gebhart/patrepeval huggingface dataset:
Sources of fatty acids stored in liver and secreted via lipoproteins in patients with nonalcoholic fatty liver disease (2005)

Nonalcoholic fatty liver disease (NAFLD) is characterized by the accumulation of excess liver triacylglycerol (TAG), inflammation, and liver damage. The goal of the present study was to directly quantify the biological sources of hepatic and plasma lipoprotein TAG in NAFLD. Patients (5 male and 4 female; 44 +/- 10 years of age) scheduled for a medically indicated liver biopsy were infused with and orally fed stable isotopes for 4 days to label and track serum nonesterified fatty acids (NEFAs), dietary fatty acids, and those derived from the de novo lipogenesis (DNL) pathway, present in liver tissue and lipoprotein TAG. Hepatic and lipoprotein TAG fatty acids were analyzed by gas chromatography/mass spectrometry. NAFLD patients were obese, with fasting hypertriglyceridemia and hyperinsulinemia. Of the TAG accounted for in liver, 59.0% +/- 9.9% of TAG arose from NEFAs; 26.1% +/- 6.7%, from DNL; and 14.9% +/- 7.0%, from the diet. The pattern of labeling in VLDL was similar to that in liver, and throughout the 4 days of labeling, the liver demonstrated reciprocal use of adipose and dietary fatty acids. DNL was elevated in the fasting state and demonstrated no diurnal variation. These quantitative metabolic data document that both elevated peripheral fatty acids and DNL contribute to the accumulation of hepatic and lipoprotein fat in NAFLD.
A Single Institution, Randomized, Prospective Trial of Cyclosporine Versus Azathioprine-Antilymphocyte Globulin for Immunosuppression in Renal Allograft Recipients (1985)

Between September 26, 1980 and December 31, 1983, 230 splenectomized, transfused renal allograft recipients were randomized to treatment with either cyclosporin-prednisone (N = 121, 68 diabetic and 53 nondiabetic recipients; 73 cadaver and 48 related donor grafts) or azathioprine-prednisone-antilymphocyte globulin (N = 109, 61 diabetic and 48 nondiabetic recipients; 69 cadaver and 40 related donor grafts). The results were analyzed on March 31, 1984. Actuarial patient survival rates at 2 years were 88% in the cyclosporin and 91% in the azathioprine groups (p = 0.649). Graft survival rates at 2 years were 82% in all cyclosporin and 77% in all azathioprine-treated recipients (p = 0.150); the corresponding figures in the recipients of related donor grafts were 87% vs. 83% (p = 0.656), and in the recipients of cadaver donor grafts were 78% vs. 73% (p = 0.178). The 2-year graft survival rates were 81% in cyclosporin and 74% in azathioprine-treated diabetic recipients (p = 0.150) and 83% in cyclosporin and 81% in azathioprine-treated nondiabetic recipients (p = 0.604). Within the cyclosporin and azathioprine treatment groups, the differences in graft survival rates between diabetic and nondiabetic recipients were not significant (p = 0.822 and 0.423, respectively). Although there were no significant differences in graft survival rates, the cumulative incidence of rejection episodes within the first post-transplant year was significantly lower in the cyclosporin (34%) than in the azathioprine (60%) treated recipients (p = 0.001). In recipients of technically successful cadaver kidney grafts, the incidence of acute tubular necrosis (ATN) was 31% in cyclosporin and 30% in azathioprine-treated recipients (p = 0.822). Graft survival rates in azathioprine- and cyclosporin-treated recipients who did or did not undergo ATN were 72% vs. 89% (p = 0.011). The mean (+/- S.D.) serum creatinine levels (mg/dl) at 1 year were higher in cyclosporin (2.0 +/- 0.6) than in azathioprine (1.5 +/- 0.5) treated recipients (p = less than 0.001). A reduction in cyclosporin dose because of nephrotoxicity was required in 96 of the cyclosporin-treated patients (70%), and 25 were switched to treatment with azathioprine (21%). The incidence of all infections in cyclosporin-treated patients was approximately half of that in azathioprine-treated patients, and only nine per cent of the cyclosporin-treated patients were diagnosed to have cytomegalovirus infections during the first post-transplant year vs. 28% in azathioprine-treated patients (p = 0.002).(ABSTRACT TRUNCATED AT 400 WORDS)
BRCA1 Mutations in Primary Breast and Ovarian Carcinomas (1994)

Loss of heterozygosity data from familial tumors suggest that BRCA1, a gene that confers susceptibility to ovarian and early-onset breast cancer, encodes a tumor suppressor. The BRCA1 region is also subject to allelic loss in sporadic breast and ovarian cancers, an indication that BRCA1 mutations may occur somatically in these tumors. The BRCA1 coding region was examined for mutations in primary breast and ovarian tumors that show allele loss at the BRCA1 locus. Mutations were detected in 3 of 32 breast and 1 of 12 ovarian carcinomas; all four mutations were germline alterations and occurred in early-onset cancers. These results suggest that mutation of BRCA1 may not be critical in the development of the majority of breast and ovarian cancers that arise in the absence of a mutant germline allele.
Transmission mode desorption electrospray ionization (2008)

A new mode of operation for desorption electrospray ionization (DESI) analysis of liquids or solid residues from evaporated solvents is presented. Unlike traditional DESI, the electrospray is not deflected off of a surface but instead is transmitted through a sampling mesh at a 0 degrees angle between the electrospray tip, sample mesh, and capillary inlet of a mass spectrometer. In this configuration, deposited samples can be analyzed rapidly without rigorous optimization of spray distances or angles and without the preparation time associated with solvent evaporation. The new transmission mode desorption electrospray ionization (TM-DESI) technique is not applicable to bulk materials, but instead is a method designed to simplify the sample preparation process for liquid samples and sample extracts. The technique can reduce analysis time to seconds while consuming only microliters of sample. The results presented summarize the optimization of the technique, highlight key figures of merit for several model compounds, and illustrate potential applications to high throughput screening of liquid mixtures in both extraction solvents and biological matrices.
Maximum likelihood soft decoding of binary block codes and decoders for the Golay codes (1989)

Maximum-likelihood soft-decision decoding of linear block codes is addressed. A binary multiple-check generalization of the Wagner rule is presented, and two methods for its implementation, one of which resembles the suboptimal Forney-Chase algorithms, are described. Besides efficient soft decoding of small codes, the generalized rule enables utilization of subspaces of a wide variety, thereby yielding maximum-likelihood decoders with substantially reduced computational complexity for some larger binary codes. More sophisticated choice and exploitation of the structure of both a subspace and the coset representatives are demonstrated for the (24, 12) Golay code, yielding a computational gain factor of about 2 with respect to previous methods. A ternary single-check version of the Wagner rule is applied for efficient soft decoding of the (12, 6) ternary Golay code.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Human Nod1 Confers Responsiveness to Bacterial Lipopolysaccharides (2001)

The immune response to microbial pathogens is initiated by recognition of specific pathogen components by host cells both at the cell surface and in the cytosol. While the response triggered by pathogen products at the surface of immune cells is well characterized, that initiated in the cytosol is poorly understood. Nod1 is a member of a growing family of intracellular proteins with structural homology to apoptosis regulators Apaf-1/Ced-4 and a class of plant disease-resistant gene products. Here we show that bacterial lipopolysaccharides, but not other pathogen components tested, induced TLR4- and MyD88-independent NF-kappaB activation in human embryonic kidney 293T cells expressing trace amounts of Nod1. Nod2, another Nod family member, also conferred responsiveness to bacterial components but with a response pattern different from that observed with Nod1. As it was reported for plant disease-resistant R proteins, the leucine-rich repeats of Nod1 and Nod2 were required for lipopolysaccharide-induced NF-kappaB activation. A lipopolysaccharide binding activity could be specifically coimmunopurified with Nod1 from cytosolic extracts. These observations suggest that Nod1 and Nod2 are mammalian counterparts of plant disease-resistant gene products that may function as cytosolic receptors for pathogen components derived from invading bacteria.
Analysis of ultrasonic waveforms using Shannon entropy (2003)

A symbol-oriented information-theoretical approach to signal analysis based on application of thermodynamic concepts is described. Images formed from temperature-dependent thermodynamic analogs of entropy, thermodynamic energy, the partition function, and specific heat at constant volume are considered. It is shown that this can be a preferred alternative to conventional digital signal analysis by making an experimental comparison of these images to images based on a more conventional signal energy approach. In all these images, which were made by c-scanning a family of thin graphite/epoxy laminates containing a foreign object within two plies of the specimen surface, the thermodynamic analogs exhibit significant increases (up to fourfold) in detection sensitivity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A novel, SiPM-array-based, monolithic scintillator detector for PET (2009)

Silicon photomultipliers (SiPMs) are of great interest to positron emission tomography (PET), as they enable new detector geometries, for e.g., depth-of-interaction (DOI) determination, are MR compatible, and offer faster response and higher gain than other solid-state photosensors such as avalanche photodiodes. Here we present a novel detector design with DOI correction, in which a position-sensitive SiPM array is used to read out a monolithic scintillator. Initial characterization of a prototype detector consisting of a 4 x 4 SiPM array coupled to either the front or back surface of a 13.2 mm x 13.2 mm x 10 mm LYSO:Ce(3+) crystal shows that front-side readout results in significantly better performance than conventional back-side readout. Spatial resolutions <1.6 mm full-width-at-half-maximum (FWHM) were measured at the detector centre in response to an approximately 0.54 mm FWHM diameter test beam. Hardly any resolution losses were observed at angles of incidence up to 45 degrees , demonstrating excellent DOI correction. About 14% FWHM energy resolution was obtained. The timing resolution, measured in coincidence with a BaF(2) detector, equals 960 ps FWHM.
Induction of erythroid differentiation in murine virus infected eythroleukemia cells by highly polar compounds. (1975)

Murine-virus-infected erythroleukemia cells cultured in a medium with dimethylsulfoxide or N,N-dimethylformamide are induced to differentiate to erythroid cells. A number of highly polar compounds have a similar effect in inducing erythroid differentiation of the virus-infected cells, as assayed by the appearance of hemoglobin. These compounds are 1-methyl-1-2-piperidone, N,N-dimethylacetamide, N-methylpyrrolidinone, N-methylacetamide, 2-pyrrolidinone, propionamide, pyridine-N-oxide, piperidone, N-methylformamide, acetamide, and triethylene glycol. It has been previously reported that dimethylsulfoxide must be present during DNA synthesis and, possibly, shortly therafter, to induce differentiation. These findings are consistent with the hypothesis that dimethylsulfoxide and related polar compounds act by changing the conformation of DNA or a DNA-protein complex, causing an alteration in transcription that leads to the expression of the program of erythroid differentiation.
The Synthetic Gene Designer: a Flexible Web Platform to Explore Sequence Space of Synthetic Genes for Heterologous Expression (2006)

"Codon optimization" is a general approach that seeks to improve heterologous expression when a gene is moved into a foreign genome that exhibits different codon usage from its native genome. However, it is still unclear exactly what it means to optimize codons for protein expression: diverse interpretations exist, and exploratory research continues. Thus, to facilitate flexible redesign of genes for heterologous expression, we have developed a bona fide web application: the "synthetic gene designer". Compared with existing codon optimization software, the synthetic gene designer provides greater flexibility in several key features of codon optimization strategy. The software, together with online tutorials and help, is available at http://www.evolvingcode. net/codon/sgd.php.
Calibration of SAW Based Capacitive Sensor Using Lumped Component and High Precision Gap Measurement (2012)

SAW device is widely used as filters, sensors, actuators in various technologies. And capacitive sensor is tremendously used to measure pressure, gap, etc. The application of SAW device as signal conditioner of capacitive sensor reduces noise level and enables high precision measurement. The response increase of SAW based capacitive sensor is produced just before the two capacitive electrode contacts by the existence of parasitic resistance of capacitive electrode. In this paper, we analyze the effects of parasitic resistance and propose the calibrating method using lumped component and execute the high precision gap measurement using calibrated system. And xx nm resolution and yy <TEX>${\mu}m$</TEX> stroke was attained.
Nitric oxide increases persistent sodium current in rat hippocampal neurons (1999)

1. The effects of nitric oxide (NO) donors on whole-cell, TTX-sensitive sodium currents and single sodium channels in excised patches were examined in rat hippocampal neurons. The whole-cell sodium current consisted of a large transient component (INa,t) and a smaller, inactivation-resistant, persistent component (INa,p). 2. In acutely dissociated neurons, the amplitude of the whole-cell INa, p increased by 60-80 % within a few minutes of exposure to either of two NO donors, sodium nitroprusside (SNP, 100 microM) or S-nitroso-N-acetyl-DL-penicillamine (SNAP, 100 microM). 3. The amplitude of INa,t was not changed significantly by the same concentrations of SNP and SNAP, indicating that NO had a selective effect on INa,p. 4. Both NO donors significantly increased the mean persistent current in excised inside-out patches from cultured hippocampal neurons. SNP at 10-100 microM increased average mean persistent current at a pipette potential (Vp) of +30 mV from -0.010 +/- 0.014 pA (control) to -2.91 +/- 1.41 pA (n = 10). SNAP at 3-100 microM increased the average mean inward current in six inside-out patches from -0.07 +/- 0.02 to -0.30 +/- 0.08 pA (Vp = +30 mV). 5. The increase in persistent Na+ channel activity recorded in inside-out patches in the presence of SNP or SNAP could be reversed by the reducing agent dithiothreitol (DTT, 2-5 mM) or by lidocaine (1-10 microM). 6. The average mean current recorded in the presence of SNP was 10-fold higher than that elicited by SNAP. The time delay before an increase was observed was shorter with SNP (4.0 +/- 0.8 min, n = 8) than with SNAP (8.4 +/- 1.6 min, n = 7). 7. A component of the SNP molecule added on its own, 5 mM sodium cyanide (NaCN), increased mean current in excised inside-out patches (Vp = +30 mV) from -0.06 +/- 0.04 to -0.58 +/- 0.21 pA (n = 19). This increase in channel activity could be blocked by 10 microM lidocaine and 2-5 mM DTT. 8. These results suggest that NO may directly increase the activity of neuronal persistent Na+ channels, but not transient Na+ channels, through an oxidizing action directly on the channel protein or on a closely associated regulatory protein in the plasma membrane.
Biochemical Analysis of the Secreted and Virion Glycoproteins of Ebola Virus (1998)

The glycoproteins expressed by a Zaire species of Ebola virus were analyzed for cleavage, oligomerization, and other structural properties to better define their functions. The 50- to 70-kDa secreted and 150-kDa virion/structural glycoproteins (SGP and GP, respectively), which share the 295 N-terminal residues, are cleaved near the N terminus by signalase. A second cleavage event, occurring in GP at a multibasic site (RRTRR downward arrow) that is likely mediated by furin, results in two glycoproteins (GP1 and GP2) linked by disulfide bonding. This furin cleavage site is present in the same position in the GPs of all Ebola viruses (R[R/K]X[R/K]R downward arrow), and one is predicted for Marburg viruses (R[R/K]KR downward arrow), although in a different location. Based on the results of cross-linking studies, we were able to determine that Ebola virion peplomers are composed of trimers of GP1-GP2 heterodimers and that aspects of their structure are similar to those of retroviruses, paramyxoviruses, and influenza viruses. We also determined that SGP is secreted from infected cells almost exclusively in the form of a homodimer that is joined by disulfide bonding.
Flk-1 as a target for tumor growth inhibition. (1996)

A number of growth factor receptor tyrosine kinases have been implicated in angiogenesis, including epidermal growth factor receptor, fibroblast growth factor receptor, platelet-derived growth factor receptor, Flk-1/KDR, Flt-1, Tie-1, and Tek/Tie-2. Flk-1/KDR, a receptor for vascular endothelial growth factor (VEGF), is expressed exclusively in endothelial cells. Using dominant-negative methods, Flk-1 was shown to play a role in angiogenesis and the growth of a variety of tumor types. Because of this, a drug discovery effort was established to identify Flk-1 kinase inhibitors. For initial screening, an ELISA in, a 96-well format was used to measure VEGF-induced Flk-1 tyrosine phosphorylation in whole cells. Compounds that inhibited ligand-induced receptor autophosphorylation were confirmed by antiphosphotyrosine immunoblotting. Inhibition of VEGF-stimulated DNA synthesis in human endothelial cells was also assessed. Inhibitors were further evaluated for their effects on vessel formation using the chorioallantoic membrane assay. Using these methods, antiangiogenesis compounds that inhibit Flk-1 tyrosine kinase activity, endothelial cell mitogenesis, and blood vessel formation in the chorioallantoic membrane assay have been found.
Silk Materials – A Road to Sustainable High Technology (2012)

This review addresses the use of silk protein as a sustainable material in optics and photonics, electronics and optoelectronic applications. These options represent additional developments for this technology platform that compound the broad utility and impact of this material for medical needs that have been recently described in the literature. The favorable properties of the material certainly make a favorable case for the use of silk, yet serve as a broad inspiration to further develop biological foundries for both the synthesis and processing of Nature's materials for technological applications.
A membrane planar diode for 200 GHz mixing applications (2006)

The design and fabrication of a monolithically integrated subharmonic mixer for 200 GHz is described. The 1.5 /spl mu/m diameter Schottky diodes are formed on a 5 micron thick GaAs membrane suspended across the RF waveguide. Predicted mixer performance shows improved conversion loss compared with that of conventional flip-chip diodes.
[Characteristics of poloxamer thermosensitive in situ gel of dexamethasone sodium phosphate]. (2008)

Thermosensitive in situ gel is a novel drug delivery system which can form gel in situ after injection of the polymer solution into the body and releases the drug in a controlled manner, thus provides a promising strategy for localized drug delivery. The aim of the present work is to investigate the characteristics including gelation temperature, sol-gel transition temperature (T(s-g)), gel strength, stable viscosity, erosion and drug release behavior of the thermosensitive in situ gel which are composed of different concentrations of poloxamer Pluronic F127 and F68. The gelation temperature was determined by tube-reverse method. Rheological measurements were carried out to evaluate T(s-g), stable viscosity and gel strength. Erosion of the gels and release of dexamethasone sodium phosphate (DSP) from the gels were investigated by membrane-free method and HPLC. Increased F127 concentration in gel decreased the gelation temperature, T(s-g) as well as erosion of the gel and drug release rate, while viscosity and gel strength rose accordingly. However, increased F68 in gel could lead to the opposite result. The poloxamer solution below T(s-g) is Newtonian fluid with comparatively low viscosity, but shows the characteristics of the pseudoplastic fluid when temperature rises near to T(s-g). Drug release was controlled by the erosion of the gel matrix, and both of them followed the zero-order kinetics. An optimized formation containing 22.5% F127 and 2.5% F68 showed more desirable characteristics which meet the clinical requirements and is of potential in future clinical therapy.
Insights into the Mechanism and Catalysis of the Native Chemical Ligation Reaction (2006)

Native chemical ligation of unprotected peptide segments involves reaction between a peptide-alpha-thioester and a cysteine-peptide, to yield a product with a native amide bond at the ligation site. Peptide-alpha-thioalkyl esters are commonly used because of their ease of preparation. These thioalkyl esters are rather unreactive so the ligation reaction is catalyzed by in situ transthioesterification with thiol additives. The most common thiol catalysts used to date have been either a mixture of thiophenol/benzyl mercaptan, or the alkanethiol MESNA. Despite the use of these thiol catalysts, ligation reactions typically take 24-48 h. To gain insight into the mechanism of native chemical ligaton and in order to find a better catalyst, we investigated the use of a number of thiol compounds. Substituted thiophenols with pK(a) > 6 were found to best combine the ability to exchange rapidly and completely with thioalkyl esters, and to then act as effective leaving groups in reaction of the peptide-thioester with the thiol side chain of a cysteine-peptide. A highly effective and practical catalyst was (4-carboxylmethyl)thiophenol ('MPAA'), a nonmalodorous, water-soluble thiol. Use of MPAA gave an order of magnitude faster reaction in model studies of native chemical ligation and in the synthesis of a small protein, turkey ovomucoid third domain (OMTKY3). MPAA should find broad use in native chemical ligation and in the total synthesis of proteins.
Human umbilical cord mesenchymal stem cells confer potent immunosuppressive effects in Sjögren’s syndrome by inducing regulatory T cells (2019)

Human UC-MSCs are capable of inducing CD4<sup>+</sup>Foxp3<sup>+</sup> T cells in both NOD mice and human <i>in vitro</i>. Human UC-MSCs effectively interfere with the autoimmune attack in the course of SS by inducing an <i>in vivo</i> state of T cell unresponsiveness and the upregulation of Tregs.