gebhart/patrepeval huggingface dataset:
Potential solvent for reconditioning polyolefin waste materials (2012)

Abstract Waste polymer reconditioning was examined by a method of dissolution/reprecipitation on low- and high-density polyethylene (PE) and polypropylene (PP). Toluene and petroleum ether, in different proportions, were used as solvents, and n-hexane was used as a non-solvent. Commercial polymer products used on an everyday basis were used with a virgin polymer, to optimize the qualities of the final product, and 98% polymer was recovered in each case. Fourier transform infrared spectroscopy (FTIR) images and tensile mechanical properties of the samples, before and after recycling, were analyzed. The potential recycling-based degradation of the polymer was further investigated by measuring the thermal properties (melting point and crystallinity) before and after recycling, using differential scanning calorimetry (DSC). High reconditioning was observed in most recycled samples, with no significant difference from the virgin materials. The studied technique seems to be viable for waste polyolefin polymer recycling.
Activation of renin-angiotensin system does not cause skeletal muscle cramps during hemodialysis. (1990)

Activation of the renin-angiotensin system usually occurs during hemodialysis and in hemodialyzed normal dogs parallels reductions in blood flow to a tissue group that is largely composed of skeletal muscle. To determine if excessive activation of this system might cause dialysis-associated skeletal muscle cramps in some patients, we conducted a double-blind, randomized and balanced trial in which 5 patients with frequent dialysis-associated cramps were each given either a 25 mg oral dose of captopril or placebo 1 h before 8 consecutive dialyses. Captopril increased the frequency of dialyses complicated by skeletal muscle cramps in 1 patient and did not affect cramp frequency in the other 4 patients. Predialysis plasma renin activity (PRA) averaged 3.9 ng/ml/h (+/- SD) and was the same as in unselected hemodialysis patients. Following captopril, PRA increased by an average of 2.2 +/- 0.7 times, similar to the 2.6-fold increase that was reported when this drug was used to prevent dialysis-associated hypertensive crises. However, hemodialysis by itself did not activate the renin-angiotensin system as consistently in patients with frequent dialysis-associated skeletal muscle cramps as in unselected hemodialysis patients and the ratio of post- to predialysis PRA averaged 1.0 +/- 0.6. We conclude that the renin-angiotensin system does not mediate, and that its activation during hemodialysis may actually help prevent, dialysis-associated skeletal muscle cramps.
Molecular Dynamics Simulations for Complexation of DNA with 2 kDa PEI Reveal Profound Effect of PEI Architecture on Complexation (2012)

A series of all-atom molecular dynamics (MD) simulations of the complexation between DNA and 2 kDa branched and linear polyethylenimines (PEIs) are reported in this study. The simulations revealed distinct binding modes of branched and linear PEIs to DNA, with branched PEIs adhering to the DNA surface like beads and linear PEIs adhering to the DNA surface like cords. The dynamics of each PEI's binding state to the DNA during the simulations and how the PEIs neutralize the DNA were quantified. For both branched and linear PEIs, the addition of salt ions similar to physiological conditions were found to have only a small effect on DNA/PEI complexation compared to salt-free conditions. The simulation results reported here will be helpful to understand the mechanism of action for the PEI-based gene carriers.
Atomistic Structure of Monomolecular Surface Layer Self-Assemblies: Toward Functionalized Nanostructures (2011)

The concept of self-assembly is one of the most promising strategies for the creation of defined nanostructures and therefore became an essential part of nanotechnology for the controlled bottom-up design of nanoscale structures. Surface layers (S-layers), which represent the cell envelope of a great variety of prokaryotic cells, show outstanding self-assembly features in vitro and have been successfully used as the basic matrix for molecular construction kits. Here we present the three-dimensional structure of an S-layer lattice based on tetrameric unit cells, which will help to facilitate the directed binding of various molecules on the S-layer lattice, thereby creating functional nanoarrays for applications in nanobiotechnology. Our work demonstrates the successful combination of computer simulations, electron microscopy (TEM), and small-angle X-ray scattering (SAXS) as a tool for the investigation of the structure of self-assembling or aggregating proteins, which cannot be determined by X-ray crystallography. To the best of our knowledge, this is the first structural model at an amino acid level of an S-layer unit cell that exhibits p4 lattice symmetry.
Some issues of power MOSFETs (1982)

Several recent studies of power MOSFETs are discussed in this paper: (a) The second-breakdown of power MOSFETs is shown to be triggered by the turn-on of the parasitic bipolar transistor, (b) The I-V characteristics of power MOSFETs operating in reverse mode (such as when used as a synchronous rectifier) are studied, (c) A H5°-spreadingangle model for the calculation of epi-resistance is shown to be more accurate than any previously published model for linear source geometry. More importantly, this model has been extended to cellular source geometries.
Impact of Pain on Depression Treatment Response in Primary Care (2004)

Pain is present in two thirds of depressed primary care patients begun on antidepressant therapy, and the severity of pain is a strong predictor of poor depression and health-related quality of life outcomes at 3 months. Better recognition, assessment, and treatment of comorbid pain may enhance outcomes of depression therapy.
Perfluorocarbons: Life sciences and biomedical uses <b>Dedicated to the memory of Professor Guy Ourisson, a true RENAISSANCE man.</b> (2007)

Abstract Perfluorocarbons are primarily characterized by outstanding chemical and biological inertness, and intense hydrophobic and lipophobic effects. The latter effects provide a powerful noncovalent, labile binding interaction that can promote selective self‐ assembly. Perfluoro compounds do not mimic nature, yet they can offer abiotic building blocks for the de novo design of functional biopolymers and alternative solutions to physiologically vital issues. They offer new tags useful for molecular recognition, selective sorting, and templated binding (e.g., selective peptide and nucleic acid pairing). They also stabilize membranes and provide micro‐ and nanocompartmented fluorous environments. Perfluorocarbons provide inert, apolar carrier fluids for lab‐on‐a‐chip experiments and assays using microfluidic technologies. Low water solubility, combined with high vapor pressure, allows stabilization of injectable microbubbles that serve as contrast agents for diagnostic ultrasound imaging. High gas solubilities are the basis for an abiotic means for intravascular oxygen delivery. Other biomedical applications of fluorocarbons include lung surfactant replacement and ophthalmologic aids. Diverse colloids with fluorocarbon phases and/or shells are being investigated for molecular imaging using ultrasound or magnetic resonance, and for targeted drug delivery. Highly fluorinated polymers provide a range of inert materials (e.g., fluorosilicons, expanded polytetrafluoroethylene) for contact lenses, reconstructive surgery (e.g., vascular grafts), and other devices. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1185–1198, 2007.
5-Gb/s performance of integrated light source consisting of lambda /4-shifted DFB laser and EA modulator with SI InP BH structure (1990)

The fabrication process and characteristics, including 5-Gb/s transmission, of an integrated light source consisting of a lambda /4-shifted distributed feedback laser and an electroabsorption (EA) modulator are discussed. By introducing a semi-insulating (SI) InP on the butt-joint region, both the large electrical isolation resistance (>10 M Omega ) between the laser and the modulator and a high optical coupling efficiency (>80%) between them are achieved. A typical threshold current was 50-70 mA, and single-mode operation at 1.576 mu m was maintained up to 5.5-mW output power. The modulation voltage to swing between 90% transmission and 10% transmission was 6.2-12 V, depending on the modulator length in the range 1000-400 mu m. The 3-dB bandwidth is 7.7 GHz and a linewidth enhancement factor ( alpha ) of 0.9 is estimated from the sideband-to-carrier ratio of the spectra.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<title>Currency features for visually impaired people</title> (1996)

The estimated 3.7 million Americans with low vision experience a uniquely difficult task in identifying the denominations of U.S. banknotes because the notes are remarkably uniform in size, color, and general design. The National Research Council's Committee on Currency Features Usable by the Visually Impaired assessed features that could be used by people who are visually disabled to distinguish currency from other documents and to denominate and authenticate banknotes using available technology. Variation of length and height, introduction of large numerals on a uniform, high-contrast background, use of different colors for each of the six denominations printed, and the introduction of overt denomination codes that could lead to development of effective, low-cost devices for examining banknotes were all deemed features available now. Issues affecting performance, including the science of visual and tactile perception, were addressed for these features, as well as for those features requiring additional research and development. In this group the committee included durable tactile features such as those printed with transparent ink, and the production of currency with holes to indicate denomination. Among long-range approaches considered were the development of technologically advanced devices and smart money.
A Comparative Evaluation of <i>In Vitro</i> Skin Sensitisation Tests: The Human Cell-line Activation Test (h-CLAT) <i>versus</i> the Local Lymph Node Assay (LLNA) (2010)

We previously developed the human cell-line activation test (h-CLAT) in vitro skin sensitisation test, based on our reported finding that a 24-hour exposure of THP-1 cells (a human monocytic leukaemia cell line) to sensitisers is sufficient to induce the augmented expression of CD86 and CD54. The aim of this study is to confirm the predictive value of h-CLAT for skin sensitisation activity by employing a larger number of test chemicals. One hundred chemicals were selected, according to their categorisation in the local lymph node assay (LLNA), as being: extreme, strong, moderate and weak sensitisers, and non-sensitisers. The correlation of the h-CLAT results with the LLNA results was 84%. There were some false negatives (e.g. benzoyl peroxide, hexyl cinnamic aldehyde) and some false positives (e.g. 1-bromobutane, diethylphthalate). Eight out of the 9 false negatives (89%) were water-insoluble chemicals. The h-CLAT could positively predict not only extreme and strong sensitisers, but also moderate and weak sensitisers, though the detection rates of weak sensitisers and non-sensitisers were comparatively low. Some sensitisers enhanced both CD86 and CD54 levels, and some enhanced the level of only one of them. The use of the combination of CD86 and CD54 induction as a positive indicator, improved the accuracy of the test. In conclusion, the h-CLAT is expected to be a useful cell-based in vitro method for predicting skin sensitisation potential.
Pipecolic acid biosynthesis in Rhizoctonia leguminicola. I. The lysine saccharopine, delta 1-piperideine-6-carboxylic acid pathway. (1990)

The biosynthesis of pipecolic acid from L-lysine in the fungal parasite, Rhizoctonia leguminicola has been reinvestigated. Pipecolate is then utilized to form the toxic octahydroindolizine alkaloids, slaframine and swainsonine. Incorporation studies of L-versus D-[U-14C]lysine into R. leguminicola metabolites confirmed earlier findings that L-lysine is the predominant substrate for pipecolate formation and D-lysine for alpha-N-acetyllysine (concerned in lysine catabolism). However [alpha-15N]lysine, not [epsilon-15N]lysine as previously reported, labeled pipecolate. Such findings implied that delta 1-piperideine-6-carboxylate, not delta 1-piperideine-2-carboxylate, was formed from lysine and was the immediate precursor of pipecolate. Evidence from cell-free enzyme systems established the following biosynthetic events: L-lysine A----saccharopine B----delta 1-piperideine-6-carboxylate C----pipecolate. Products of reactions A and C were identified from biological and chemical considerations. Reaction B was carried out by a previously undescribed flavin enzyme termed saccharopine oxidase. The product of reaction B, which reacted with p-dimethylaminobenzaldehyde, was reduced with Na-CNB2H3. Its NMR spectrum was identical with that of deuteriated pipecolate prepared from authentic delta 1-piperideine-6-carboxylate, but not from authentic delta 1-piperideine-2-carboxylate. Reaction B represents a branching of primary lysine metabolism from saccharopine to a secondary pathway leading to pipecolate and to octahydroindolizine alkaloids in R. leguminicola.
Structural and Electronic Properties of Old and New A<sub>2</sub>[M(pin<sup>F</sup>)<sub>2</sub>] Complexes (2013)

Seven new homoleptic complexes of the form A2[M(pin(F))2] have been synthesized with the dodecafluoropinacolate (pin(F))(2-) ligand, namely (Me4N)2[Fe(pin(F))2], 1; (Me4N)2[Co(pin(F))2], 2; ((n)Bu4N)2[Co(pin(F))2], 3; {K(DME)2}2[Ni(pin(F))2], 4; (Me4N)2[Ni(pin(F))2], 5; {K(DME)2}2[Cu(pin(F))2], 7; and (Me4N)2[Cu(pin(F))2], 8. In addition, the previously reported complexes K2[Cu(pin(F))2], 6, and K2[Zn(pin(F))2], 9, are characterized in much greater detail in this work. These nine compounds have been characterized by UV-vis spectroscopy, cyclic voltammetry, elemental analysis, and for paramagnetic compounds, Evans method magnetic susceptibility. Single-crystal X-ray crystallographic data were obtained for all complexes except 5. The crystallographic data show a square-planar geometry about the metal center in all Fe (1), Ni (4), and Cu (6, 7, 8) complexes independent of countercation. The Co species exhibit square-planar (3) or distorted square-planar geometries (2), and the Zn species (9) is tetrahedral. No evidence for solvent binding to any Cu or Zn complex was observed. Solvent binding in Ni can be tuned by the countercation, whereas in Co only strongly donating Lewis solvents bind independent of the countercation. Indirect evidence (diffuse reflectance spectra and conductivity data) suggest that 5 is not a square-planar compound, unlike 4 or the literature K2[Ni(pin(F))2]. Cyclic voltammetry studies reveal reversible redox couples for Ni(III)/Ni(II) in 5 and for Cu(III)/Cu(II) in 8 but quasi-reversible couples for the Fe(III)/Fe(II) couple in 1 and the Co(III)/Co(II) couple in 2. Perfluorination of the pinacolate ligand results in an increase in the central C-C bond length due to steric clashes between CF3 groups, relative to perhydropinacolate complexes. Both types of pinacolate complexes exhibit O-C-C-O torsion angles around 40°. Together, these data demonstrate that perfluorination of the pinacolate ligand makes possible highly unusual and coordinatively unsaturated high-spin metal centers with ready thermodynamic access to rare oxidation states such as Ni(III) and Cu(III).
Conversion of ES cells to columnar epithelia by hensin and to squamous epithelia by laminin (2004)

Single-layered epithelia are the first differentiated cell types to develop in the embryo, with columnar and squamous types appearing immediately after blastocyst implantation. Here, we show that mouse embryonic stem cells seeded on hensin or laminin, but not fibronectin or collagen type IV, formed hemispheric epithelial structures whose outermost layer terminally differentiated to an epithelium that resembled the visceral endoderm. Hensin induced columnar epithelia, whereas laminin formed squamous epithelia. At the egg cylinder stage, the distal visceral endoderm is columnar, and these cells begin to migrate anteriorly to create the anterior visceral endoderm, which assumes a squamous shape. Hensin expression coincided with the dynamic appearance and disappearance of columnar cells at the egg cylinder stage of the embryo. These expression patterns, and the fact that hensin null embryos (and those already reported for laminin) die at the onset of egg cylinder formation, support the view that hensin and laminin are required for terminal differentiation of columnar and squamous epithelial phenotypes during early embryogenesis.
A <i>CDC45</i> Homolog in Arabidopsis Is Essential for Meiosis, as Shown by RNA Interference–Induced Gene Silencing (2003)

CDC45 is required for the initiation of DNA replication in yeast and cell proliferation in mammals and functions as a DNA polymerase alpha loading factor in Xenopus. We have cloned a CDC45 homolog from Arabidopsis whose expression is upregulated at the G1/S transition and in young meiotic flower buds. One-third of Arabidopsis 35S:CDC45 T1 RNA interference lines are partially to completely sterile, and the proportion of sterile plants is increased by using a dmc1 promoter. T1 plants have decreased levels of the CDC45 transcript and contain 21- to 23-bp RNA fragments specific to the CDC45 gene. T2 transgenic lines, in which small RNA fragments are still present, were used to analyze S-phase entry by 5-bromodeoxyuridine incorporation, which was not altered compared with that in the wild type. However, microarray data show that other cell cycle genes are upregulated or downregulated. T2 plants also have highly reduced fertility. The severity of the phenotype is correlated with the levels of the CDC45 transcript and small RNA fragments. Severe chromosome fragmentation arising during meiosis, which is not the result of a defect in the repair of SPO11-induced double strand breaks, leads to abnormal chromosome segregation and defective pollen and ovule development.
Scalable parallel OPTICS data clustering using graph algorithmic techniques (2013)

OPTICS is a hierarchical density-based data clustering algorithm that discovers arbitrary-shaped clusters and eliminates noise using adjustable reachability distance thresholds. Parallelizing OPTICS is considered challenging as the algorithm exhibits a strongly sequential data access order. We present a scalable parallel OPTICS algorithm (Poptics) designed using graph algorithmic concepts. To break the data access sequentiality, POPTICS exploits the similarities between the OPTICS algorithm and Prim's Minimum Spanning Tree algorithm. Additionally, we use the disjoint-set data structure to achieve a high parallelism for distributed cluster extraction. Using high dimensional datasets containing up to a billion floating point numbers, we show scalable speedups of up to 27.5 for our OpenMP implementation on a 40-core shared-memory machine, and up to 3,008 for our MPI implementation on a 4,096-core distributed-memory machine. We also show that the quality of the results given by POPTICS is comparable to those given by the classical OPTICS algorithm.
The Non-Producer Phenotype of the Human Immunodeficiency Virus Type 1 Provirus F12/HIV-1 is the Result of Multiple Genetic Variations (1996)

A cell clone (Hut-78/F12) chronically infected with a non-producer human immunodeficiency virus type 1 (HIV-1) variant showed an abnormal pattern of virus structural proteins and released no detectable virus particles. Exchanges of homologous parts of the F12/HIV provirus and a replication-competent HIV (strain NL4-3) were undertaken to define the genetic determinants of the F12/HIV phenotype. The non-infectious phenotype was reproduced by replacing an NL4-3 genomic fragment encoding the C terminus of gp 120 and the N terminus of gp41 with the corresponding parts of the F12/HIV provirus. Conversely, a much more extended genomic fragment (encompassing the vif, pol and env genes) was necessary to convert the F12/HIV phenotype. These results demonstrate that the F12/HIV non-producer phenotype is the result of mutations scattered along most of the genome, rendering the conversion to an infectious phenotype a very unlikely event. The F12/HIV genome is thus a reliable model for preclinical studies of anti-HIV gene therapy.
Asynchronous multiple-access interference suppression using variable block adaptive filtering in time-varying multipath channels (2005)

A computationally-efficient fuzzy-logic controlled block adaptive filtering (FLC-BAF) technique is developed for asynchronous DS-CDMA systems with antenna arrays in multipath Rayleigh-fading channels. This time-varying block filtering scheme employs a (2-to-1)-fuzzy inference system (FIS) to determine the processing blocksize Q. Consequently, this FLC-BAF approach accomplishes a substantial reduction of the computational cost without compromising bit-error-rate (BER) performance and dynamic-tracking characteristic. Simulations are conducted to illustrate the BER and convergence/tracking superiority and to provide a comparative evaluation of the proposed algorithm to other known block processing algorithms.
Changes in Protonation Associated with Substrate Binding and Cob(I)alamin Formation in Cobalamin-Dependent Methionine Synthase (1997)

Methionine synthase catalyzes the transfer of a methyl group from methylcobalamin enzyme to homocysteine, generating methionine and cob(I)alamin enzyme, and then from methyltetrahydrofolate to cob(I)alamin enzyme, generating tetrahydrofolate and regenerating the methylcobalamin enzyme. The reactions catalyzed by methionine synthase require deprotonation of the substrate, homocysteine, and protonation of the product tetrahydrofolate, with no net change in proton stoichiometry for a complete turnover cycle. In addition, formation of the intermediate cob(I)alamin enzyme requires a change in the cobalt ligand geometry from 6-coordinate to 4-coordinate, and this rearrangement may require the transient protonation of protein residues to stabilize the cob(I)alamin enzyme. In the E. coli enzyme, the lower face of the methylcobalamin cofactor is coordinated by histidine 759, which is hydrogen bonded to aspartate 757 and then to serine 810, forming a "ligand triad". It has previously been shown that reduction of cob(II)alamin enzyme to cob(I)alamin is associated with the uptake of a proton from solution, and it has been postulated that this proton resides within the His759-Asp757 pair. Cob(I)alamin can also be generated by demethylation of methylcobalamin enzyme by homocysteine; it was not known whether this mode of cob(I)alamin formation was associated with proton uptake. In this paper, we use equilibrium titrations and kinetic analyses in the presence of the pH indicator dye phenol red, along with studies of the pH dependence of oxidation/reduction equilibria, to identify and characterize mechanistic steps associated with proton uptake and release in both the turnover and reactivation of the enzyme. We confirm that cob(I)alamin formation by reduction of cob(II)alamin enzyme is associated with proton uptake and show that mutation of Asp757 to Glu abolishes the pH dependence of this reduction. Demethylation of methylcobalamin enzyme also leads to cob(I)alamin formation and is also shown to be associated with proton uptake. By observing pre-steady-state reactions with homocysteine and methyltetrahydrofolate in the presence of phenol red, we show that this proton uptake occurs at a rate that is equal to the rate of formation of the cob(I)alamin enzyme. In addition, we show that binding of homocysteine to the enzyme results in the rapid release of a proton, presumably the homocysteine thiol proton. In contrast, binding methyltetrahydrofolate to the enzyme does not result in proton uptake, suggesting that the proton destined for the product tetrahydrofolate is already present on the free methylcobalamin enzyme.