gebhart/patrepeval huggingface dataset:
Macrophage nitric oxide synthase: relationship between enzyme-bound tetrahydrobiopterin and synthase activity (1992)

Nitric oxide synthase (NOS) (EC 1.14.23) catalyzes the oxidation of L-arginine to citrulline and nitric oxide. The complex reaction carried out by NOS, which involves NADPH, O2, and enzyme-bound FAD, FMN, and tetrahydrobiopterin (BH4), has only recently begun to be elucidated. Herein we report the characterization of the pterin requirement of murine macrophage NOS. Although purified NOS activity was not dependent on BH4, activity was significantly enhanced by BH4 in a concentration-dependent fashion. NOS purified in the absence of added BH4 was found to contain substoichiometric concentrations of enzyme-bound pterin, where increased concentrations of bound pterin correlated with an increase in activity when assayed in the absence of exogenous BH4. However, NOS purified in the presence of BH4 followed by gel filtration exhibited a 1 mol of pterin:1 mol of NOS 130-kDa subunit stoichiometry and activity that was essentially independent of exogenous BH4. Experiments to probe a redox role for the pterin were carried out using pterin analogues. 6(R,S)-Methyltetrahydropterin was found to increase NOS activity in enzyme purified in the absence of BH4. However, the deaza analogue, 6(R,S)-methyl-5-deazatetrahydropterin, was not only incapable of supporting enzymatic turnover but also inhibited citrulline formation in a concentration-dependent manner. Overall, these results support a role for BH4 in the NOS reaction that involves stabilization of the enzyme and redox chemistry wherein a 1:1 stoichiometry between bound pterin and NOS subunit results in maximum activity.
RNA Extraction from Archival Formalin-Fixed Paraffin-Embedded Tissue: A Comparison of Manual, Semiautomated, and Fully Automated Purification Methods (2009)

The fully automated RNA-purification method showed the best reproducibility in gene expression analyses of neighboring sections of tissue blocks between 3 and 20 years of age and required the least overall and hands-on times. This method appears well suited for high-throughput RNA analyses in both routine clinical testing and translational research studies with archived FFPE material.
Prestack depth migration by symmetric nonstationary phase shift (2001)

Abstract A new depth migration method suitable for heterogeneous media is presented. The well-known phase shift plus interpolation (PSPI) method and the recently introduced nonstationary phase-shift (NSPS) method are combined into a single symmetric operator with improved accuracy and stability and with similar computational effort. For prestack depth migration, the symmetric operator is used in a recursive wavefield extrapolation to compute incident and reflected wavefields at any desired depth, and the ratio of the incident and reflected wavefields at a particular depth is used to estimate seismic reflectivity. When the velocity model is made piecewise constant laterally, the symmetric extrapolation operator can be computed efficiently using ordinary phase-shift extrapolation for a series of reference velocities and appropriate spatial windowing. Migration of the Marmousi synthetic data set by symmetric nonstationary phase shift (SNPS) provides an image that compares favorably with an image of the zero-offset reflectivity derived from the Marmousi velocity model.
Development of a Low-EMI Advanced Variable Speed Drive for Shipboard Applications (2007)

The U.S. Navy fleet has yet to widely adopt variable speed motor drives (VSDs), despite maturation of commercial inverter technologies. The stringent electric power (MIL-STD-1399) and electromagnetic interference (MIL-STD-461) requirements are a significant obstacle for standard VSDs, which require large and heavy filters to comply with these specifications. A commercial AC-link VSD was modified, tested, and shown to have compliant harmonic levels and conducted EMI levels.
Covering a Robot Fingertip With uSkin: A Soft Electronic Skin With Distributed 3-Axis Force Sensitive Elements for Robot Hands (2017)

Distributed tactile sensing is crucial to perform stable, subtle, and precise manipulation so that a robot can recognize and handle objects properly. However, currently existing skin sensors still have common problems such as complex and expensive production or are difficult to integrate into robot hands. In particular, a practical distributed soft skin sensor system that can cover various parts of the robot hand, measure force in 3-axis, with a subcentimeter spatial density, and digital output at the same time does not exist yet. This letter discusses uSkin, a soft, distributed, 3-axis force sensor for robot hands and presents its implementation for multicurved fingertips. The sensor is low-cost, easy to manufacture, and can measure normal and shear forces. The experimental results revealed that this sensor has 10% hysteresis for perpendicular force with a maximum range of 6 N. The Signal to Noise Ratio (SNR) value of 54 dB for 0.4 N load was achieved, which constitutes the state of the art for this kind of sensors. Evaluation experiments also showed that the distributed 3-axis load cells could produce vectors that represent the shape of objects. This opens the possibility that the sensor can be used for classifying different shapes. Furthermore, the fingertip sensor was installed on the Allegro hand and the changing force measurements when the robot is grasping an object are presented.
Direct soft x-ray response of a charge-coupled image sensor (1977)

To determine the feasibility of actively recovering data from x-ray imaging instruments used in the laser fusion program of Lawrence Livermore Laboratory, we have used a commercial, silicon video sensor to detect patterns of soft x rays (1–8 keV). The sensor is a two-dimensional, frame transfer, charge-coupled device (CCD), modified to allow direct access of x rays to the sensitive silicon. We discuss the x-ray sensitivity, linearity, and dynamic range of the CCD.
Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells (2013)

This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
Induction of noncatalytic TrkB neurotrophin receptors during axonal sprouting in the adult hippocampus (1993)

Brain-derived neurotrophic factor (BDNF) and its signal transducing receptor, the TrkB tyrosine protein kinase, are expressed at high levels in the hippocampus of the adult brain, suggesting a role for BDNF mechanisms in neuronal plasticity. To test this hypothesis, we used defined lesions of perforant path and fimbria-fornix, two major hippocampal afferents, to remove synapses on dendrites of dentate gyrus granule cells and pyramidal cells of Ammon's horn and induce synaptic rearrangements. These combined lesions remove afferent connections from entorhinal cortex and septum and produce massive sprouting of axons of the commissural/associational pathways into the molecular layer of the hippocampal dentate gyrus. At days 1, 3, and 6, the lesions decreased BDNF mRNA expression ipsilaterally to approximately 50% of control, with complete recovery at 14 d. The lesions did not alter trkB mRNA levels in neuronal layers of the hippocampus; however, they resulted in a pronounced induction of trkB mRNA expression in hippocampal non-neuronal cells 6-14 d after lesioning. The induction corresponded in time and place to the synaptic reorganization in the lesioned hippocampus. The mRNA species newly induced by the lesions corresponded to those transcripts encoding the noncatalytic TrkB receptor isoform that lacks the cytoplasmic protein kinase domain. Expression of mRNAs coding for neurotrophin-3 and the TrkC tyrosine protein kinase were not altered by the lesions. The findings suggest that truncated noncatalytic TrkB molecules expressed on the surface of glial cells play an important role in plasticity of the adult brain, possibly regulating the concentration of bioactive neurotrophins or the responsiveness of neurotrophin receptors. Alternatively, they may play a role in presenting neurotrophin molecules to growing axons.
Wavelet and subband transforms: fundamentals and communication applications (1997)

Subband and wavelet transforms have been a subject of great interest, especially in the fields of signal processing and applied mathematics. This article presents a tutorial on this subject, emphasizing the fundamentals and the reason for its success, importance, and potential. Subband and wavelet transform applications in communications are also reviewed. These application areas include interference excision, spread spectrum codes based on subband transform bases, CDMA, and discrete multitone transceivers.
DECOUPLE: defect current detection in deep submicron I/sub DDQ/ (2002)

I/sub DDQ/ test concept for deep submicron (DSM) devices named DECOUPLE (Defect Current Observation Under the Proportion of intrinsic Leakage currents) is proposed. A new clustering method obtained two defect free groups from a production data set by abstracting from a signature of intrinsic leakage current that is independent of process variations. Possible pass/fail tests, diagnosis, and detection of parametric defect currents are discussed on the data set. Another example of the pass/fail tests on a second product is presented.
<i>CDKL5</i> gene‐related epileptic encephalopathy: electroclinical findings in the first year of life (2011)

Infants with CDKL5-related early epileptic encephalopathy can present in the first year of life with an unusual electroclinical pattern of 'prolonged' generalized tonic-clonic seizures.
Blue Native Polyacrylamide Gel Electrophoresis to Monitor Inflammasome Assembly and Composition (2013)

Inflammasomes are large cytosolic multi-protein complexes that form in response to infection and other stimuli, and play an important role in the innate immune response. Traditional methods for assaying inflammasome activation have relied on detection of autoproteolysis of the cysteine protease caspase-1, or proteolytic processing of its substrate, the inflammatory cytokine IL-1β. These measurements report on the final output of inflammasome activation, but do not assess inflammasome assembly and composition. Here we describe the application of blue native gel electrophoresis as a tool for investigating stimulus-dependent inflammasome assembly and for identification of individual components within the multi-protein complex.
Mobilizing COVID-19 Science (2020)

While there are many uncertainties about the ensuing COVID-19 pandemic, scientific mobilization that integrates knowledge from across the wide-ranging intersection of applicable expertise will optimize our response strategy. As we continue to coordinate these efforts, sociological contributions can continue to identify improved social coordination opportunities, even while practicing social distancing.
Can kiwis and koalas as cultural primes induce perceptual bias in Australian English speaking listeners? (2019)

The presence of culturally significant objects has been shown to induce biases in speech perception consistent with features of the dialect relevant to the object. Questions remain about the transferability of this effect to different dialect contexts, and the efficacy of the task in inducing the effect. This paper details an Australian-context experiment modelled on Hay and Drager’s (2010) New Zealand-context stuffed toy study. Seventy-five listeners heard spoken Australian English (AusE) phrases with phrase-final monosyllabic words containing either kit, dress, or trap vowels. Each phrase was followed by audio presentation of a six-step synthesized vowel continuum, from New Zealand English (NZE)-like to exaggerated AusE-like tokens. Listeners attempted to match one of the synthesized variants to the speaker’s realization of the target vowel. Listeners were exposed to one of two priming conditions, established by stuffed toy kiwis (New Zealand) and stuffed toy koalas (Australia), or a control condition (no toy). Contrary to Hay and Drager (2010), token selections did not differ significantly between the New Zealand and Australian priming conditions. However, reversing the order of continuum presentation did significantly affect token selection for kit vowels, raising questions about the task design itself. Results suggest that the influence of regional primes on speech perception may be more limited than previously thought.
Radiotherapy of malignant melanoma cerebral metastases - results of treatment (2004)

A i m. The aim of the study was to evaluate the efficacy of radiotherapy in the treatment of malignant melanoma brain metastases. Material and methods . 20 patients with malignant melanoma brain metastases treated with palliative radiotherapy at the Centre of Oncology in Krakow between 1990 and 2000. In 8 cases the patients were irradiated twice daily (39 Gy in 13 fractions of 300 cGy) and in 12 cases once daily (20-40 Gy in 5-10 fractions of 400 cGy). Results . The overall 2-year survival rate in the entire group of 20 palliatively irradiated patients was 5%. The median survival was 5.5 months. Conclusio n. Radiation therapy is effective in the palliative management of malignant melanoma brain metastases. Wyniki leczenia napromienianiem chorych z przerzutami czerniaka z∏oEliwego do mozgu C e l. Ocena roli radioterapii w leczeniu chorych na czerniaka z∏oEliwego z przerzutami do mozgu na podstawie doEwiadczeƒ Centrum Onkologii w Krakowie. Materia∏ i m etody . W latach 1990-2000 w Centrum Onkologii w Krakowie leczono napromienianiem 20 chorych na czerniaka z∏oEliwego skory z przerzutami do mozgu. U wszystkich chorych zastosowano paliatywne napromienianie ca∏ego mozgu. 8 chorych napromieniano dwa razy dziennie dawka 39 Gy w 13 frakcjach po 300 cGy. 12 chorych napromieniano raz dziennie i otrzymali oni dawk´ 20-40 Gy w 5-10 frakcjach po 400 cGy.
FORMATION OF CARBAMATE DERIVATIVES BY REACTION OF CHLOROMETHYLOXIRANE OR PHENYLOXIRANE WITH CARBON DIOXIDE AND ALIPHATIC AMINES (1978)

Abstract Reactions of chloromethyloxirane or phenyloxirane with carbon dioxide and aliphatic amines in methanol afforded corresponding hydroxyoxazinone or hydroxycarbamate derivatives under mild conditions.
JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form (1988)

JCAMP-DX is a standard file form for exchange of infrared spectra and related chemical and physical information between spectrometer data systems of different manufacture, main-frame time-sharing systems, general purpose lab computers, and personal computers. It is compatible with all media: telephone, magnetic and optical disk, magnetic tape, and even the printed page (via optical reader). All data are stored as labeled fields of variable length using printable ASCII characters. A JCAMP-DX spectrum is a text file which can be viewed, corrected, and annotated with a text editor. The present focus is on infrared spectra, but JCAMP-DX can easily accommodate Raman, UV, NMR, mass, and other types of spectra, x-ray powder patterns, chromatograms, thermograms, and other plots which require the capability of representing contours as well as peak position and intensity. JCAMP-DX also provides for combining adequate information about the sample and method of observation with its spectrum.
The Kinetic Mechanism of Glycerokinase (1974)

Abstract The steady state kinetics of glycerokinase from Candida mycoderma has been studied at pH 7.0 by initial velocity and product inhibition techniques and by dead-end inhibition by the inert coordination complex, chromium ATP. The mechanism appears to be Ordered Bi Bi with glycerol adding before the magnesium nucleotide and l-glycerol 3-phosphate being released last. With different nucleotides as substrates the dissociation constant for glycerol is constant, but the Kms of the nucleotides vary from 9 µm for MgATP to 2400 µm for MgXTP. In addition to glycerol (Km, 15 µm), dihydroxyacetone (Km, 5 mm) and l-glyceraldehyde (Km, 3.7 mm) are phosphorylated. d-Glyceraldehyde (Km, 0.5 mm) is not phosphorylated but incluces hydrolysis of MgATP. Glycerol is competitive versus l-glycerol 3-phosphate and noncompetitive versus MgADP. CrATP is competitive versus MgATP and is uncompetitive versus glycerol or MgADP. The dissociation constant of CrATP from the enzymeglycerol complex is 0.5 to 0.7 µm. In an ordered mechanism the sum of the vertical coordinates of the crossover points in initial velocity patterns for forward and reverse reactions, divided by the sum of reciprocal velocities in both directions, is a dimensionless number varying from 0 for a mechanism where second product release is solely rate limiting, to 1 for a rapid equilibrium ordered mechanism where catalysis and/or first product release is solely rate limiting. Where the two maximum velocities are not equal, this number indicates the rate-limiting step in the slower direction only. For glycerokinase this analysis and comparison of inhibition constants for CrATP versus MgATP and MgADP show that in the reverse direction, glycerol release is 2 to 5 times faster than catalysis and/or release of MgATP.
<i>In Situ</i> Synthesis and Alignment of Au Nanoparticles within Hexagonally Packed Cylindrical Domains of Diblock Copolymers in Bulk (2009)

We present a simple method to prepare hexagonally packed metallic nanocylinders based on gold nanoparticles embedded in a copolymeric matrix. The gold nanoparticles are generated selectively within the P4VP-rich cylindrical domains of a polystyrene-b-poly-4-vinylpyridine (PS-b-P4VP) diblock copolymer. In order to achieve this selectivity, a gold precursor (HAuCl4) is coupled to the pyridine blocks of a spherical PS327-b-P4VP27 block copolymer. In consequence, the hybrid block copolymer is able to self-assemble in a hexagonally packed cylinders morphology. The application of mechanical oscillatory shear improved markedly the alignment of these nanocylinders, while simultaneously the gold precursor was reduced in situ into gold nanoparticles. Following rheological characterization in the linear viscoelastic regime, a set of alignment parameters were comprehensively selected and checked with a series of transmission electron microscopy (TEM) micrographs. An optimal temperature of alignment was found after systematic evaluation of samples sheared at different temperatures. The block copolymer exhibited an increase in the domain period as a consequence of chain rearrangements around the newly formed gold nanoparticles. The hexagonally packed morphology was preserved, and under the optimal conditions single grain sizes showed significant improvement to macroscale order in comparison to nonaligned samples. In contrast to current multistep lithographic techniques, the present method constitutes a simple path to produce three-dimensional organic-inorganic conductive nanowires with periodicities at the macroscopic level.
The intracellular transport of low density lipoprotein-derived cholesterol is defective in Niemann-Pick type C fibroblasts. (1989)

Niemann-Pick disease type C (NPC) is characterized by substantial intracellular accumulation of unesterified cholesterol. The accumulation of unesterified cholesterol in NPC fibroblasts cultured with low density lipoprotein (LDL) appears to result from the inability of LDL to stimulate cholesterol esterification in addition to impaired LDL-mediated downregulation of LDL receptor activity and cellular cholesterol synthesis. Although a defect in cholesterol transport in NPC cells has been inferred from previous studies, no experiments have been reported that measure the intracellular movement of LDL-cholesterol specifically. We have used four approaches to assess intracellular cholesterol transport in normal and NPC cells and have determined the following: (a) mevinolin-inhibited NPC cells are defective in using LDL-cholesterol for growth. However, exogenously added mevalonate restores cell growth equally in normal and NPC cells; (b) the transport of LDL-derived [3H]cholesterol to the plasma membrane is slower in NPC cells, while the rate of appearance of [3H]acetate-derived, endogenously synthesized [3H]cholesterol at the plasma membrane is the same for normal and NPC cells; (c) in NPC cells, LDL-derived [3H]cholesterol accumulates in lysosomes to higher levels than normal, resulting in defective movement to other cell membranes; and (d) incubation of cells with LDL causes an increase in cholesterol content of NPC lysosomes that is threefold greater than that observed in normal lysosomes. Our results indicate that a cholesterol transport defect exists in NPC that is specific for LDL-derived cholesterol.
Binding of Boron and Alkali Metal Cations by a Pseudocryptand (1995)

A synthetic analogue of the natural antibiotic boromycin is described. The negatively charged pseudocryptand 1 possessing a spiroborate moiety binds the potassium cation with the highest stability thus far observed with synthetic receptors. Furthermore, compound 1 displays high selectivity for potassium over other alkali metal cations.
Down-regulation of interferon γ-activated STAT1 by UV light (1997)

STAT1 is a cytoplasmic transcription factor that is phosphorylated by Janus kinases (Jak) in response to interferon-gamma (IFNgamma). Phosphorylated STAT1 translocates to the nucleus, where it turns on specific sets of IFNgamma-inducible genes. Here, we show that UV light interferes with tyrosine phosphorylation of STAT1, thereby hindering IFNgamma from exerting its biological effects. This effect is not due to a down-regulation of the IFNgamma receptor because phosphorylation of upstream-located Jak1 and Jak2 was not suppressed by UV light. In contrast, UV light had no effect on the phosphorylation of STAT3, which is activated by the proinflammatory cytokine interleukin 6. The UV light effect on STAT1 phosphorylation could be antagonized by vanadate, indicating at least partial involvement of a protein tyrosine phosphatase. Therefore, this study indicates a mechanism by which UV light can inhibit gene activation and suggests STAT1 as a new extranuclear UV target closely located to the membrane.