gebhart/patrepeval huggingface dataset:
Fluorescent-conjugated polymer superquenching facilitates highly sensitive detection of proteases (2004)

Sensor formats have been developed for detecting the activity of proteolytic enzymes based on fluorescent conjugated polymer superquenching. These sensors employ a reactive peptide sequence within a tether linking a quencher to a biotin. The peptide binds to sensors containing colocated biotin-binding protein and fluorescent polymer by means of biotin-biotin binding protein interactions, resulting in a strong quenching of polymer fluorescence. Enzyme-mediated cleavage of the peptide results in a reversal of the fluorescence quenching. These assays for protease activity are simple, sensitive, fast, and have the specificity required for screening chemical libraries for novel protease inhibitors in a high-throughput screening assay environment. These assays have been demonstrated for enterokinase, caspase-3/7, and beta-secretase.
The Relationship between Active Ghrelin Levels and Human Obesity Involves Alterations in Resting Energy Expenditure (2004)

Ghrelin is a gastric hormone that exerts a stimulatory effect on appetite and fat accumulation. Ser(3) octanoylation is regarded as a prerequisite for ghrelin biological activity, although des-octanoylated forms may retain biological functions in vitro. Circulating ghrelin levels are usually low in obesity and in states of positive energy balance. Hence, the aim of our study was to analyze plasma active and serum total ghrelin levels in 20 obese (ages, 22-42 yr; body mass index, 41.3 +/- 1.1 kg/m(2)) and 20 lean subjects (ages, 22-43 yr; body mass index, 22.4 +/- 0.6 kg/m(2)) as well as their relationship to measures of glucose homeostasis, body fat, and resting energy expenditure (REE). The measured/predicted REE percentage ratio was calculated to subdivide groups into those with positive (> or = 100% ) and negative (<100%) ratio values. In obese patients, plasma active (180 +/- 18 vs. 411 +/- 57 pg/ml; P < 0.001) and serum total ghrelin levels (3650 +/- 408 vs. 5263 +/- 643 pg/ml; P < 0.05) were significantly lower when compared with lean subjects. Hence, ghrelin activity, defined as the proportion of active over total ghrelin levels, was similarly reduced in the obese state (6.1 +/- 0.9% vs. 8.4 +/- 1%; P < 0.05). There was a significant correlation between active and total ghrelin (r = 0.62; P < 0.001), and between total ghrelin and insulin (r = -0.53; P < 0.001) or insulin resistance using the homeostatis model of assessment-insulin resistance (r = -0.49; P < 0.001) approach. Significantly higher active ghrelin levels (214 +/- 22 vs. 159 +/- 30 pg/ml; P < 0.05) and ghrelin activity (8 +/- 1.7% vs. 4.9 +/- 0.9%; P < 0.05) were observed in patients with positive compared with negative measured/predicted REE ratio values. Our study shows that obesity is associated with an impairment of the entire ghrelin system. The observation that ghrelin is further decreased in cases of abnormal energy profit adds new evidence to the relationship between ghrelin activity and energy balance in obesity.
Continuous infusion, general anesthesia and other intensive care treatment for uncontrolled status epilepticus (2014)

Uncontrolled episodes of status epilepticus require intensive care treatment and the literature describes a common pathway of care used by many. However, cases of truly refractory and super-refractory status epilepticus are seen infrequently at any given institution. One strategy to improve the quality of evidence is to develop prospective, national and multinational case registries to determine the range of presentations and causes, efficacy of treatments, and clinical outcomes.
A unified statistical framework for sequence comparison and structure comparison (1998)

We present an approach for assessing the significance of sequence and structure comparisons by using nearly identical statistical formalisms for both sequence and structure. Doing so involves an all-vs.-all comparison of protein domains [taken here from the Structural Classification of Proteins (scop) database] and then fitting a simple distribution function to the observed scores. By using this distribution, we can attach a statistical significance to each comparison score in the form of a P value, the probability that a better score would occur by chance. As expected, we find that the scores for sequence matching follow an extreme-value distribution. The agreement, moreover, between the P values that we derive from this distribution and those reported by standard programs (e.g., BLAST and FASTA validates our approach. Structure comparison scores also follow an extreme-value distribution when the statistics are expressed in terms of a structural alignment score (essentially the sum of reciprocated distances between aligned atoms minus gap penalties). We find that the traditional metric of structural similarity, the rms deviation in atom positions after fitting aligned atoms, follows a different distribution of scores and does not perform as well as the structural alignment score. Comparison of the sequence and structure statistics for pairs of proteins known to be related distantly shows that structural comparison is able to detect approximately twice as many distant relationships as sequence comparison at the same error rate. The comparison also indicates that there are very few pairs with significant similarity in terms of sequence but not structure whereas many pairs have significant similarity in terms of structure but not sequence.
Nanodiamond imaging: molecular imaging with optically detected spin resonance of nitrogen-vacancy centers in nanodiamonds (2013)

Nanodiamond imaging is a new molecular imaging modality that takes advantage of nitrogen-vacancy (NV) defects in nanodiamonds to image the distribution of nanodiamonds within a living organism with high sensitivity and high resolution. Nanodiamond is a nontoxic material that is easily conjugated to biomolecules, such that the distribution of nanodiamond within a living organism can be used to elicit physiological information. Unlike the tracers used in other molecular imaging modalities such as positron emission tomography (PET) and single photon emission computed tomography (SPECT), nanodiamonds are stable and thus allow longitudinal imaging of the same organism over a long time span. Unlike fluorescence-based molecular imaging that has a resolution degraded by photon scattering, the resolution of nanodiamond imaging is defined by the strength of a magnetic gradient. <br/> To form an image, a magnetic field-free region is created, such as exists halfway between two identical magnets with north poles facing each other. Optical excitation pumps the NVs into a bright fluorescence state, and microwaves transfer them to a dark state, but only for those NVs within the field-free region and resonant with the microwaves. By rastering the field-free region across the sample, the changes in fluorescence yield the nanodiamond concentration. Images of nanodiamond phantoms within chicken breast have been recorded with a prototype system. By modifying the nanodiamond particles and enhancing the imaging system, it should be possible to approach 100 &mu;m resolution and to increase the sensitivity to a 10 nanomolar carbon concentration per root Hz in a mm<sup>3</sup> voxel.
Optison (FS069) Disrupts the Blood-Brain Barrier in Rats (2000)

Optison is a new echocardiographic contrast agent, designed for IV injection, that is very useful in delineating cardiac structures during ultrasound examination. Because Optison could be a valuable adjunct in the diagnosis and evaluation of congenital heart disease, this study was undertaken to assess its effects on the blood-brain barrier when introduced directly in the cerebral circulation, as might occur with some congenital lesions. In this study, Sprague-Dawley rats were anesthetized, and Optison, at various dosages, was injected into the carotid artery. After this, Evans blue dye, a marker for blood-brain barrier disruption, was injected at different time intervals. Gross and histologic examination of the animals' brains revealed disruption of the blood-brain barrier that appeared to be Optison-dosage-dependent. Although the mechanism for this disruption is unclear, it may be related to the use of octofluoropropane gas used in the Optison as a contrast medium. Further studies are necessary to determine the pathologic consequences of Optison's effects on the blood-brain barrier.
Crystallization and preliminary X-ray diffraction analysis of the complex of a human anti-ephrin type-A receptor 2 antibody fragment and its cognate antigen (2010)

The recombinant N-terminal domain of human ephrin type-A receptor 2 (rEphA2) has been crystallized in complex with the recombinantly produced Fab fragment of a fully human antibody (1C1; IgG1/kappa). These are the first reported crystals of an ephrin receptor bound to an antibody. The orthorhombic crystals belonged to space group C222(1) (the 00l reflections obey the l = 2n rule), with unit-cell parameters a = 78.93, b = 120.79, c = 286.20 A. The diffraction of the crystals extended to 2.0 A resolution. However, only data to 2.55 A resolution were considered to be useful owing to spot overlap caused by the long unit-cell parameter. The asymmetric unit is most likely to contain two 1C1 Fab-rEphA2 complexes. This corresponds to a crystal volume per protein weight (V(M)) of 2.4 A(3) Da(-1) and a solvent content of 49.5%. The three-dimensional structure of this complex will shed light on the molecular basis of 1C1 specificity. This will also contribute to a better understanding of the mechanism of action of this antibody, the current evaluation of which as an antibody-drug conjugate in cancer therapy makes it a particularly interesting case study.
India's Pro-Arab Policy: A Study in Continuity (1992)

Preface and Acknowledgments Historical Background Reasons for a Pro-Arab Policy The Palestine Question India, Pakistan and Arab Reciprocity Continuation of a Traditional Policy Conclusion Selected Bibliography Index
Relationship Between Insulin Resistance and an Endogenous Nitric Oxide Synthase Inhibitor (2002)

A significant relationship exists between insulin resistance and plasma concentrations of ADMA. Pharmacological intervention with rosiglitazone enhanced insulin sensitivity and reduced ADMA levels. Increases in plasma ADMA concentrations may contribute to the endothelial dysfunction observed in insulin-resistant patients.
Miniaturised "Low Profile" module integrated converter for photovoltaic applications with integrated magnetic components (1999)

This paper deals with reliability aspects of module integrated power converters (MIC) for grid-connected photovoltaic power applications. The presented "low profile design" of a MIC has almost twice the power density and a 70% longer lifetime than commercially available MICs. In order to miniaturise and increase the reliability of the MIC, all magnetic components have been realised using planar cores and windings integrated into the PCB. Additionally, the power converter's resonant inductor has been integrated into the transformer by using the leakage inductance as the inductor. The leakage inductance of planar transformers with integrated windings can be adjusted very precisely.
A Computational Study of Nicotine Conformations in the Gas Phase and in Water (2000)

The conformational preferences of nicotine in three protonation states and in the gas phase as well as aqueous solution are investigated using several computational procedures. Conformational aspects emphasized are N-methyl stereochemistry, relative rotation of the pyridine and pyrrolidine rings, and pyrrolidine ring conformation. All methods consistently predicted that the N-methyl trans species are most stable for all protonation states in both gas phase and in water. However, the cis/trans energy gap is significantly reduced in water. Additionally, the two pyridine ring rotamers, which are energetically equivalent in the gas phase, experience different solvation energies in water.
Posterior Vitreous Detachment Induced by Microplasmin (2004)

Both after death and in vivo, microplasmin induces a dose-dependent cleavage between the vitreous cortex and the ILM without morphologic alterations of the retina. In the feline eye, there is no cellular response of retinal glial cells or neurons.
Mass spectrometric study of ion adsorption on poly(ethylene terephthalate) and polypropylene surfaces (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMass spectrometric study of ion adsorption on poly(ethylene terephthalate) and polypropylene surfacesRonald D. Macfarlane, Catherine J. McNeal, and Charles R. MartinCite this: Anal. Chem. 1986, 58, 6, 1091–1097Publication Date (Print):May 1, 1986Publication History Published online1 May 2002Published inissue 1 May 1986https://pubs.acs.org/doi/10.1021/ac00297a025https://doi.org/10.1021/ac00297a025research-articleACS PublicationsRequest reuse permissionsArticle Views113Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Monolithic Chip System with a Microfluidic Channel for In Situ Electron Microscopy of Liquids (2014)

Electron microscopy of enclosed liquid samples requires the thinnest possible membranes as enclosing windows as well as nanoscale liquid sample thickness to achieve the best possible resolution. Today liquid sample systems for transmission electron microscopy (TEM) are typically made from two sandwiched microchips with thin membranes. We report on a new microfabricated chip system based on a monolithic design that enables membrane geometry on the scale of a few micrometers. The design is intended to reduce membrane deflection when the system is under pressure, a microfluidic channel for improved flow geometry, and a better space angle for auxiliary detectors such as energy-dispersive X-ray spectroscopy. We explain the system design and fabrication and show the first successful TEM images of liquid samples in the chips.
The Effects ofN,N-Diethyl-4-Methyl-3-Oxo-4-Aza-5α-Androstane-17yβ-Carboxamide, a 5α-Reductase Inhibitor and Antiandrogen, on the Development of Baldness in the Stumptail Macaque* (1987)

We used a primate model of male-pattern baldness to test the efficacy of a topically applied 5 alpha-reductase inhibitor and antiandrogen (4-MA) in the prevention of baldness. Six periadolescent stumptail macaques were given daily topical applications of either 4-MA in dimethylsulfoxide or dimethylsulfoxide alone for 27 months. The three control monkeys developed varying degrees of baldness, while the three 4-MA-treated monkeys retained their juvenile pattern of hair growth. The percentage of actively growing hair follicles in the frontal scalp did not change in the 4-MA-treated group [46 +/- 6 (+/- SE) vs. 48 +/- 4], while a significant decrease occurred in the control group (63 +/- 6 vs. 25 +/- 12; P less than 0.025). Skin 5 alpha-reductase activity was reduced in the scalp of the 4-MA-treated monkeys. We conclude that topical 4-MA can prevent the development of baldness in the stumptail macaque, a primate model of androgen-dependent baldness.
Amelioration of delayed neuronal death in the hippocampus by nerve growth factor (1991)

Selective neuronal death in the CA1 sector of the hippocampus [delayed neuronal death (DND)] develops several days after transient global cerebral ischemia in rodents. Because NGF plays a potential role in neuronal survival, it was decided to study its effect in DND. We report here that intraventricular injection of NGF either before or after 5 min forebrain ischemia in the Mongolian gerbil significantly reduced the occurrence of DND. The tissue content of NGF in the hippocampus was decreased 2 d after ischemia and recovered to the preischemic level by 1 week. By the Golgi staining technique, changes first began in the dendrites of affected neurons as early as 3 hr. Such changes could be ameliorated by NGF treatment. Although previous knowledge of NGF is limited to the survival of cholinergic neurons in the CNS, it is assumed that other mechanisms must be operating in the hippocampus, for example, postsynaptic modification at dendrites or aberrant expression of NGF receptors possibly at the initial excitation period by glutamate. Furthermore, because previous work has shown that inhibition of protein synthesis reduces the occurrence of DND, a program leading to cell death might also be operating via de novo synthesis of certain protein(s), collectively termed "killer protein," because of a lack of NGF.
TiO2 Nanophotonic Sensors for Efficient Integrated Evanescent Raman Spectroscopy (2016)

Waveguide-based evanescent Raman sensors are an attractive chemical-detection technology due to their compact format, increased signal over micro-Raman spectrometers, and nanoscale surface sensitivity. To improve the device’s performance, herein we experimentally demonstrate strategies to increase the efficiency of waveguide-based evanescent Raman sensors over the state-of-the-art silicon-nitride devices by more than an order of magnitude. First, we use pumping at visible wavelengths (532 nm versus 785 nm, which is commonly used) to exploit the Raman cross-section’s λ–4 dependence. Second, we use titanium dioxide (TiO2), which combines comparatively low visible background luminescence with a high refractive index to concentrate light near the waveguide’s surface. These visibly pumped TiO2 sensors display >50× more Stokes signal per input pump power over that of silicon-nitride devices. Lastly, we explore ring resonators and observe on-resonance Stokes emission with peak rates >30× higher than an equivalent length straight waveguide. We attribute the higher Stokes emission to a combination of pump and emission enhancements and propose using this approach to increase the Stokes signal in future devices.
Photodynamic Therapy (1998)

Photodynamic therapy involves administration of a tumor-localizing photosensitizing agent, which may require metabolic synthesis (i.e., a prodrug), followed by activation of the agent by light of a specific wavelength. This therapy results in a sequence of photochemical and photobiologic processes that cause irreversible photodamage to tumor tissues. Results from preclinical and clinical studies conducted worldwide over a 25-year period have established photodynamic therapy as a useful treatment approach for some cancers. Since 1993, regulatory approval for photodynamic therapy involving use of a partially purified, commercially available hematoporphyrin derivative compound (Photofrin) in patients with early and advanced stage cancer of the lung, digestive tract, and genitourinary tract has been obtained in Canada, The Netherlands, France, Germany, Japan, and the United States. We have attempted to conduct and present a comprehensive review of this rapidly expanding field. Mechanisms of subcellular and tumor localization of photosensitizing agents, as well as of molecular, cellular, and tumor responses associated with photodynamic therapy, are discussed. Technical issues regarding light dosimetry are also considered.
International Society for Cellular Therapy perspective on immune functional assays for mesenchymal stromal cells as potency release criterion for advanced phase clinical trials (2015)

Mesenchymal stromal cells (MSCs) as a pharmaceutical for ailments characterized by pathogenic autoimmune, alloimmune and inflammatory processes now cover the spectrum of early- to late-phase clinical trials in both industry and academic sponsored studies. There is a broad consensus that despite different tissue sourcing and varied culture expansion protocols, human MSC-like cell products likely share fundamental mechanisms of action mediating their anti-inflammatory and tissue repair functionalities. Identification of functional markers of potency and reduction to practice of standardized, easily deployable methods of measurements of such would benefit the field. This would satisfy both mechanistic research as well as development of release potency assays to meet Regulatory Authority requirements for conduct of advanced clinical studies and their eventual registration. In response to this unmet need, the International Society for Cellular Therapy (ISCT) addressed the issue at an international workshop in May 2015 as part of the 21st ISCT annual meeting in Las Vegas. The scope of the workshop was focused on discussing potency assays germane to immunomodulation by MSC-like products in clinical indications targeting immune disorders. We here provide consensus perspective arising from this forum. We propose that focused analysis of selected MSC markers robustly deployed by in vitro licensing and metricized with a matrix of assays should be responsive to requirements from Regulatory Authorities. Workshop participants identified three preferred analytic methods that could inform a matrix assay approach: quantitative RNA analysis of selected gene products; flow cytometry analysis of functionally relevant surface markers and protein-based assay of secretome. We also advocate that potency assays acceptable to the Regulatory Authorities be rendered publicly accessible in an "open-access" manner, such as through publication or database collection.
Saccharomicins, Novel Heptadecaglycoside Antibiotics Effective against Multidrug-Resistant Bacteria (1998)

Two novel heptadecaglycoside antibiotics, saccharomicins A (1) and B (2), were isolated from a new species of Saccharothrix. Their structures were determined by a combination of chemical degradation and spectroscopic methods. Saccharomicin B (2) was identified as N-(m,p-dihydroxycinnamoyl) taurine p-O-[α-4-epi-vancosaminopyranosyl(1→4)-α-4-epi-vancosaminopyranosyl(1→4)-α-digitoxopyranosyl(1→4)-α- 4-epi-vancosaminopyranosyl(1→4)-α-digitoxopyranosyl(1→3)-β-fucopyranosyl(1→4)-β-saccharosaminopyranosyl(1→4)-α-digitoxopyranosyl(1→3)]-[α-4-epi-vancosaminopyranosyl(1→4)]-β-fucopyranosyl(1→4)-β- saccharosaminopyranosyl(1→4)-α-rhamnopyranosyl(1→3)-β-fucopyranosyl(1→4)-β-saccharosaminopyranosyl(1→4)-β-fucopyranosyl(1→4)-β-saccharosaminopyranosyl(1→4)-β-2-sulfate-fucopyranoside. Saccharomicin A (1) differs from saccharomicin B (2) only in the 10th sugar residue, where α-digitoxopyranosyl(1→3) is replaced with α-rhamnopyranosyl(1→3). The novel amino sugar residue, designated saccharosamine, was identified by NMR spectroscopy and X-ray crystallography. Both saccharomicins A (1) and B (2) showed antimicrobial activity against Gram-positive bacteria.