gebhart/patrepeval huggingface dataset:
Synchrotron Infrared Measurements of Protein Phosphorylation in Living Single PC12 Cells during Neuronal Differentiation (2012)

Protein phosphorylation is a post-translational modification that is essential for the regulation of many important cellular activities, including proliferation and differentiation. Current techniques for detecting protein phosphorylation in single cells often involve the use of fluorescence markers, such as antibodies or genetically expressed proteins. In contrast, infrared spectroscopy is a label-free and noninvasive analytical technique that can monitor the intrinsic vibrational signatures of chemical bonds. Here, we provide direct evidence that protein phosphorylation in individual living mammalian cells can be measured with synchrotron radiation-based Fourier transform-infrared (SR-FT-IR) spectromicroscopy. We show that PC12 cells stimulated with nerve growth factor (NGF) exhibit statistically significant temporal variations in specific spectral features, correlating with changes in protein phosphorylation levels and the subsequent development of neuron-like phenotypes in the cells. The spectral phosphorylation markers were confirmed by bimodal (FT-IR/fluorescence) imaging of fluorescently marked PC12 cells with sustained protein phosphorylation activity. Our results open up new possibilities for the label-free real-time monitoring of protein phosphorylation inside cells. Furthermore, the multimolecule sensitivity of this technique will be useful for unraveling the associated molecular changes during cellular signaling and response processes.
Marked Decrease in Sleepiness in Patients with Sleep Apnea by Etanercept, a Tumor Necrosis Factor-α Antagonist (2004)

The proinflammatory cytokines, TNFalpha and IL-6, are elevated in obstructive sleep apnea (OSA) and have been proposed as mediators of excessive daytime sleepiness in humans. We tested the effects of etanercept, a medication that neutralizes TNFalpha and is approved by the FDA for the treatment of rheumatoid arthritis, in eight obese male apneics. These patients participated in a pilot, placebo-controlled, double-blind study during which nighttime polysomnography, multiple sleep latency test, and fasting blood glucose and plasma levels of IL-6, C-reactive protein, insulin, and adiponectin were obtained. There was a significant and marked decrease in sleepiness by etanercept, which increased sleep latency during the multiple sleep latency test by 3.1 +/- 1.0 min (P < 0.05) compared with placebo. Also, the number of apneas/hypopneas per hour was reduced significantly by the drug compared with placebo (52.8 +/- 9.1 vs. 44.3 +/- 10.3; adjusted difference, -8.4 +/- 2.3; P < 0.05). Furthermore, IL-6 levels were significantly decreased after etanercept administration compared with placebo (3.8 +/- 0.9 vs. 1.9 +/- 0.4 pg/ml; adjusted difference, -1.9 +/- 0.5; P < 0.01). However, no differences were observed in etanercept vs. placebo in the levels of fasting blood glucose and plasma C-reactive protein, insulin, and adiponectin. We conclude that neutralizing TNFalpha activity is associated with a significant reduction of objective sleepiness in obese patients with OSA. This effect, which is about 3-fold higher than the reported effects of continuous positive airway pressure on objective sleepiness in patients with OSA (0.9 vs. 3.1 min), suggests that proinflammatory cytokines contribute to the pathogenesis of OSA/sleepiness.
New Range of Vectors with a Stringent 5-Fluoroorotic Acid-Based Counterselection System for Generating Mutants by Allelic Replacement in Staphylococcus aureus (2012)

We have developed a range of vectors for allelic replacements in Staphylococcus aureus to facilitate genetic work in this opportunistic pathogen. The central feature of the vector range is a selection/counterselection system that takes advantage of the 5-fluoroorotic acid (FOA) resistance and pyrimidine prototrophy caused by the loss and gain, respectively, of the pyrF and pyrE genes. This system allows for stringent counterselection of the vectors during the second homologous recombination of a classic allelic replacement. The basic vector pRLY2, which contains the pyrFE genes from Bacillus subtilis, was combined with chloramphenicol, erythromycin, and tetracycline resistance genes and four different versions of nonreplicative or conditionally replicative origins of replication. The choice between these 12 different pRLY vectors allows for high versatility and ensures that the vectors can be used in virtually any genetic background. Finally, as proof of concept, we present six deletions or modifications of components in the S. aureus degradosome as well as the operon containing the cshB DEAD box helicase.
Prediction-based highly sensitive CRISPR off-target validation using target-specific DNA enrichment (2020)

CRISPR effectors, which comprise a CRISPR-Cas protein and a guide (g)RNA derived from the bacterial immune system, are widely used for target-specific genome editing. When the gRNA recognizes genomic loci with sequences that are similar to the target, deleterious mutations can occur. Off-target mutations with a frequency below 0.5% remain mostly undetected by current genome-wide off-target detection techniques. Here we report a method to effectively detect extremely small amounts of mutated DNA based on predicted off-target-specific amplification. In this study, we used various genome editors to induce intracellular genome mutations, and the CRISPR amplification method detected off-target mutations at a significantly higher rate (1.6~984 fold increase) than an existing targeted amplicon sequencing method. In the near future, CRISPR amplification in combination with genome-wide off-target detection methods will allow detection of genome editor-induced off-target mutations with high sensitivity and in a non-biased manner.
Quinoline, quinazoline and acridone alkaloids (2000)

Covering: July 1998 to June 1999. Previous review: 1999, 16, 697.
Laser and Microwave Observations of Sea-Surface Condition for Fetch-Limited 17- to 25-m/s Winds (1970)

The variability of sea-surface conditions has been observed from a low-flying aircraft by a laser-wave profiling system and a scanning horizontally polarized 19.35-GHz passive microwave radiometer for fetch-limited wind speeds of 17 to 25 m/s in the North Sea. Wave profiles obtained with the laser system have been analyzed and show that wave growth occurs simultaneously at all frequencies and that an equilibrium value for the higher frequency components is eventually reached, but not before substantially higher (overshoot) values are obtained. Simultaneous observations of the microwave brightness temperature at vertical incidence show an increase with wind speed (or roughness of the sea surface) of 1°K/m/s. This increase, not in accord with theory, is shown to be a function of the percentage of foam coverage of the ocean surface.
Development of a New Electrodeposition Process for Plating of Zn-Ni-X (X = Cd, P) Alloys Permeation Characteristics of Zn-Ni-Cd Ternary Alloys (2000)

It is shown that an electrodeposited Zn‐Ni‐Cd alloy coating produced from sulfate electrolyte inhibits the discharge of hydrogen on carbon steel. The newly developed ternary alloys have approximately ten times higher corrosion resistance when compared to a Zn‐Ni alloy. Hydrogen permeation characteristics of Zn‐Ni‐Cd alloy coatings were studied and compared with those of a bare and a Zn‐Ni alloy coated steel. The transfer coefficient, α, exchange current density, , thickness dependent adsorption‐absorption rate constant, k'', recombination rate constant, , surface hydrogen coverage, , were obtained by applying a mathematical model to experimental results. Alloys obtained from baths containing higher concentration than 3 g/L of in the sulfate plating bath are seen to have superior permeation inhibition properties compared to the Zn‐Ni alloy coating and bare steel. The hydrogen permeation current was zero under normal corroding conditions for Zn‐Ni‐Cd alloy and it increased to at a cathodic overpotential of 250 mV. The hydrogen permeation current density for steel and Zn‐Ni alloy under similar conditions were 62.1 and , respectively. © 2000 The Electrochemical Society. All rights reserved.
A Comparison of Additivity Axioms in Timed Transition Systems. (1993)

This paper discusses some axioms from the literature which have been used to define properties of timed transition systems. The additivity axiom proposed by (amongst others) Wang, and Nicollin and Sifakis is compared with the trajectory axiom of Lynch and Vaandrager. Some conditions for an additive transition system to be trajectoried are discussed. These are proved sufficient by using some simple terminology from category theory to show how this problem about timed transition systems can be turned into an equivalent problem about monotone functions on partially ordered sets. We also discuss trajectory (bi)simulation, which is a variant of Ho-Stuart&apos;s path bisimulation, and use similar techniques to discuss when (bi)simulation is equivalent to trajectory (bi)simulation.
Crystallization of Amorphous Lactose (1992)

ABSTRACT Crystallization of amorphous lactose was studied at constant water content and at constant relative humidity above glass transition temperature (Tg). The rate of crystallization was followed using differential scanning calorimetry. Crystallization at constant water content increased the amount of water in the remaining amorphous matrix, which decreased T g and accelerated crystallization. At constant relative humidity crystallization proceeded at a rate determined by T ‐T g which increased with crystallinity. Temperature dependence of time to complete crystallization was confirmed to follow Williams‐Landel‐Ferry (WLF) equation. The results can be used to evaluate diffusion and crystallization kinetics of amorphous carbohydrates.
Transport Through Carbon Nanotube Wires (2001)

This viewgraph presentation gives an overview of the the current carrying capacity of nanotube wires. Information is given on the motivation for the research, models and assumptions, Bragg reflection and Zener tunneling effects, and the influence of defects. Results show that dI/dv versus V does not increase in a manner commensurate with the increase in the number of subbands; in small diameter nanotubes, Zener tunneling is ineffective; Zener tunneling contributes to current with increase in nanotube diameter; and the increase in dI/dV with bias is much smaller than the increase in the number of subbands.
Vowels formants analysis allows straightforward detection of high arousal emotions (2011)

Recently, automatic emotion recognition from speech has achieved growing interest within the human-machine interaction research community. Most part of emotion recognition methods use context independent frame-level analysis or turn-level analysis. In this article, we introduce context dependent vowel level analysis applied for emotion classification. An average first formant value extracted on vowel level has been used as unidimensional acoustic feature vector. The Neyman-Pearson criterion has been used for classification purpose. Our classifier is able to detect high-arousal emotions with small error rates. Within our research we proved that the smallest emotional unit should be the vowel instead of the word. We find out that using vowel level analysis can be an important issue during developing a robust emotion classifier. Also, our research can be useful for developing robust affective speech recognition methods and high quality emotional speech synthesis systems.
Distributed Aggregation Algorithms with Load-Balancing for Scalable Grid Resource Monitoring (2007)

Scalable resource monitoring and discovery are essential to the planet-scale infrastructures such as grids and PlanetLab. This paper proposes a scalable grid monitoring architecture that builds distributed aggregation trees (DAT) on a structured P2P network like Chord. By leveraging Chord topology and routing mechanisms, the DAT trees are implicitly constructed from native Chord routing paths without membership maintenance. To balance the DAT trees, we propose a balanced routing algorithm on Chord that dynamically selects the parent of a node from its finger nodes by its distance to the root. This paper shows that this balanced routing algorithm enables the construction of almost completely balanced DATs, when nodes are evenly distributed in the Chord identifier space. We have evaluated the performance and scalability of a DAT prototype implementation with up to 8192 nodes. Our experimental results show that the balanced DAT scheme scales well to a large number of nodes and corresponding aggregation trees. Without maintaining explicit parent-child membership, it has very low overhead during node arrival and departure. We demonstrate that the DAT scheme performs well in grid resource monitoring.
A Highly Sensitive Enzyme Immunoassay for Mouse β Nerve Growth Factor (1983)

A sensitive two-site enzyme immunoassay system for mouse beta nerve growth factor (NGF) was developed, based on the sandwiching of the antigen between anti-mouse beta NGF antibody IgG coated to a polystyrene tube and anti-mouse beta NGF antibody Fab'-linked beta-D-galactosidase (beta-D-galactoside hydrolase, EC 3.2.1.23). This method has the following advantages: (a) the procedures are simple and rapid compared to bioassay or two-site radioimmunoassay; (b) antibody Fab'-beta-D-galactosidase complex is more stable than 125I-labeled antibody; (c) purified beta NGF is detectable at a concentration as low as 10 pg/ml. Our enzyme immunoassay was used to examine the levels of NGF in some tissues of mice. The submaxillary gland contained a high concentration of NGF. However, other tissues, such as the heart, brain, and skeletal muscle, and serum did not contain detectable NGF. These results support recent findings by other investigators that NGF was not found in the organs/tissues other than the submaxillary gland of mice.
Water solubilization, determination of the number of different types of single-wall carbon nanotubes and their partial separation with respect to diameters by complexation with η-cyclodextrin (2003)

Complexation of single-wall carbon nanotubes with 12-membered cyclodextrins enables not only their solubilization in water but also their partial separation with respect to diameters and determination of the number of nanotube types on the basis of NMR spectra.
Elastic-constant variability in stainless-steel 304 (1980)

Variability of elastic constants in stainless-steel 304 was determined by measuring longitudinal and transverse ultrasonic velocities in 20 samples acquired randomly. Three kinds of variations—sample to sample, directional within a sample, and repeated measurements on a single sample—are reported for four elastic constants: the bulk modulus, Young’s modulus, shear modulus, and Poisson’s ratio. Because of surprisingly small variations, 1% or less, the principal problem became measurement sensitivity and reproducibility. To overcome this problem, a high-resolution measurement system was devised using general-purpose equipment augmented with a very simple impedance-transforming amplifier and an FET transmission gate. With this system the often-reported troublesome transit-time correction disappeared. Effects due to frequency and directionality were negligible.
HiPPAI: High Performance Portable Accelerator Interface for SoCs (2009)

Specialized hardware accelerators are enabling today's System on Chip (SoC) platforms to target various applications. In this paper we show that as these SoCs evolve in complexity and usage, the programming models for such platforms need to evolve beyond the traditional driver oriented architecture. Using a test set up that employs a programmable FPGA based accelerator to implement one of the critical computation functions of a Mobile Augmented Reality based workload, we describe the performance drawbacks that a conventional programming model brings to compute environments employing hardware accelerators. We show that these performance issues become more critical as the interface latencies continue to improve over time with better hardware integration and efficient interconnect technologies. Under these usage scenarios, we show with measurements that the software overheads enforced by the current programming model, like those associated with system calls, memory copy and memory address translations account for a major part of the performance overheads. We then propose a novel High Performance Portable Accelerator Interface (HiPPAI) for SoC platforms using hardware accelerators to reduce the software overheads mentioned above. In addition, we position the new programming interface to allow for function portability between software and hardware function accelerators to reduce the application development effort. Our proposed model relies on two major building blocks for performance improvement. A uniform virtual memory addressing model based on hardware IOMMU support and direct user mode access to accelerators. We demonstrate how these enhancements reduce the overheads of system calls and address translations at the user/kernel boundary in traditional software stacks and enable function portability.
Migraine: diagnosis, management, and new treatment options. (2002)

Primary care physicians must manage migraine patients with treatments that demonstrate a balance between efficacy and tolerability.
A Click‐Chemistry‐Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry (2019)

Mass spectrometry is the method of choice for the characterisation of proteomes. Most proteins operate in protein complexes, in which their close association modulates their function. However, with standard MS analysis, information on protein-protein interactions is lost and no structural information is retained. To gain structural and interactome data, new crosslinking reagents are needed that freeze inter- and intramolecular interactions. Herein, the development of a new reagent, which has several features that enable highly sensitive crosslinking MS, is reported. The reagent enables enrichment of crosslinked peptides from the majority of background peptides to facilitate efficient detection of low-abundant crosslinked peptides. Due to the special cleavable properties, the reagent can be used for MS<sup>2</sup> and potentially for MS<sup>3</sup> experiments. Thus, the new crosslinking reagent, in combination with high-end MS, should enable sensitive analysis of interactomes, which will help researchers to obtain important insights into cellular states in health and diseases.
Cardiopulmonary Resuscitation Outcomes in Hospitalized Community‐Dwelling Individuals and Nursing Home Residents Based on Activities of Daily Living (2013)

Functional and residential status are important predictors of survival after in-hospital cardiac arrest. Contrary to the hypothesis but reassuring from a quality-of-care perspective, less-aggressive attempts at resuscitation do not appear to contribute to poorer outcomes in individuals dependent in ADL, regardless of residential status.
A FORTRAN preprocessor to support encapsulated data abstraction definitions (1979)

In an encapsulated data abstraction definition a data type and the set of all operations which may access or modify instances of the type are defined together.
The growth of CdHgTe on GaAs and fabrication of high-quality photodiodes (1990)

The use of metal organic vapor phase epitaxy (MOVPE) for the growth of device quality CdHgTe (MCT) on GaAs has been studied extensively. This is the first report of diode formation by mercury diffusion in the MOVPE grown material. It is also the first report of medium-wavelength infrared (MWIR) photodiodes made in the material. The effect of altering the cadmium to tellurium alkyl ratios on the growth of a CdTe buffer on (100) and (111)GaAs was investigated. For every alkyl ratio used, it was possible to grow (111) or (100)CdTe on (100)GaAs. (100)CdTe/(100)GaAs samples exhibited very sharp, well-defined photoluminescence spectra and x-ray rocking curve full width half-maximum (FWHM) peaks of &lt;90 arc s were found for layers of 6–10 μm thick. Generally the (111)CdTe/(111)GaAs layers were dominated by twins, but the growth of untwinned (111)CdTe and MCT is reported. CdTe, high x MCT, and combinations of CdTe and HgTe layers were used as buffers for (100)MCT growth to reduce the hillock density. The combinations of CdTe and HgTe layers gave rise to the lowest hillock density (at best 30–100/cm2) over a large area (25×25 mm2). FWHMs of 80–90 arc s are routinely achieved for (100)MCT layers. Linear diode arrays have been fabricated with 77 K R0A values typically of 3×103 Ω cm2 for 7.5 μm cutoff. The detectivity of a 5.5 μm cutoff diode was 1.5×1011 cm Hz1/2 W−1 at 77 K, and 1.3×1010 cm Hz1/2 W−1 at 193 K. This is comparable to the performance obtained with the best traveling heater method devices.
The Portals 4.0 Network Programming Interface (2012)

This report presents a specification for the Portals 4.0 network programming interface. Portals 4.0 is intended to allow scalable, high-performance network communication between nodes of a parallel computing system. Portals 4.0 is well suited to massively parallel processing and embedded systems. Portals 4.0 represents an adaption of the data movement layer developed for massively parallel processing platforms, such as the 4500-node Intel TeraFLOPS machine. Sandia’s Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4.0 is targeted to the next generation of machines employing advanced network interface architectures that support enhanced offload capabilities.
WHAT KEEPS WRITING ALIVE IN OUR CLASSROOMS? (1993)

Experimentation in writing and reading were highly valued by the teachers and students in the classrooms in this article. To not know how to do something is the behavioral norm in these classrooms. The teachers set aside daily time for the students to learn to read from books of their choice and to write on topics of their choice. When the teachers and students discuss their reading and writing, the diversity of their voices shows the value they place on individual differences. Self‐evaluation becomes a skill students use to assess their progress and to set goals for their continued growth.