gebhart/patrepeval huggingface dataset:
Low Fidelity Mutants in the O-Helix of Thermus aquaticus DNA Polymerase I (1997)

We screened 67 mutants in the O-helix of Thermus aquaticus (Taq) DNA polymerase I (pol I) for altered fidelity of DNA synthesis. These mutants were obtained (Suzuki, M., Baskin, D., Hood, L., and Loeb, L. A. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 9670-9675) by substituting an oligonucleotide containing random sequences for codons 659-671, and selecting for complementation of a growth defect in Escherichia coli caused by temperature-sensitive host pol I. Thirteen mutants decreased fidelity in a screen that employed primer extension reactions lacking one of four complementary deoxynucleoside triphosphates (dNTPs). Three mutants were purified and exhibited 29-68% of wild-type specific activity. Homogeneous polymerases A661E, A661P, and T664R extended primers further than the wild-type, synthesizing past template nucleotides for which the complementary dNTP was absent. The data indicate that both misinsertion of incorrect nucleotides and extension of mispaired primer termini were increased. In a lacZalpha forward mutation assay, A661E and T664R yielded mutation frequencies at least 7- and 25-fold greater, respectively, than that of the wild-type polymerase. These findings emphasize the importance of the O-helix in substrate recognition and are compatible with a role for pyrophosphate release in enhancing fidelity of DNA synthesis.
Lithography at a wavelength of 193 nm (1997)

The trend in microelectronics toward printing features 0.25 µm and below has motivated the development of lithography at the 193-nm wavelength of argon fluoride excimer lasers. This technology is in its early stages, but a picture is emerging of its strengths and limitations. The change in wavelength from 248 to 193 nm requires parallel progress in projection systems, optical materials, and photoresist chemistries and processes. This paper reviews the current status of these various topics, as they have been engineered under a multiyear program at MIT Lincoln Laboratory.
Biological and Chemical Applications of Fluorescence Correlation Spectroscopy:  A Review (2001)

ADVERTISEMENT RETURN TO ISSUECurrent Topics/Persp...Current Topics/PerspectivesNEXTBiological and Chemical Applications of Fluorescence Correlation Spectroscopy: A Review†Samuel T. Hess, Shaohui Huang, Ahmed A. Heikal, and Watt W. WebbView Author Information Department of Physics and School of Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, New York 14853 Cite this: Biochemistry 2002, 41, 3, 697–705Publication Date (Web):December 20, 2001Publication History Received26 September 2001Revised1 November 2001Published online20 December 2001Published inissue 1 January 2002https://pubs.acs.org/doi/10.1021/bi0118512https://doi.org/10.1021/bi0118512review-articleACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views9831Altmetric-Citations545LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Diffusion,Fluorescence,Fluorescence spectroscopy,Genetics,Molecules Get e-Alerts
Survey of Chemical Reactivity of C60, Electrophile and Dieno—polarophile Par Excellence (1992)

Buckminsterfullerene, C60, was found to add a large variety of neutral and charged nucleophiles, a couple of dienes, and a number of dipoles. The reagents mentioned within are propylamine, dodecylamine, tert-butylamine, ethylenediamine, morpholine, triethyl phosphite, hydride (lithium triethyl borohydride), phenyllithium, phenylmagnesium bromide, tert-butyllithium, tert-butylmagnesium bromide, anthracene, cyclopentadiene, p-nitrophenylazide, ethyl diazoacetate, phenyldiazomethane, diphenyldiazomethane, and the ylide (CH3)2S+CH-CO2Et. When a large molar excess of reagent relative to fullerene is used, as many as 10—12 new bonds are formed. For primary amine addition (with the exception of tert-butylamine), the mechanism involves single-electron transfer as a first step. Mass spectrometry shows facile reactivity of C60 in the gas phase with CH4 in both positive and negative ionization.
Mast Cell Tryptase Induces Microglia Activation via Protease-activated Receptor 2 Signaling (2012)

Our results suggest that tryptase can induce microglia activation and pro-inflammatory mediator release via PAR-2-MAPK-NF-kappa B signaling pathway, which will contribute to the development of microglia-mediated inflammation in brain.
Invariant natural killer T cells in lupus patients promote IgG and IgG autoantibody production (2014)

IgG autoantibodies, including antibodies to double-stranded DNA (dsDNA), are pathogenic in systemic lupus erythematosus (SLE), but the mechanisms controlling their production are not understood. To assess the role of invariant natural killer T (iNKT) cells in this process, we studied 44 lupus patients. We took advantage of the propensity of PBMCs from patients with active disease to spontaneously secrete IgG in vitro. Despite the rarity of iNKT cells in lupus blood (0.002-0.05% of CD3-positive T cells), antibody blockade of the conserved iNKT TCR or its ligand, CD1d, or selective depletion of iNKT cells, inhibited spontaneous secretion of total IgG and anti-dsDNA IgG by lupus PBMCs. Addition of anti-iNKT or anti-CD1d antibody to PBMC cultures also reduced the frequency of plasma cells, suggesting that lupus iNKT cells induce B-cell maturation. Like fresh iNKT cells, expanded iNKT-cell lines from lupus patients, but not healthy subjects, induced autologous B cells to secrete antibodies, including IgG anti-dsDNA. This activity was inhibited by anti-CD40L antibody, as well as anti-CD1d antibody, confirming a role for CD40L-CD40 and TCR-CD1d interactions in lupus iNKT-cell-mediated help. These results reveal a critical role for iNKT cells in B-cell maturation and autoantibody production in patients with lupus.
Tomato SP-Interacting Proteins Define a Conserved Signaling System That Regulates Shoot Architecture and Flowering (2001)

Divergent architecture of shoot models in flowering plants reflects the pattern of production of vegetative and reproductive organs from the apical meristem. The SELF-PRUNING (SP) gene of tomato is a member of a novel CETS family of regulatory genes (CEN, TFL1, and FT) that controls this process. We have identified and describe here several proteins that interact with SP (SIPs) and with its homologs from other species: a NIMA-like kinase (SPAK), a bZIP factor, a novel 10-kD protein, and 14-3-3 isoforms. SPAK, by analogy with Raf1, has two potential binding sites for 14-3-3 proteins, one of which is shared with SP. Surprisingly, overexpression of 14-3-3 proteins partially ameliorates the effect of the sp mutation. Analysis of the binding potential of chosen mutant SP variants, in relation to conformational features known to be conserved in this new family of regulatory proteins, suggests that associations with other proteins are required for the biological function of SP and that ligand binding and protein-protein association domains of SP may be separated. We suggest that CETS genes encode a family of modulator proteins with the potential to interact with a variety of signaling proteins in a manner analogous to that of 14-3-3 proteins.
Unrestricted Hepatocyte Transduction with Adeno-Associated Virus Serotype 8 Vectors in Mice (2004)

Recombinant adeno-associated virus (rAAV) vectors can mediate long-term stable transduction in various target tissues. However, with rAAV serotype 2 (rAAV2) vectors, liver transduction is confined to only a small portion of hepatocytes even after administration of extremely high vector doses. In order to investigate whether rAAV vectors of other serotypes exhibit similar restricted liver transduction, we performed a dose-response study by injecting mice with beta-galactosidase-expressing rAAV1 and rAAV8 vectors via the portal vein. The rAAV1 vector showed a blunted dose-response similar to that of rAAV2 at high doses, while the rAAV8 vector dose-response remained unchanged at any dose and ultimately could transduce all the hepatocytes at a dose of 7.2 x 10(12) vector genomes/mouse without toxicity. This indicates that all hepatocytes have the ability to process incoming single-stranded vector genomes into duplex DNA. A single tail vein injection of the rAAV8 vector was as efficient as portal vein injection at any dose. In addition, intravascular administration of the rAAV8 vector at a high dose transduced all the skeletal muscles throughout the body, including the diaphragm, the entire cardiac muscle, and substantial numbers of cells in the pancreas, smooth muscles, and brain. Thus, rAAV8 is a robust vector for gene transfer to the liver and provides a promising research tool for delivering genes to various target organs. In addition, the rAAV8 vector may offer a potential therapeutic agent for various diseases affecting nonhepatic tissues, but great caution is required for vector spillover and tight control of tissue-specific gene expression.
Activity and spectroscopic properties of bovine liver catalase in sodium bis(2‐ethylhexyl)sulfosuccinate/isooctane reverse micelles (1993)

Spectroscopic properties such as ultraviolet-visible spectroscopy, circular dichroism, steady-state fluorescence and the catalytic activity of bovine liver catalase (BLC) have been studied in reverse-micelles microemulsions formed by sodium bis(2-ethylhexyl)sulfosuccinate (AOT) in isooctane. Activity measurements were carried out with the highly water soluble hydrogen peroxide as substrate as a function of temperature and pH, at various concentrations of substrate, enzyme, AOT and at different w0 values (w0 = [H2O]/[AOT]). The folding of catalase in reverse micelles is not drastically altered, although there are changes in the local surrounding of the prosthetic group. Kinetic measurements have been carried out under first-order conditions at low substrate concentration. They indicate that the measured substrate decomposition rate is limited by the exchange of substrate molecules between the substrate-filled and the enzyme-containing micelles. The specificity constant, ks = kcat/KM, as related to water pool concentrations, k(s,wp)rm, was, at all w0 values, considerably lower than ks measured in buffer (ksb). In contrast, overall values of ks in reverse micelles, k(s,ov)rm, were always 2-4-times higher than ksb. This apparent superactivity can, however, be ascribed to concentration effects. No 'bell-curve' to describe the w0 dependence of catalase activity in reverse micelles was found, k or ks increasing monotonously up to w0 = 50.
[A case of retroperitoneal extramedullary plasmacytoma]. (2003)

A 69-year-old woman visited a hospital with a complaint of left abdominal dull pain. A computed tomographic scan demonstrated a large tumor with central necrosis in the left retroperitoneum, and an angiography revealed hypervascular tumor which was fed from splenic, left renal, left gastric and left colic arteries. Renal cell carcinoma with extrarenal progression was pre-operatively suspected, and a resection was attempted. However, since the celiac artery was involved in the tumor, only a biopsy was performed. The histopathological finding of the biopsy specimen was a plasmacytoma. A combination of chemotherapy and radiation therapy resulted in a marked reduction of the tumor. There was no evidence of tumor progression one year after the chemotherapy.
Microbiologically influenced corrosion in copper and nickel seawater piping systems (1990)

Abstract : Sections of CDA 706 piping and Monel 400 tubing were severely pitted after exposure to marine and estuarine waters, respectively. Surfaces of both alloys were uniformly covered with thick surface deposits, ranging in color form blue-green to reddish brown to black. Pits developed under surface deposits containing 0.0001 - 0.00001 sulfate-reducing bacteria (SRB) in association with other bacteria. Pits were irregular in shape, lacking a consistent morphology. The observed corrosion was attributed to a combination of differential aeration cells, a large cathode::small anode surface area, concentration of chlorides, development of acidity within the pits, and the specific reactions of the base metals with sulfides produced by the SRB. Chlorine and sulfur appear to have reacted selectively with iron and nickel in the alloys. Nickel has been selectivity removed from pitted areas leaving a copper rich spongy pit interior.
Modern Antenna Design (2005)

Preface. 1. Properties of Antennas. 2. Radiation Structures and Numerical Methods. 3. Arrays. 4. Aperture Distributions and Arrays Synthesis. 5. Dipoles, Slots, and Loops. 6. Microstrip Antennas. 7. Horn Antennas. 8. Reflector Antennas. 9. Lens Antennas. 10. Traveling Wave Antennas. 11. Frequency-Independent Antennas. 12. Phased Arrays. Index.
An Application of the Fractal Theory in the Design of Heat Sink for Precision Measurement Instrument (2005)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Maillard Products as Biomarkers in Cancer (2008)

Because tumors exert increased glycolysis rates, a high intracellular carbonyl stress with the formation of Maillard products may evolve. Therefore, we studied the presence of N epsilon-(carboxymethyl)lysine (CML) modification in breast cancer tissues from 20 patients and found significant cytoplasmatic staining in tumor cells that was independent of the tumor stage, tumor type, and microanatomic localization. Studying breast cancer cell lines, we also found strong cytoplasmatic CML staining that was again independent of their invasive or metastatic behavior. Our results reveal that tumor cells show a strong cytoplasmatic immunoreactivity to CML without evident association with breast carcinoma type, differentiation, tumor stage, or intratumoral localization. We conclude that CML formation is a general tumor cell-associated process.
Protein-O-glycosylation in yeast: protein-specific mannosyltransferases (1997)

S. cerevisiae contains at least six genes (PMT1-6) for dolicholphosphate-D-mannose: protein-O-D-mannosyltransferases. The in vivo mannosylation of seven O-mannosylated yeast proteins has been analyzed in a number of pmt mutants. The results clearly indicate that the various protein O-mannosyltransferases have different specificities for protein substrates. Five of the proteins tested (chitinase, a-agglutinin, Kre9p, Bar1p, Pir2p/hsp 150) are mainly underglycosylated in pmt1 and pmt2 mutants, whereby qualitative differences exist among the various proteins. Two of the O-mannosylated proteins (Ggp1p and Kex2p) are not at all affected in pmt1 and pmt2 mutants but are clearly underglycosylated when PMT4 is mutated. Although the PMT4 gene product is shown to be responsible for O-mannosylating a Ser-rich region of Ggp1p in vivo, a penta-seryl-peptide is not an in vitro substrate for this transferase. A PMT3 mutation does affect O-mannosylation of chitinase only in the genetic background of a pmt1pmt2 double mutation, indicating that PMT1 and PMT2 can compensate for a deleted PMT3 gene.
Improved outcome of allogeneic bone marrow transplantation due to breastfeeding-induced tolerance to maternal antigens (2009)

Exposure of offspring to noninherited maternal antigens (NIMAs) during pregnancy may have an impact on transplantations performed later in life. Using a mouse model, we recently showed that bone marrow transplantation (BMT) from NIMA-exposed offspring to the mother led to a reduction of graft-versus-host disease (GVHD). Since offspring can also be exposed to NIMAs by breastfeeding after birth, we tested whether breast milk could mediate the tolerogenic NIMA effect. We found that oral exposure to NIMAs by breastfeeding alone was sufficient to reduce GVHD, and that in utero exposure to NIMAs is required for maximum reduction of GVHD. The tolerogenic milk effects disappeared when donor mice were injected with CD25 monoclonal antibodies during the lactation period, suggesting a CD4(+)CD25(+) regulatory T cell-dependent mechanism. Our results suggest a previously unknown impact of breastfeeding on the outcome of transplantation.
Fiber Optic Sensing: Evolution to Value (2014)

Abstract Harsh environments and access limitations continually challenge well surveillance in oil and gas production. Knowledge of subsurface characteristics, such as fluid flow, helps mitigate safety and operational risk while enhancing economic viability. As operators pursue technically challenging reservoirs, the development and use of advanced sensor technology has become crucial to exploring, developing and producing hydrocarbon reserves - while maintaining system integrity from the producing zone to transportation. Research and technical commercialization in fiber optic sensing has the potential to enhance many aspects of flow integrity and assurance, including barrier monitoring, reservoir and flow characterization, leading to increased safety, production protection, and production enhancement. Fiber optic sensing has evolved over time at BP. This is with respect to diversity of applications and realization of benefits, while increasing our learning from implementation challenges. We will use this context to highlight the research, commercial ecosystem and business aspects of fiber optic sensing– particularly to provide a perspective on future uses of this technology. Using an integrated approach, the goal of this paper is to increase awareness and promote adoption. We do this by making a case for accelerating integration, collaboration and standardization among the operators, service providers, equipment manufacturers and systems integrators to stimulate and to drive efficiencies and value.
CD40-activated human B cells: an alternative source of highly efficient antigen presenting cells to generate autologous antigen-specific T cells for adoptive immunotherapy. (1997)

Multiple clinical trials have shown the efficacy of adoptively transferred allogeneic antigen-specific T cells for the treatment of viral infections and relapsed hematologic malignancies. In contrast, the therapeutic potential of autologous antigen-specific T cells has yet to be established since it has been technically difficult to generate sufficient numbers of these T cells, ex vivo. A major obstacle to the success of this objective derives from our inability to simply and rapidly isolate and/or expand large numbers of highly efficient antigen presenting cells (APCs) for repetitive stimulations of antigen-specific T cells in vitro. We show that autologous CD40-activated B cells represent a readily available source of highly efficient APC that appear to have several important advantages over other APCs for ex vivo T cell expansion including: (a) methodological simplicity necessary to generate continuously large numbers of APCs from just 50 cm3 of peripheral blood without loss of APC function; (b) capacity to induce high peak T cell proliferation and interferon-gamma production without IL-10 production; (c) ease in cryopreservation; and (d) markedly reduced cost. We, therefore, contend that CD40-activated B cells are an alternative source of highly efficient APCs with which to generate antigen-specific T cells ex vivo for autologous adoptive immunotherapy.
Increased Production of Prostaglandin D2 in Patients with Systemic Mastocytosis (1980)

SYSTEMIC mastocytosis is a disorder of unknown origin, characterized by abnormal proliferation of tissue mast cells involving various organs and associated with a variety of clinical symptoms and signs.1 Episodic attacks of flushing, frequently accompanied by hypotension and tachycardia, are a predominant manifestation of systemic mastocytosis, which at times can result in life-threatening shock.Although the symptoms of mastocytosis have generally been attributed to the release of histamine from mast cells, only partial amelioration of symptoms has been described in the few isolated case reports on the effects of histamine-antagonist therapy of this disorder.2 , 3 After the recent demonstration that combined . . .
Reward/Punishment Reversal Learning in Older Suicide Attempters (2010)

Older suicide attempters display impaired reward/punishment-based learning. The authors propose a hypothesis that older suicide attempters make overly present-focused decisions, ignoring past experiences. Modification of this "myopia for the past" may have therapeutic potential.
Trimethylsilyl-Directed 1,3-Dipolar Cycloaddition Reactions in the Solid-Phase Synthesis of 1,2,3-Triazoles (2005)

[reaction: see text] A regioselective method for the preparation of 1,5-trisubstituted 1H-1,2,3-triazoles via a 1,3-dipolar cycloaddition of 1-trimethylsilylacetylenes with organoazides is described. Immobilization of the azide on REM resin and subsequent cycloaddition afforded a 2 x 2 x 4 x 3 membered 1,5-disubstituted 1H-1,2,3-triazole library with an average purified yield of 68%.
Prevalence of Hearing Loss in Older Adults in Beaver Dam, Wisconsin: The Epidemiology of Hearing Loss Study (1998)

There are no recent population-based data on the prevalence of hearing loss in older adults using standard audiometric testing. The population-based Epidemiology of Hearing Loss Study was designed to measure the prevalence of hearing loss in adults aged 48-92 years, residing in Beaver Dam, Wisconsin. Hearing thresholds were measured with standardized protocols using pure-tone air- and bone-conduction audiometry in sound-treated booths. The examination also included an otoscopic evaluation, screening tympanogram, and a questionnaire on hearing-related medical history, noise exposure, other potential risk factors, and self-perceived hearing handicap. Of the 4,541 eligible people, 3,753 (82.6%) participated in the hearing study (1993-1995). The average age of participants was 65.8 years, and 57.7% were women. The prevalence of hearing loss was 45.9%. The odds of hearing loss increased with age (odds ratio (OR) = 1.88 for 5 years, 95% confidence interval (CI) 1.80-1.97) and were greater for men than women (OR = 4.42, 95% CI 3.73-5.24). The male excess of hearing loss remained statistically significant after adjusting for age, education, noise exposure, and occupation (OR = 3.65). These results demonstrate that hearing loss is a very common problem affecting older adults. Epidemiologic studies are needed to understand the genetic, environmental, and sex-related determinants of age-related hearing loss and to identify potential intervention strategies.