in practical synthetic yields even in the formation of multi-membered ring when the shorter electrophile and the longest α,ω-bis(tosylamide) reacted.
Anti-Inflammatory Activity of Superoxide Dismutases: Studies on Adjuvant Induced Polyarthritis in Rats (1986)

The anti-arthritic activities of various superoxide dismutases and of liposomal bovine Cu-SOD have been compared in the adjuvant induced Lewis Inbred Rat model. Various approaches, including plethysmometric measurements, red cell sedimentation rates, while cell counts, levels of IgA and IgG immunoglobulins and scoring by visual, radiographic and scintigraphic techniques all concord in a demonstration of different activities for different SODs. The most efficient are liposomal bovine Cu-SOD and E. coli Mn-SOD, a moderate activity being shown by free bovine Cu-SOD. Poor or zero results are obtained with human Mn-SOD, human Cu-SOD or the homologous rat Cu-SOD.
Development and Validation of a Real-Time PCR for Chlamydia suis Diagnosis in Swine and Humans (2014)

Pigs are the natural host for Chlamydia suis, a pathogen which is phylogenetically highly related to the human pathogen C. trachomatis. Chlamydia suis infections are generally treated with tetracyclines. In 1998, tetracyline resistant C. suis strains emerged on U.S. pig farms and they are currently present in the Belgian, Cypriote, German, Israeli, Italian and Swiss pig industry. Infections with tetracycline resistant C. suis strains are mainly associated with severe reproductive failure leading to marked economical loss. We developed a sensitive and specific TaqMan probe-based C. suis real-time PCR for examining clinical samples of both pigs and humans. The analytical sensitivity of the real-time PCR is 10 rDNA copies/reaction without cross-amplifying DNA of other Chlamydia species. The PCR was successfully validated using conjunctival, pharyngeal and stool samples of slaughterhouse employees, as well as porcine samples from two farms with evidence of reproductive failure and one farm without clinical disease. Chlamydia suis was only detected in diseased pigs and in the eyes of humans. Positive humans had no clinical complaints. PCR results were confirmed by culture in McCoy cells. In addition, Chlamydia suis isolates were also examined by the tet(C) PCR, designed for demonstrating the tetracycline resistance gene tet(C). The tet(C) gene was only present in porcine C. suis isolates.
Surface modeling using quadtrees (1996)

Two quadtree variants effective in modeling 2 1 2 -D surfaces are presented. The restricted quadtree can handle regularly sampled data. For irregular data, embedding a TIN inside a PMR quadtree is suggested. Together, these schemes facilitate the handling of most types of input within a single framework. Algorithms for the construction of both data structures from their respective data formats are described and analyzed. The possible application of each of the models to the problem of visibility determination is considered and its performance is theoretically evaluated. The support of the Department of Energy under Grant DEFG02-95ER25237 and the National Science Foundation under Grant IRI-92-16970 is gratefully acknowledged, as is the help of Sandy German in preparing this paper. Preface This dissertation deals with modeling of surfaces, i.e., data structures that can facilitate the storage and manipulation of objects resembling topographical surfaces using computers. Such surfac...
Leakage Monitoring Technique in Near-Threshold Systems with a Time-Based Bootstrapped Ring Oscillator (2013)

The paper presents a built-in self-testing (BIST) technique for leakage monitoring using a time-based bootstrapped sensor at near-threshold supply. In order to observe critical leakage behavior in near-threshold systems, the BIST circuit duplicates the leakage current and a leakage quantizer converts the sensed current into digital outputs. Moreover, a bootstrapped ring oscillator (BTRO) serves as an ultra low-voltage sensor to operate even in deep sub-threshold region. It suppresses most of the leakage current and has high energy efficiency to convert sensed leakage current to oscillation frequency. As a result, it monitors leakage current from the circuit under test (CUT) and quantizes the leakage to high resolution digital outputs. In addition, our design also can be used to monitor the process variation in the ultra low-voltage application. The design and test technique is simulated in 90 nm 1P9M SPRVT CMOS process. As compared to state-of-art works, the proposed sensor can operate even at 0.2 to 0.4V VDD in different corners. Besides, it achieves 11-bit resolution under 10us testing time.
<i>Paenibacillus marinum</i>sp. nov., a thermophilic xylanolytic bacterium isolated from a marine hot spring in Tunisia (2013)

Among a large collection of Tunisian hot springs bacterial isolates a bacterial strain, THE22(T) , with xylanolytic properties was identified. The bacterium was isolated from a natural hot spring "Ain Echefa" at Mediteranean sea (Korbous, North-Eastern Tunisia). The novel strain was Gram positive, spore-forming, rod-shaped, facultatively anaerobic and grew optimally under conditions of 55 °C, 1% (w/v) NaCl and pH 7-8. The 16S rRNA gene sequence analysis showed that strain THE22(T) fell within the radiation of the cluster comprising Paenibacillus species with Paenibacillus phyllosphaerae PALXIL04(T) as the closest phylogenetic neighbour (95.8%). The predominant components in the fatty methyl ester profile were iso-C16:0 (34.46%), C16:0 (19.64%), anteiso-C15:0 (19.18%) and anteiso-C17:0 (18.11%). The major respiratory quinone was menaquinone-7 (MK-7). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The base composition of DNA was 56 mol%. Based on the polyphasic taxonomic data, strain THE-22(T) (=DSM 18499(T) = LMG 23758(T) ) was recognized as a novel species within the genus Paenibacillus. The name Paenibacillus marinum sp. nov. is proposed.
A2B Adenosine Receptors Increase Cytokine Release by Bronchial Smooth Muscle Cells (2003)

Adenosine (Ado) has been suggested to play a role in inflammatory airway diseases such as asthma and chronic obstructive pulmonary disease. The goal of this study was to determine the effect of Ado and its receptor subtypes on cytokine release by bronchial smooth muscle cells. The A2B Ado receptor (AdoR) was expressed at the highest level among the four AdoR subtypes. Activation of the A2B AdoR by an Ado analog, 5'-(N-ethylcarboxamido)-adenosine (NECA), increased cAMP accumulation with potency (EC50 value) of 21.2 +/- 0.2 microM. The effect of NECA on the expression of the inflammatory cytokines was determined using a cDNA array consisting of 23 cytokine genes and confirmed using real-time reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay. NECA increased the release of interleukin-6 and monocyte chemotactic protein-1 proteins with EC50 values of 1.26 +/- 0.25 microM and 0.40 +/- 0.08 microM, respectively, and the maximal folds of induction were 20.8 +/- 1.7- and 6.4 +/- 0.7-fold, respectively. Selective agonists for the A1, A2A, and A3 AdoR subtypes had no effect on cytokine release. The effects of NECA were attenuated by selective antagonists of the A2B AdoR. Thus, Ado increases the release of interleukin-6 and monocyte chemotactic protein-1 from bronchial smooth muscle cells via activation of the A2B AdoR. Our findings provide a novel mechanism whereby Ado acts as a proinflammatory mediator in the airway.