gebhart/patrepeval huggingface dataset:
Characterization of a dengue type-specific epitope on dengue 3 virus envelope protein domain III (2010)

Dengue virus (DENV) is a mosquito-borne disease caused by four genetically and serologically related viruses termed DENV-1, -2, -3 and -4. The DENV envelope (E) protein ectodomain can be divided into three structural domains designated ED1, ED2 and ED3. The ED3 domain contains DENV type-specific and DENV complex-reactive antigenic sites. To date, nearly all antigenic studies on the E protein have focused on DENV-2. In this study, the epitope recognized by a DENV-3 type-specific monoclonal antibody (mAb 14A4-8) was mapped to the DENV-3 ED3 domain using a combination of physical and biological techniques. Epitope mapping revealed that amino acid residues V305, L306, K308, E309, V310, K325, A329, G381 and I387 were critical for the binding of mAb 14A4-8 and amino acid residues T303, K307, K386, W389 and R391 were peripheral residues for this epitope. The location of the mAb 14A4-8 epitope overlaps with the DENV complex-reactive antigenic site in the DENV-3 ED3 domain.
The REDOR transform: direct calculation of internuclear couplings from dipolar-dephasing NMR data (1995)

Rotational-echo double-resonance (REDOR) is a dipolar-dephasing NMR technique that provides measurement of dipolar couplings between nuclei in solids, and therefore allows calculation of internuclear distances. Time-domain REDOR dephasing signals do not oscillate in a periodic manner, and the analysis of frequency- and time-domain signals is complicated when discrete or continuous distributions of couplings are present. We introduce a new analytic transform method, analogous to a Fourier transform, that produces resonances at the dipolar coupling frequencies present in the REDOR signal. Computer simulations are used to demonstrate and explore details of the REDOR transform.
Endogenous ascorbate regenerates vitamin E in the retina directly and in combination with exogenous dihydrolipoic acid (1995)

Vitamin E ($aL-tocopherol) is the major lipid-soluble antioxidant of retinal membranes whose deficiency causes retinal degeneration. Its antioxidant function is realized via scavenging peroxyl radicals as a result of which phenoxyl radicals of $aL-tocopherol are formed. Our hypothesis is that $aL-tocopherol phenoxyl radicals can be reduced by endogenous reductants in the retina, providing for $aL-tocopherol recycling. The results of this study demonstrate for the first time that: (i) endogenous ascorbate (vitamin C) in retinal homogenates and in rod outer segments is able to protect endogenous $aL-tocopherol against oxidation induced by UV-irradiation by reducing the phenoxyl radical of $aL-tocopherol, (ii) in the absence of ascorbate, neither endogenous nor exogenously added glutathione (GSH) is efficient in protecting $aL-tocopherol against oxidation; (iii) GSH does not substantially enhance the protective effect of ascorbate against $aL-tocopherol oxidation; (iv) exogenous dihydrolipoic acid (DHLA), although inefficient in direct reduction of the $aL-tocopherol phenoxyl radical, is able to enhance the protective effect of ascorbate by regenerating it from dehydroascorbate. Thus, regeneration of $aL-tocopherol from its phenoxyl radical can enhance its antioxidant effectiveness in the retina. The recycling of $aL-tocopherol opens new avenues for pharmacological approaches to enhance antioxidants of the retina.
How Text Segmentation Algorithms Gain from Topic Models (2012)

This paper introduces a general method to incorporate the LDA Topic Model into text segmentation algorithms. We show that semantic information added by Topic Models significantly improves the performance of two word-based algorithms, namely TextTiling and C99. Additionally, we introduce the new TopicTiling algorithm that is designed to take better advantage of topic information. We show consistent improvements over word-based methods and achieve state-of-the art performance on a standard dataset.
The Influence of Vehicle Design Parameters on Characteristic Speed and Understeer (1967)

<div class="htmlview paragraph">Vehicle understeer is rigorously defined and discussed as it pertains to directional control of an automobile. Methods are presented for predicting understeer quality in proposed vehicle designs and for measuring understeer quality in existing vehicles. The methods make possible complete and accurate quantitative descriptions of vehicle understeer.</div>
Perspective of Cytokine Regulation for Periodontal Treatment: Fibroblast Biology (2003)

Efforts to understand the pathogenesis of periodontal diseases have been underway for decades. Studies of immunological aspects in addition to the structural components of gingival fibroblasts showed that the fibroblasts actively participate in immune and inflammatory events in periodontal diseases. Future strategies for the prevention and treatment of periodontal diseases should biologically regulate fibroblast activities. These cells are surrounded by monocyte-derived proinflammatory cytokines such as interleukin-1 beta (IL-1beta), tumor necrosis factor-alpha (TNF-alpha), and lymphocyte-derived interleukin-6 (IL-6) in inflamed gingival tissue. Recent anti-cytokine therapy for inflammatory diseases including rheumatoid arthritis aimed to inhibit the binding of cytokines to targeted cells such as fibroblasts and condrocytes. IL-1beta and TNF-alpha are thought to be therapeutic targets because these cytokines are essential for the initiation of inflammatory immune reactions and are produced for prolonged periods in inflammatory diseases. IL-6 is also a target, because it is abundantly present in inflammatory lesions and activates fibroblasts in the presence of soluble IL-6 receptor. In addition, these cytokines accelerate gingival fibroblasts to produce collagenolytic enzymes, resulting in tissue destruction. Soluble receptors for IL-1beta and TNF-alpha are suggested to be candidates for therapeutic molecules, but soluble receptor for IL-6 is suggested to be a factor-stimulating fibroblast. This paper will review the utilization of soluble receptors specific to inflammatory cytokines which potentially stimulate fibroblasts to regulate biological events involved in the pathogenesis of periodontal diseases.
Plasmon-Enhanced Raman and Resonance Raman Scattering and Single Molecule Detection in Langmuir-Blodgett Monolayers (2011)

The present work explores vibrational Raman spectroscopy. Vibrational Raman and vibrational infrared are the most commonly used spectroscopies for detection and identification of molecules with their vibrational fingerprint. Under certain conditions, molecules display unique florescence and Raman scattering behavior when they are close to metal nanostructures sustaining localized surface plasmon resonances (LSPR), giving rise to surface-enhanced Raman scattering (SERS) and surface-enhanced resonance Raman scattering (SERRS). The utilization of LSPR in metallic nanoparticles, in particular silver and gold nanostructures, is a remarkable means of improving the efficiency of Raman scattering enhancing optical signals in SERS and SERRS. Correspondingly, the fabrication and characterization of silver and gold island films are first presented, and SERS signals enhancement of an organic dye on these metal nanostructured films are demonstrated. The excitations are characterized by UV-Vis absorption spectroscopy, while the morphology is revealed by atomic force microscopy (AFM). To control the surface coverage of the metal nanostructures, the Langmuir-Blodgett (LB) technique is used to coat the SERS substrate with monomolecular layers of several target systems, such as dyes and phospholipids. The most important results in this work are in the field of single molecule detection (SMD) using two spectroscopic approaches: LB-SERRS and LB-SERS. LB-SERRS improves the scattering efficiency from the electronic resonances (resonance Raman) of dye using silver island film with a plasmon absorption overlapping the molecular absorption. Several experiments are designed to the statistical average of LB-SERRS spectra, and the statistical breakdown observed in spectral characteristics when SMD is approached. The development of other SERS-substrates was attempted to control plasmonic using LSPR. A convenient method was pursued using a self-assembly of silver colloidal nanoparticles on a silanized glass surface. The SERS spectral evidence is presented to validate the substrate development. Surface-enhanced florescence (SEF) was also used for single molecule studies. Shell-isolated nanoparticles (SHINs) are used to produce SEF that named SHINEF. Using mixed LB monolayers of perylene tetracarboxylic (PTCD) derivatives, we report single molecule fluorescence and single molecule SERRS. In addition, overtones and combinations of fundamental vibrational modes are seen with atypical relative intensity in the LB-SERRS spectra of PTCDs.
Squeezable tunneling junctions (1986)

Squeezable tunneling junctions establish the current state of the art for resistance stability of mechanically adjustable tunneling structures at ΔR/R ≈ 0.1%. This is sufficient for use in connection with spectroscopies as subtle as phonon spectroscopy, but it is marginal and cannot at present be maintained to high enough bias voltage to permit molecular vibrational spectroscopy. Squeezable junctions have been used for characterizing bulk samples and for differential capacitance-voltage analyses of semiconductors.
Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center (2016)

Dioxygenase (dOx) utilizes stereospecific oxidation on aromatic molecules; consequently, dOx has potential applications in bioremediation and stereospecific oxidation synthesis. The reactive components of dOx comprise a Rieske structure Cys2[2Fe-2S]His2 and a non-heme reactive oxygen center (ROC). Between the Rieske structure and the ROC, a universally conserved Asp residue appears to bridge the two structures forming a Rieske-Asp-ROC triad, where the Asp is known to be essential for electron transfer processes. The Rieske and ROC share hydrogen bonds with Asp through their His ligands; suggesting an ideal network for electron transfer via the carboxyl side chain of Asp. Associated with the dOx is an itinerant charge carrying protein Ferredoxin (Fdx). Depending on the specific cognate, Fdx may also possess either the Rieske structure or a related structure known as 4-Cys-[2Fe-2S] (4-Cys). In this study, we extensively explore, at different levels of theory, the behavior of the individual components (Rieske and ROC) and their interaction together via the Asp using a variety of density function methods, basis sets, and a method known as Generalized Ionic Fragment Approach (GIFA) that permits setting up spin configurations manually. We also report results on the 4-Cys structure for comparison. The individual optimized structures are compared with observed spectroscopic data from the Rieske, 4-Cys and ROC structures (where information is available). The separate pieces are then combined together into a large Rieske-Asp-ROC (donor/bridge/acceptor) complex to estimate the overall coupling between individual components, based on changes to the partial charges. The results suggest that the partial charges are significantly altered when Asp bridges the Rieske and the ROC; hence, long range coupling through hydrogen bonding effects via the intercalated Asp bridge can drastically affect the partial charge distributions compared to the individual isolated structures. The results are consistent with a proton coupled electron transfer mechanism.
Translocation of Apocytochrome c across the Outer Membrane of Mitochondria (1995)

Apocytochrome c follows a unique pathway into mitochondria. Import does not require the general protein translocation machinery, protease-sensitive components of the outer membrane, or a membrane potential across the inner membrane. We investigated the membrane binding and translocation steps of the import reaction using purified outer membrane vesicles (OMV) from Neurospora crassa mitochondria. OMV specifically bound, but did not import apocytochrome c. If, however, specific antibodies were enclosed inside OMV, apocytochrome c was accumulated in soluble form in the lumen. Import was reversible, since apocytochrome c became accessible to external protease after release from the antibodies. Thus, OMV are competent of translocating apocytochrome c into their lumen, but lack a binding partner which traps the apoprotein. In intact mitochondria, cytochrome c heme lyase (CCHL), a peripheral protein of the inner membrane, serves such a function by stably associating with apocytochrome c in a complex which is detectable by co-immunoprecipitation. We suggest a model for the import mechanism of apocytochrome c in which the apoprotein specifically associates with and reversibly passes across the outer membrane. Translocation is rendered unidirectional by stable association with CCHL which serves as a "trans side receptor." Finally, heme is attached by CCHL and the holoprotein folds into its native structure.
Trench gate emitter switched thyristors (2002)

A new MOS-gated Emitter Switched Thyristor (EST) structure using trench gate technology is reported for the first time. In this new trench gate EST, the voltage drop across the series lateral MOSFET is reduced due to an increase in channel density resulting in forward voltage drops equal to thyristors and MCTs. In addition, the parasitic thyristor that is inherent in the conventional EST is completely eliminated in this structure, allowing higher maximum controllable current densities for ESTs. The trench gate allows homogenous current distribution in the EST and preserves the unique feature of gate controlled current saturation of the thyristor current. The characteristics of 600 V forward blocking trench EST obtained from two dimensional numerical simulations is described and compared with that of the trench IGBT and MCT. Resistive load simulations for the trench EST indicate turn-off times comparable to trench IGBTs and MCTs.
Development of a Wireless Capacitive Sensor for Ambulatory ECG Monitoring over Clothes (2007)

We present a wireless capacitive sensor for ambulatory ECG monitoring. The device is capable of detecting electrocardiographic potential through underwear. It is based on capacitive coupling involving the electrode, the underwear, and the skin. Validation of the system revealed the following: (1) The frequency response of the device with the underwear revealed that the gain of the detected signal was reduced, but distortion of the signal within the pass-band (from 6 to 45 Hz) was minimal even with the underwear. (2) The signal displayed a periodic waveform synchronized with the simultaneously recorded ECG, even when the underwear was inserted between the electrode and the skin. (3) Although the signal was seemed deteriorated slightly while walking, R-waves were recognized easily. Although there is still room for improvement in terms of its practical use, the proposed approach appears promising for application to ambulatory ECG monitoring.
Identification of a MHC Class II-Restricted Human gp100 Epitope Using DR4-IE Transgenic Mice (2000)

CD4+ T cells play a central role in the induction and persistence of CD8+ T cells in several models of autoimmune and infectious disease. To improve the efficacy of a synthetic peptide vaccine based on the self-Ag, gp100, we sought to provide Ag-specific T cell help. To identify a gp100 epitope restricted by the MHC class II allele with the highest prevalence in patients with malignant melanoma (HLA-DRB1*0401), we immunized mice transgenic for a chimeric human-mouse class II molecule (DR4-IE) with recombinant human gp100 protein. We then searched for the induction of CD4+ T cell reactivity using candidate epitopes predicted to bind to DRB1*0401 by a computer-assisted algorithm. Of the 21 peptides forecasted to bind most avidly, murine CD4+ T cells recognized the epitope (human gp10044-59, WNRQLYPEWTEAQRLD) that was predicted to bind best. Interestingly, the mouse helper T cells also recognized human melanoma cells expressing DRB1*0401. To evaluate whether human CD4+ T cells could be generated from the peripheral blood of patients with melanoma, we used the synthetic peptide h-gp10044-59 to sensitize lymphocytes ex vivo. Resultant human CD4+ T cells specifically recognized melanoma, as measured by tumor cytolysis and the specific release of cytokines and chemokines. HLA class II transgenic mice may be useful in the identification of helper epitopes derived from Ags of potentially great clinical utility.
Glucose-6-Phosphate Dehydrogenase Modulates Cytosolic Redox Status and Contractile Phenotype in Adult Cardiomyocytes (2003)

Reactive oxygen species (ROS)-mediated cell injury contributes to the pathophysiology of cardiovascular disease and myocardial dysfunction. Protection against ROS requires maintenance of endogenous thiol pools, most importantly, reduced glutathione (GSH), by NADPH. In cardiomyocytes, GSH resides in two separate cellular compartments: the mitochondria and cytosol. Although mitochondrial GSH is maintained largely by transhydrogenase and isocitrate dehydrogenase, the mechanisms responsible for sustaining cytosolic GSH remain unclear. Glucose-6-phosphate dehydrogenase (G6PD) functions as the first and rate-limiting enzyme in the pentose phosphate pathway, responsible for the generation of NADPH in a reaction coupled to the de novo production of cellular ribose. We hypothesized that G6PD is required to maintain cytosolic GSH levels and protect against ROS injury in cardiomyocytes. We found that in adult cardiomyocytes, G6PD activity is rapidly increased in response to cellular oxidative stress, with translocation of G6PD to the cell membrane. Furthermore, inhibition of G6PD depletes cytosolic GSH levels and subsequently results in cardiomyocyte contractile dysfunction through dysregulation of calcium homeostasis. Cardiomyocyte dysfunction was reversed through treatment with either a thiol-repleting agent (L-2-oxothiazolidine-4-carboxylic acid) or antioxidant treatment (Eukarion-134), but not with exogenous ribose. Finally, in a murine model of G6PD deficiency, we demonstrate the development of in vivo adverse structural remodeling and impaired contractile function over time. We, therefore, conclude that G6PD is a critical cytosolic antioxidant enzyme, essential for maintenance of cytosolic redox status in adult cardiomyocytes. Deficiency of G6PD may contribute to cardiac dysfunction through increased susceptibility to free radical injury and impairment of intracellular calcium transport. The full text of this article is available online at http://www.circresaha.org.
A Dual-Polarized Microstrip Patch Antenna Using Hybrid Feed (2010)

Abstract A new dual-polarized microstrip patch antenna fed by probe feed and aperture coupled feed is presented. The hybrid feed, a T-shaped microstrip feedline, is adopted to improve the isolation between two ports, and the “hour-glass” shaped slot is used to improve the input impedance of the proposed antenna. The measured center frequency is 2.37 GHz, the return loss for port 1 is −16.08 dB and −21.92 dB for port 2, and the isolation between the two ports is −24.24 dB. Finally, four slots are embedded along the centerline of the ground plane so that the bandwidth of antenna is greatly improved. Good agreement between the measured and simulated results has been achieved.
DNA Cleavage Is Not Required for the Binding of Quinolone Drugs to the DNA Gyrase−DNA Complex (1996)

The primary target for the quinolone group of antibacterial agents is DNA gyrase. One model for the interaction of quinolone drugs with gyrase and DNA suggests that the drugs bind to the single-stranded regions revealed following DNA cleavage by the enzyme. We have tested this hypothesis by using mutants which have the active-site tyrosine in the gyrase A subunit altered to phenylalanine or serine. We have found that proteins bearing these mutations are still able to bind drug, suggesting that DNA cleavage is not a prerequisite for drug binding. We have also found that the blocking of transcription by RNA polymerase in vitro by the gyrase-quinolone complex on DNA does not occur when the active-site tyrosine is mutated to serine; i.e., polymerase blocking requires DNA cleavage.
Intelligent Lighting Control for Vision-Based Robotic Manipulation (2011)

The ability of a robot vision system to capture informative images is greatly affected by the condition of lighting in the scene. This paper reveals the importance of active lighting control for robotic manipulation and proposes novel strategies for good visual interpretation of objects in the workspace. Good illumination means that it helps to get images with large signal-to-noise ratio, wide range of linearity, high image contrast, and true color rendering of the object's natural properties. It should also avoid occurrences of highlight and extreme intensity unbalance. If only passive illumination is used, the robot often gets poor images where no appropriate algorithms can be used to extract useful information. A fuzzy controller is further developed to maintain the lighting level suitable for robotic manipulation and guidance in dynamic environments. As carried out in this paper, with both examples of numerical simulations and practical experiments, it promises satisfactory results with the proposed idea of active lighting control.
Effect of various compounds on the reaction of tris-(2-chloroethyl)amine with ribonucleic acid in vitro and on its toxicity in mice. (1981)

The effect of tris-(2-chloroethyl)-amine (HN-3) on RNA and DNA was investigated spectrophotometrically. The shift in the absorbance spectrum caused by the addition of HN-3 was used to test a variety of compounds for their ability to inhibit RNA alkylation. The effect of HN-3 on the activity of several enzymes was also investigated. The activities of ribonuclease A, desoxyribonuclease I, acetylcholinesterase, diaphorase, glutathione reductase, adenosine desaminase, glyoxalase I, 3-hydroxyacyl-CoA-dehydrogenase, xanthine oxidase, glucose-6-phosphate dehydrogenase, hexokinase and the microsomal N-oxygenation of aniline were not changed by HN-3, whereas the activity of cytochrome-c-reductase exhibited a dose dependent diminution in the presence HN-3. Of 105 compounds tested only 14, namely, sodium thiosulfate, dithioxanthine, thiosalicylic acid, 1,2,4-triazole-5-thiol, 2-thiocytosine, 2-thiohistadine, 2,3-dithiosuccinic acid, thioglycolic acid, 3-mercapto-D-valine,6-amino-2-thiouracil, thionicotine amide, dithiothreitol, sodium sulfite, and ergothioneine prevented the alkylation of RNA. All of them also reacted with HN-3 in absence of RNA. No correlation was found between the reaction constant of the reaction compound:HN-3 in the absence of RNA and the concentration of the compound which inhibited RNA alkylation by 50%. The compounds which were effective in vitro were also tested in mice for their ability to reduce HN-3 toxicity in vivo. Only sodium thiosulfate, d-penicillamine, and dithiosuccinic acid were effective. A 3.9fold increase in the LD50 of HN-3 was achieved in mice treated with sodium thiosulfate 3330 mg/kg i.p., a 1.7fold with 2125 mg dithiosuccinic acid/kg, and a 2fold increase with 2500 mg/kg d-penicillamine. The compound tested was injected i.p. 0.5 to 1 min after the s.c. injection of HN-3.
Acoustic assisted, field-induced strain in ferromagnetic shape memory alloys (2004)

A technique has been developed that uses acoustic energy to assist a magnetic field in driving twin boundary motion in a NiMnGa single crystal. Acoustic assisted magnetic-field-induced strain has been observed to increase the magnetic-field-induced strain response by up to one order of magnitude. This effect is most pronounced for magnetic field drives near the twin boundary threshold field. Increasing frequency of the acoustic wave input is shown to increase strain up to about 4 kHz after which there is a small decline in FSMA strain for higher frequencies.