gebhart/patrepeval huggingface dataset:
Minimizing the surface effect of PDMS–glass microchip on polymerase chain reaction by dynamic polymer passivation (2006)

Abstract Polydimethyl siloxane (PDMS)–glass microchip has a very strong surface effect on polymerase chain reaction (PCR), leading to a very poor PCR yield. In the work reported here, practical dynamic passivation of surfaces of PDMS–glass microchip using polyethylene glycol (PEG) or polyvinylpyrrolidone (PVP) was achieved using a conventional thermocycler. The passivation procedure was cost‐effective and easy to conduct. The effects of polymer molecular weight and polymer concentration on tube PCR efficiency were investigated primarily to prescreen out suitable polymers and polymer concentrations in the PCR mixture. The result from tube PCR indicated that both PEG and PVP could affect the performance of Taq polymerase. A final concentration of 0.025% (w/v) or 0.4% (w/v) polymer in the PCR mixture can enhance the tube PCR, while 1% (w/v) polymer was found to inhibit the reaction. PEG was more effective in tube PCR, although PVP performed better in chip PCR. Instead of employing the polymer directly in the PCR mixture, i.e. the conventional in situ passivation approach, another approach of dynamic passivation by pre‐injecting polymers into the microchip achieved better performance. The efficiency of pre‐passivation was found to follow the order: PVP10000&gt;PVP55000, PEG8000&gt; PEG10000&gt;PEG400. After pre‐passivation with PVP10000, PVP55000 and PEG8000, the PCR efficiency can recover to 93%, 86% and 83%, respectively, of that obtained from tube PCR. Copyright © 2006 Society of Chemical Industry
A Critical Review of Aqueous Solubilities, Vapor Pressures, Henry’s Law Constants, and Octanol–Water Partition Coefficients of the Polychlorinated Biphenyls (1986)

Relationships between the environmentally relevant physical chemical properties of the polychlorinated biphenyls, namely, aqueous solubility, vapor pressure, Henry’s law constant, and octanol–water partition coefficient are discussed. Reported experimental data are tabulated and critically reviewed. Recommended values are given for 42 of the 209 congeners; however, procedures are suggested for estimating the properties of the other congeners. Properties of mixtures are not treated.
A cis-acting element is necessary and sufficient for translational regulation of human ferritin expression in response to iron. (1987)

Ferritin plays a key role in determining the intracellular fate of iron and is highly regulated by the iron status of the cell. We have identified a cis-acting element in the transcribed but nontranslated 5' leader sequence of human ferritin heavy-chain mRNA. In transiently transfected murine fibroblasts, the presence of a 157-nucleotide region of the 5' leader sequence was found to be necessary for iron-dependent regulation of ferritin biosynthesis. Further, this 5' leader region is sufficient to transfer iron-mediated translational control to the expression of a heterologous gene product, chloramphenicol acetyltransferase.
Multidisciplinary management for esophageal and gastric cancer (2016)

The management of esophageal and gastric cancer is complex and involves multiple specialists in an effort to optimize patient outcomes. Utilizing a multidisciplinary team approach starting from the initial staging evaluation ensures that all members are in agreement with the plan of care. Treatment selection for esophageal and gastric cancer often involves a combination of chemotherapy, radiation, surgery, and palliative interventions (endoscopic and surgical), and direct communication between specialists in these fields is needed to ensure appropriate clinical decision making. At the University of Colorado, the Esophageal and Gastric Multidisciplinary Clinic was created to bring together all experts involved in treating these diseases at a weekly conference in order to provide patients with coordinated, individualized, and patient-centered care. This review details the essential elements and benefits of building a multidisciplinary program focused on treating esophageal and gastric cancer patients.
Design and development of a high-speed electrooptic A/D converter (1979)

A detailed analysis of a high-speed electrooptic guided wave analog-to-digital (A/D) converter has been performed. It is concluded that the development of converters in the 4-6 bit <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-2-GS/s</tex> range should be feasible. Analyses are presented which detail the design considerations for the electrooptic modulator chip, the laser sampler, and the analog signal amplifier. A design plan is presented for a 6-bit <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-GS/s</tex> converter which utilizes an array of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6 LiTaO_3</tex> interferometric waveguide modulators to perform the conversion and a frequency-doubled mode-locked Nd:YAG laser to perform the sampling of analog signals having 500-MHz bandwidths. Preliminary waveguide device results are also reported, including the successful demonstration of an interferometric modulator with a 17-dB (98-percent) extinction ratio.
A Model for Escherichia coli DNA Polymerase III Holoenzyme Assembly at Primer/Template Ends (2000)

The gamma complex of the Escherichia coli DNA polymerase III holoenzyme assembles the beta sliding clamp onto DNA in an ATP hydrolysis-driven reaction. Interactions between gamma complex and primer/template DNA are investigated using fluorescence depolarization to measure binding of gamma complex to different DNA substrates under steady-state and presteady-state conditions. Surprisingly, gamma complex has a much higher affinity for single-stranded DNA (K(d) in the nM range) than for a primed template (K(d) in the microM range) under steady-state conditions. However, when examined on a millisecond time scale, we find that gamma complex initially binds very rapidly and with high affinity to primer/template DNA but is converted subsequently to a much lower affinity DNA binding state. Presteady-state data reveals an effective dissociation constant of 1.5 nM for the initial binding of gamma complex to DNA and a dissociation constant of 5.7 microM for the low affinity DNA binding state. Experiments using nonhydrolyzable ATPgammaS show that ATP binding converts gamma complex from a low affinity "inactive" to high affinity "active" DNA binding state while ATP hydrolysis has the reverse effect, thus allowing cycling between active and inactive DNA binding forms at steady-state. We propose that a DNA-triggered switch between active and inactive states of gamma complex provides a two-tiered mechanism enabling gamma complex to recognize primed template sites and load beta, while preventing gamma complex from competing with DNA polymerase III core for binding a newly loaded beta.DNA complex.
Phenol Antioxidant Quantity and Quality in Foods:  Fruits (2001)

The free and bound phenols have been measured in 20 fruits commonly consumed in the American diet. Phenols were measured colorimetrically using the Folin-Ciocalteu reagent with catechin as the standard after correction for ascorbic acid contribution. On a fresh weight basis, cranberry had the highest total phenols, and was distantly followed by red grape. Free and total phenol quality in the fruits was analyzed by using the inhibition of lower density lipoprotein oxidation promoted by cupric ion. Ascorbate had only a minor contribution to the antioxidants in fruits with the exception of melon, nectarine, orange, white grape, and strawberry. The fruit extracts' antioxidant quality was better than the vitamin antioxidants and most pure phenols, suggesting synergism among the antioxidants in the mixture. Using our assay, fruits had significantly better quantity and quality of phenol antioxidants than vegetables. Fruits, specifically apples and cranberries, have phenol antioxidants that can enrich lower density lipoproteins and protect them from oxidation. The average per capita consumption of fruit phenols in the U.S. is estimated to be 255 mg/day of catechin equivalents.
Inhibitory Effect of Anti-pyretic and Anti-inflammatory Herbs on Herpes Simplex Virus Replication (2001)

The increasing clinical use of acyclovir, ganciclovir, and foscarnet against herpes simplex virus (HSV), varicella-zoster virus, and cytomegalovirus has been associated with the emergence of drug-resistant herpesvirus strains. To develop anti-HSV compounds from plants, 31 herbs used as antipyretic and anti-inflammatory agents in Chinese medicine were screened. Five different preparations (cold aqueous, hot aqueous, ethanolic, acid ethanolic, and methanolic) from 31 herbs were analyzed by plaque reduction assay, and 7 extracts. which showed significant antiviral activities, were further elucidated for their antiviral mechanisms. Our results showed that ethanolic extract of Rheum officinale and methanolic extract of Paeonia suffruticosa prevented the process of virus attachment and penetration. Aqueous extract of P. suffruticosa and ethanolic extract of Melia toosendan inhibited virus attachment to cell surface. Aqueous extract of Sophora flavescens and methanolic extract of M. toosendan showed no effect on virus attachment and penetration. These data indicated that these 4 herbs have a potential value as a source of new powerful anti-HSV compounds.
Structural characterization of the FKHR gene and its rearrangement in alveolar rhabdomyosarcoma (1995)

The FKHR gene, which contains a forkhead DNA-binding motif, is fused to either PAX3 or PAX7 by the t(2;13) or t(1;13) translocation in alveolar rhabdomyosarcoma,respectively. These tumors express chimeric transcripts encoding the N-terminal portion of either PAX protein fused to the C-terminal portion of FKHR. To understand the structural basis and functional consequences of these translocations, we characterized the wild-type FKHR gene and its rearrangement in alveolar rhabdomyosarcomas. By isolating and analyzing phage, cosmid and YAC clones, we determined that FKHR consists of three exons spanning 140 kb and that several highly similar loci are present in other genomic regions. Exon 1 encodes the N-terminus of the forkhead domain and is embedded within demethylated CpG island. RNA analyses reveal FKHR transcripts initiate from a TATA-less promoter within this island. Exon 2 encodes the C-terminus of the forkhead domain and a transcription activation domain, whereas exon 3 encodes a large 3' untranslated region. The intron 1-exon 2 boundary precisely matches the FHKR fusion point in the chimeric transcripts found in alveolar rhabdomyosarcomas. Using pulsed-field and fluorescence in situ hybridization analyses, we demonstrate that the 130kb FKHR intron 1 is rearranged in t(2;13)-containing alveolar rhabdomyosarcomas. Our findings indicate that FKHR intron 1 provides a large target for DNA rearrangemnt. Rearrangement of this intron with PAX3 produces two important functional consequences: in-frame fusion of N-terminal PAX3 sequences to the FKHR transcriptional activation domain and disruption of the FKHR DNA binding domain.
Synthetic glycopeptides for the development of tumour‐selective vaccines (2003)

Based on structural information reported for the tumour-associated epithelial mucin MUC1, glycopeptides have been synthesized which contain tumour-associated saccharide antigens. such as the Thomsen-Friedenreich (T), TN or sialyl TN antigen. in combination with peptide sequences of the tandem repeat region of MUC1. Solid-phase syntheses have been carried out using N-Fmoc protected O-glycosyl serine and threonine building blocks and an allylic anchor which is stable to basic and acidic conditions, but can be cleaved under neutral conditions in a palladium(0)-catalysed allyl transfer reaction. In addition. a (2-3)sialyl T antigen threonine building block was prepared by a chemoenzymatic strategy and used in the synthesis of an N-terminal glycopeptide antigen of leukosialin (CD43). The proliferation of cytotoxic T cells could be induced using a construct consisting of a MUC1-glycopeptide antigen and a T cell epitope.
Cish actively silences tcr signaling in CD8+ T cells to maintain tumor tolerance (2015)

Meeting abstracts Improving the functional avidity of effector T cells is critical in overcoming inhibitory factors within the tumor microenvironment and eliciting tumor regression. We have found that Cish, a member of the Suppressor of Cytokine Signaling (SOCS) family, is induced by TCR
The homeobox gene Hox 7.1 has specific regional and temporal expression patterns during early murine craniofacial embryogenesis, especially tooth development in vivo and in vitro (1991)

Hox 7.1 is a murine homeobox-containing gene expressed in a range of neural-crest-derived tissues and areas of putative epithelial-mesenchymal interactions during embryogenesis. We have examined the expression of Hox 7.1 during craniofacial development in the mouse embryo between days 8 and 16 of development. Whereas facial expression at day 10 of gestation is broadly localised in the neural-crest-derived mesenchyme of the medial nasal, lateral nasal, maxillary and mandibular processes, by day 12 expression is restricted to the mesenchyme immediately surrounding the developing tooth germs in the maxillary and mandibular processes. Hox 7.1 expression in the mesenchyme of the dental papilla and follicle is maximal at the cap stage of development and progressively declines in the bell stage prior to differentiation of odontoblasts and ameloblasts. Hox 7.1 expression in tooth germs is independent of overall embryonic stage of development but is dependent on stage of development of the individual tooth. Similar patterns of transient Hox 7.1 expression can also be detected in tooth germs in vitro in organ cultures of day 11 first branchial arch explants cultured for up to 7 days. Hox 7.1 is also expressed early in development (days 10/11) in the epithelium of the developing anterior pituitary (Rathke's pouch), the connective tissue capsule and meninges of the developing brain, and specific regions of neuroepithelium in the developing brain.
Universal digital portable radio communications (1987)

Providing voice and data communications to people away from their wireline telephones has become a major communication frontier. This frontier is being penetrated by evolving approaches to portable communications, e.g., cordless telephones, mobile radiotelephone, and radio paging. However, these approaches have many limitations; none can provide universal portable communications services. This paper discusses limitations of the evolving approaches and considers objectives and approaches for providing more universal digital portable communications as an integrated part of telephone exchange networks. These more universal communications could be accomplished by using demand-assigned radio links for the last thousand feet or so of telephone loops and sharing the remainder of the fixed distribution facilities. Fixed radio ports as integrated parts of telephone distribution networks could be placed throughout service regions. Efficient use of the radio spectrum could be insured by the planned reuse of radio frequencies throughout the regions. The severe multipath radio propagation environment within and around buildings that strongly influences the design of portable communications systems is described in the paper. System configurations and radio link techniques, that can provide reliable communications in the multipath environment, are discussed. Radio system calculations are illustrated for radio ports with 30-ft-high antennas in residential areas. The calculations indicate that radio link availability would be greater than 99 percent for 2000-ft port separations and 5-mW portable transmitters. Reuse of frequencies would require dividing the allocated frequency band into segments for use at adjacent ports. Calculations suggest that link availability in the cochannel interference environment would be greater than 99 percent, if 25 to 35 segments were used in residential areas.
Quinolinic Acid: An Endogenous Metabolite That Produces Axon-Sparing Lesions in Rat Brain (1983)

A current hypothesis links the neuroexcitatory properties of certain acidic amino acids to their ability to cause selective neuronal lesions. Intracerebral injection of the neuroexcitatory tryptophan metabolite, quinolinic acid, has behavioral, neurochemical, and neuropathological consequences reminiscent of those of exogenous excitotoxins, such as kainic and ibotenic acids. Its qualities as a neurotoxic agent suggest that quinolinic acid should be considered as a possible pathogenic factor in neurodegenerative disorders.
Extensive cellular uptake into endothelial cells of an amphipathic β‐sheet forming peptide (1997)

Extensive internalization into endothelial cells has been found for a water soluble amphipathic 26-mer beta-sheet peptide (FLUOS-DPKGDPKGVTVTVTVTVTGKGDPKPD-NH2; VT5). With the D-Val13,D-Thr14 di-D-amino acid analog of VT5 (DD-VT5), exhibiting an identical primary structure but no propensity to adopt a beta-sheet conformation, only about 5% of the cellular uptake of VT5 was found. The mechanism of entry of VT5 into the cells remained unclear, but proved to be energy, temperature and pH dependent and, therefore, clearly distinct from that reported for helical amphipathic peptides. No detectable cytotoxicity, high solubility in water and the found extensive entry into endothelial cells make VT5 appear a good lead for developing new types of vectors for delivering oligonucleotides and peptides into intact cells.
Reconfigurable holographic optical interconnections using a phase-only nematic liquid crystal spatial light modulator (1991)

The authors implement various optical interconnection functions using multilevel phase-only holograms written in a nematic liquid crystal panel capable of nearly continuous phase modulation. These include nearest/next nearest neighbor interconnects, space-invariant one to many interconnects (fan-out elements), and a perfect shuffle. Nearly diffraction-limited focal spots and approximately 15% total diffraction efficiencies are obtained.
Metabolically engineered bacteria for producing hydrogen via fermentation (2007)

Hydrogen, the most abundant and lightest element in the universe, has much potential as a future energy source. Hydrogenases catalyse one of the simplest chemical reactions, 2H(+) + 2e(-) ↔ H(2), yet their structure is very complex. Biologically, hydrogen can be produced via photosynthetic or fermentative routes. This review provides an overview of microbial production of hydrogen by fermentation (currently the more favourable route) and focuses on biochemical pathways, theoretical hydrogen yields and hydrogenase structure. In addition, several examples of metabolic engineering to enhance fermentative hydrogen production are presented along with some examples of expression of heterologous hydrogenases for enhanced hydrogen production.
Modeling and Field Trials of the Effective Tractoring Force of Axial Vibration Tools (2014)

Abstract There are a significant number of extended reach wells that cannot be effectively intervened to total depth due to tubing string lock-up. If the horizontal section of the wellbore is sufficiently long, the axial compressive load conveying the tubing into the wellbore will cause the tubing to buckle. Buckling initiates in a sinusoidal mode and progresses to a helical mode. Once the tubing buckles helically, the string quickly locks-up due to increased normal forces and frictional interaction with the wellbore. Several commercial vibration devices attempt to extend intervention depths in extended reach wells. One of the primary modes of vibration employed in these devices is axial. We have developed a simulation tool to enhance understanding of how axial vibration devices extend reach. In the first section, we introduce a 1D finite rigid body dynamic model. This computational tool models the propagation of axial excitation in the presence of borehole frictional contact. In the second section, we demonstrate that the reach extension of axial vibration tools can be represented by an effective tractoring force, which is dependent upon vibration amplitude and injection speed. In the third section, we present field trial results of an axial vibration tool currently under development. Using tool output measured via a downhole force gauge, we compare reach extension seen in the field trials with modeling predictions.
Microbiologically Influenced Corrosion Handbook (1994)

Introduction to microbiologically influenced corrosion Microbiology Metallurgy Electrochemistry Case histories Detection, diagnosis and monitoring Prevention Mitigation Testing.
Retrieval of forest spatial pattern from SAR images (2002)

The spatial structure presented by forest stands and openings is of interest to scientists studying forest ecosystem dynamics. The ability to characterize forest spatial properties in terms of patch size and surface type is useful for initializing ecosystem models as well as, understanding the processes contributing to forest development. In this study, forest units with low biomass were classified from synthetic aperture radar images into several categories based on their spatial structure and different scattering mechanisms. In addition to non-forest classes several classes were identified with varying tree heights and/or tree densities that reflect natural and anthropogenic induced conditions. Optimal variables derived from Stokes matrices of P, L and C-band AIRSAR images were selected based on the separabilities between designated classes. After image classification, the number, area, and perimeter of each patch for these categories were calculated. The spatial patterns were also categorized in terms of simple spatial statistics including fractal dimensions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Treatment of Relapsing Paralysis in Experimental Encephalomyelitis by Targeting Th1 Cells through Atorvastatin (2003)

Statins, known as inhibitors of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, exhibit numerous functions related to inflammation, such as MHC class II down-regulation, interference with T cell adhesion, and induction of apoptosis. Here we demonstrate that both subcutaneous and oral administration of atorvastatin inhibit the development of actively induced chronic experimental autoimmune encephalomyelitis in SJL/J mice and significantly reduce the inflammatory infiltration into the central nervous system (CNS). When treatment was started after disease onset, atorvastatin reduced the incidence of relapses and protected from the development of further disability. Both the reduced autoreactive T cell response measured by proliferation toward the encephalitogenic peptide PLP139-151 and the cytokine profile indicate a potent blockade of T helper cell type 1 immune response. In in vitro assays atorvastatin not only inhibited antigen-specific responses, but also decreased T cell proliferation mediated by direct TCR engagement independently of MHC class II and LFA-1. Inhibition of proliferation was not due to apoptosis induction, but linked to a negative regulation on cell cycle progression. However, early T cell activation was unaffected, as reflected by unaltered calcium fluxes. Thus, our results provide evidence for a beneficial role of statins in the treatment of autoimmune attack on the CNS.
Immunity to intracellular bacteria (1992)

Immunity to intracellular bacteria including Mycobacterium tuberculosis, Mycobacterium leprae, and Listeria monocytogenes depends on specific T cells. Evidence to be described suggests that CD4 alpha/beta T cells, CD8 alpha/beta T cells and gamma/delta T cells which interact with each other and with macrophages contribute to acquired resistance against as well as pathogenesis of intracellular bacterial infections.