gebhart/patrepeval huggingface dataset:
Type II restriction endonucleases—a historical perspective and more (2014)

This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
A 60GHz Class-E tuned power amplifier with PAE &#x003E;25% in 32nm SOI CMOS (2012)

A Class-E tuned CMOS power amplifier (PA) operating in the 60 GHz band is presented. Design, layout, and parasitic modeling considerations to attain high-efficiency millimeter-wave PA operation are discussed. Both single-ended and differential versions of the single-stage PA are implemented in a 32nm SOI CMOS process. Peak power added efficiency of 27% (30%), power gain of 8.8dB (10dB), and saturated output power >;9dBm (12.5dBm) are measured at 60GHz from the single-ended (differential) PA with 0.9V supply.
MUC1 Oncoprotein Activates the FOXO3a Transcription Factor in a Survival Response to Oxidative Stress (2004)

The MUC1 transforming protein is aberrantly overexpressed by most human carcinomas. Recent studies demonstrated that MUC1 confers a protective function against oxidative stress-induced apoptosis; however, the mechanisms responsible for this response are not known. The present work demonstrates that MUC1 regulates FKHRL1/FOXO3a, a member of the forkhead family of transcription factors that induces oxidant scavenging and DNA repair. We show that MUC1 attenuates activation of the phosphoinositide 3-kinase --> phospho-Akt/PKB pathway in HCT116 colon carcinoma cells and thereby decreases FOXO3a phosphorylation. MUC1 is expressed as an N-terminal ectodomain that is tethered to the cell surface by a C-terminal transmembrane subunit. The results demonstrate that the MUC1 cytoplasmic domain is sufficient to induce FOXO3a activation and attenuation of oxidative stress. We also demonstrate that stable down-regulation of endogenous MUC1 in ZR-75-1 breast cancer cells inactivates FOXO3a, increases intracellular oxidant levels, and sensitizes cells to H(2)O(2)-induced necrosis. These findings indicate that MUC1 regulates the FOXO3a signaling pathway in a survival response to oxidative stress.
Genetic Heterogeneity of Hypervariable Region 1 of the Hepatitis C Virus (HCV) Genome and Sensitivity of HCV to Alpha Interferon Therapy (2000)

Hepatitis C virus (HCV) populations persist in vivo as a mixture of heterogeneous viruses called quasispecies. The relationship between the genetic heterogeneity of these variants and their responses to antiviral treatment remains to be elucidated. We have studied 26 virus strains to determine the influence of hypervariable region 1 (HVR-1) of the HCV genome on the effectiveness of alpha interferon (IFN-alpha) therapy. Following PCR amplification, we cloned and sequenced HVR-1. Pretreatment serum samples from 13 individuals with chronic hepatitis C whose virus was subsequently eradicated by treatment were compared with samples from 13 nonresponders matched according to the major factors known to influence the response, i.e., sex, genotype, and pretreatment serum HCV RNA concentration. The degree of virus variation was assessed by analyzing 20 clones per sample and by calculating nucleotide sequence entropy (complexity) and genetic distances (diversity). Types of mutational changes were also determined by calculating nonsynonymous substitutions per nonsynonymous site (K(a)) and synonymous substitutions per synonymous site (K(s)). The paired-comparison analysis of the nucleotide sequence entropy and genetic distance showed no statistical differences between responders and nonresponders. By contrast, nonsynonymous substitutions were more frequent than synonymous substitutions (P </= 0.05) in responders, but there was no significant difference in nonresponders. Nonsynonymous substitutions tended to be more frequent than synonymous substitutions in women (P = 0.06) but not in men. Nucleotide entropy and genetic distances were significantly related to serum RNA concentration (P </= 0.01). Our findings suggest that after controlling for the major determinants of interferon response, neither complexity nor diversity of the HVR-1 region is associated per se with virus eradication. Because a higher proportion of nonsynonymous substitutions than synonymous substitutions was found only in responders, host anti-HCV-specific immune response rather than viral factors may be playing an important role in the interferon response.
Activation of Hepatocyte Growth Factor and Urokinase/Plasminogen Activator by Matriptase, an Epithelial Membrane Serine Protease (2000)

Matriptase is an epithelial-derived, integral membrane serine protease. The enzyme was initially isolated from human breast cancer cells and has been implicated in breast cancer invasion and metastasis. In the current study, using active matriptase isolated from human milk, we demonstrate that matriptase is able to cleave various synthetic substrates with arginine or lysine as their P1 sites and prefers small side chain amino acids, such as Ala and Gly, at P2 sites. For the most reactive substrates, N-tert-butoxycarbonyl (N-t-Boc)-gamma-benzyl-Glu-Ala-Arg-7-amino-4-methylcoumarin (AMC) and N-t-Boc-Gln-Ala-Arg-AMC, the K(m) values were determined to be 3. 81 and 4.89 microm, respectively. We further demonstrated that matriptase can convert hepatocyte growth factor/scattering factor to its active form, which can induce scatter of Madin-Darby canine kidney epithelial cells and can activate c-Met tyrosine phosphorylation in A549 human lung carcinoma cells. In addition, we noted that matriptase can activate urokinase plasminogen activator but has no affect on plasminogen. These results suggest that matriptase could act as an epithelial, upstream membrane activator to recruit and activate stromal-derived downstream effectors important for extracellular matrix degradation and epithelial migration, two major events of tissue remodeling, cancer invasion, and metastasis.
Spray dried plasma as an alternative to antibiotics in piglet feeds, mode of action and biosafety (2016)

The use of growth promoting and therapeutic antibiotics in piglet feed has been a concerning subject over the last few decades because of the risk of generating antimicrobial resistance that could be transferred to humans. As a result, many products have been proposed as potential alternatives to the use of antibiotics, and among these, spray dried plasma is considered one of the most promising. However, there have been concerns about its biosafety, particularly during periods of emergence or re-emergence of swine diseases in different regions of the world, such as the recent porcine epidemic diarrhea virus outbreak in North America. The objectives of this paper are to review recent publications about the use of spray dried plasma as an alternative to antibiotics in weaned pig diets, the possible mechanisms of action of spray dried plasma, and the existing evidence related to the biosafety of spray dried animal plasma. Particular attention is given to studies in which spray dried plasma has been directly compared to antibiotics or other alternative antimicrobial products. Several studies on the possible modes of action for spray dried plasma, such as preservation of gut barrier function or modulation of the immune response, are also reviewed. Finally, the paper focuses on the review of the existing studies on the risks of disease transmission with the use of spray dried plasma from porcine origin. Overall, spray dried plasma is a promising alternative to in-feed antimicrobials for piglets, particularly during the early stages of the post-weaning phase. Additionally, there is enough evidence to support that commercial spray dried porcine plasma is a safe product for pigs.
Evidence for the involvement of vicinal sulfhydryl groups in insulin-activated hexose transport by 3T3-L1 adipocytes. (1985)

Following the differentiation of 3T3-L1 preadipocytes insulin acutely activates the rate of 2-deoxy-[1-14C]glucose uptake in the mature 3T3-L1 adipocyte by 15- to 20-fold. Phenylarsine oxide, a trivalent arsenical that forms stable ring complexes with vicinal dithiols, prevents insulin-activated hexose uptake in a concentration-dependent manner (Ki = 7 microM) but has no inhibitory effect on basal hexose uptake. 2,3-Dimercaptopropanol at a level nearly stoichiometric to that of phenylarsine oxide prevents or rapidly reverses the inhibition of hexose uptake; 2-mercaptoethanol, even in high stoichiometric excess over the arsenical, does not reverse inhibition of hexose uptake. When phenylarsine oxide is added after adipocytes have been fully activated by insulin, 2-deoxy-[1-14C]glucose uptake rate decays slowly at a rate corresponding to that caused by the withdrawal of insulin (t1/2 = 10 min). Using the same conditions under which phenylarsine oxide blocked activation, the Km for deoxyglucose uptake, the rate at which 125I-insulin became cell-associated, and the 125I-insulin binding isotherm for solubilized insulin receptor were not affected by phenylarsine oxide. These results support the transporter translocation model for insulin-activated hexose transport and implicate vicinal sulfhydryl groups in a post-insulin binding event essential for the translocation of glucose transporters to the plasma membrane.
B-cell stimulatory factor 1 activates resting B cells. (1985)

B-cell stimulatory factor 1 (BSF-1) is a T-cell-derived lymphokine that acts together with low concentrations of anti-IgM antibodies to stimulate resting B cells to enter the G1 phase of the cell cycle and to synthesize DNA. We show here that supernatants from EL-4 cells, rich in BSF-1 activity, and BSF-1 purified by high-pressure liquid chromatography (HPLC-BSF-1) act on resting B cells, in the absence of anti-IgM antibodies, to prepare them to respond to anti-IgM and BSF-1. A 24-hour preculture with BSF-1 speeds the entry into S phase of B cells subsequently cultured with anti-IgM and BSF-1 by approximately equal to 12 hours and causes substantial increase in cell volume of all resting B cells. Both of these effects, stimulated either by EL-4 supernatants or by HPLC-BSF-1, are inhibited by a monoclonal anti-BSF-1 antibody. These results lead us to propose that BSF-1 should be regarded as a B-cell activation factor.
Effects of Prostaglandin E<sub>2</sub> on Alveolar Bone Resorption during Orthodontic Tooth Movement (1988)

Twenty Sprague-Dawley rats weighing 280-300 g were divided into two groups of ten animals each. They were treated by daily submucosal injections of 50 micrograms prostaglandin E2 (PGE2) per kilogram body weight into the region below the apex of the left first maxillary molar (experimental), or vehicle into the region below the apex of the right first molar (control), for a period of 5 days. The animals of the first group were sacrificed immediately following the treatment period, while those of the second group were sacrificed 5 days after the treatment period. Twenty-two hours prior to sacrifice, a piece of latex orthodontic elastic was secured to the adjacent area between the first and second maxillary molars of both sides of each rat by using two mosquito hemostats. The periodontal ligament (PDL) mesial to the mesiobuccal root of the first maxillary molar was assayed for changes in PDL cell factors. The results showed that immediately following the 5-day treatment period the left PDL had a significant decrease in the total number of fibroblasts and a significant increase in the total number of both osteoclasts and nuclei per osteoclast, while no significant changes in the osteoblasts when compared with those of the right control PDL. The left PDL of animals which were sacrificed 5 days after the treatment period revealed a significant decrease in the number of total fibroblasts and only a slight decrease in both numbers of total osteoclasts and total nuclei per osteoclast, but again no significant changes in osteoblasts when compared with those of the right control PDL.(ABSTRACT TRUNCATED AT 250 WORDS)
Structure of amplified DNA in different Syrian hamster cell lines resistant to N-(phosphonacetyl)-L-aspartate. (1983)

Syrian hamster cell lines selected in multiple steps for resistance to high levels of N-(phosphonacetyl)-L-aspartate (PALA) contain many copies of the gene coding for the pyrimidine pathway enzyme CAD. Approximately 500 kilobases of additional DNA was coamplified with each copy of the CAD gene in several cell lines. To investigate its structure and organization, we cloned ca. 162 kilobases of coamplified DNA from cell line 165-28 and ca. 68 kilobases from cell line B5-4, using a screening method based solely on the greater abundance of amplified sequences in the resistant cells. Individual cloned fragments were then used to probe Southern transfers of genomic DNA from 12 different PALA-resistant mutants and the wild-type parents. A contiguous region of DNA ca. 44 kilobases long which included the CAD gene was amplified in all 12 mutants. However, the fragments cloned from 165-28 which were external to this region were not amplified in any other mutant, and the external fragments cloned from B5-4 were not amplified in two of the mutants. These results suggest that movement or major rearrangement of DNA may have accompanied some of the amplification events. We also found that different fragments were amplified to different degrees within a single mutant cell line. We conclude that the amplified DNA was not comprised of identical, tandemly arranged units. Its structure was much more complex and was different in different mutants. Several restriction fragments containing amplified sequences were found only in the DNA of the mutant cell line from which they were isolated and were not detected in DNA from wild-type cells or from any other mutant cells. These fragments contained novel joints created by rearrangement of the DNA during amplification. The cloned novel fragments hybridized only to normal fragments in every cell line examined, except for the line from which each novel fragment was isolated or the parental population for that line. This result argues that "hot spots" for forming novel joints are rare or nonexistent.
Formulation Design of Self-Microemulsifying Drug Delivery Systems for Improved Oral Bioavailability of Celecoxib (2004)

Celecoxib is a hydrophobic and highly permeable drug belonging to class II of biopharmaceutics classification system. Low aqueous solubility of celecoxib leads to high variability in absorption after oral administration. Cohesiveness, low bulk density and compressibility, and poor flow properties of celecoxib impart complications in it's processing into solid dosage forms. To improve the solubility and bioavailability and to get faster onset of action of celecoxib, the self-microemulsifying drug delivery system (SMEDDS) was developed. Composition of SMEDDS was optimized using simplex lattice mixture design. Dissolution efficiency, t(85%), absorbance of diluted SMEDDS formulation and solubility of celecoxib in diluted formulation were chosen as response variables. The SMEDDS formulation optimized via mixture design consisted of 49.5% PEG-8 caprylic/capric glycerides, 40.5% mixture of Tween20 and Propylene glycol monocaprylic ester (3:1) and 10% celecoxib, which showed significantly higher rate and extent of absorption than conventional capsule. The relative bioavailability of the SMEDDS formulation to the conventional capsule was 132%. The present study demonstrated the suitability of mixture design to optimize the compositions for SMEDDS. The developed SMEDDS formulations have the potential to minimize the variability in absorption and to provide rapid onset of action of celecoxib.
The frequency of sexual problems among family practice patients. (1988)

Two hundred-twelve patients attending a family practice center participated in a questionnaire study of their sexual identity and function. Using conservative definitions of problems, 75% were identified as having at least one specific sexual problem area. Most of these problems were functional in nature and involved desire, arousal, or orgasm. While the frequency of sexual problems was high in both sexes among all age groups, identity problems were primarily seen among the young, and desire problems among older adults. The prevalence rate of reporting sexual problems did not differ significantly by sex. However, females reported more specific sexual problems than males. Only 26% of the subjects summarized their overall sexual lives as problematic and the vast majority of patients thought their family physicians were able to help with such problems. This study reaffirms the high prevalence of sexual disorders in the population. Given adequate training, family physicians may be the ideal providers of assistance for these problems.
Sol-Gel Science: The Physics and Chemistry of Sol-Gel Processing (1990)

Preface. Acknowledgments. Introduction. Hydrolysis and Condensation I: Nonsilicates. Hydrolysis and Condensation II: Silicates. Particulate Sols and Gels. Gelation. Aging of Gels. Theory of Deformation and Flow in Gels. Drying. Structural Evolution during Consolidation. Surface Chemistry and Chemical Modification. Sintering. Comparison of Gel-Derived and Conventional Ceramics. Film Formation. Applications. Index.
Generation of panoramic image based on planar image features using side-view in-vehicle camera (2009)

In this paper, we propose a method for generation of panoramic image suitable for a building wall surface using the side-view in-vehicle camera. In the proposed method, alignments and geometric normalizations are performed on the basis of planar features of the images. This allows no need for rigorous calibration for camera setting, such as camera postures and positions. Therefore, the proposed method is comparatively tolerant of image distortions which arise from the movement of a car. Experimental results show that the proposed method provides promising panoramic image.
Inhibition of MIF Bioactivity by Rational Design of Pharmacological Inhibitors of MIF Tautomerase Activity (2002)

The pro-inflammatory mediator macrophage migration inhibitory factor (MIF) is produced by immune and endocrine cells and inhibits the antiinflammatory activities of glucocorticoids. MIF also catalyzes the tautomerization of the non-naturally occurring D-isomer of dopachrome, phenylpyruvate, and certain catecholamines, suggesting that MIF might exert its biological effects via enzymatic action on a substrate. However, no physiologically relevant substrate for MIF has been identified. Site-directed mutagenesis studies have not consistently supported a requirement for an intact, functional catalytic site as a prerequisite for MIF bioactivity. We hypothesized that the catalytically active site, but not the enzymatic activity per se, nevertheless plays a critical role in MIF pro-inflammatory activity. Accordingly, we designed small druglike molecules that bind at the catalytically active tautomerase site of MIF and tested the complex for MIF bioactivity. We describe herein the rational design and synthesis of a class of imine conjugates produced by coupling amino acids to a range of benzaldehyde derivatives that inhibit MIF tautomerase and biological activities. We found that aromatic amino acid Schiff bases were better inhibitors of MIF enzymatic and bioactivities compared to the aliphatic ones. For instance, the IC(50) inhibition of MIF tautomerase activity by aromatic amino acid Schiff base methyl esters was achieved at a concentration between 1.65 and 50 microM, suggesting a critical role for the additional binding of the aromatic residues within the vicinity of the active site. The most potent inhibitor of MIF tautomerase activity was 2-[(4-hydroxybenzylidene)amino]-3-(1H-indol-3-yl)propionic acid methyl ester (8), with an IC(50) of 1.65 microM. We found that compound 8 binding to MIF active site resulted in the inhibition of MIF bioactivity in three established bioassays: ERK-1/2 MAP kinase activation, p53-dependent apoptosis, and proliferation of serum-starved cells. Compound 8 inhibited MIF interaction with its as yet unidentified cognate cell surface receptor as shown by flow cytometry, concluding a critical role for the tautomerase active site in receptor binding. Thus the inhibitory effect of compound 8 on MIF bioactivities strongly correlated with the inhibition of MIF tautomerase activity, a connection not made previously through use of small-molecule MIF inhibitors. The inhibitory activity of amino acid-benzaldehyde Schiff base-type MIF antagonists is the first step toward a meaningful structure/function analysis of inhibitors of MIF cellular bioactivities.
A collaborative extensible user environment for simulation and knowledge management (2015)

In scientific simulation, scientists use measured data to create numerical models, execute simulations and analyze results from advanced simulators executing on high performance computing platforms. This process usually requires a team of scientists collaborating on data collection, model creation and analysis, and on authorship of publications and data. This paper shows that scientific teams can benefit from a user environment called Akuna that permits subsurface scientists in disparate locations to collaborate on numerical modeling and analysis projects. The Akuna application is built on the Velo software platform that provides a desktop client environment for conducting and analyzing simulations, a knowledge management server for project and data management, annotation, collaboration, job execution, and event-based communication, and a Tool Integration Framework for connecting any type of software application — from desktop tools to simulator codes — into the Velo framework. Akuna is a customized Velo deployment that is tailored for subsurface modeling and is designed to support any type of simulator. Simulator extensibility is achieved by providing a customizable suite of desktop tools for simulator setup and execution that utilize Velo's Tool Integration Framework and are based on data-driven user interface generation. This paper describes the collaborative aspects of the Velo platform, how Velo was customized for Akuna, and Akuna's extensible “toolset” framework that creates a collaborative research environment for subsurface modelers. A use case example is provided, which demonstrates creating and executing a 3D subsurface simulation.
A Decade of Direct-to-Consumer Advertising of Prescription Drugs (2007)

Spending on direct-to-consumer advertising has continued to increase in recent years in spite of the criticisms leveled against it. Our findings suggest that calls for a moratorium on such advertising for new drugs would represent a dramatic departure from current practices.