gebhart/patrepeval huggingface dataset:
Anaerobic Biodegradation of Aromatic Hydrocarbons: Pathways and Prospects (2008)

Aromatic hydrocarbons contaminate many environments worldwide, and their removal often relies on microbial bioremediation. Whereas aerobic biodegradation has been well studied for decades, anaerobic hydrocarbon biodegradation is a nascent field undergoing rapid shifts in concept and scope. This review presents known metabolic pathways used by microbes to degrade aromatic hydrocarbons using various terminal electron acceptors; an outline of the few catabolic genes and enzymes currently characterized; and speculation about current and potential applications for anaerobic degradation of aromatic hydrocarbons.
Synthesis of Benzobisoxazole-Linked Two-Dimensional Covalent Organic Frameworks and Their Carbon Dioxide Capture Properties (2016)

Developing novel synthetic strategies to construct crystalline polymeric materials with excellent chemical stability and high carbon capture capacity has become a challenging process. Herein, we report the synthesis of two novel 2D benzobisoxazole-linked covalent organic frameworks (BBO-COFs) utilizing C<sub>3</sub>-symmetric formyl- and C<sub>2</sub>-symmetric <i>o</i>-aminophenol-substituted molecular building blocks. The BBO-COFs exhibit excellent water stability, high surface areas, and great CO<sub>2</sub> uptake capacities. This general synthetic method affords the opportunity to prepare ordered BBO-based polymeric materials for carbon capture, chemical sensing, and organic electronic applications.
Phase-diversity correction of turbulence-induced space-variant blur (1994)

Space-variant blur is encountered when objects extend beyond the isoplanatic patch associated with the intervening atmospheric turbulence. The method of phase diversity, used to estimate jointly the object and the aberrations, is generalized to accommodate turbulence-induced space-variant blur. This generalization utilizes a parametric model for the blur function that is constructed with multiple phase screens. Simulation results are presented that demonstrate the recovery of near-diffraction-limited imagery from phase-diversity imagery that has been degraded with rather severe anisoplanatism.
Bright Bioluminescent BRET Sensor Proteins for Measuring Intracellular Caspase Activity (2017)

FRET-based caspase activity probes have become important tools to monitor apoptotic cell signaling. However, their dependence on external illumination is incompatible with light sensitive cells and hampers applications that suffer from autofluorescence and light scattering. Here we report the development of three caspase sensor proteins based on Bioluminescence Resonance Energy Transfer (BRET) that retain the advantages of genetically encoded, ratiometric optical probes but do not require external illumination. These sensors consist of the bright and stable luciferase NanoLuc and the fluorescent protein mNeonGreen, fused together via a linker containing a recognition site for caspase-3, -8, or -9. <i>In vitro</i> characterization showed that each caspase sensor displayed a robust 10-fold decrease in BRET ratio upon linker cleavage, with modest caspase specificity. Importantly, whereas scattering and background fluorescence precluded FRET-based detection of intracellular caspase activity in plate-reader assays, such measurements could be easily performed using our caspase BRET sensors in a high throughput format. The brightness of the BRET sensors also enabled long-term single-cell imaging, allowing BRET-based recording of cell heterogeneity in caspase activity in a heterogenic cell population.
Human Primary Osteocyte Differentiation in a 3D Culture System (2009)

Studies on primary osteocytes, which compose >90-95% of bone cells, embedded throughout the mineralized matrix, are a major challenge because of their difficult accessibility and the very rare models available in vitro. We engineered a 3D culture method of primary human osteoblast differentiation into osteocytes. These 3D-differentiated osteocytes were compared with 2D-cultured cells and with human microdissected cortical osteocytes obtained from bone cryosections. Human primary osteoblasts were seeded either within the interspace of calibrated biphasic calcium phosphate particles or on plastic culture dishes and cultured for 4 wk in the absence of differentiation factors. Osteocyte differentiation was assessed by histological and immunohistological analysis after paraffin embedding of culture after various times, as well as by quantitative RT-PCR analysis of a panel of osteoblast and osteocyte markers after nucleic acid extraction. Histological analysis showed, after only 1 wk, the presence of an osteoid matrix including many lacunae in which the cells were individually embedded, exhibiting characteristics of osteocyte-like cells. Real-time PCR expression of a set of bone-related genes confirmed their osteocyte phenotype. Comparison with plastic-cultured cells and mature osteocytes microdissected from human cortical bone allowed to assess their maturation stage as osteoid-osteocytes. This model of primary osteocyte differentiation is a new tool to gain insights into the biology of osteocytes. It should be a suitable method to study the osteoblast-osteocyte differentiation pathway, the osteocyte interaction with the other bone cells, and orchestration of bone remodeling transmitted by mechanical loading and shear stress. It should be used in important cancer research areas such as the cross-talk of osteocytes with tumor cells in bone metastasis, because it has been recently shown that gene expression in osteocytes is strongly affected by cancer cells of different origin. It could also be a very efficient tool for drug testing and bone tissue engineering applications.
Tailoring Synthesis Conditions of Carbon Xerogels towards Their Utilization as Pt-Catalyst Supports for Oxygen Reduction Reaction (ORR) (2012)

Carbon xerogels characterized by different textural, structural and chemical properties were synthesized and used as supports for Pt catalysts for the application in polymer electrolyte fuel cells. Synthesis conditions were varied in order to synthesize carbon xerogels following the sol-gel method. These included the reactants ratio (precursor/formaldehyde), the catalyst concentration (precursor/catalyst ratio) and type (basic and acid), the precursor type (resorcinol and pyrogallol) and the solvent (aqueous or acetone based). Stoichiometric mixtures of resorcinol and formaldehyde yielded well polymerized gels and highly developed structures. Slow gelation, favored by the presence of acetone as solvent in the sol and low catalyst concentration, resulted in higher polymerization extent with a highly mesoporous or even macroporous texture and more ordered structure, as evidenced by XPS and Raman spectroscopy. Small Pt particles of ca. 3.5 nm were obtained by using carbon xerogels characterized by an ordered surface structure. The specific activity towards the oxygen reduction reaction, i.e., the limiting catalytic process in low temperature fuel cells, is significantly favored by highly ordered carbon xerogels due to a metal-support enhanced interaction. Nevertheless, surface defects favor the distribution of the metallic particles on the surface of carbon, which in the end influences the effectiveness of the catalyst. Accelerated degradation tests were conducted to evaluate catalyst stability under potential cycling conditions. The observed decay of performance was considerably lower for the catalysts based on ordered carbon xerogels stabilizing Pt particles in a higher extent than the other xerogels and the commercial carbon black support.
Differentiation-related Expression of ICAM-1 by Rat Alveolar Epithelial Cells (1993)

Local regulation of immune and inflammatory responses within the alveolar space is a critical aspect of normal pulmonary host defense. The type I and type II epithelial cells that line the alveolar space are in intimate contact with lymphocytes and macrophages within the alveolar space and are ideally situated to provide regulatory signals to these effector cells. The present studies were undertaken to investigate the expression by rat alveolar epithelial cells in vitro and in vivo of intercellular adhesion molecule-1 (ICAM-1), an adhesion molecule that is involved in migration and activation of T cells and macrophages. An antibody specifically blocking rat ICAM-1 (mAb 1A29) inhibited the adherence of activated T lymphoblasts to monolayers of type II alveolar epithelial cells. The expression of ICAM-1 protein by alveolar epithelial cells in vitro was confirmed both by immunofluorescence microscopy and by Western blot analysis. However, in each instance, ICAM-1 was not detected in type II cells the day of isolation, but appeared at low levels after 1 day and in abundance throughout the monolayer after 2 days, with sustained expression thereafter. This suggested that ICAM-1 expression might be a type I cell feature, which was induced as isolated type II cells underwent transformation towards the type I cell-like phenotype in vitro. Using immunofluorescence microscopy on frozen sections of normal lung, ICAM-1 was found in a linear distribution along the alveolar space, consistent with expression on type I cells.(ABSTRACT TRUNCATED AT 250 WORDS)
Continuous wave single transverse mode vertical-cavity surface-emitting lasers fabricated by helium implantation and zinc diffusion (1992)

A single transverse mode vertical-cavity surface emitting laser with moderate power has been fabricated using helium implantation and zinc diffusion. Devices with a 4 μm diameter active region exhibited a fundamental transverse mode (TEM00) operation with a maximum continuous wave output power of 1.5 mW and a quantum efficiency as high as 70%.
Nonlinear damping and quasi-linear modelling (2015)

The mechanism of energy dissipation in mechanical systems is often nonlinear. Even though there may be other forms of nonlinearity in the dynamics, nonlinear damping is the dominant source of nonlinearity in a number of practical systems. The analysis of such systems is simplified by the fact that they show no jump or bifurcation behaviour, and indeed can often be well represented by an equivalent linear system, whose damping parameters depend on the form and amplitude of the excitation, in a 'quasi-linear' model. The diverse sources of nonlinear damping are first reviewed in this paper, before some example systems are analysed, initially for sinusoidal and then for random excitation. For simplicity, it is assumed that the system is stable and that the nonlinear damping force depends on the nth power of the velocity. For sinusoidal excitation, it is shown that the response is often also almost sinusoidal, and methods for calculating the amplitude are described based on the harmonic balance method, which is closely related to the describing function method used in control engineering. For random excitation, several methods of analysis are shown to be equivalent. In general, iterative methods need to be used to calculate the equivalent linear damper, since its value depends on the system's response, which itself depends on the value of the equivalent linear damper. The power dissipation of the equivalent linear damper, for both sinusoidal and random cases, matches that dissipated by the nonlinear damper, providing both a firm theoretical basis for this modelling approach and clear physical insight. Finally, practical examples of nonlinear damping are discussed: in microspeakers, vibration isolation, energy harvesting and the mechanical response of the cochlea.
Use of Torrymeter for measurement of freshness of some commercially important Indian marine fishes (1994)

The freshness of mackerel (Rastrelliger kanagurta), oil sardine {Sardinella longiceps), common shark (Scoliodon laticadus), croaker (Johnius sp.). lizard fish (Saurida tumbil) and seer fish (Scomberomorws commerson), iced immediately after catch, was assesed by using Torrymeier as well as by other biochemical and microbiological tests and compared with sensory scores obtained. The Torrymeter readings generally showed good correlation with sensory scores for all the species studied except shark. The decrease of Torrymeter readings was fairly consistant and gradual only in initial storage period, indicating the usefulness of Torrymeter in measuring the initial loss of freshness of icestored fish. It was observed that fat content of fish in some way interferes with the reading of the instrument.
Dopant effects on the superconductivity of YBa2Cu3O7 ceramics (1988)

We investigated the effects of SrTiO3 and 17 different oxide dopants, namely Ca, Sc, La, and Zr with possible substitution in the yttrium sites, K, Sr, and Pb in the barium sites, Li, Mg, Fe, Co, Ni, Zn, Al, Ti, Nb, and Si in the copper sites on the superconductivity of YBa2Cu3O7. These dopants can be classified into four categories depending on their solubilities and substitution in the different cation sublattices of YBa2Cu3O7 perovskite. Dopants in the first category dissolve and substitute in the copper sublattice and they can significantly reduce the transition temperature of the superconductivity of YBa2Cu3O7. For example, three dopants in this category, namely Zn, Mg, and Li, at 2 mole % dopant level, reduce the transition temperatures to 66, 65, and 82 K, respectively. The second category dopants substitute in the barium and yttrium sites, and these dopants, e.g., Sr at 2 mole % concentration, do not have any significant effect on the transition temperature of the superconductivity of YBa2Cu3O7. While dopants, e.g., AlO1.5 and SiO2, in the third category have a limited solubility in YBa2Cu3O7, they have a strong tendency to decompose the superconducting phase by leaching out some components of YBa2Cu3O7. The transition temperature of the undecomposed superconducting phase remains unaffected at ∼91 K even though the susceptibility signal is reduced substantially. Since the dopants in the fourth category have a limited solubility and very little reactivity with YBa2Cu3O7, they are present simply as an inert second phase among the superconducting matrix.
Business Process Coordination: State of the Art, Trends, and Open Issues (2001)

Over the past decade, there has been a lot of work in developing middleware for integrating and automating enterprise business processes. Today, with the growth in e-commerce and the blurring of enterprise boundaries, there is renewed interest in business process coordination, especially for inter-organizational processes. This paper provides a historical perspective on technologies for intra- and interenterprise business processes, reviews the state of the art, and exposes some open research issues. We include a discussion of process-based coordination and event/rule-based coordination, and corresponding products and standards activities. We provide an overview of the rather extensive work that has been done on advanced transaction models for business processes, and of the fledgling area of business process intelligence. 1.
Arthroscopic Microfracture for Osteochondral Lesions of the Talus (2019)

Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
MOLECULAR DYNAMICS SIMULATION AND ITS APPLICATION TO NANO-RHEOLOGY (2013)

Over the last 15 years molecular dynamics (MD) simulations have become one of the important tools to tackle many of the complex problems that are faced by rheologists and engineers. The advent of modern areas of science such as nanotechnology and the need to understand physical phenomena including rheology and tribology at the molecular scale have helped the growth of research both experimentally and computationally at nano-scales. Molecular dynamics simulations among other molecular simulation methods have been used for computational research in those areas. Application of molecular dynamics to rheology has helped to understand the behaviour of polymers qualitatively; also important progress has been made in predicting quantitative rheological properties such as the viscosity of simpler liquids (such as alkanes). In particular the application of MD to the behaviour of confined fluids and lubricants at nano-scales has revealed some important properties and explained the underlying physics of observed phenomena that include enhanced viscosity and relaxation times and the role of normal stress differences in supporting large loads. MD has been a valuable tool in studying the relationship of the molecular structure and the rheological properties. In this review we will give an introduction about the method and will discuss some of the progress made to date. Our main focus will be on the application of MD in the nano-rheology of ultra-thin confined films.
A feedback class-C VCO with robust startup condition over PVT variations and enhanced oscillation swing (2011)

This paper presents a feedback class-C VCO with PVT-robustness and enhanced oscillation swing. The proposed VCO starts oscillation as a differential LC-VCO for robust startup, and automatically adapts to an amplitude-enhanced class-C VCO in steady-state for lower phase noise. The proposed VCO is implemented in a 0.18-μm CMOS process. The measured phase noise at room temperature is -125 dBc/Hz @ 1MHz offset with a power dissipation of 3.4 mW, from a carrier frequency of 4.84 GHz. The figure-of-merit is -193 dBc/Hz.
Redox signaling in cardiac myocytes (2011)

The heart has complex mechanisms that facilitate the maintenance of an oxygen supply-demand balance necessary for its contractile function in response to physiological fluctuations in workload as well as in response to chronic stresses such as hypoxia, ischemia, and overload. Redox-sensitive signaling pathways are centrally involved in many of these homeostatic and stress-response mechanisms. Here, we review the main redox-regulated pathways that are involved in cardiac myocyte excitation-contraction coupling, differentiation, hypertrophy, and stress responses. We discuss specific sources of endogenously generated reactive oxygen species (e.g., mitochondria and NADPH oxidases of the Nox family), the particular pathways and processes that they affect, the role of modulators such as thioredoxin, and the specific molecular mechanisms that are involved-where this knowledge is available. A better understanding of this complex regulatory system may allow the development of more specific therapeutic strategies for heart diseases.
Knowledge, Objectivity and the Paradigm Case Argument* (1977)

(1977). Knowledge, Objectivity and the Paradigm Case Argument* Educational Philosophy and Theory: Vol. 9, No. 2, pp. 19-30.
Reduced List-Decoding of Reed--Solomon Codes Using Reliability Information (2014)

We decode Reed-Solomon codes using soft information provided at the receiver. The Extended Euclidean Algorithm (EEA) is considered as an initial step to obtain an intermediate result. The final decoding result is obtained by interpolating the output of the EEA at the least reliable positions of the received word. We refer to this decoding method as reduced list-decoding, since not all received positions are used in the interpolation as in other list-decoding methods, such as the Guruswami-Sudan and Wu algorithms. Consequently the complexity of the interpolation step is reduced considerably. The probability of failure can be minimised by adjusting certain parameters, making it comparable with the Kötter-Vardy algorithm but having a much lower complexity.
Skip Decision and Reference Frame Selection for Low-Complexity H.264/AVC Surveillance Video Coding (2014)

H.264/advanced video coding surveillance video encoders use the Skip mode specified by the standard to reduce bandwidth. They also use multiple frames as reference for motion-compensated prediction. In this paper, we propose two techniques to reduce the bandwidth and computational cost of static camera surveillance video encoders without affecting detection and recognition performance. A spatial sampler is proposed to sample pixels that are segmented using a Gaussian mixture model. Modified weight updates are derived for the parameters of the mixture model to reduce floating point computations. A storage pattern of the parameters in memory is also modified to improve cache performance. Skip selection is performed using the segmentation results of the sampled pixels. The second contribution is a low computational cost algorithm to choose the reference frames. The proposed reference frame selection algorithm reduces the cost of coding uncovered background regions. We also study the number of reference frames required to achieve good coding efficiency. Distortion over foreground pixels is measured to quantify the performance of the proposed techniques. Experimental results show bit rate savings of up to 94.5% over methods proposed in literature on video surveillance data sets. The proposed techniques also provide up to 74.5% reduction in compression complexity without increasing the distortion over the foreground regions in the video sequence.
Nuclear DNA Content and Chromosome Numbers in Switchgrass (1998)

Switchgrass, Panicum virgatum L., one of the three dominant grasses of the North American tall grass prairie, is a genetically and morphologically diverse species with an array of ploidy levels, or set of chromosomes, and ecotypes. The relationship between DNA content and ploidy level has been controversial. The objectives of this study were to provide clear photodocumentation of switchgrass chromosome numbers and to clarify the relationship between nuclear DNA content and chromosome number. Defining the relationship between ploidy level and nuclear DNA content will facilitate the use of molecular biology techniques, such as flow cytometry, in plant breeding and evolutionary biology. The switchgrass tetraploids examined, which contain 4 sets of chromosomes, had 36 chromosomes with a nuclear DNA content of 3.1 pg/nuclei, while octaploids (8 sets of chromosomes) had 72 chromosomes with 6.1 pg/nuclei. Tetraploid plants from lowland ecotypes had the same nuclear DNA content as tetraploid plants from upland ecotypes. Normal diploid chromosome pairing occurred at meiosis for all tetraploid and octaploid plants examined. Our results indicate that the lowland and upland ecotypes have the same basic genome, and that the octaploids most likely evolved from the tetraploids by a natural doubling of chromosomes, and did so long enough ago for meiosis to be stabilized. Further research is needed to explore the evolutionary origins of switchgrass.
Association of Expression Aberrances and Genetic Polymorphisms of <i>Lysyl Oxidase</i> with Areca-Associated Oral Tumorigenesis (2007)

LOX exerts oncogenic roles in areca-associated OSCC. This potential could be affected by the existence of LOX propeptide domain or genetic polymorphism.
Modeling fixed‐bed coal gasifiers (1992)

Abstract A one‐dimensional model of countercurrent fixed‐bed coal gasification has been developed, and results have been compared to experimental data from commercial‐scale gasifiers. The steady‐state model considers separate gas and solid temperatures, axially variable solid and gas flow rates, variable bed void fraction, coal drying, devolatilization based on chemical functional group composition, oxidation and gasification of char, and partial equilibrium in the gas phase. Generalized treatment of gas‐phase chemistry and accounting for variable bed void fraction were necessary to predict realistic axial temperature and pressure profiles in an atmospheric fixed‐bed gasifier. Model evaluation includes sensitivity of axial temperature profiles to model options, model parameters and operational parameters. Model predictions agree reasonably well with experimental temperature and pressure profile data for gasification of eight coal types ranging from lignite to bituminous. The relative importance of char oxidation resistances to bulk film diffusion, ash diffusion, and chemical reaction is identified.