gebhart/patrepeval huggingface dataset:
Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability (2013)

Histone deacetylases (HDACs) are critical in the control of gene expression, and dysregulation of their activity has been implicated in a broad range of diseases, including cancer, cardiovascular, and neurological diseases. HDAC inhibitors (HDACi) employing different zinc chelating functionalities such as hydroxamic acids and benzamides have shown promising results in cancer therapy. Although it has also been suggested that HDACi with increased isozyme selectivity and potency may broaden their clinical utility and minimize side effects, the translation of this idea to the clinic remains to be investigated. Moreover, a detailed understanding of how HDACi with different pharmacological properties affect biological functions in vitro and in vivo is still missing. Here, we show that a panel of benzamide-containing HDACi are slow tight-binding inhibitors with long residence times unlike the hydroxamate-containing HDACi vorinostat and trichostatin-A. Characterization of changes in H2BK5 and H4K14 acetylation following HDACi treatment in the neuroblastoma cell line SH-SY5Y revealed that the timing and magnitude of histone acetylation mirrored both the association and dissociation kinetic rates of the inhibitors. In contrast, cell viability and microarray gene expression analysis indicated that cell death induction and changes in transcriptional regulation do not correlate with the dissociation kinetic rates of the HDACi. Therefore, our study suggests that determining how the selective and kinetic inhibition properties of HDACi affect cell function will help to evaluate their therapeutic utility.
Spontaneous oxygen radical generation by sickle erythrocytes. (1982)

Since the various membrane abnormalities of sickle erythrocytes might result from excessive accumulation of oxidant damage, we have measured the generation of superoxide, peroxide, and hydroxyl radical by normal and sickle erythrocytes using assays involving reduction of cytochrome c, aminotriazole inhibition of catalase, and methane evolution from dimethyl sulfoxide, respectively. Compared with normal erythrocytes, sickle erythrocytes spontaneously generate approximately twice as much superoxide, peroxide, and hydroxyl radical. One possible source of hydroxyl radical generation was identified as hemichrome, excessive amounts of which are bound to sickle erythrocyte membranes. Hemichrome did not generate hydroxyl radical when exposed to superoxide alone or peroxide alone. However, in the presence of both superoxide and peroxide, hemichrome greatly facilitated hydroxyl radical generation. Supporting this, normal erythrocyte membranes induced to acquire sickle hemichrome concomitantly acquired an enhanced ability to mediate hydroxyl radical generation. Finally, sickle erythrocyte membranes greatly enhanced superoxide/peroxide-driven hydroxyl radical generation as compared with normal erythrocyte membranes. These data suggest that an excessive accumulation of oxidant damage in sickle erythrocyte membranes might contribute to the accelerated membrane senescence of these cells. They further indicate that accumulation of oxidant damage could be a determinant of normal erythrocyte membrane senescence.
Comprehensive Drill-Rate Management Process To Maximize Rate of Penetration (2006)

Abstract The operator's drill rate management process is designed to maximize rate of penetration (ROP) in every foot of hole drilled. Due to its quantitative nature and the degree to which it is incorporated into all phases of the drill well process, the operator believes it to be the industry's first comprehensive ROP design process. The workflow is being implemented uniformly across an organization drilling approximately 4.5 million feet of hole per year in a wide range of rock types, directional profiles, and international locations. The results to date have been similar in most applications with significant gains in ROP, bit life, and reduction in tool failures related to vibrations. The workflow evolved from surveillance techniques the operator developed to utilize Mechanical Specific Energy (MSE) surveillance to evaluate drilling performance in real-time(1),(2). MSE surveillance proved to be an effective aid in identifying bit and system inefficiency. However, having this knowledge does not ensure the team knows why the inefficiency is occurring, or how to correct it. There are organizational processes that must also be considered when mitigation of the problem involves increased mechanical risk, significant changes in established practices, or a high level of technical training. MSE is a technology, while the ROP management process is a broad workflow designed to ensure MSE and numerous other sources of data are used effectively to maximize ROP. Consistent implementation of the workflow has been shown to achieve consistent increases in ROP. The key elements of the workflow required to achieve this performance are discussed. Over 40 categories of ROP-limiters have been identified, of which only 4 are directly related to the bit. The ROP in a large portion of footage drilled is constrained by factors other than bit performance, which are referred to as non-bit limiters. The workflow addresses both bit and non-bit limiters equally, and includes a simple model to aid drill teams in prioritizing the large number of potential ROP-limiters so resources available for surveillance and redesign are used most effectively. Performance improvements have been sustained since the staged rollout began in late 2004, and additional gains are continuing. Performance data is included, as well as a discussion of key implementation learnings.
한국인의 원초적 공동체사회의식과 사회과교육 (1999)

이 연구는 언어학적 연구방법을 통하여 한국인의 원초적 공동체사회의식의 특성을 밝히고, 새로운 사회변동에 슬기롭게 대응할 수 있는 바람직한 사회의식의 개발을 위한, 사회과의 학습지도방안을 탐색하고자 시도한 것이다. 먼저 언어학적 연구과정에서는 한국인의 원초적 사회의식이 언어적 상징을 통하여 표출되어 온 각 부분들의 의미구조를 분석하고, 이들을 연결·비교·종합하는 고찰과정을 통하여 그 지향적 특성을 밝혀보고자 하였다. 이 연구과정을 통하여 밝혀진 내용을 다음과 같이 요약할 수 있다. 1) 우리의식은 이해와 사랑으로 뭉친 공동체의식의 제1차적 표현유형이었다. 여기에는 「우리-울-얼-어리」 등이 소리와 뜻의 양면에 걸쳐서 연결되었다. 2) 마을공동체의 자치생활은 우리 의식을 공동체사회의식으로 승화·발전시켜준 가장 기초적인 바탕이었다. 여기서 마을의 어간인 「말」은 「물·몰·믈」과 관련되었으며, 그 상징의 원초적인 핵심어는 「물」이었던 것으로 이해되었다. 물이 이와 같이 마을의 명칭에 상징화된 것은 사람들이 서로 이해하고 협력하여, 서로간에 차별·단절·소외가 없는 공동체 사회를 이룩하려는 생활의식이 투영된 것으로 인식되었다. 3) 그 밖에 사회의식에 관련된 용례로써, 물의 의미적 요소들은 지명·인명·부족명·관직명·왕호·성읍명·부족국가명 및 나라의 통상명칭, 누리 등의 의미구조에도 투영되었다. 4) 우리 민족의 원초적인 공동체사회의식은 건전하고 이상지향적인 것이었다. 그러나 그것이 여러 가지 사회요인들에 의하여 건전하게 발전되지 못해 온 것으로 파악되었다. 5) 끝으로 미래지향적인 바람직한 공동체의식을 개발하기 위하여, 교재내용의 개선과 학습방법 및 평가과정을 연결-조정하는 통합모형의 연구과제를 제시하였다.
Beneficial effects of intravenous iron therapy in a rat model of heart failure with preserved systemic iron status but depleted intracellular cardiac stores (2018)

Iron deficiency (ID) commonly occurs in chronic heart failure (HF) and is associated with poor prognosis. Neither its causes nor pathophysiological significance are clearly understood. We aimed to assess iron status and the effect of iron supplementation in the rat model of post-myocardial infarction (MI) HF. Four weeks after induction of MI to induce HF or sham surgery, rats received intravenous iron (ferric carboxymaltose) or saline, 4 doses in 1-week intervals. HF alone did not cause anemia, systemic or myocardial ID, but reduced myocardial ferritin, suggesting depleted cardiomyocyte iron stores. Iron therapy increased serum Fe, ferritin and transferrin saturation as well as cardiac and hepatic iron content in HF rats, but did not increase myocardial ferritin. This was accompanied by: (1) better preservation of left ventricular (LV) ejection fraction and smaller LV dilation, (2) preservation of function of Ca<sup>2+</sup> handling proteins in LV cardiomyocytes and (3) reduced level of inflammatory marker, CRP. Furthermore, iron supplementation did not potentiate oxidative stress or have toxic effects on cardiomyocyte function, but increased activity of antioxidant defenses (cardiac superoxide dismutase). Despite lack of systemic or myocardial ID we found evidence of depleted cardiomyocyte iron stores in the rat model of HF. Furthermore we observed positive effect of iron supplementation and confirmed safety of iron supplementation in this setting.
Human Cytomegalovirus Open Reading Frame TRL11/IRL11 Encodes an Immunoglobulin G Fc-Binding Protein (2001)

Several herpesviruses encode Fc receptors that may play a role in preventing antibody-mediated clearance of the virus in vivo. Human cytomegalovirus (HCMV) induces an Fc-binding activity in cells upon infection, but the gene that encodes this Fc-binding protein has not been identified. Here, we demonstrate that the HCMV AD169 open reading frame TRL11 and its identical copy, IRL11, encode a type I membrane glycoprotein that possesses IgG Fc-binding capabilities.
Transduction mechanisms in airway sensory nerves (2006)

The induction of action potentials in airway sensory nerves relies on events leading to the opening of cation channels in the nerve terminal membrane and subsequent membrane depolarization. If the membrane depolarization is of sufficient rate and amplitude, action potential initiation will occur. The action potentials are then conducted to the central nervous system, leading to the initiation of various sensations and cardiorespiratory reflexes. Triggering events in airway sensory nerves include mechanical perturbation, inflammatory mediators, pH, temperature, and osmolarity acting through a variety of ionotropic and metabotropic receptors. Action potential initiation can be modulated (positively or negatively) through independent mechanisms caused mainly by autacoids and other metabotropic receptor ligands. Finally, gene expression of sensory nerves can be altered in adult mammals. This neuroplasticity can change the function of sensory nerves and likely involve both neurotrophin and use-dependent mechanisms. Here we provide a brief overview of some of the transduction mechanisms underlying these events.
Microfluidic large-scale integration on a chip for mass production of monodisperse droplets and particles (2007)

In this study, we report the mass production of monodisperse emulsion droplets and particles using microfluidic large-scale integration on a chip. The production module comprises a glass microfluidic chip with planar microfabricated 16-256 droplet-formation units (DFUs) and a palm-sized stainless steel holder having several layers for supplying liquids into the inlets of the mounted chip. By using a module having 128 cross-junctions (i.e., 256 DFUs) arranged circularly on a 4 cm x 4 cm chip, we could produce droplets of photopolymerizable acrylate monomer at a throughput of 320.0 mL h(-1). The product was monodisperse, having a mean diameter of 96.4 microm, with a coefficient of variation (CV) of 1.3%. Subsequent UV polymerization off the module yielded monodisperse acrylic microspheres at a throughput of approximately 0.3 kg h(-1). Another module having 128 co-flow geometries could produce biphasic Janus droplets of black and white segments at 128.0 mL h(-1). The product had a mean diameter of 142.3 microm, with a CV of 3.3%. This co-flow module could also be applied in the mass production of homogeneous monomer droplets.
Nonviral siRNA Delivery to the Lung: Investigation of PEG−PEI Polyplexes and Their In Vivo Performance (2009)

This study describes the physicobiological characterization of PEI- and PEG-PEI polyplexes containing partially 2'-OMe modified 25/27mer dicer substrate siRNAs (DsiRNAs) and their in vivo behavior regarding biodistribution and systemic bioavailability after pulmonary application as well as their ability to knock down gene expression in the lung. Biophysical characterization included circular dichroism of siRNA in polyplexes, condensation efficiency of polymers and in vitro stability. After in vivo application, biodistribution and kinetics of radiolabeled polyplexes were quantified and recorded over time in three-dimensional SPECT images and by end point scintillation counting. The influence on lung tissue and on the humoral and cellular immunosystem was investigated, and finally knockdown of endogenous gene expression in the lung was determined qualitatively. While all of the polymers used in our study were proven to effectively condense siRNA, stability of the complexes depended on the PEG grafting degree. Interestingly, PEI 25 kDa, which showed the least interaction with mucin or surfactant in vitro, performed poorly in vivo. Our nuclear imaging approach enabled us to follow biodistribution of the instilled nanocarriers over time and indicated that PEGylated nanocarriers are more suitable for lung application. While moderate proinflammatory effects were attributed to PEI25k-PEG(2k)(10) nanocarriers, none of the treatments caused histological abnormalities. Our preliminary in vivo knockdown experiment suggests that PEG-PEI/siRNA complexes are promising nanomedicines for pulmonary siRNA delivery. These results encouraged us to further investigate possible adverse effects and to quantify in vivo gene silencing in the lung after intratracheal instillation of PEG-PEI/siRNA complexes.
Framework for Multivariate Selectivity Analysis, Part II: Experimental Applications (2005)

In Part I of this paper, a framework for multivariate selectivity was introduced that is both calculable from first principles and experimentally tractable. In this part, we employ the proposed selectivity framework for analyzing both in vitro and in vivo near-infrared experimental data. Two in vitro data sets are used to compare different methods for estimating selectivity and to demonstrate the benefits obtained from validation data with expanded interferant concentration ranges. The in vitro data also demonstrate that the experimentally estimated selectivities provide insights into the properties of the calibration models that are difficult or impossible to infer by other means. The merits of the proposed selectivity function are further demonstrated using a complex in vivo application: the noninvasive measurement of ethanol in humans. Results indicate that in vivo calibration model sensitivity, selectivity, and concentration correlations can be systematically interrogated using the proposed selectivity framework and judicious use of experimental measurements. These analyses not only provide selectivity and sensitivity information, but also the variance components of the total MSEP, which is invaluable information for both method development and analytical method characterization.
Design, Synthesis, and Spectroscopic Properties of Peptide-Bridged Fluorescence Energy-Transfer Cassettes (1999)

A general partial solid-phase synthetic scheme was developed for the synthesis of energy-transfer cassettes with the donor and acceptor dyes bridged by a peptide. In these cassettes, 6-carboxyfluorescein (Fam) served as a donor. For the second dye, 6-carboxy-X-rhodamine (Rox) was used as a fluorescent acceptor or erythrosin B as a quencher. Different peptides bearing Rox at the amino terminus and Fam linked through different diamines to the carboxyl terminus were synthesized to examine the effects of the chain length and rigidity on energy-transfer efficiency. The ratio of emission intensities at 605 nm of the acceptor dye (ROX) in the cassette Rox-GPPPEPPP-p-xylylenediamine-Fam versus free ROX with 488 nm excitation was approximately 14 and is similar to that obtained for optimized oligonucleotide primers bearing the same dyes [Ju, J., Ruan, C., Fuller, C. W., Glazer, A. N., and Mathies, R. A. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 4347-4351].
PEPTIDE HORMONES IN PLANTS (2006)

In recent years, numerous biochemical and genetic studies have demonstrated that peptide signaling plays a greater than anticipated role in various aspects of plant growth and development. A substantial proportion of these peptides are secretory and act as local signals mediating cell-to-cell communication. Specific receptors for several peptides were identified as being membrane-localized receptor kinases, the largest family of receptor-like molecules in plants. These findings illustrate the importance of peptide signaling in the regulation of plant growth, functions that were previously ascribed to the combined action of small lipophilic compounds referred to as "traditional plant hormones." Here, we outline recent advances in the current understanding of biologically active peptides in plants, currently regarded as a new class of plant hormones.
An Approach to Combined Laplacian and Optimization-Based Smoothing for Triangular, Quadrilateral, and Quad-Dominant Meshes. (1998)

Abstract. Automatic finite element mesh generation techniques have become commonly used tools for the analysis of complex, real-world models. All of these methods can, however, create distorted and even unusable elements. Fortunately, several techniques exist which can take an existing mesh and improve its quality. Smoothing (also referred to as mesh relaxation) is one such method, which repositions nodal locations, so as to minimize element distortion. In this paper, an overall mesh smoothing scheme is presented for meshes consisting of triangular, quadrilateral, or mixed triangular and quadrilateral elements. This paper describes an efficient and robust combination of constrained Laplacian smoothing together with an optimization-based smoothing algorithm. The smoothing algorithms have been implemented in ANSYS ® and performance times are presented along with several example models.
Selective Catalytic Reduction for Treating the NO<sub>x</sub> Emissions from Lean-Burn Gasoline Engines: Performance Assessment (2008)

&lt;div class="htmlview paragraph"&gt;Selective catalytic reduction (SCR) with NH&lt;sub&gt;3&lt;/sub&gt; provides an attractive alternative to lean NO&lt;sub&gt;x&lt;/sub&gt; traps for controlling the NO&lt;sub&gt;x&lt;/sub&gt; emissions from lean-burn gasoline engines. This paper summarizes a laboratory study to assess the effects of temperature, space velocity, and the concentrations of NO, NH&lt;sub&gt;3&lt;/sub&gt;, and O&lt;sub&gt;2&lt;/sub&gt; on the NO&lt;sub&gt;x&lt;/sub&gt; conversion of an iron/zeolite SCR catalyst. A fresh sample was evaluated on slow temperature ramps with 5% O&lt;sub&gt;2&lt;/sub&gt; and 250, 500, or 1000 ppm of NO and NH&lt;sub&gt;3&lt;/sub&gt;. The NO&lt;sub&gt;x&lt;/sub&gt; conversion at low temperatures decreased with increasing NO and NH&lt;sub&gt;3&lt;/sub&gt; concentrations due to kinetic limitations. Conversely, the conversion at high temperatures increased with increasing NO and NH&lt;sub&gt;3&lt;/sub&gt; concentrations because the portion of NH&lt;sub&gt;3&lt;/sub&gt; oxidized by O&lt;sub&gt;2&lt;/sub&gt; decreased with increasing NO concentration. Thermally aged samples were evaluated at different steady-state temperatures and at different space velocities where the NO concentration was held constant at 250, 500, or 1000 ppm and the NH&lt;sub&gt;3&lt;/sub&gt; concentration was controlled at ten levels ranging from 143 to 1085 ppm. The NH&lt;sub&gt;3&lt;/sub&gt;/NO ratios producing the minimum slip of NH&lt;sub&gt;3&lt;/sub&gt;+NO&lt;sub&gt;x&lt;/sub&gt; were approximately 1.0 or higher for most temperatures and NO concentrations when the space velocity was 25K hr&lt;sup&gt;-1&lt;/sup&gt; or below, allowing high NO&lt;sub&gt;x&lt;/sub&gt; conversions to be achieved. When the space velocity was 47K hr&lt;sup&gt;-1&lt;/sup&gt; and higher, kinetic limitations and the need to limit the NH&lt;sub&gt;3&lt;/sub&gt; slip resulted in optimum NH&lt;sub&gt;3&lt;/sub&gt;/NO ratios less than 1.0, which limited the potential NO&lt;sub&gt;x&lt;/sub&gt; conversion. The NO&lt;sub&gt;x&lt;/sub&gt; conversion dropped with decreasing O&lt;sub&gt;2&lt;/sub&gt; concentration, particularly at low temperatures, and the conversion was very low when the O&lt;sub&gt;2&lt;/sub&gt; was removed from the feedgas.&lt;/div&gt;
Subatomic Features on the Silicon (111)-(7×7) Surface Observed by Atomic Force Microscopy (2000)

The atomic force microscope images surfaces by sensing the forces between a sharp tip and a sample. If the tip-sample interaction is dominated by short-range forces due to the formation of covalent bonds, the image of an individual atom should reflect the angular symmetry of the interaction. Here, we report on a distinct substructure in the images of individual adatoms on silicon (111)-(7x7), two crescents with a spherical envelope. The crescents are interpreted as images of two atomic orbitals of the front atom of the tip. Key for the observation of these subatomic features is a force-detection scheme with superior noise performance and enhanced sensitivity to short-range forces.
The Humane Interface: New Directions for Designing Interactive Systems (2000)

Deep thinking is rare in this field where most companies are glad to copy designs that were great back in the 1970s. The Humane Interface is a gourmet dish from a master chef. Five mice! --Jakob Nielsen, Nielsen Norman Group Author of Designing Web Usability: The Practice of SimplicityThis unique guide to interactive system design reflects the experience and vision of Jef Raskin, the creator of the Apple Macintosh. Other books may show how to use today's widgets and interface ideas effectively. Raskin, however, demonstrates that many current interface paradigms are dead ends, and that to make computers significantly easier to use requires new approaches. He explains how to effect desperately needed changes, offering a wealth of innovative and specific interface ideas for software designers, developers, and product managers.The Apple Macintosh helped to introduce a previous revolution in computer interface design, drawing on the best available technology to establish many of the interface techniques and methods now universal in the computer industry. With this book, Raskin proves again both his farsightedness and his practicality. He also demonstrates how design ideas must be built on a scientific basis, presenting just enough cognitive psychology to link the interface of the future to the experimental evidence and to show why that interface will work.Raskin observes that our honeymoon with digital technology is over: We are tired of having to learn huge, arcane programs to do even the simplest of tasks; we have had our fill of crashing computers; and we are fatigued by the continual pressure to upgrade. The Humane Interface delivers a way for computers, information appliances, and other technology-driven products to continue to advance in power and expand their range of applicability, while becoming free of the hassles and obscurities that plague present products. 0201379376B07092001
Immunomagnetic Cell Separation (2003)

In metastasis research, it may sometimes be necessary to separate populations of tumor cells from a mixed cell population such as a tumor, peripheral blood, or bone marrow. In addition, the normal counterparts of populations of tumor cells can be separated to allow direct comparisons to be made (1).In recent years magnetic bead separation techniques have become increasingly popular for these purposes.