gebhart/patrepeval huggingface dataset:
Mining the Proteome of <i>Leishmania donovani</i> for the Development of Novel MHC Class I Restricted Epitope for the Control of Visceral Leishmaniasis (2017)

Although, the precise host defence mechanism(s) is not completely understood, T cell-mediated immune responses is believed to play a pivotal role in controlling parasite infection. Here we target the stage dependent over expressed gene. Here, the consensus based computational approach was adopted for the screening of potential major histocompatibility complex class I restricted epitopes. Based on the computational analysis and previously published report, a set 19 antigenic proteins derived from Leishmania donovani were screened for further characterization as vaccine candidates. A total of 49 epitopes were predicted, which revealed a comprehensive binding affinity to the 40 different MHC class I supertypes. Based on the population coverage and HLA cross presentation, nine highly promiscuous epitopes such as LTYDDVWTV (P1), FLFPQRTAL(P2), FLFSNGAVV (P3), YIYNFGIRV (P4), YMTAAFAAL (P5), KLLRPFAPL (P6), FMLGWIVTI (P7), SLFERNKRV (P8), and SVWNRIFTL (P9) which have either a high or an intermediate TAP binding affinity were selected for further analysis. Theoretical population coverage analysis of polytope vaccine (P1-P9) revealed more than 92% population. Stimulation with the cocktail of peptide revealed a proliferative CD8<sup>+</sup> T cell response and increased IFN-γ production. An upregulated NF-κB activity is thought to be play a pivotal role in T cell proliferation against the selected peptide. The Th1-type cytokine profile (presence of IFN-γ and absence of IL-10) suggests the potentiality of the cocktail of epitope as a subunit vaccine against leishmaniasis. However, the efficiency of these epitopes to trigger other Th1 cytokines and chemokines in a humanized mice model could explore its plausibility as a vaccine candidate. J. Cell. Biochem. 119: 378-391, 2018. © 2017 Wiley Periodicals, Inc.
A novel physiological mechanism of glycine‐induced immunomodulation: Na <sup>+</sup> ‐coupled amino acid transporter currents in cultured brain macrophages (2004)

Glycine is known to modulate immune cell responses. However, the physiological mechanisms underlying inhibitory effects of glycine on macrophages are not well understood. Here we show that glycine is capable of inducing inward currents in brain macrophages (microglia). In contrast to glycine, the glycine receptor agonist taurine failed to elicit currents. Glycine-evoked currents of brain macrophages were unaffected by strychnine, Cl(-)-free extracellular solution, N-[3-(4'-fluorophenyl)-3-(4'-phenylphenoxy)propyl])sarcosine (NFPS) and amoxapine, but were abolished upon omission of extracellular Na(+). Furthermore, glycine caused increases in the intracellular Na(+) concentration and pronounced membrane depolarization. Glycine-evoked depolarization was Na(+) dependent and occurred independently of the intracellular Cl(-) concentration. Similarly to glycine, glutamine and alpha-(methylamino)isobutyric acid (MeAIB) elicited inward currents in brain macrophages. In the presence of either glutamine or MeAIB, glycine-induced currents were inhibited. It is concluded that neither functional glycine receptors nor glycine transporters are expressed in brain macrophages. We suggest that glycine mediates its effects by activation of system A Na(+)-coupled neutral amino acid transporters.
Computer-Aided Drug Discovery and Development (2011)

Computer-aided approaches have been widely used in pharmaceutical research to improve the efficiency of the drug discovery and development pipeline. To identify and design small molecules as clinically effective therapeutics, various computational methods have been evaluated as promising strategies, depending on the purpose and systems of interest. Both ligand and structure-based drug design approaches are powerful technologies, which can be applied to virtual screening for lead identification and optimization. Here, we review the progress in this field and summarize the application of some new technologies we developed. These state-of-the-art tools have been used for the discovery and development of active agents for various diseases, in particular for cancer therapies. The described protocols are appropriate for all drug discovery stages, but expertise is still needed to perform the studies based on the targets of interest.
Rapid Determination of Deoxynivalenol (Vomitoxin) by Liquid Chromatography Using Modified Romer Column Cleanup (1984)

A modification of the Romer method for determining deoxynivalenol (DON) provides rapid sample cleanup and includes liquid chromatographic (LC) quantitation. The method was evaluated using wheat, wheat flour, and other wheat products. The sample is extracted with acetonitrile-water (84 + 16), and an aliquot of the extract is subjected to activated charcoal-alumina column chromatography. The extract is then evaporated and diluted to volume with mobile phase, and DON is quantitated using liquid chromatography. The relative standard deviation based on duplicate samples is 6.07%. The detection limit is 30 ppb based on 2 X signal/noise ratio. Results by this method compared with the results obtained by the Scott GC method showed a correlation coefficient of 0.992 with a mean vomitoxin content of 779 ppb by this method and 716 ppb by the Scott method for 14 samples.
Analysis of multielement semiconductor lasers (1983)

An analysis of laser action in a multielement resonator structure is presented. Resonance wavelengths, threshold gains, energy density distributions, and quality of the modes are obtained from a linear model. A multimode rate equation approach then describes the dynamical behavior and gives absolute values for the modal output. It is shown that structures with only a few active elements can have a high mode selectivity providing single-longitudinal-mode operation of semiconductor lasers under high-frequency current modulation. For example, the suppression of unwanted secondary modes in an eight-element laser can be larger than 23 dB.
Even Good Bots Fight: The Case of Wikipedia (2017)

Each file contains the history of all the articles in the WP. Articles are separated by their names within the file. Each line of the file below the name of an article, contains a delimiter "^^^" followed by the timestamp of each edit, a binary flag of 0/1 corresponding to a normal/revert edit, an accenting integer code, starting from 1, assigned to each new revision, whose text is not similar to any of the previous ones, otherwise the same code as the previous version with the similar text, and finally the editor of the version.
A Reliable Ultra-Fast Three Step Short Circuit Protection Method for E-mode GaN HEMTs (2019)

The Enhancement-mode (E-mode) Gallium Nitride High-Electron Mobility Transistor (GaN HEMT) has several hundred nanosecond level short circuit withstand time, much shorter than that of the silicon (Si) devices. Reliable ultra-fast protection solutions for the GaN HEMTs are in great demand. In this paper, a three-step GaN HEMT short circuit protection solution is proposed, including ultra-fast detection, active gate clamping and de-saturation circuit confirmation. First, the GaN HEMT short circuit capability under various gate voltages has been explained. Based on the safe protection boundary, the three- step protection solution is proposed. Experimental results prove that with the proposed protection method, the short circuit fault can be detected within 36 ns, and the short circuit energy is reduced with the ultra-fast detection and gate voltage clamping. Eventually, the GaN HEMT can be successfully protected from fatal failure up-to 400 V dc bus.
A Randomized Clinical Trial of a Brief Hypnosis Intervention to Control Side Effects in Breast Surgery Patients (2007)

Hypnosis was superior to attention control regarding propofol and lidocaine use; pain, nausea, fatigue, discomfort, and emotional upset at discharge; and institutional cost. Overall, the present data support the use of hypnosis with breast cancer surgery patients.
Fracture Diagnostics With Tube Wave Reflection Logs (1994)

Summary The Tube-Wave Reflection Log (TWRL) is a new fracture diagnostic method that is based on cased-hole acoustic logging. It relies on reflection and attenuation effects in tube waves resulting from fluid flow through perforations into hydraulic fractures. Information about the location, conductivity, and height of fractures can be deduced from these effects. Introduction The TWRL uses low-frequency tube waves to detect and provide information about fractured intervals behind perforated casing. Tube waves are interface waves that propagate in unperforated casing with little attenuation at a speed roughly equal to the fluid compressional velocity. The TWRL concept relies on the sensitivity of tube waves to changes in wellbore-wall permeability. An increase in permeability causes an increase in attenuation and a decrease in velocity of the tube waves owing to fluid flow in and out of the permeable zone. These phenomena are well known. A hydraulically induced fracture, in communication with a cased borehole through perforations, acts as a high-permeability zone in an otherwise impermeable wellbore. Throughout this zone, the tube waves are attenuated and slowed down owing to fluid flow into and out of the fracture. Tube-wave reflections also occur at the top and bottom of the fracture zone because of impedance contrasts.
Toward an Understanding of Ion Transport through the Na,K‐ATPase (2003)

In the Na,K-ATPase the charge-translocating reaction steps were found to be binding of the third Na(+) ion to the cytoplasmic side and the release of all three Na(+) ions to the extracellular side as well as binding of the two K(+) ions on the extracellular side. The conformation transition E(1) --> E(2) was only of minor electrogenicity; all other reaction steps produced no significant charge movements. In the SR Ca-ATPase and the gastric H,K-ATPase, all ion-binding and -release steps were identified to move charge through the membrane. The high-resolution structure of the SR Ca-ATPase in state E(1) revealed the position of the ion-binding sites in the transmembrane part of the protein. If the same arrangement is assumed for the Na pump, the missing expected charge movements in state E(1) may to be assumed to be apparent effects. With the proposal that binding of 2 Na(+) or 2 K(+) is compensated correspondingly by H(+) ions, agreement between structural and functional aspects is obtained. Investigations of the pH-dependence of ion-binding steps indicate competition between the ions and electrogenic H(+) binding in support of this concept.
A comparative trial of botulinum toxin type A and methylprednisolone for the treatment of myofascial pain syndrome and pain from chronic muscle spasm (2000)

Myofascial pain syndrome (MPS) is a common illness, characterised by acute or chronic focal pain, muscle stiffness and fatigue. The pathophysiology of MPS remains unclear. Previous preliminary studies have demonstrated therapeutic efficacy of the muscle relaxant botulinum toxin type A (BTX-A) in the treatment of MPS. A single-centre, randomised trial compared the effects of BTX-A with the steroid methylprednisolone (both administered intramuscularly with 0.5% bupivacaine), in 40 patients suffering from chronic myofascial pain in the piriformis, iliopsoas or scalenus anterior muscles. Thirty days after receiving an injection of either BTX-A or steroid followed by post-injection physiotherapy, pain severity had decreased significantly from baseline in both treatment groups, with no significant difference between the two treatment groups. However, the baseline pain score was significantly higher in the BTX-A treatment group compared with the steroid group (7.9 vs. 7.3), and the reduction in pain score between baseline and 30 days post-injection was greater in the BTX-A group compared with the steroid group (-3.9 vs. -3.5; P=0.06). At 60 days post-injection, the pain severity score for the BTX-A-treated patients was statistically significantly lower than the pain score for the steroid-treated population (2.3 vs. 4.9). Furthermore, the reduction in pain score in the BTX-A group at 60 days post-injection was greater than at 30 days (-5.5 vs. -3.9), whereas the effect of the steroid had begun to wane. These results indicate the superior efficacy of BTX-A over conventional steroid treatment in patients suffering from MPS, when combined with appropriate physiotherapy.
Inhibitory Control and Affective Processing in the Prefrontal Cortex: Neuropsychological Studies in the Common Marmoset (2000)

The orbitofrontal cortex has been ascribed a role in the inhibitory control, as well as in the emotional control, of behaviour. While damage to the orbitofrontal cortex in humans and non-human primates can cause inflexibility, impulsiveness and emotional disturbance, the relationship between these effects are unclear. Excitotoxic lesion studies in marmosets comparing the effects of cell loss within specific regions of the prefrontal cortex on performance of a range of behavioural tests reveal that mechanisms of response inhibition are not unique to the orbitofrontal cortex. Instead they are present in distinct cognitive domains for lowerorder as well as higher-order processing throughout the prefrontal cortex. Thus, the lateral prefrontal cortex is involved in the selection and control of action based upon higher-order rules while the orbitofrontal and medial prefrontal cortex may be involved in different but complementary forms of lower-order rule learning, their roles dissociable, as a result of their differential contribution to different types of associative learning.
Extracting and Normalizing Entity-Actions from Users' Comments (2012)

With the growing popularity of opinion-rich resources on the Web, new opportunities and challenges arise and aid people in actively using such information to understand the opinions of others. Opinion mining process currently focuses on extracting the sentiments of the users on products, social, political and economical issues. In many instances, users not only express their sentiments but also contribute their ideas, requests and suggestions through comments. Such comments are useful for domain experts and are referred to as actionable content. Extracting actionable knowledge from online social media has attracted a growing interest from both academia and the industry. We define a new problem in this line which is extracting entity-actionable knowledge from the users’ comments. The problem aims at extracting and normalizing the entity-action pairs. We propose a principled approach to solve this problem and detect exactly matched entities with 75.1% F-score and exactly matched actions with 76.43% F-score. We could achieve an average precision of 81.15% for entity-action normalization.
MICROSTRUCTURAL DEVELOPMENT DURING THE LIQUID-PHASE SINTERING OF CEMENTED CARBIDES (1972)

Measurements have been made of the contiguity, the dihedral angle, and the continuity of the carbide phase in alloys of a number of transition-metal carbides with cobalt, which were prepared by liquid-phase sintering. During sintering, the carbide contiguity in a given alloy develops towards an equilibrium value, which is directly related to the dihedral angle between carbide grains and therefore to the relative values of the interfacial energy and the contiguous boundary energy. A direct relationship between the contiguity and the angle of contact of the liquid on the carbide, however, does not exist. The contiguity at the start of sintering depends to some extent on the history of the specimen before liquid-phase sintering and in most cases is higher than the equilibrium value. Observations were made which indicate that the carbide grains in the majority of cemented carbides exist as a continuous skeleton. Arguments are presented to show that neither the presence of such a skeleton nor the presence of contiguity need be entirely inconsistent with accepted theories of densification.
Excessive heart rate increase during mild mental stress in preparation for exercise predicts sudden death in the general population (2009)

An important heart rate increase produced by a mild mental stress predicts long-term risk for sudden cardiac death. Heart rate changes before an exercise test may provide a simple tool for risk stratification.
An opportunistic power-saving mode and scheduler design for wireless local area networks (2006)

Minimizing energy consumption is crucial for portable wireless stations because they operate on a limited battery supply. The mechanism called power-saving mode (PSM) allows a network interface on a wireless station to enter the sleep mode whenever possible to reduce its energy consumption. At the same time, there has been a growing popularity in multi-rate wireless systems that can exploit the time-varying nature of the radio environment to increase the overall performance of the system under certain QoS/fairness requirements of users. The primary objective in these so-called systems is to increase the system throughput by giving priority to a mobile station experiencing better channel condition. In this work, we propose an opportunistic Power-Saving Mode and a corresponding scheduler design for wireless local area networks, which improves the energy consumption of PSM stations while maintaining throughput maximization, by exploiting time-varying channel conditions. We identify the challenges in the design and implementation of the PSM and the scheduler. We design a channel probing scheme and a scheduler called OEES (Opportunistic Energy Efficient Scheduler), which considers throughput maximization first and then focuses on minimizing energy consumption. Extensive simulations show that our scheme saves a significant amount of energy while maintaining throughput maximization.
Effects of Milk Products Fermented by Bifidobacterium longum on Blood Lipids in Rats and Healthy Adult Male Volunteers (2003)

The effects of milk products fermented by Bifidobacterium longum strain BL1, a probiotic strain, on blood lipids in rats and humans were studied. Rats were fed a cholesterol-enriched experimental diet, supplemented with lyophilized powders of 1) acid milk (control), 2) milk fermented with a mixed culture of ordinary yogurt starters composed of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus (SL), and 3) bifidobacterium milk fermented with the probiotic B. longum strain BL1, respectively. The bifidobacterium milk feeding brought about significant lowering of the serum concentrations of total cholesterol, low-density lipoprotein cholesterol, and triglycerides, in comparison with the control, while no change in high-density lipoprotein cholesterol concentration was observed. On the other hand, supplementation with SL milk resulted in only slight, nonsignificant decreases in serum lipid concentrations in comparison with the control. In the human study, 32 subjects with serum total cholesterol ranging from 220 to 280 mg/dl were randomly assigned to two treatments: 1) intake of a low-fat drinking yogurt prepared with ordinary yogurt starters composed of S. thermophilus and L. delbrueckii subsp. bulgaricus (P-group) and 2) intake of a low-fat drinking yogurt prepared with the two ordinary yogurt starters plus B. longum strain BL1 (B-group). After intake for 4 wk at 3 x 100 ml/day, reduction of serum total cholesterol was observed in approximately half of the B-group subjects; a particularly significant decrease in serum total cholesterol was found among subjects with moderate hypercholesterolemia (serum total cholesterol > 240 mg/dl). However, the serum lipid concentrations in the P-group subjects were almost stable during the experimental periods. The present results indicate the potential of the probiotic B. longum strain BL1 in serum lipid improvement.
Practical and Successful Prevention of Annular Pressure Buildup on the Marlin Project (2003)

Summary In late 1999, BP plc experienced a well failure in the Marlin development in deepwater Gulf of Mexico. Within hours of starting production, the production tieback casing collapsed, causing failure of the production tubing. Pressurization of outer annuli because of production thermal effects was identified as the most likely cause of the failure.
Phase II Study of Carboplatin in Non-small Cell Lung Cancer (1989)

Forty four patients with advanced non-small cell lung cancer (NSCLC) were treated with carboplatin (CBDCA; cis-diammine-1, 1-cyclobutane dicarboxylate platinum II) at a dose of 400-450 mg/m2 intravenously every four weeks in a phase II study. Forty three patients were evaluated for response and toxicity. Two patients achieved responses resulting in an overall response rate of 4.7% (95% confidence limits: 0.6-15.8%); one of these had not been treated previously and the other had been treated previously with vinblastine. The durations of their responses were 5 and 7 months, respectively. The response rate in 28 previously untreated patients was 3.6% (1/28; 95% confidence limits: 0.1-18.3%). Myelosuppression was the most commonly found toxicity, and thrombocytopenia especially was dose-limiting. Thrombocytopenia (less than 75,000/mm3) was observed in 12 patients (28%). Leukopenia (less than 3,000/mm3) was observed in 14 patients (33%). No serious infection or bleeding occurred, however. Treatment with 400-450 mg CBDCA/m2 was well tolerated in the good risk patients in this study. Mild to moderate emesis was observed in 28 patients (65%). No renal toxicity, neurotoxicity or ototoxicity was seen. It was demonstrated that CBDCA had little efficacy in NSCLC at the dose and schedule given in the present study.
Experimental and Theoretical Study of the Phase Equilibria in Ternary Aqueous Mixtures of 1,4-Butanediol with Alcohols at 298.2 K (2009)

Ternary liquid−liquid equilibrium (LLE) data for the mixtures of water + 1,4-butanediol + organic solvent (cyclohexanol, 2-ethyl-1-hexanol, and 1-decanol) were determined at 298.2 K and atmospheric pressure. These three ternary systems exhibit type-1 behavior of LLE. The immiscibility region was found to be larger for the branched aliphatic alcohol, 2-ethyl-1-hexanol. The experimental ternary LLE data were correlated using the UNIQUAC and NRTL models, and the binary interaction parameters were obtained. The reliability of the experimental tie-line data was tested through the Othmer−Tobias and Bachman correlation equations. Distribution coefficients and separation factors were calculated to evaluate the extracting capability of the solvents. The LLE results show that 2-ethyl-1-hexanol may be considered to be a reliable organic solvent for the extraction of 1,4-butanediol from aqueous solutions.
Analysis of the Human G Protein–Coupled Receptor Kinase 2 (GRK2) Gene Promoter (2000)

Our results suggest that the expression of GRK2 in vascular cells is tightly controlled at the transcriptional level by the interplay between several extracellular messengers, which may trigger alterations of normal GRK2 levels in some physiopathological circumstances, thus promoting changes in the efficacy of the GPCR signal transduction.
Truthful auctions for pricing search keywords (2006)

We present a truthful auction for pricing advertising slots on a web-page assuming that advertisements for different merchants must be ranked in decreasing order of their (weighted) bids. This captures both the Overture model where bidders are ranked in order of the submitted bids, and the Google model where bidders are ranked in order of the expected revenue (or utility) that their advertisement generates. Assuming separable click-through rates, we prove revenue-equivalence between our auction and the non-truthful next-price auctions currently in use.
Evaluation of Imiquimod 5% Cream to Modify the Natural History of Herpes Labialis: A Pilot Study (2005)

Application of imiquimod 5% cream to herpes labialis lesions was associated with a delay in the time to the first recurrence after treatment, but severe local inflammation occurred in some individuals.