gebhart/patrepeval huggingface dataset:
A Label-Free, Sensitive, Real-Time, Semiquantitative Electrochemical Measurement Method for DNA Polymerase Amplification (ePCR) (2015)

Oligonucleotide hybridization to a complementary sequence that is covalently attached to an electrochemically active conducting polymer (ECP) coating the working electrode of an electrochemical cell causes an increase in reaction impedance for the ferro-ferricyanide redox couple. We demonstrate the use of this effect to measure, in real time, the progress of DNA polymerase chain reaction (PCR) amplification of a minor component of a DNA extract. The forward primer is attached to the ECP. The solution contains other PCR components and the redox couple. Each cycle of amplification gives an easily measurable impedance increase. Target concentration can be estimated by cycle count to reach a threshold impedance. As proof of principle, we demonstrate an electrochemical real-time quantitative PCR (e-PCR) measurement in the total DNA extracted from chicken blood of an 844 base pair region of the mitochondrial Cytochrome c oxidase gene, present at ∼1 ppm of total DNA. We show that the detection and semiquantitation of as few as 2 copies/μL of target can be achieved within less than 10 PCR cycles.
Purification and Properties of l-Lysine Monooxygenase from Pseudomonas fluorescens (1974)

Abstract l-Lysine monooxygenase has been isolated in nearly pure form from a lysine adapted strain of Pseudomonas fluorescens. The enzyme, which catalyzes the oxidative decarboxylation of l-lysine to form δ-aminovaleramide, has a molecular weight of approximately 246,000, and contains four subunits of equal size and four FAD prosthetic groups. Enzymic activity is greatly inhibited by a variety of buffers at low lysine concentrations, while at saturating l-lysine levels, this sensitivity is lost, and buffers have very little effect on the activity. The absorption spectrum is typical of a simple flavoprotein, with absorption maxima at 276, 385, and 462 nm. Two electron equivalents per mole are required to completely reduce the enzyme-bound flavin by dithionite, indicating that FAD is the only electron acceptor associated with the enzyme. During the course of reduction by dithionite, the semiquinone form of the flavin is produced. The ionization state of this species is a function of pH, with red or anionic semiquinone seen at pH values above 8 and the blue or neutral form at pH 5.5. l-Lysine monooxygenase, then, is one of the few flavoproteins exhibiting a pK near neutrality for the semiquinone oxidation state. The fluorescence properties of this enzyme are also unusual in that while the oxidized state is practically devoid of visible fluorescence, the reduced state exhibits flavin fluorescence, with an emission maximum at 505 nm and an excitation maximum at 360 nm. This reduced enzyme fluorescence is quenched by the addition of the substrates l-lysine or l-ornithine.
Boron-Based Hydrogen Storage: Ternary Borides and Beyond (2016)

DOE continues to seek reversible solid-state hydrogen materials with hydrogen densities of ≥11 wt% and ≥80 g/L that can deliver hydrogen and be recharged at moderate temperatures (≤100 °C) and pressures (≤100 bar) enabling incorporation into hydrogen storage systems suitable for transportation applications. Boron-based hydrogen storage materials have the potential to meet the density requirements given boron’s low atomic weight, high chemical valance, and versatile chemistry. However, the rates of hydrogen exchange in boron-based compounds are thus far much too slow for practical applications. Although contributing to the high hydrogen densities, the high valance of boron also leads to slow rates of hydrogen exchange due to extensive boron-boron atom rearrangements during hydrogen cycling. This rearrangement often leads to multiple solid phases occurring over hydrogen release and recharge cycles. These phases must nucleate and react with each other across solid-solid phase boundaries leading to energy barriers that slow the rates of hydrogen exchange. This project sought to overcome the slow rates of hydrogen exchange in boron-based hydrogen storage materials by minimizing the number of solid phases and the boron atom rearrangement over a hydrogen release and recharge cycle. Two novel approaches were explored: 1) developing matched pairs of ternary borides and mixed-metal borohydrides that could exchange hydrogen with only one hydrogenated phase (the mixed-metal borohydride) and only one dehydrogenated phase (the ternary boride); and 2) developing boranes that could release hydrogen by being lithiated using lithium hydride with no boron-boron atom rearrangement.
Birefringent Hemozoin Identifies Malaria (1986)

The diagnosis of malaria is still sometimes difficult because of the insensitivity of microscopic screening at low levels of parasitemia. The malarial pigment, hemozoin, is a crystalline product of the digestion of hemoglobin by the parasites. Under polarized light at 500X magnification, brilliantly birefringent granules of the pigment were detected in Wright's stained smears, and the parasites easily localized, in 18 cases of malarial infection. Fresh, wet, coverslipped preparations of cultures of Plasmodium falciparum also were examined under polarized light. Serial dilutions of the cultures showed that, even at the very low level of 0.01% parasitemia, intracellular birefringent granules were detected in an average of 45 +/- 16 (SE) seconds at 500X magnification. Using polarized light is a simple, fast, sensitive, and specific method for localizing intracellular pigmented malaria parasites in wet preparations of blood.
Speech intelligibility in various spatial configurations of backgroundnoise (2005)

This study is concerned with the influence of spatial separation of disturbing sources of noise on the speech intelligibility. Spatial separation of speech and disturbing sources without changing their acoustic power may contribute to the significant improvement in the speech intelligibility. This problem has been recently analysed in many papers [1-5]. These works have confirmed an important role of the spatial configuration of sources. However, there have been no work investigating this problem for nonsense words (logatoms) that may provide more rigorous tests of this phenomenon. Moreover, this problem has not been analysed for Polish speech. It is important to emphasize that the acoustic and phonetic properties of Polish speech are somewhat different from those of English one. Therefore, the attempt to investigate the influence of the spatial separation of sound sources was made in this study. In the situation with more than one spatially separated disturbances, there may occur a so-called spatial suppression phenomenon, that is ``mutual suppression'' of disturbing sounds in the auditory system that brings about an increase in the speech intelligibility. This phenomenon is also called the spatial unmasking of speech [5, 6]. The research consist in determination of the speech intelligibility in the presence of one or two statistically independent speech-shaped noise sources varying in configuration. Only two pairs of the spatial configurations were investigated. Character of the dependences obtained in the study implies that the spatial suppression occurs in certain configurations of sources only. This effect brings about an increase in the speech intelligibility and can be explained on the basis of the binaural masking level difference (BMLD). It seems then that the BMLD may be a more general phenomenon and includes not only difference in the detection threshold of a pure tone masked by noise but also the improvement in the speech intelligibility, while speech is presented at the background of disturbing signals. Key words: speech intelligibility, speech perception, spatial separation, spatial suppression.
Gas Exchange Efficiency of a Membrane Oxygenator with Use of a Vibrating Flow Pump (1995)

We have developed a newly designed blood pump, named the vibrating flow pump (VFP), which can generate high frequency oscillated flow. The driving frequency is 10-50 Hz, and flow volume is linearly controlled electric power (current and voltage). The VFP was applied as the pump for extracorporeal circulation (ECC) in acute animal experiments. The gas exchange efficiency of the membrane oxygenator with the VFP and a roller pump (RP) was evaluated. Under general anesthesia with halothane, 7 adult goats underwent ECC; an inflow cannula was inserted into the right atrium, an outflow cannula was sutured to the descending thoratic aorta, and total ECC was performed with a flow of about 80 ml/min/kg. The ECC system with the VFP showed excellent gas exchange efficiency compared with that of the RP. The hemodynamics of ECC using the VFP were easily maintained within normal limits. These results suggest that the VFP is very useful as a pump for ECC; thus, a compact-sized ECC system may be achieved.
Human cathepsin S: chromosomal localization, gene structure, and tissue distribution (1994)

The human lysosomal cysteine proteinases, cathepsins H, L, and B, have been mapped to chromosomes 15, 9, and 8, respectively, and the genomic structures of cathepsins L and B have been determined. We report here the chromosomal localization and partial gene structure for a recently sequenced human cysteine proteinase, cathepsin S. A 20-kilobase pair genomic clone of the human cathepsin S gene was isolated from a human fibroblast genomic library and used to map the human cathepsin S gene to chromosome 1q21 by fluorescence in situ hybridization. This clone contains exons 1 through 5, introns 1 through 4, part of intron 5, and > 7 kilobase pairs of the 5'-flanking sequence. The gene structure of human cathepsin S is similar to that of cathepsin L through the first 5 exons, except that cathepsin S introns are substantially larger. Sequencing of the 5'-flanking region revealed, similar to human cathepsin B, no classical TATA or CAAT box. In contrast to cathepsin B, cathepsin S contains only two SP1 and at least 18 AP1 binding sites that potentially could be involved in regulation of the gene. This 5'-flanking region also contains CA microsatellites. The presence of AP1 sites and CA microsatellites suggest that cathepsin S can be specifically regulated. Results of Northern blotting using probes for human cathepsins B, L, and S are consistent with this hypothesis; only cathepsin S shows a restricted tissue distribution, with highest levels in spleen, heart, and lung. In addition, immunostaining of lung tissue demonstrated detectable cathepsin S only in lung macrophages. The high level of expression in the spleen and in phagocytes suggests that cathepsin S may have a specific function in immunity, perhaps related to antigen processing.
Microsomal phosphatidic acid phosphohydrolase of rat mammary tissue: I. General properties (1980)

The microsomal bound phosphatidic acid phosphohydrolase from lactating rat mammary tissue had a specific activity of six nmoles per mg protein per minute. The optimum pH was 7.0; magnesium at 1.3 mM was required for maximum activity, and at low substrate concentrations magnesium lowered the Km of the enzyme for phosphatidic acid. Diglycerides exerted little effect while diglyceride ether stimulated enzyme activity. Inorganic salts, i.e., potassium phosphate and potassium chloride, enhanced rates of phosphatidic acid hydrolysis under standard assay conditions.
Parallel sort and join for high speed database machine operations (1981)

This paper proposes a parallel joining and sorting algorithm that completes in about log N steps for N records. The algorithm is intended for large database systems. The algorithm and its required processor interconnection are simple and realistic. Thus, a performance improvement of three to four orders of magnitude can be realistically expected by applying this algorithm to database machines. Analysis is primarily made by simulations.
Formaldehyde-treated casein–safflower oil supplement for dairy cows: I. Effect on milk composition (1972)

Summary The effects of feeding lactating cows a daily supplement of 1 kg formaldehyde-treated casein–safflower oil (1:1, w/w) on the milk composition are reported. Three breeds, Jersey, Sahiwal and Sahiwal × Jersey crossbred were used. The formaldehyde treatment not only eliminated the suppressing effect on the milk, fat and protein yields and on the fat and protein contents usually encountered when such a level of unsaturated oil is fed to lactating cows, but also resulted, on the average, in 15 and 6% increases in the fat and protein contents respectively. The formaldehyde-treated dietary supplement also caused a decline of 5% in the solids-not-fat content, presumably due to a decrease in the lactose content. It is suggested that the formaldehyde treatment protects the casein from the ruminal proteolysis and this in turn prevents the encapsulated unsaturated oil from biohydrogenation and eliminates the diverse effects on rumen microflora and environment.
Cognitive Technology for Ultra-Wideband/WiMax Coexistence (2007)

Cognitive radios have been advanced as a technology for the opportunistic use of under-utilized spectrum wherein secondary devices sense the presence of the primary user and use the spectrum only if it is deemed empty. The distinguishing aspect of cognitive radios is the ability to sense the primary user and modify their transmission parameters to avoid interference to the primary. In this paper we explore the use of cognitive technology to enable the operation of ultra-wideband (UWB) devices in WiMax bands. In this particular example UWB devices must incorporate cognitive technology to detect and avoid (DAA) WiMax devices in certain regulatory domains. We start by discussing various options for detection and avoidance. We then describe the obstacles faced in achieving robust detection and avoidance with an on-chip implementation of basic DAA functionality. This implementation is based on the energy detector and can reliably detect WiMax uplink transmissions. Finally, we present empirical results for the operation of a single cognitive technology enabled UWB device with a WiMax system. This interaction also highlights the problem of dealing with listen before speak primaries where secondary transmission could interfere by denying the primary access to the medium.
Revealing anelasticity and structural rearrangements in nanoscale metallic glass films using <i>in situ</i> TEM diffraction (2016)

We used a novel diffraction-based method to extract the local, atomic-level elastic strain in nanoscale amorphous TiAl films during <i>in situ</i> transmission electron microscopy deformation, while simultaneously measuring the macroscopic strain. The complementary strain measurements revealed significant anelastic deformation, which was independently confirmed by strain rate experiments. Furthermore, the distribution of first nearest-neighbor distances became narrower during loading and permanent changes were observed in the atomic structure upon unloading, even in the absence of macroscopic plasticity. The results demonstrate the capability of <i>in situ</i> electron diffraction to probe structural rearrangements and decouple elastic and anelastic deformation in metallic glasses.
Controlled Polymerization in Mesoporous Silica toward the Design of Organic−Inorganic Composite Nanoporous Materials (2005)

Free-radical polymerization inside mesoporous silica has been investigated in order to open a route to functional polymer-silica composite materials with well-defined mesoporosity. Various vinyl monomers, such as styrene, chloromethyl styrene, 2-hydroxyethyl methacrylate, and methacrylic acid, were polymerized after impregnation into mesoporous silicas with various structures, which were synthesized using polyalkylene oxide-type block copolymers. The location of the polymers was systematically controlled with detailed structures of the silica framework and the polymerization conditions. Particularly noteworthy is the polymer-silica composite structure obtained by in situ polymerization after the selective adsorption of monomers as a uniform film on silica walls. The analysis of XRD data and the N(2) adsorption isotherms indicates the formation of uniform polymer nanocoating. The resultant polymer-silica composite materials can easily be post-functionalized to incorporate diverse functional groups in high density, due to the open porous structure allowing facile access for the chemical reagent. The fundamental characteristics of the composite materials are substantiated by testing the biomolecule's adsorption capacity and catalytic reactivity. Depending on the structure and composition of polymers, the resultant polymer-silica composite materials exhibit notably distinct adsorption properties toward biomolecules, such as proteins. Furthermore, it is demonstrated that the nanocoatings of polymers deposited on the mesopore walls have remarkably enhanced catalytic activity and selectivity, as compared to that of bulk polymer resins. We believe that, due to facile functionalization and attractive textural properties, the mesoporous polymer-silica composite materials are very useful for applications, such as adsorption, separation, host-guest complexes, and catalysis.
Oxygen Reduction on Silver Low-Index Single-Crystal Surfaces in Alkaline Solution:  Rotating Ring Disk<sub>Ag(</sub><i><sub>h</sub></i><i><sub>kl</sub></i><sub>)</sub> Studies (2006)

The rotating ring disk method is applied to investigate the oxygen reduction reaction on Ag single-crystal surfaces in alkaline solution over the temperature range 293-333 K. At all temperatures, the oxygen reduction reaction proceeds through the 4e- reaction pathway with a very small (approximately 0.5-2%) peroxide formation. At the same temperature and overpotentials, the kinetics of the ORR always increases in the order (100) < or = (111) < (110), indicating that the reaction is structure-sensitive. We present an interpretation of the structure sensitivity based on the supposition that it arises from (i) a potential-dependent adsorption of spectator hydroxyl ions and (ii) variations in activation energies, which are determined by the O2 adsorption on Ag single-crystal surfaces covered by adsorbed oxygenated species.
Ocular myasthenia gravis (1996)

Ocular myasthenia gravis may mimic any pupil-spared, painless, nonproptotic ophthalmoplegia with or without ptosis. This review references recent papers regarding clinical features, diagnostic techniques, and treatment for ocular myasthenia gravis.
ChemInform Abstract: A Facile and Template‐Free Hydrothermal Synthesis of Mn<sub>3</sub>O<sub>4</sub> Nanorods on Graphene Sheets for Supercapacitor Electrodes with Long Cycle Stability. (2012)

Abstract Graphene/Mn 3 O 4 composites for use in supercapacitors are hydrothermally synthesized from an ethylene glycol suspension of an aqueous dispersion of graphene sheets and KMnO 4 (autoclave, 120 °C, 4 h).
Cellular charge of Cryptococcus neoformans: contributions from the capsular polysaccharide, melanin, and monoclonal antibody binding (1997)

Cryptococcus neoformans is a human pathogenic fungus which is unusual in two respects: it has a polysaccharide capsule similar to that found in encapsulated bacteria and it can produce melanin. Capsular and melanization phenotypes are associated with virulence. In this study we analyzed the contributions of the capsular polysaccharide, melanization, and antibody binding to the capsule to the cellular charge of C. neoformans. Cell charge was inferred from measurements of zeta potential. The results indicate that (i) C. neoformans cells are significantly more negatively charged than Saccharomyces cerevisiae cells, (ii) the polysaccharide capsule of C. neoformans is responsible for the high negative charge of the cells, (iii) C. neoformans melanin is negatively charged, (iv) melanization in C. neoformans is associated with an increased negative charge per cell, and (v) antibody binding to the capsule of C. neoformans significantly alters the cell charge. These results suggest that alterations in cell charge attributable to polysaccharide capsule formation, melanization, and antibody binding may affect C. neoformans virulence given that macrophage phagocytosis is effected by the zeta potential of microorganisms.
Dynamic Response of Prevacuolar Compartments to Brefeldin A in Plant Cells (2006)

Little is known about the dynamics and molecular components of plant prevacuolar compartments (PVCs) in the secretory pathway. Using transgenic tobacco (Nicotiana tabacum) Bright-Yellow-2 (BY-2) cells expressing membrane-anchored yellow fluorescent protein (YFP) reporters marking Golgi or PVCs, we have recently demonstrated that PVCs are mobile multivesicular bodies defined by vacuolar sorting receptor proteins. Here, we demonstrate that Golgi and PVCs have different sensitivity in response to brefeldin A (BFA) treatment in living tobacco BY-2 cells. BFA at low concentrations (5-10 microg mL(-1)) induced YFP-marked Golgi stacks to form both endoplasmic reticulum-Golgi hybrid structures and BFA-induced aggregates, but had little effect on YFP-marked PVCs in transgenic BY-2 cells at both confocal and immunogold electron microscopy levels. However, BFA at high concentrations (50-100 microg mL(-1)) caused both YFP-marked Golgi stacks and PVCs to form aggregates in a dose- and time-dependent manner. Normal Golgi or PVC signals can be recovered upon removal of BFA from the culture media. Confocal immunofluorescence and immunogold electron microscopy studies with specific organelle markers further demonstrate that the PVC aggregates are distinct, but physically associated, with Golgi aggregates in BFA-treated cells and that PVCs might lose their internal vesicle structures at high BFA concentration. In addition, vacuolar sorting receptor-marked PVCs in root-tip cells of tobacco, pea (Pisum sativum), mung bean (Vigna radiata), and Arabidopsis (Arabidopsis thaliana) upon BFA treatment are also induced to form similar aggregates. Thus, we have demonstrated that the effects of BFA are not limited to endoplasmic reticulum and Golgi, but extend to PVC in the endomembrane system, which might provide a quick tool for distinguishing Golgi from PVC for its identification and characterization, as well as a possible new tool in studying PVC-mediated protein traffic in plant cells.
A model of transcriptional regulatory networks based on biases in the observed regulation rules (2002)

Abstract Control rules governing transciption of eukaryotic genes can be modeled as Boolean function, and these rules are strongly biased toward large numbers of “canalizing” inputs. The ensemble of networks with the observed canalizing bias predicts cells are in an ordered regime with convergent flow in transcription state space, a percolating subnetwork of genes fixed on or off an isolated islands of twinkling genes turning on or off, and a near power‐law distribution of cascades of gene activity changes following perturbations. The data suggest that a given cell state or type can be represented as an attractor of transcriptional activity or flow over time. © 2002 Wiley Periodicals, Inc.
Calcium Antagonists: Classification and Properties (1982)

Calcium antagonists (slow channel blockers, slow Ca2+ antagonists) are a heterogeneous group of substances with widely differing tissue specificities, potency and properties. Some of them exhibit other properties in addition to that of Ca2+ antagonism. In general these drugs can be considered as a subgroup of a much larger group of compounds which impede the entry of Ca2+ irrespective of the route of entry. The 'slow channel blockers' can be subdivided on the basis of their differing tissue specificities. The purpose of this article is to explore the possibility that a classification which is based on differing tissue specificities may reflect differing modes of action.