gebhart/patrepeval huggingface dataset:
Kinetic Mechanism of Monomeric Non-claret Disjunctional Protein (Ncd) ATPase (1997)

The non-claret disjunctional protein (Ncd) is a kinesin-related microtubule motor that moves toward the negative end of microtubules. The kinetic mechanism of the monomer motor domain, residues 335-700, satisfied a simple scheme for the binding of 2'-3'-O-(N-methylanthraniloyl) (MANT) ATP, the hydrolysis step, and the binding and release of MANT ADP, where T, D, and Pi refer to nucleotide triphosphate, nucleotide diphosphate, and inorganic phosphate, respectively, and MtN is the complex of an Ncd motor domain with a microtubule site. Rate constants k1 and k-4 are the rates of a first order step, an isomerization induced by nucleotide binding. The apparent second order rate constants for the binding steps are 1.5 x 10(6) M-1 s-1 for MANT ATP and 3.5 x 10(6) M-1 s-1 for MANT ADP (conditions, 50 mM NaCl, pH 6.9, 21 degrees C). The rate constant of the hydrolysis step (k2) was obtained from quench flow measurements of the phosphate burst phase corrected for the contribution of the rate of product release to the transient rate constant. The rate of phosphate dissociation was not measured; the value was assigned to account for a steady state rate of 3 s-1. The MtN complex is dissociated by ATP at a rate of 10 s-1 based on light scattering measurements. Dissociation constants of Ncd-nucleotide complexes from microtubules increased in the order adenosine 5'-O-(thiotriphosphate) (ATPgammaS) < ADP-AlF4 < ATP < ADP < ADP-vanadate. Comparison of the properties of Ncd with a monomeric kinesin K332 (Ma and Taylor (1997) J. Biol. Chem. 272, 717-723) showed a close similarity, except that the rate constants for the hydrolysis and ADP release steps and the steady state rate are approximately 15-20 times smaller for Ncd. There are two differences that may affect the reaction pathway. The rate of dissociation of MtN by ATP is comparable to the rate of the hydrolysis step, and N.T may dissociate in the cycle, whereas for kinesin, dissociation occurs after hydrolysis. The rate of dissociation of MtN by ADP is larger than the rate of ADP release from MtN.D, whereas for the microtubule-kinesin complex, the rate of dissociation by ADP is smaller than the rate of ADP release. The monomeric Mt.Ncd complex is not processive.
The use of 4‐hetaryliden‐ and 4‐aryliden‐5(4<i>H</i>)‐oxazolones as dienophiles. Appropriate reagents for the synthesis of cyclic analogues of natural amino acids (1997)

Abstract This report describes the behavior of 4‐hetaryliden‐ and 4‐aryliden‐5(4 H )‐oxazolones as dienophiles in the Diels‐Alder reaction with several dienes. The application of this reaction to the synthesis of different conformationally constrained cyclic analogues of natural amino acids of pharmacological interest is also described.
Hetero-Epitaxial Growth of Boron Monophosphide on Silicon Substrate Using B<sub>2</sub>H<sub>6</sub>-PH<sub>3</sub>-H<sub>2</sub>System (1974)

Boron monophosphide (BP) was epitaxially grown on Si substrates with (100), (110) and (111) faces, by thermal decomposition of a B2H6-PH3 mixture in hydrogen in the temperature range of 950°C to 1050°C. The crystallographic orientation of the BP was the same as that of the Si substrates. n- and p-type BP were obtained under different growth conditions. The carrier concentrations without any additional doping were from 1018 to 1021 cm-3 and their mobilities were from 150 to 80 cm2/Vsec.
Joint university and industry investigation of polyimide for thin film organic dielectrics for VLSI interlevel applications (2003)

An investigation of acetylene functional polyimide oligomers has demonstrated some of the advantages connected with their use as the starting materials for an interlayer dielectric film in the fabrication of IC devices. Results are presented on two acetylene functional, fully imidized polyimide oligomers. One oligomer is an isoimide structure which can be deposited to form a thin film by spin coating from solvent at high solids levels. The second oligomer is a fully normal imidized structure which contains fluorine atoms and hence shows excellent solubility before cure and generates a low dielectric constant film after cure. The use of these polyimide oligomers as ion implant masks for boron and phosphorus was also demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
DNA damage as a basis for 4'-demethylepipodophyllotoxin-9-(4,6-O-ethylidene-beta-D-glucopyranoside) (etoposide) cytotoxicity. (1983)

The precise mechanism of action of 4'-demethylepipodophyllotoxin-9-(4,6-O-ethylidene-beta-D-glucopyranoside) (VP-16), an important chemotherapeutic agent, has yet to be determined. VP-16 has been shown to cause single-strand breaks (SSBs) in DNA, but their relationship to cytotoxicity has not been determined. We have investigated the action of VP-16 using mouse leukemia L1210 cells in culture. By using the alkaline elution technique, we reaffirmed the occurrence of SSBs in DNA over the drug concentration range 1 to 60 microM. We were able to demonstrate additional types of DNA damage in the form of DNA double-strand breaks and DNA-protein cross-links within the same dose range. The number of double-strand breaks formed per SSB was consistent over this dose range and greater than that found after exposure of L1210 cells to gamma-irradiation. DNA SSBs and double-strand breaks were also shown to occur in isolated nuclei, indicating that cytoplasmic components are not required for this drug action. Colony formation by L1210 cells in soft agar decreased over a drug concentration range similar to that which produced DNA damage. The correlation between the effective dose range in the colony-forming assay and the DNA scission experiments supports the hypothesis that DNA breakage is responsible for drug cytotoxicity. The demonstration of strand scission in isolated nuclei may provide an experimental model for elucidating the exact mechanism of action of VP-16.
Apolipoprotein A-IV in diabetes mellitus. (1995)

Apolipoprotein A-IV is considered to play a role in triglyceride-rich lipoprotein metabolism, in reverse cholesterol transport, and in facilitation of CETP (Cholesterolyl Ester Transfer Protein) activity. Moreover, apoA-IV is genetically polymorphic in humans, in whom two major isoproteins (apoA-IV 1 and apoA-IV 2) are present and have differences that influence the apoA-IV phenotype in lipid metabolism. In non-insulin-dependent-diabetes, increased apoA-IV levels are found, mainly related to hypertriglyceridemia and to a lesser extent to HDL cholesterol level; apoA-IV phenotype distribution is not different from controls; in the control population, the potential protective lipid profile (characterized by increased HDL and HDL2 cholesterol levels) related to the apoA-IV 1-2 phenotype, is no longer found in NIDDM patients (the metabolic state of NIDDM appears to have effected the potential protective lipid profile related to the apoA-IV 1-2 phenotype); and plasma apoA-IV levels is associated with increased prevalence for macrovascular disease. In non-insulin-dependent diabetes treated with insulin, apoA-IV levels are increased. Unlike results for NIDDM patients undergoing oral treatment, the increase in apoA-IV level is not related to hypetriglyceridemia, so that the effect on lipid metabolism may be different.
Probabilistic Modeling of Glued-Laminated Timber Beams (1992)

An existing glued-laminated (glulam) timber beam simulation model was refined in this research.This refined model, referred to as PROLAM, incorporates results from recent research on localized lumber and end joint properties.Simulated beams are analyzed for strength using a transformed section method and analyzed for stiffness using a complementary virtual work technique.Other features of PROLAM include user options to proof test individual grades of lumber and to analyze the propagation of end joint and lamination failures that occur during a beam failure.PROLAM was validated using independent glulam beam test data provided by the American Institute of Timber Construction.The simulated beam results were found to be in close agreement with the actual beam test results.In addition, predictions of allowable bending stress compared favorably with published design values.
A Flow Visualization Study of the NCVC Centrifugal Blood Pump (1994)

A compact centrifugal pump, NCVC-1, has an open-type impeller with 6 curved vanes, and it is characterized by no shaft and no seal. A tunnel is placed in the center of the impeller-rotor assembly to irrigate the back space behind the rotor. To evaluate the flow, we performed 3 visualization methods: tracer, oil film, and injection streak line method. The flow, observed by the tracer method in NCVC-1, indicated little turbulence along vanes. A volute chamber proved effective to reduce vortex formation in the outlet. Oil film pattern revealed no flow separation on vanes at 5 L/min. Washout flow behind the rotor is essential to prevent thrombus formation and was shown as inward spiral flow without any stagnation. These data suggested that a combination of visualization techniques was useful to analyze various flow conditions, and the NCVC-1 has excellent flow characteristics with little turbulence and little flow stagnation, which must be beneficial to low hemolysis and high antithrombogenicity.
Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions (2010)

Point mutations resulting in the substitution of a single amino acid can cause severe functional consequences, but can also be completely harmless. Understanding what determines the phenotypical impact is important both for planning targeted mutation experiments in the laboratory and for analyzing naturally occurring mutations found in patients. Common wisdom suggests using the extent of evolutionary conservation of a residue or a sequence motif as an indicator of its functional importance and thus vulnerability in case of mutation. In this work, we put forward the hypothesis that in addition to conservation, co-evolution of residues in a protein influences the likelihood of a residue to be functionally important and thus associated with disease. While the basic idea of a relation between co-evolution and functional sites has been explored before, we have conducted the first systematic and comprehensive analysis of point mutations causing disease in humans with respect to correlated mutations. We included 14,211 distinct positions with known disease-causing point mutations in 1,153 human proteins in our analysis. Our data show that (1) correlated positions are significantly more likely to be disease-associated than expected by chance, and that (2) this signal cannot be explained by conservation patterns of individual sequence positions. Although correlated residues have primarily been used to predict contact sites, our data are in agreement with previous observations that (3) many such correlations do not relate to physical contacts between amino acid residues. Access to our analysis results are provided at http://webclu.bio.wzw.tum.de/~pagel/supplements/correlated-positions/.
Variable ordering of binary decision diagrams for multi-level logic minimization (1993)

Binary Decision Diagram (BDD) is now widely used in CAD fields, especially in formal verification and logic synthesis. In this paper, variable ordering methods of BDD for the application of multi-level logic minimization are presented. The variable ordering algorithm for sum-of-products representation is based on cover patterns and selects most binate variables first, and the one for multi-level logic representation is based on depth first traversal of circuits. In both cases, the obtained variable orderings are optimized by exchanging a variable with its neighbor in the ordering. Experimental results show the effectiveness of our methods
Congenital Stenosis of the Pulmonary Artery Branches (1964)

Eighteen cases of stenosis of the branches of the pulmonary artery, seen at the Mayo Clinic, have been reviewed and subdivided into two main types: Type I, stenosis of the main branches of the pulmonary artery, 11 cases, and type II, stenosis of multiple peripheral branches of the pulmonary arteries, seven cases. Of special interest were two cases in which thrombosis occurred as a complication and one case in which surgical relief of multiple areas of stenosis in the peripheral branches of the pulmonary arteries was accomplished. Unexplained pulmonary hypertension necessitates further investigation, which includes cardiac catheterization for measurement of intracardiac pressure and frequently selective angiocardiography. Main branch or peripheral pulmonary artery stenosis should be suspected when a continuous murmur is heard or when poststenotic dilatations of the pulmonary artery branches or areas of decreased pulmonary vasculature can be perceived in the roentgenogram. Angiocardiography is the only technic that permits detailed anatomic evaluation of the entire pulmonary vasculature, especially in the cases associated with severe infundibular or valvular pulmonic stenosis. Stenosis of the branches of the pulmonary artery must be taken into account, when surgical repair of associated cardiovascular defects is considered. These lesions also might complicate anastomotic procedures involving the pulmonary artery in cyanotic patients.
Monitoring key CMP process parameters to improve manufacturing productivity (2002)

A discussion of three different methods of monitoring CMP process parameters are presented that can help lead to improved manufacturing productivity. The three methods include data capture of down force from load cell output, direct pressure uniformity measurements from wafer carrier surfaces and wafer shape measurements of pre-polished wafers.
All‐nitride monochromatic amber‐emitting phosphor‐converted light‐emitting diodes (2009)

Abstract Phosphor conversion of light‐emitting diode (LED) radiation has been used in many configurations and combinations to generate white light. The concept of down conversion of, e.g., blue LED emission, offers also the possibility to provide efficient generation of monochromatic, high‐color‐purity light, especially in wavelength ranges in which direct radiation from non‐converted LEDs is relatively inefficient, i.e., in the “yellow gap”. In the case described here, a blue‐emitting LED is ‘fully’ converted to amber emission with a peak wavelength of 595 nm and a color purity of >96%, while demonstrating an external quantum efficiency exceeding that of direct AlGaInP LEDs of the same wavelength by a factor of almost two at room temperature, and the lumen output under equal drive conditions at 85 °C by more than a factor of four. An essential component in this high performance is, besides the choice of the right – nitride – phosphor, the use of this phosphor in a densely sintered ceramic form which has considerable optical advantages over powders. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Getting light through black composites: embedded triboluminescent structural damage sensors (2001)

Triboluminescent materials offer a viable route to real time structural damage sensing. The sensors can be externally attached to the surface of metals or composites, or embedded within composites. In situ monitoring of structural damage in composites is particularly relevant since severe internal damage can exist with little indication of this damage on the composite surface. The main issue related to embedding triboluminescent sensors within composites is how to access efficiently the optical signal generated upon structural damage and how to guide efficiently this optical damage signal to a remote detector. Earlier work relied on side-coupling of the triboluminescent light into a curved conventional silica fibre and/or end-coupling into the silica fibre, if the damage to the host structure had also broken the fibre. Both these light collection methods are, of course, inefficient and resulted in an optical damage signal with a very poor signal-to-noise (S/N) ratio. By using novel photoluminescent polymeric and silica fibres, we have shown that it is possible to efficiently capture and guide the optical damage signal from an embedded triboluminescent sensor to a remote detector. These fibres resulted in a signal with a S/N ratio that was orders of magnitude larger than that achieved using the conventional silica fibre. Furthermore, we have shown that the light collection/guiding technique can even be used effectively with triboluminescent sensors embedded within black carbon fibre reinforced plastic (CFRP) composites. Finally, we have demonstrated that for resins and glass fibre reinforced plastic (GFRP) composites, triboluminescent sensors act as truly global damage sensors, whereas for CFRP composites, the damage sensing is localized to areas close to the embedded photoluminescent fibre.
Stoichiometric dry etching of mercury cadmium telluride using a secondary afterglow reactor (1989)

A secondary afterglow reactor has been used for the dry etching of mercury cadmium telluride. In this reactor, methane is injected into the flowing afterglow of a microwave discharge in a fluorine source gas. The resulting reaction of F+CH4 produces methyl radicals, which etch mercury cadmium telluride at rates of up to 400 Å/min. Examination of etched surfaces by energy dispersive x-ray analysis and electron beam electroreflectance (EBER) reveals no change of stoichiometry over the unetched surface. EBER analysis further indicates no damage to the crystallinity of the surface. The etched surfaces exhibit crystalline anisotropy. Recent advances in mercury cadmium telluride device fabrication have focused on vacuum processes. The development of a nondamaging, stoichiometric dry etch process provides the potential of processing mercury cadmium telluride focal plane arrays in a continuous vacuum environment.
Alpha-amidation of peptide hormones in lung cancer. (1991)

Small-cell lung cancer (SCLC), the most common neuroendocrine tumor in humans, provides an excellent model system for analyzing the role of growth factors in lung cancer. SCLCs secrete a wide range of peptide hormones, including some that stimulate tumor cell growth, such as gastrin-releasing peptide and insulin-like growth factor I. Many of these peptides are synthesized as prohormones that acquire biological activity only after specific post-translational modifications. Here, we review our current understanding of the biological role of neuroendocrine peptides in lung carcinogenesis and consider how a mechanistic knowledge of one particular modification, carboxy-terminal alpha-amidation, may permit identification of novel growth factors for lung cancer cells. We also describe potential applications of this knowledge as a basis for prevention-oriented approaches to the disease.
Double-blind evaluation of oral L-prolyl-Lleucyl-glycine amide in Parkinson's disease. (1976)

A 4-month double-blind study comparing the effect of increasing oral doses (up to 1.0 g daily) of synthetic L-proyl-L-leucyl-glycine amide (PLG) and placebo in 20 parkinsonian patients showed no significant improvement in objective scores of functional disability. However, important trends and some significant results were observed with the lower doses of PLG. These essentially negative results may be attributed to poor intestinal absorption of the compound, a short biologic half-life in the blood, or administration of oral doses that were much higher than required, or a combination of factors. In further studies with this peptide, which are encouraged, the intravenous route should be used until the question of intestinal absorption is resolved.
Look Before You Leap: Bridging Model-Free and Model-Based Reinforcement Learning for Planned-Ahead Vision-and-Language Navigation (2018)

Existing research studies on vision and language grounding for robot navigation focus on improving model-free deep reinforcement learning (DRL) models in synthetic environments. However, model-free DRL models do not consider the dynamics in the real-world environments, and they often fail to generalize to new scenes. In this paper, we take a radical approach to bridge the gap between synthetic studies and real-world practices---We propose a novel, planned-ahead hybrid reinforcement learning model that combines model-free and model-based reinforcement learning to solve a real-world vision-language navigation task. Our look-ahead module tightly integrates a look-ahead policy model with an environment model that predicts the next state and the reward. Experimental results suggest that our proposed method significantly outperforms the baselines and achieves the best on the real-world Room-to-Room dataset. Moreover, our scalable method is more generalizable when transferring to unseen environments.
A Novel Proteinaceous Kex 2 Proteinase Inhibitor, Kexstatin, from<i>Streptomyces platensis</i>Q268 (1996)

We found a novel proteinaceous Kex 2 proteinase inhibitor, named kexstatin, in the culture supernatant of Streptomyces platensis Q268. The purified kexstatin was homogeneous by SDS-PAGE and the molecular weight was estimated to be 13,000. The N-terminal amino acid sequence of kexstatin has high similarity to Streptomyces subtilisin inhibitor (SSI), suggesting that kexstatin belongs to the SSI family. Kexstatin was a strong inhibitor of Kex 2 proteinase and subtilisin but not thermolysin, trypsin, or chymotrypsin. The IC50 value of kexstatin against 1 microgram of Kex 2 proteinase was 1.4 micrograms.
Unique strains of SV40 in commercial poliovaccines from 1955 not readily identifiable with current testing for SV40 infection. (1999)

SV40 was first identified as a contaminant of poliovaccines used from 1955 until 1963. Recently, SV40 has been detected in several human tumors. The virus detected in human tumors often contained only one 72-bp enhancer in the regulatory region, in contrast to the SV40 originally isolated from poliovaccines, which contained two 72-bp enhancers. The origin of viruses with one 72-bp enhancer in humans was unknown, because it was thought that these viruses were not present in poliovaccines. It was also thought that all poliovaccine vials produced from 1955 until 1963 had been discarded, thus the possibility that one 72-bp virions contaminated those vials could not be tested. We unexpectedly obtained what appear to be the last available vials of poliovaccine produced in 1955. In these vials, we detected and sequenced SV40 containing only one 72-bp enhancer in the regulatory region. The tissue culture cytopathic test currently used in the United States to screen oral poliovaccines was designed to detect rapidly proliferating SV40 virions containing two 72-bp enhancers. We found that this test is not sensitive enough to detect low amounts of the slow-replicating SV40 virions containing one 72-bp enhancer. This virus was easily detected in the same cells by immunostaining and PCR. Twelve current vials of poliovaccines tested uniformly negative for SV40, suggesting that the precaution of preparing poliovaccines from kidneys obtained from monkeys bred in isolated colonies prevented SV40 contamination. Our data demonstrate that humans were exposed to SV40 viruses with both one 72-bp enhancer and two 72-bp enhancers SV40 through contaminated vaccines. Our data also suggest that instead of cytopathic tests, immunohistochemical and/or molecular studies should be used to screen poliovaccines for SV40 to completely eliminate the risk of occasional contamination.