gebhart/patrepeval huggingface dataset:
A Cleavage-potentiated Fragment of Tear Lacritin Is Bactericidal (2014)

Antimicrobial peptides are important as the first line of innate defense, through their tendency to disrupt bacterial membranes or intracellular pathways and potentially as the next generation of antibiotics. How they protect wet epithelia is not entirely clear, with most individually inactive under physiological conditions and many preferentially targeting Gram-positive bacteria. Tears covering the surface of the eye are bactericidal for Gram-positive and -negative bacteria. Here we narrow much of the bactericidal activity to a latent C-terminal fragment in the prosecretory mitogen lacritin and report that the mechanism combines membrane permeabilization with rapid metabolic changes, including reduced levels of dephosphocoenzyme A, spermidine, putrescine, and phosphatidylethanolamines and elevated alanine, leucine, phenylalanine, tryptophan, proline, glycine, lysine, serine, glutamate, cadaverine, and pyrophosphate. Thus, death by metabolic stress parallels cellular attempts to survive. Cleavage-dependent appearance of the C-terminal cationic amphipathic α-helix is inducible within hours by Staphylococcus epidermidis and slowly by another mechanism, in a chymotrypsin- or leupeptin protease-inhibitable manner. Although bactericidal at low micromolar levels, within a biphasic 1-10 nM dose optimum, the same domain is mitogenic and cytoprotective for epithelia via a syndecan-1 targeting mechanism dependent on heparanase. Thus, the C terminus of lacritin is multifunctional by dose and proteolytic processing and appears to play a key role in the innate protection of the eye, with wider potential benefit elsewhere as lacritin flows from exocrine secretory cells.
Implication of the RAGE–EN‐RAGE axis in endometriosis (2010)

Our findings strengthen the hypothesis of an underlying inflammation in the pathophysiology of endometriosis and suggest exploring anti-inflammatory therapies as adjunct treatment.
Robust Land Use Characterization of Urban Landscapes using Cell Phone Data (2011)

Abstract. Mobile devices have become one of the main sensors of human behavior, and as such, can be used as proxies to study urban environments. In this paper we describe a method to automatically identify land uses from call detail record databases. Given the inherent diversity of human activities in urban landscapes, we use fuzzy clustering techniques to identify land uses in a robust way, characterizing only those geographical areas with well defined behaviors. Finally, we validate the results obtained using expert knowledge. 1
Dealing with verbal abuse (2001)

Walter Brennan offers guidance on how to manage one of the more insidious forms of aggression
PHARMACOLOGICAL STUDIES OF PANAX GINSENG LEAVES (1973)

Pharmacological properties of a crude saponin fraction (GF-DS-I) and saponins (GF-DS-II) which were obtained from Panax Ginseng leaves, were estimated by blind screening consisting of three tests: 1) neuropharmacological observations in mice, 2) tests on the respiratory and cardiovascular system in rats, and 3) tests on the guinea-pig isolated ileum. GF-DS-I appeared to have CNS-depressive, neuroleptic, analgesic, hypertensive, cholinergic, and histamine-like activities, while GF-DS-II, had CNS-depressive, neuroleptic, analgesic, hypotensive, atropine-like and papaverine-like activities. These neuroleptic activities, were examined and confirmed by tests on motor activity, exploratory movements, muscle tone, motor coordination, hypothermia and potentiation of CNS-depressant, and pole climbing, anticonvulsant and analgesic tests. No effects were seen on hemolysis.
Biased Signaling Pathways in β <sub>2</sub> -Adrenergic Receptor Characterized by <sup>19</sup> F-NMR (2012)

Extracellular ligand binding to G protein-coupled receptors (GPCRs) modulates G protein and β-arrestin signaling by changing the conformational states of the cytoplasmic region of the receptor. Using site-specific (19)F-NMR (fluorine-19 nuclear magnetic resonance) labels in the β(2)-adrenergic receptor (β(2)AR) in complexes with various ligands, we observed that the cytoplasmic ends of helices VI and VII adopt two major conformational states. Changes in the NMR signals reveal that agonist binding primarily shifts the equilibrium toward the G protein-specific active state of helix VI. In contrast, β-arrestin-biased ligands predominantly impact the conformational states of helix VII. The selective effects of different ligands on the conformational equilibria involving helices VI and VII provide insights into the long-range structural plasticity of β(2)AR in partial and biased agonist signaling.
Computational Modeling of Localized Laser Energy Deposition in Quiescent Air (2002)

A model for Nd:YAG laser energy deposition in air is developed. Laser beam optics, inversebremsstrahlung absorption, plasma reflection, air breakdown chemistry and the fluid dynamics of the blast wave are modeled. The energy deposition process is simulated using this model. The eects of varying absorptivity and reflectivity on the plasma structure are studied. The simulated plasma and the detonation wave are compared with the experimental results. The CFD results are capable of capturing the main features of laser induced spark formation and the shape of the detonation wave, but the fluid dynamics that follow are not suciently represented in quantitative terms, due to excessuve numerical dissipation.
Interferon-gamma-mediated activation of STAT1alpha regulates growth factor-induced mitogenesis. (1996)

Immunomodulatory cytokines and growth factors act in a complex network to regulate diverse biologic processes. Pre-treatment of two types of human vascular pericytes, liver fat-storing cells or glomerular mesangial cells, with IFN-gamma dramatically enhanced DNA synthesis in response to PDGF or EGF. IFN-gamma by itself had very little effect on DNA synthesis. At least 24-h exposure of the cells to IFN-gamma is required for enhancement of growth factor-induced mitogenesis. IFN-gamma pretreatment did not influence PDGF or EGF receptor autophosphorylation, activation of phospholipase Cgamma1, and phosphatidylinositol 3-kinase, or mitogen-activated protein kinase activity. However, IFN-gamma pretreatment markedly potentiated the DNA binding activity of STAT1alpha in response to PDGF or EGF. Incubation of cells with antisense oligonucleotides targeting STATlalpha mRNA resulted in inhibition of DNA synthesis induced by the combination of IFN-gamma and PDGF or EGF. These data indicate that interaction between IFN-gamma and growth factors at the level of STAT1alpha results in increased DNA synthesis, and establish a role for STAT1alpha in this important biologic function of growth factors.
Routine Endoscopy Using a Magnifying Endoscope for Gastric Cancer Diagnosis (2002)

The fine mucosal patterns and the features of capillary vessels, which were identified with the magnifying endoscope, correlated well with the pathological diagnosis. Magnifying endoscopy will be very useful in predicting the histological diagnosis during routine endoscopic procedures.
Studies of magnetic sensitivity in the yellowfin tuna, Thunnus albacares (1983)

Ph.D.
Preparation and Identification of ACE Inhibitory Peptides from the Marine Macroalga Ulva intestinalis (2019)

Angiotensin I-converting enzyme (ACE) inhibitory peptides derived from seaweed represent a potential source of new antihypertensive. The aim of this study was to isolate and purify ACE inhibitory peptides (ACEIPs) from the protein hydrolysate of the marine macroalga <i>Ulva intestinalis</i>. <i>U. intestinalis</i> protein was hydrolyzed by five different proteases (trypsin, pepsin, papain, α-chymotrypsin, alcalase) to prepare peptides; compared with other hydrolysates, the trypsin hydrolysates exhibited the highest ACE inhibitory activity. The hydrolysis conditions were further optimized by response surface methodology (RSM), and the optimum conditions were as follows: pH 8.4, temperature 28.5 °C, enzyme/protein ratio (E/S) 4.0%, substrate concentration 15 mg/mL, and enzymolysis time 5.0 h. After fractionation and purification by ultrafiltration, gel exclusion chromatography and reverse-phase high-performance liquid chromatography, two novel purified ACE inhibitors with IC<sub>50</sub> values of 219.35 μM (0.183 mg/mL) and 236.85 μM (0.179 mg/mL) were obtained. The molecular mass and amino acid sequence of the ACE inhibitory peptides were identified as Phe-Gly-Met-Pro-Leu-Asp-Arg (FGMPLDR; MW 834.41 Da) and Met-Glu-Leu-Val-Leu-Arg (MELVLR; MW 759.43 Da) by ultra-performance liquid chromatography-tandem mass spectrometry. A molecular docking study revealed that the ACE inhibitory activities of the peptides were mainly attributable to the hydrogen bond and Zn(II) interactions between the peptides and ACE. The results of this study provide a theoretical basis for the high-valued application of <i>U. intestinalis</i> and the development of food-derived ACE inhibitory peptides.
The use of chitin and chitosan as drug carriers. (1981)

The suitability of chitin and chitosan for use as vehicles for the sustained release of drugs was examined. Indomethacin and papaverine hydrochloride were used as model drugs in this evaluation. Sustained release of the drugs from the dried gels was obtained. Drugs dispersed in the chitosan gels were released at a constant rate (zero order). Chitin and chitosan could be useful vehicles for the sustained release of drugs.
Role of Pyruvate Carboxylase, Phosphoenolpyruvate Carboxykinase, and Malic Enzyme during Growth and Sporulation of Bacillus subtilis (1973)

Abstract In extracts of Bacillus subtilis, CO2 fixation occurs primarily through the apparently constitutive enzyme carboxylase, which is strongly activated by acetyl-CoA. This enzyme is necessary for growth on glucose but is not required for sporulation, as was established with a carboxylase mutant. The malic enzyme can use either NAD or, less effectively, NADP as cofactor. The ratio of these activities remains constant through enzyme purification and during enzyme induction by l-malate. Enzyme synthesis is not repressed by glucose. Malic enzyme and carboxylase form a pyruvate shunt to the citric acid cycle, which apparently is necessary during growth on malate for the production of oxalacetate in substrate amounts; malic dehydrogenase functions mainly to provide energy via the citric acid cycle. A specific and sensitive [γ-32P]ATP assay for P-enolpyruvate carboxykinase has been developed. Using this assay, a purified enzyme preparation gave a Km for oxalacetate of about 25 µm. Enzyme synthesis is repressed by glucose. P-enolpyruvate carboxykinase mutants have established that the enzyme is needed for gluconeogenesis and, under normal growth conditions, for sporulation. Sporulation can be restored by the continuous feeding of gluconate.
Prognostic factors for patients with diffuse large <scp>B</scp> cell lymphoma and transformed indolent lymphoma undergoing autologous stem cell transplantation in the positron emission tomography era (2012)

In the positron emission tomography (PET) era, traditional prognostic factors may not apply for patients with relapsed/refractory (R/R) diffuse large B cell lymphoma (DLBCL) undergoing autologous stem cell transplantation (ASCT). Moreover, little is known about prognostic factors in patients transplanted for transformed indolent lymphoma (TIL). We conducted a retrospective study of 143 patients with R/R DLBCL and TIL who were transplanted in the last decade and had a post-salvage PET scan. We examined prognostic factors in both groups, and constructed a prognostic score for DLBCL patients. For patients with DLBCL, post-salvage PET response was an important prognostic factor. Advanced age and symptomatic relapse were also significantly associated with outcome. A simple score could stratify patients into three risk groups with 4-year post-ASCT overall survival of 84%, 59%, and 10%, and 4-year progression-free survival of 67%, 41% and 0% (P<0.0001 for both). However, none of those factors (including PET response to salvage) appeared relevant for patients with TIL, despite their comparable overall outcome. Our prognostic score for DLBCL patients undergoing ASCT may be useful for prognostication, for stratification in clinical trials, and to motivate the design of new strategies for patients in the high-risk group, who may not derive benefit from standard ASCT.
Improving distributed join efficiency with extended bloom filter operations (2007)

Bloom filter based algorithms have proven successful as very efficient technique to reduce communication costs of database joins in a distributed setting. However, the full potential of bloom filters has not yet been exploited. Especially in the case of multi-joins, where the data is distributed among several sites, additional optimization opportunities arise, which require new bloom filter operations and computations. In this paper, we present these extensions and point out how they improve the performance of such distributed joins. While the paper focuses on efficient join computation, the described extensions are applicable to a wide range of usages, where bloom filters are facilitated for compressed set representation.
Formation of Indole-3-Carboxylic Acid by <i>Chromobacterium violaceum</i> (1976)

l-Tryptophan is converted to indole-3-carboxylic acid by growing cultures and resting cell suspensions of Chromobacterium violaceum
Effect of additive particles on mechanical, thermal, and cell functioning properties of poly(methyl methacrylate) cement (2014)

The most common bone cement material used clinically today for orthopedic surgery is poly(methyl methacrylate) (PMMA). Conventional PMMA bone cement has several mechanical, thermal, and biological disadvantages. To overcome these problems, researchers have investigated combinations of PMMA bone cement and several bioactive particles (micrometers to nanometers in size), such as magnesium oxide, hydroxyapatite, chitosan, barium sulfate, and silica. A study comparing the effect of these individual additives on the mechanical, thermal, and cell functional properties of PMMA would be important to enable selection of suitable additives and design improved PMMA cement for orthopedic applications. Therefore, the goal of this study was to determine the effect of inclusion of magnesium oxide, hydroxyapatite, chitosan, barium sulfate, and silica additives in PMMA on the mechanical, thermal, and cell functional performance of PMMA. American Society for Testing and Materials standard three-point bend flexural and fracture tests were conducted to determine the flexural strength, flexural modulus, and fracture toughness of the different PMMA samples. A custom-made temperature measurement system was used to determine maximum curing temperature and the time needed for each PMMA sample to reach its maximum curing temperature. Osteoblast adhesion and proliferation experiments were performed to determine cell viability using the different PMMA cements. We found that flexural strength and fracture toughness were significantly greater for PMMA specimens that incorporated silica than for the other specimens. All additives prolonged the time taken to reach maximum curing temperature and significantly improved cell adhesion of the PMMA samples. The results of this study could be useful for improving the union of implant-PMMA or bone-PMMA interfaces by incorporating nanoparticles into PMMA cement for orthopedic and orthodontic applications.
Penile reconstruction/formation (2008)

Technical advances in penile reconstruction have been highlighted. The few long-term follow-up studies available confirm the difficulty of such surgery, in terms of complications and the limits of the final achievable outcomes. The surgery necessitates several steps and a high number of revisions. Scientific progress in penile reconstruction seems slow, with a lack of controlled studies, high rate of loss to follow-up (especially in sex reassignment surgery) and a lack of validated assessment measures. However, a few recent studies are making the problems clearer, especially in patient selection and the avoidance of raising false expectations in patients.
Chloramphenicol induction of cat-86 requires ribosome stalling at a specific site in the leader. (1988)

The plasmid gene cat-86 specifies chloramphenicol-inducible chloramphenicol acetyltransferase in Bacillus subtilis. Induction by the antibiotic is primarily due to activation of the translation of cat-86-encoded mRNA. It has been suggested that the inducer stalls ribosomes at a discrete location in the leader region of cat-86 mRNA, which causes the destabilization of a downstream RNA secondary structure that normally sequesters the cat-86 ribosome binding site. It is the destabilization of this RNA secondary structure that permits translation of the cat-86 coding sequence. In the present report, we show that ribosomes that were stalled in the cat-86 leader by starvation of host cells for the amino acid specified by leader codon 6 induced gene expression to a level above that detected when cells were starved for the amino acids specified by leader codons 7 and 8. Starvation for amino acids specified by leader codons 3, 4, or 5 failed to activate cat-86 expression. These results indicate that the stalled ribosome that is most active in cat-86 induction has its aminoacyl site occupied by leader codon 6. To determine if chloramphenicol also stalled ribosomes in the cat-86 regulatory leader such that the aminoacyl site was occupied by codon 6, we separately changed leader codons 3, 4, 5, and 6 to the translation termination (ochre) codon TAA. Each of the mutated genes was tested for its ability to be induced by chloramphenicol. The results show that replacement of leader codons 3, 4, or 5 by the ochre codon blocked induction, whereas replacement of leader codon 6 by the ochre codon permitted induction. Collectively, these observations lead to the conclusion that cat-86 induction requires ribosome stalling in leader mRNA, and they identify leader codon 6 as the codon most likely to be occupied by the aminoacyl site of a stalled ribosome that is active in the induction.
The Biological Impact of Flash Pasteurization Over a Wide Temperature Interval* (2000)

Trials on the impact of flash pasteurization on beer quality showed that higher pasteurization temperatures with shorter holding times are favourable for beer quality. However, the killing effect in the temperature range up to 90°C has not been elucidated so far. Pasteurization temperatures of 50°; 60°; 72°; 84° and 90°C and pasteurization units of 0; 15; 80 and 500 PU were used. The associated residence times were calculated according to Del Vecchio et al.'s formula. The experiments with beer-relevant yeasts and bacteria showed that Saccharomyces yeasts are much easier to inactivate than Lactobacilli and Pediococci. Furthermore, it can be stated that the commonly used PU calculation according to Del Vecchio reflects the actual killing characteristics in the temperature range from 60° to 72°C quite precisely. Although flash pasteurization with low PU figures at temperatures higher than 72°C and with very high amounts of bacteria may be insufficient, because the real inactivation effect is lower than indicated, there is no need to increase the PU load when changing to higher pasteurization temperatures and shorter holding times in practical application.
Steel Coiled Tubing Defect Evaluation Using Magnetic Flux Leakage Signals (2014)

Abstract Mechanical defects, such as manufacturing imperfections, grinding marks, corrosion pits, slip marks, kinking, gouges, etc, whether occurred in the factory or in the field, can be readily found on CT strings. Extensive studies have demonstrated the detrimental effects of mechanical defects, over the integrity of the coiled tubing, both in the lab and in the field. Researchers in the field have been proposing theoretical models for the severity assessment of mechanical defects, particularly as it relates to the remaining fatigue life. For such models, the defect sizing is usually a prerequisite. In order to improve coiled tubing pipe management, it is important to assess the size of a defect, and its severity. MFL (magnetic flux leakage) based devices are volumetric and non-contact technology that is now commercially available for inspection and monitoring of CT strings. These devices have been demonstrated to be sufficiently sensitive in identifying mechanical defects. However, defect characterization and evaluation based on the devices’ MFL signals is rarely seen. To fully utilize these MFL based inspection devices for coiled tubing pipe management, it is important to establish correlation between the MFL inspection signals and the geometry and severity of the underlying mechanical defects. The current work developed a three dimensional Finite Element Analysis (FEA) model to calculate magnetic flux leakage for mechanical defects on steel coiled tubing. The fidelity of the FEA model was verified against analytical and experimental results over a series of benchmark defects. By using the analytical and FEA models, parametric studies were performed to evaluate how the MFL signals are affected by various factors. The results were used to identify defect geometry features based on MFL signals. Physical limits behind these results were identified and analyzed. Ways to overcome such limits were proposed. Further, a novel approach was presented and validated to reconstruct three-dimensional MFL field based on a single MFL component measurement. The benefit of using multiple MFL components was demonstrated for defect characterization.
A lithographic mask manufacturability and pattern fidelity aware OPC algorithm (2016)

Optical Proximity Correction (OPC) is still the main stream among Resolution Enhancement Techniques (RETs) for printing advanced technology nodes in optical lithography in the foreseeable future. However, to keep pace with the continuous shrinkage of feature dimensions, OPC algorithms are getting more aggressive to achieve acceptable pattern fidelity on the silicon wafer. This results in outputting complex mask patterns whose manufacturability is degraded. In this paper, we propose an intensity based OPC algorithm to improve mask manufacturability with preserving acceptable pattern fidelity following linearly interpolated intensity error model. Experimental results show the effectiveness of our algorithm on the public benchmarks.
Substituted polythiophenes designed for optoelectronic devices and conductors (1999)

Polythiophenes are a very versatile class of conjugated polymers. Substituted polythiophenes can be tailored for various applications by designing the side groups to give the polymer different desired properties. Our work on preparing polythiophenes designed to have high stability in the doped state is described. We also discuss our efforts on tuning the colour of the emission from polythiophenes for use in polymer light-emitting diodes. Design criteria for the synthesis of polythiophenes with high luminescence efficiency for use in light-emitting diodes and lasers are also described. Finally, the design of polythiophenes for use in photodiodes is discussed.