gebhart/patrepeval huggingface dataset:
Isothermal DNA Amplification Coupled with DNA Nanosphere-Based Colorimetric Detection (2005)

We present a simple, rapid method for detecting short DNA sequences that combines a novel isothermal amplification method (EXPAR) with visual, colorimetric readout based on aggregation of DNA-functionalized gold nanospheres. The reaction is initiated by a trigger oligonucleotide, synthetic in nature for this proof-of-principle study, which is exponentially amplified at 55 degrees C and converted to a universal reporter oligonucleotide capable of bridging two sets of DNA-functionalized gold nanospheres. This reaction provides >10(6)-fold amplification/conversion in under 5 min. When combined with a solution containing DNA nanospheres, the bridging reporter causes nanosphere aggregation. The resulting color change from red to dark purple or blue is enhanced through spotting the solution onto a C18 reversed-phase thin-layer chromatography plate. The reaction can easily be adapted for detection of different trigger oligonucleotides using the same set of DNA nanospheres. It permits detection of as low as 100 fM trigger oligonucleotide in under 10 min total assay time, with minimal reagent consumption and requirement for instrumentation. We expect that combining this simple, versatile assay with trigger generation from a genomic target DNA sequence of interest will be a powerful tool in the development of rapid and simple point-of-care molecular diagnostic applications.
Diastolic function of the heart in untreated primary hypertension. (1984)

To study left ventricular (LV) diastolic function of the heart in relation to blood pressure (BP) and other signs of hypertensive cardiac and peripheral vascular changes, isovolumic relaxation time and early diastolic filling were determined in four BP groups of untreated 49-year-old men: normotensive subjects (n = 20), men with borderline hypertension (n = 30), mild hypertension (n = 45), and moderate to severe hypertension (n = 24). Isovolumic relaxation time, measured as the distance between aortic closure (A2, phonocardiography) and mitral valve opening (echocardiography), and early diastolic filling, measured as the distance between mitral valve opening and the O point of the apexcardiogram, tended to increase with BP level, and the total interval from aortic closure to the O point (A2O interval) was significantly prolonged in the two groups with mild and moderate to severe hypertension. A prolonged A2O interval (greater than or equal to 117% of expected value at observed heart rate) was seen in several hypertensives, who had no obvious increase in LV wall thickness on M mode echocardiography. This suggests that a prolonged LV relaxation time may be an early sign of cardiac involvement in primary hypertension. In the group with moderate to severe hypertension, an increase in LV wall thickness was seen together with an increase in resistance at maximal dilation in the calf. This supports the theory that when changes in cardiac structure develop they occur in parallel with structural changes also in the periphery.
Formation and Properties of Peroxynitrite as Studied by Laser Flash Photolysis, High-Pressure Stopped-Flow Technique, and Pulse Radiolysis (1997)

Flash photolysis of alkaline peroxynitrite solutions results in the formation of nitrogen monoxide and superoxide. From the rate of recombination it is concluded that the rate constant of the reaction of nitrogen monoxide with superoxide is (1.9 +/- 0.2) x 10(10) M-1 s-1. The pKa of hydrogen oxoperoxonitrate is dependent on the medium. With the stopped-flow technique a value of 6.5 is found at millimolar phosphate concentrations, while at 0.5 M phosphate the value is 7.5. The kinetics of decay do not follow first-order kinetics when the pH is larger than the pKa, combined with a total peroxynitrite and peroxynitrous acid concentration that exceeds 0.1 mM. An adduct between ONOO- and ONOOH is formed with a stability constant of (1.0 +/- 0.1) x 10(4) M. The kinetics of the decay of hydrogen oxoperoxonitrate are not very pressure-dependent: from stopped-flow experiments up to 152 MPa, an activation volume of 1.7 +/- 1.0 cm3 mol-1 was calculated. This small value is not compatible with homolysis of the O-O bond to yield free nitrogen dioxide and the hydroxyl radical. Pulse radiolysis of alkaline peroxynitrite solutions indicates that the hydroxyl radical reacts with ONOO- to form [(HO)ONOO].- with a rate constant of 5.8 x 10(9) M-1 s-1. This radical absorbs with a maximum at 420 nm (epsilon = 1.8 x 10(3) M-1 cm-1) and decays by second-order kinetics, k = 3.4 x 10(6) M-1 s-1. Improvements to the biomimetic synthesis of peroxynitrite with solid potassium superoxide and gaseous nitrogen monoxide result in higher peroxynitrite to nitrite yields than in most other syntheses.
Licorice β-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin (2008)

Glycyrrhizin, a major bioactive compound derived from the underground parts of Glycyrrhiza (licorice) plants, is a triterpene saponin that possesses a wide range of pharmacological properties and is used worldwide as a natural sweetener. Because of its economic value, the biosynthesis of glycyrrhizin has received considerable attention. Glycyrrhizin is most likely derived from the triterpene beta-amyrin, an initial product of the cyclization of 2,3-oxidosqualene. The subsequent steps in glycyrrhizin biosynthesis are believed to involve a series of oxidative reactions at the C-11 and C-30 positions, followed by glycosyl transfers to the C-3 hydroxyl group; however, no genes encoding relevant oxidases or glycosyltransferases have been identified. Here we report the successful identification of CYP88D6, a cytochrome P450 monooxygenase (P450) gene, as a glycyrrhizin-biosynthetic gene, by transcript profiling-based selection from a collection of licorice expressed sequence tags (ESTs). CYP88D6 was characterized by in vitro enzymatic activity assays and shown to catalyze the sequential two-step oxidation of beta-amyrin at C-11 to produce 11-oxo-beta-amyrin, a possible biosynthetic intermediate between beta-amyrin and glycyrrhizin. CYP88D6 coexpressed with beta-amyrin synthase in yeast also catalyzed in vivo oxidation of beta-amyrin to 11-oxo-beta-amyrin. CYP88D6 expression was detected in the roots and stolons by RT-PCR; however, no amplification was observed in the leaves or stems, which is consistent with the accumulation pattern of glycyrrhizin in planta. These results suggest a role for CYP88D6 as a beta-amyrin 11-oxidase in the glycyrrhizin pathway.
Effect of P(VDF/TrFE) Film Thickness on the Characteristics of Pyroelectric Passive Infrared Ray Sensor for Human Body Detection (2011)

A thick 25 <TEX>${\mu}m$</TEX> thickness poled P(VDF/TrFE) film pyroelectric infrared ray sensor has been fabricated and then thin 1.6 <TEX>${\mu}m$</TEX> thickness P(VDF/TrFE) film pyroelectric infrared ray sensor has been fabricated also. These thick and thin P(VDF/TrFE) film pyroelectric infrared ray sensor was mounted in TO-5 housing to detect infrared light of 5.5 ~ 14 <TEX>${\mu}m$</TEX> wavelength for human body detecting with each other. The noise output voltage of the thick P(VDF/TrFE) film pyroelectric infrared ray sensor were 380 mV and NEP(noise equivalent power) is <TEX>$3.95{\times}10^{-7}$</TEX> W which is the similar value with the commercial pyroelectric infrared ray sensor using ceramic materials as a sensing material. The NEP and specific detectivity <TEX>$D^*$</TEX> of the thin P(VDF/TrFE) film pyroelectric infrared ray sensor were <TEX>$2.13{\times}10^{-8}$</TEX> W and <TEX>$9.37{\times}106$</TEX> cm/W under emission energy of 13 <TEX>${\mu}W/cm^2$</TEX> respectively. These result caused by lower thermal diffusion coefficient of a thin 1.6 <TEX>${\mu}m$</TEX> thickness PVDF/TrFE film than the thick 25 <TEX>${\mu}m$</TEX> thickness poled P(VDF/TrFE) film pyroelectric infrared ray sensor.
Performance of BICM-ID with Signal Space Diversity (2006)

This paper presents a performance analysis of bit-interleaved coded-modulation with iterative decoding (BICM-ID) and complex N-dimensional signal space diversity in fading channels to investigate its performance limitation, the choice of the rotation matrix and the design of a low-complexity receiver. The tight error bound is first analytically derived. Based on the design criterion obtained from the error bound, the optimality of the rotation matrix is then established. It is shown that using the class of the optimal rotation matrices, the performance of BICM-ID systems over a Rayleigh fading channel approaches that of the BICM-ID systems over an AWGN channel when the dimension of the signal constellation increases. Furthermore, by exploiting the sigma mappings for M-QAM constellations, a very simple suboptimal, but yet effective iterative receiver structure suitable for signal constellations with large dimensions is proposed. Simulation results in various cases and conditions indicate that the proposed receiver can achieve the analytical performance bounds with low complexity.
The influence of 3TC resistance mutation M184I on the fidelity and error specificity of human immunodeficiency virus type 1 reverse transcriptase (1998)

A common target for therapies against human immuno-deficiency virus type 1 (HIV-1) is the viral reverse transcriptase (RT). Treatment with the widely used nucleoside analog (-)-2', 3'-deoxy-3'-thiacytidine (3TC) leads to the development of resistance-conferring mutations at residue M184 within the YMDD motif of RT. First, variants of HIV with the M184I substitution appear transiently, followed by viruses containing the M184V substitution, which persist and become the dominant variant for the duration of therapy. In the three-dimensional crystal structure of HIV-1 RT complexed with double-stranded DNA, the M184 residue lies in the vicinity of the primer terminus, near the incoming dNTP substrate. Recent studies have shown that 3TC resistance mutations, including M184I, increase the nucleotide insertion and mispair extension fidelity. Therefore, we have examined the effects of the M184I mutation on the overall polymerase fidelity of HIV-1 RT via an M13-based forward mutation assay. We found the overall error rate of the M184I variant of HIV-1 RT to be 1.7 x 10(-5) per nucleotide. This represents a 4-fold increase in fidelity over wild-type HIV-1Hxb2RT (7.0 x 10(-5) per nucleotide) and a 2.5-fold increase in fidelity over the M184V variant (4.3 x 10(-5) per nucleotide). Of the nucleoside analog resistance mutations studied using the forward assay, the M184I variant has shown the greatest increase in fidelity observed to date. Interestingly, the M184I variant RT displays significantly altered error specificity, both in terms of error rate at specific sites and in the overall ratio of substitution to frameshift mutations in the entire target.
Prognostic factors in aggressive malignant lymphomas: description and validation of a prognostic index that could identify patients requiring a more intensive therapy. The Groupe d'Etudes des Lymphomes Agressifs. (1991)

The objectives of this study were to determine prognostic factors for response to treatment, freedom-from-relapse (FFR) survival, and overall survival of 737 aggressive malignant lymphoma patients treated with the doxorubicin, cyclophosphamide, vindesine, bleomycin, methylprednisolone, methotrexate with leucovorin, ifosfamide, etoposide, asparaginase, and cytarabine (LNH-84) regimen; to construct a prognostic index with factors isolated by multivariate analyses; and to validate this prognostic index with another set of patients. Complete response (CR) was reached in 75% of LNH-84 patients, and 30% of them relapsed. With a median follow-up of 36 months, median FFR survival and median overall survival were not reached. Low serum albumin level, high tumoral mass, weight loss, bone marrow involvement, greater than or equal to 2 extranodal sites, and increased lactic dehydrogenase (LDH) level were associated with a low response rate. Advanced stage, increased LDH level, and nonlarge-cell histologic subtypes (diffuse mixed, lymphoblastic, and small non-cleaved) were statistically associated with a high relapse rate and short FFR survival. Increased LDH level, low serum albumin level, tumoral mass larger than 10 cm, greater than or equal to 2 extranodal sites, advanced stage, and age older than 65 years were statistically associated with short overall survival. Four of these parameters, namely, LDH level, stage, number of extranodal sites, and tumoral mass, were put together to construct a prognostic index. This index partitioned LNH-84 patients into three subgroups of good, intermediate, and poor prognosis (P less than .00001): CR rates of 93%, 83%, and 61%; relapse rates of 12%, 25%, and 45%; 3-year FFR survival of 87%, 73%, and 53%, and 3-year survival of 88%, 71%, and 41%, respectively. This prognostic index was applied to a test set of patients: 155 patients treated on protocols of the Nebraska Lymphoma Study Group. Using this index, these patients had 3-year FFR survival of 70%, 40%, and 22% (P = .0002) and 3-year survival of 79%, 52%, and 31% (P = .005). In patients with aggressive lymphomas, this simple prognostic index could distinguish between patients requiring intensive treatment such as autologous bone marrow transplantation in first complete remission and those who could be treated with standard regimens.
Protective effects of FK506 against glutamate-induced neurotoxicity in retinal cell culture. (1998)

FK506 protected against glutamate neurotoxicity by inhibiting NOS activity in cultured retinal neurons.
Turbo multiuser detection: an overview (2002)

Turbo multiuser detection refers to joint channel decoding and multiuser detection using an iterative exchange of soft information between the two processes. This technique has been examined by several authors, with very promising results. This paper provides an introduction to this area.
An automated normative-based fluorodeoxyglucose positron emission tomography image-analysis procedure to aid Alzheimer disease diagnosis using statistical parametric mapping and interactive image display (2006)

Having approved fluorodeoxyglucose positron emission tomography (FDG PET) for the diagnosis of Alzheimer's disease (AD) in some patients, the Centers for Medicare and Medicaid Services suggested the need to develop and test analysis techniques to optimize diagnostic accuracy. We developed an automated computer package comparing an individual's FDG PET image to those of a group of normal volunteers. The normal control group includes FDG-PET images from 82 cognitively normal subjects, 61.89±5.67 years of age, who were characterized demographically, clinically, neuropsychologically, and by their apolipoprotein E genotype (known to be associated with a differential risk for AD). In addition, AD-affected brain regions functionally defined as based on a previous study (Alexander, et al, Am J Psychiatr, 2002) were also incorporated. Our computer package permits the user to optionally select control subjects, matching the individual patient for gender, age, and educational level. It is fully streamlined to require minimal user intervention. With one mouse click, the program runs automatically, normalizing the individual patient image, setting up a design matrix for comparing the single subject to a group of normal controls, performing the statistics, calculating the glucose reduction overlap index of the patient with the AD-affected brain regions, and displaying the findings in reference to the AD regions. In conclusion, the package automatically contrasts a single patient to a normal subject database using sound statistical procedures. With further validation, this computer package could be a valuable tool to assist physicians in decision making and communicating findings with patients and patient families.
Methylation Profiles of Multiple CpG Island Loci in Extrahepatic Cholangiocarcinoma Versus Those of Intrahepatic Cholangiocarcinomas (2007)

A close relationship exists between CpG island hypermethylation and nodal metastasis of extrahepatic cholangiocarcinomas. Methylation profiles of extrahepatic cholangiocarcinomas are somewhat similar to but distinct from those of intrahepatic cholangiocarcinomas.
Gene therapy for arthritis: principles and clinical practice (1997)

Conference Article| May 01 1997 Gene therapy for arthritis: principles and clinical practice R. Kang; R. Kang *Departments of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar S. C. Ghivizzani; S. C. Ghivizzani †Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar J. H. Herndon; J. H. Herndon *Departments of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar P. D. Robbins; P. D. Robbins †Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar C. H. Evans C. H. Evans *Departments of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, U.S.A.†Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1997) 25 (2): 533–537. https://doi.org/10.1042/bst0250533 Article history Received: November 22 1996 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation R. Kang, S. C. Ghivizzani, J. H. Herndon, P. D. Robbins, C. H. Evans; Gene therapy for arthritis: principles and clinical practice. Biochem Soc Trans 1 May 1997; 25 (2): 533–537. doi: https://doi.org/10.1042/bst0250533 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: RA, rheumatoid arthritis, OA, osteoarthritis, IL, interleukin, TNF-α, tumour necrosis factor α, IL-IRa, IL-1 receptor antagonist, Th, T-helper lymphocyte, SCID, severe combined immunodeficiency This content is only available as a PDF. © 1997 Biochemical Society1997 Article PDF first page preview Close Modal You do not currently have access to this content.
Stretching Single Stranded DNA, a Model Polyelectrolyte (2002)

The elastic properties of single stranded (ss)DNA, studied by pulling on an isolated molecule, are shown to agree with a recent model of ssDNA that takes into account base pairings and screened electrostatic repulsion of the phosphodiester backbone. By an appropriate physicochemical treatment, the pairing interactions were suppressed and ssDNA used as an experimental model for a generic polyelectrolyte. The elastic behavior of such an altered ssDNA deviates strongly from the behavior of an ideal polymer. This deviation is shown to result from the elasticity of the chain and its electrostatic self-avoiding interactions.
Effect of ribavirin, levovirin and viramidine on liver toxicological gene expression in rats (2003)

The ribavirin/interferon-alpha combination is currently the standard therapy for patients with chronic hepatitis C. However, ribavirin causes hemolytic anemia as a significant side-effect. Levovirin, an L-enantiomer of ribavirin, possesses similar immunomodulatory activity to ribavirin but lacks direct antiviral activity or hemolytic anemia. Viramidine is a liver-targeting prodrug of ribavirin with much less potential for hemolytic anemia. The aim of the present study is to profile the hepatic toxicological gene response to ribavirin, levovirin and viramidine. Rats were dosed orally with 120 mg kg(-1) day(-1) of ribavirin and viramidine and 2000 mg kg(-1) day(-1) of levovirin for 8 days. Ribavirin did not cause any significant change (>threefold) in gene expression as analyzed by the Affymetrix GeneChip technique. Levovirin decreased the mRNA level of CYP7A1 by fourfold but did not affect the expression of CYP27/CYP7B1 that functions as an alternative pathway for cholesterol metabolism. Viramidine down-regulated both expressed sequence tag 233569 and heat shock protein 86 genes threefold. The changes at mRNA level of these genes were confirmed by the reverse transcription competitive polymerase chain reaction technique. None of the compounds changed the liver/body weight ratio, the major cytochrome P-450 protein levels or enzyme activities. The data indicated that a high dose of ribavirin, levovirin or viramidine did not cause significant change at the transcription level of most of the liver toxicological genes.
The selecting: vascular adhesion molecules (1995)

The selectin family of adhesion molecules mediates the initial attachment of leukocytes to venular endothelial cells before their firm adhesion and diapedesis at sites of tissue injury and inflammation. The selectin family consists of three closely related cell-surface molecules with differential expression by leukocytes (L-selectin), platelets (P-selectin), and vascular endothelium (E- and P-selectin). The selectins have characteristic extracellular regions composed of an amino-terminal lectin domain that binds a carbohydrate ligand, an epidermal growth factor-like domain, and two to nine short repeat units homologous to domains found in complement binding proteins. In contrast to most other adhesion molecules, selectin function is restricted to leukocyte interactions with vascular endothelium. Multiple studies indicate that the selectins mediate neutrophil, monocyte, and lymphocyte rolling along the venular wall. The generation of selectin-deficient mice has confirmed these findings and provided further insight into how the overlapping functions of these receptors regulate inflammatory processes. Selectin-directed therapeutic agents are now proven to be effective in blocking many of the pathological effects resulting from leukocyte entry into sites of inflammation. Future studies are focused on how the selectins interact with the increasing array of other adhesion molecules and inflammatory mediators.