gebhart/patrepeval huggingface dataset:
Dye structure affects Taq DNA polymerase terminator selectivity (1999)

All DNA sequencing methods have benefited from the development of new F667Y versions of Taq DNA polymerase. However, terminator chemistry methods show less uniform peak height patterns when compared to primer chemistry profiles suggesting that the dyes and/or their linker arms affect enzyme selectivity. We have measured elementary nucleotide rate and binding constants for representative rhodamine- and fluorescein-labeled terminators to determine how they interact with F667 versions of Taq Pol I. We have also developed a rapid gel-based selectivity assay that can be used to screen and to quantify dye-enzyme interactions with F667Y versions of the enzyme. Our results show that 6-TAMRA-ddTTP behaves like unlabeled ddTTP, while 6-FAM-ddTTP shows a 40-fold reduction in the rate constant for polymerization without affecting ground-state nucleotide binding. Detailed mechanism studies indicate that both isomers of different fluorescein dyes interfere with a conformational change step which the polymerase undergoes following nucleotide binding but only when these dyes are attached to pyrimidines. When these same dyes are attached to purines by the same propargylamino linker arm, they show no effect on enzyme selectivity. These studies suggest that it may be possible to develop fluorescein terminators for thermocycle DNA sequencing methods for polymerases that do not discriminate between deoxy- and dideoxynucleotides.
A fully active monolayer enzyme electrode derivatized by antigen-antibody attachment (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA fully active monolayer enzyme electrode derivatized by antigen-antibody attachmentChristian Bourdillon, Christophe Demaille, Jean Gueris, Jacques Moiroux, and Jean Michel SaveantCite this: J. Am. Chem. Soc. 1993, 115, 26, 12264–12269Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://doi.org/10.1021/ja00079a005RIGHTS & PERMISSIONSArticle Views645Altmetric-Citations141LEARN 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 InReddit PDF (2 MB) Get e-Alerts Get e-Alerts
Type 1 Diabetes—Pathogenesis, Prediction, and Prevention (2009)

Type 1 diabetes affects over 1.4 million people in the US, with a rising incidence in many western nations. It is clear that there is a strong hereditary component and that autoimmunity plays a large role in disease pathogenesis. In the last two decades novel technologies have been developed to study the genetics, biochemistry, and molecular pathology of type 1 diabetes. These, in turn, have allowed for early recognition of disease as well as the potential for prevention trials and early insulin treatment. This article highlights the prediction of type 1 diabetes risk and developing immunotherapeutic concepts.
Mutations of p16Ink4/CDKN2 and p15Ink4B/MTS2 genes in biliary tract cancers. (1995)

p16Ink4 and p15Ink4B are cyclin-dependent kinase 4 inhibitors and link to the regulation of cell cycle in mammalian cells. The genes encoding these inhibitors are located at 9p21, which is a frequent site of allelic loss in various types of tumors. Twenty-five primary biliary tract cancers were examined for somatic mutations in p16Ink4/CDKN2, p15Ink4B/MTS2, p53, and K-ras genes and allelic loss of 9p21 by microsatellite analysis. Four biliary tract cancer cell lines were analyzed for homozygous deletions and point mutations. We found frequent homozygous deletions in p16Ink4/CDKN2 and p15Ink4B/MTS2 genes in the biliary tract cancer cell lines. Each cancer cell line had alteration of either p16Ink4/CDKN2, p15Ink4B/MTS2, or p53 genes. In primary tumors, 16 of 25 (64%) biliary tract cancers had point mutations in the p16Ink4/CDKN2 gene. These include 14 missense and 2 silent mutations. The frequency of mutations in gall bladder cancer and hilar bile duct cancer were 80% (8 of 10) and 63% (5 of 8), respectively. Each of codons 1, 80, and 111 was changed in two cases of these cancers. One of three intrahepatic bile duct cancers, one of two common bile duct cancers, and one of two ampullary cancers had mutations in the p16Ink4/CDKN2 gene. In contrast, no mutation in the p15Ink4B/MTS2 gene, one base change in the K-ras gene, and one loss of heterozygosity at the IFN alpha locus in 25 cancers and one base change in the p53 gene in 19 cancers were observed. These results suggest that p16Ink4/CDKN2, rather than p15Ink4B/MTS2 or p53 genes, and its inactivation may be important in biliary tract carcinogenesis.
Ca2+-Dependent Production and Release of IL-8 in Human Neutrophils (1998)

IL-8, a potent neutrophil chemoattractant that is elevated about 200-fold in exudative neutrophils isolated from localized inflammatory sites in vivo, is thought to play a major role in recruitment of neutrophils to inflammatory sites. Incubation of peripheral blood neutrophils with thapsigargin, an inhibitor of the endoplasmic reticulum Ca2+-sequestering-ATPase, causes a dose-dependent induction of IL-8 synthesis that continues for up to 8 h. Cycloheximide inhibits the thapsigargin-induced IL-8 production, suggesting the induction of protein synthesis de novo. In addition, Northern blot analysis of mRNA isolated from neutrophils indicates that thapsigargin treatment increases IL-8 mRNA in a time- and dose-dependent manner. Thapsigargin also induces a biphasic rise in the intracellular Ca2+ concentration, [Ca2+]i, which is composed of an initial (within 15 s) EGTA-insensitive elevation in [Ca2+]i, followed by a delayed (2-min) EGTA-sensitive component. Addition of EGTA before thapsigargin inhibited the induction of IL-8 production. Experiments in which EGTA was added at various times after thapsigargin treatment indicated that a sustained Ca2+ influx was required for maximum IL-8 production. Ascomycin and cyclosporin A, inhibitors of the Ca2+-dependent phosphatase, calcineurin, also inhibited thapsigargin-induced IL-8 production. Thus, in neutrophils, a prolonged increase in [Ca2+]i stimulates IL-8 transcription and synthesis, possibly through a calcineurin-dependent pathway.
Reduction of Postprandial Hyperglycemia in Subjects With IDDM by Intravenous Infusion of AC137, a Human Amylin Analogue (1995)

AC137 administration, in these patients with IDDM, reduced postprandial hyperglycemia apparently by affecting the delivery rate of glucose from the gastrointestinal tract. AC137 may prove to be a clinically useful addition to insulin regimens to facilitate the achievement of glycemic control.
Perspective of plant growth promoting rhizobacteria (PGPR) containing ACC deaminase in stress agriculture (2007)

Ethylene is a gaseous plant growth hormone produced endogenously by almost all plants. It is also produced in soil through a variety of biotic and abiotic mechanisms, and plays a key role in inducing multifarious physiological changes in plants at molecular level. Apart from being a plant growth regulator, ethylene has also been established as a stress hormone. Under stress conditions like those generated by salinity, drought, waterlogging, heavy metals and pathogenicity, the endogenous production of ethylene is accelerated substantially which adversely affects the root growth and consequently the growth of the plant as a whole. Certain plant growth promoting rhizobacteria (PGPR) contain a vital enzyme, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which regulates ethylene production by metabolizing ACC (an immediate precursor of ethylene biosynthesis in higher plants) into alpha-ketobutyrate and ammonia. Inoculation with PGPR containing ACC deaminase activity could be helpful in sustaining plant growth and development under stress conditions by reducing stress-induced ethylene production. Lately, efforts have been made to introduce ACC deaminase genes into plants to regulate ethylene level in the plants for optimum growth, particularly under stressed conditions. In this review, the primary focus is on giving account of all aspects of PGPR containing ACC deaminase regarding alleviation of impact of both biotic and abiotic stresses onto plants and of recent trends in terms of introduction of ACC deaminase genes into plant and microbial species.
Sub-10 nm imprint lithography and applications (1997)

New developments, further details, and applications of imprint lithography are presented. Arrays of 10 nm diameter and 40 nm period holes were imprinted not only in polymethylmethacrylate (PMMA) on silicon, but also in PMMA on gold substrates. The smallest hole diameter imprinted in PMMA is 6 nm. All the PMMA patterns were transferred to a metal using a liftoff. In addition, PMMA mesa’s of a size from 45 nm to 50 μm were obtained in a single imprint. Moreover, imprint lithography was used to fabricate the silicon quantum dot, wire, and ring transistors, which showed the same behavior as those fabricated using electron (e)-beam lithography. Finally, imprint lithography was used to fabricate nanocompact disks with 10 nm features and 400 Gbits/in.2 data density—near three orders of magnitude higher than current critical dimensions (CDs). A silicon scanning probe was used to read back the data successfully. The study of wear indicates that due to the ultrasmall force in tapping mode, both the nano-CD and the scanning probe will not show noticeable wear after a large number of scans.
The subunit structure of human macrophage migration inhibitory factor: evidence for a trimer (1996)

The subunit structure of human macrophage migration inhibitory factor (MIF) has been studied by preliminary X-ray analysis of wild-type and selenomethionine-MIF and dynamic light scattering. Crystal form I of MIF belongs to space group P2(1)2(1)2(1) and is grown from 2 M ammonium sulfate at pH 8.5. A native data set has been collected to 2.4 A resolution. Self-rotation studies and Van values indicate that three molecules per asymmetric unit are present. A data set to 2.8 A resolution has been collected for crystal form II, which belongs to space group P3(1)21 or P3(2)21 and grows from 2 M ammonium sulfate, 2% polyethylene glycol (average molecular mass 400) 0.1 M HEPES, pH 7.5. Three, four, five or six monomers in the asymmetric unit are consistent with Van values for this crystal form. Analysis of crystal form II containing selenomethionine-MIF indicates nine selenium sites are present per asymmetric unit. Dynamic light scattering of MIF suggests that the major form of the protein in solution is a trimer. The results of these studies are in contrast to previous reports indicating that MIF is a monomer or dimer. The subunit arrangement of MIF is similar to that of tumor necrosis factor and suggests that signal transduction might require trimerization of receptor subunits.
Distribution of GPR30, a Seven Membrane–Spanning Estrogen Receptor, in Primary Breast Cancer and its Association with Clinicopathologic Determinants of Tumor Progression (2006)

GPR30 and ER exhibited distinct patterns of association with breast tumor progression variables, including HER-2/neu, tumor size, and metastatic disease. Thus, these results support the hypothesis that GPR30 and ER have an independent influence on estrogen responsiveness in breast carcinoma.
Substrate replenishment extends protein synthesis with an in vitro translation system designed to mimic the cytoplasm (2004)

Cytoplasmic mimicry has recently led to the development of a novel method for cell-free protein synthesis called the "Cytomim" system. In vitro translation with this new system produced more than a 5-fold yield increase of chloramphenicol acetyl transferase (CAT) relative to a conventional method using pyruvate as an energy substrate. Factors responsible for activating enhanced protein yields, and causes leading to protein synthesis termination have been assessed in this new system. Enhanced yields were caused by the combination of three changes: growing the extract source cells on 2x YTPG media versus 2x YT, replacing polyethylene glycol with spermidine and putrescine, and reducing the magnesium concentration from conventional levels. Cessation of protein synthesis was primarily caused by depletion of cysteine, serine, CTP, and UTP. Substrate replenishment of consumed amino acids, CTP, and UTP extended the duration of protein synthesis to 24 h in fed-batch operation and produced 1.2 mg/mL of CAT. By also adding more T7 RNA polymerase and plasmid DNA, yields were further improved to 1.4 mg/mL of CAT. These results underscore the critical role that nucleotides play in the combined transcription-translation reaction and highlight the importance of understanding metabolic processes influencing substrate depletion.
Prostasin, a Potential Serum Marker for Ovarian Cancer: Identification Through Microarray Technology (2001)

Prostasin is overexpressed in epithelial ovarian cancer and should be investigated further as a screening or tumor marker, alone and in combination with CA 125.
Genetic background and development of skin tumors. (1989)

Inbred mouse strains that differing widely in their susceptibility to multistage skin carcinogenesis provide useful models for studying the genetic factors involved and advancing our understanding of the biochemical and molecular events associated with this process. The process of skin tumor initiation appears to be somewhat similar in various strains of mice, and most data in the literature suggest that differences in response to skin tumor promoters are a major determinant in controlling susceptibility to multistage skin carcinogenesis. A model system has been developed for examining the genetics of susceptibility to skin tumor promotion. The susceptibility to phorbol ester skin tumor promotion in crosses between DBA/2 and C57BL/6 mice is inherited as an incomplete dominant trait, and neither X-chromosome nor cytoplasmic genetic determinants appear to play a major role in determining susceptibility in these two inbred strains. In addition, two or more genetic loci contribute to the higher sensitivity of DBA/2 mice than C57BL/6 mice to TPA-induced skin tumor promotion. Further studies to characterize these genes will contribute greatly to our understanding of the mechanisms of phorbol ester skin tumor promotion. In addition, much work should now be directed at understanding the cellular, biochemical, and molecular mechanisms for differential responsiveness not only to phorbol esters but also to other classes of tumor promoters.
Use of a Constitutively Active Hypoxia-Inducible Factor-1α Transgene as a Therapeutic Strategy in No-Option Critical Limb Ischemia Patients (2007)

HIF-1alpha therapy in patients with critical limb ischemia was well tolerated, supporting further, larger, randomized efficacy trials.
Carotenoid photobleaching induced by the action, of photosynthetic reaction center II: DGMU-sensitivity (1977)

Journal Article Carotenoid photobleaching induced by the action, of photosynthetic reaction center II: DGMU-sensitivity Get access Reiko Suzuki, Reiko Suzuki Ocean Research Institute, University of TokyoNakano, Tokyo 164, Japan Search for other works by this author on: Oxford Academic Google Scholar Yoshihiko Fujita Yoshihiko Fujita Ocean Research Institute, University of TokyoNakano, Tokyo 164, Japan Search for other works by this author on: Oxford Academic Google Scholar Plant and Cell Physiology, Volume 18, Issue 3, June 1977, Pages 625–631, https://doi.org/10.1093/oxfordjournals.pcp.a075475 Published: 01 June 1977 Article history Received: 20 January 1977 Published: 01 June 1977
<title>Synthesis and spectral properties of axially bromo-substituted subphthalocyanines for optical storage</title> (2001)

Subphthalocyanines (SubPc) are composed of three isoindole units containing boron inside, which defines a molecular axis and forms a cone-shaped structure. Despite being non-planar, they show a delocalized 14(pi) -electron system similar to that present in phthalocyanines. The attractive characteristics of SubPc are their chemical stability and thermal stability. We report here the synthesis of three SubPc compounds, in which the axial substituent is a bromide. The peripheral substituent in the compounds leads to an improved solubility in common organic solvents. The results demonstrated that SubPc showed a strong and broad absorption region near 600 nm. This is advantageous for the purification and important for the applications in optical storage (DVD-R).
The role of tramadol ER in the treatment of chronic pain (2009)

Despite its high prevalence, chronic pain is suboptimally treated in approximately one half of affected patients. Failure to recognise and manage comorbid physical and psychosocial impairments may contribute to the perpetuation of chronic pain. Knowledge of the potential advantages and disadvantages of available analgesic medications will permit informed selection of the appropriate medication for the individual chronic pain patient. Ultimate therapeutic goals will also influence analgesic medication selection. For the patient with chronic pain requiring analgesic treatment for an extended period of time, long-acting analgesics are recommended. Theoretically, these agents will provide sustained analgesia by minimising the end-of-dose pain that is often seen with short-acting medications, with improved patient convenience and a potential for reduced risk of adverse events. The extended-release formulation of tramadol (tramadol ER) has proven efficacy in chronic pain conditions such as osteoarthritis and low back pain, as well as a favourable tolerability profile. In addition, tramadol ER has been shown in clinical trials to improve pain-related sleep disturbances and physical function in patients with chronic pain from osteoarthritis and low back pain.
An Interstitial Fluid Transdermal Extraction System for Continuous Glucose Monitoring (2012)

A novel microfluidic system which is fabricated with five polydimethylsiloxane layers for interstitial fluid (ISF) extraction, collection, and measurement toward the application of continuous and real-time glucose monitoring is presented in this paper. The system consists of a micro vacuum generator for ISF transdermal extraction and fluid manipulation, micro chambers for the collection of ISF, micro pneumatic valves for fluid management, and a micro flow sensor for ISF volume measurement. Sequentially controlled by the pneumatic valves, the ISF extraction, collection, and volumetric measurement functions of the system were demonstrated using the stable vacuum generated by the integrated vacuum generator. Through low-frequency ultrasound pretreated full-thickness pig skin, the normal saline solution with different glucose concentrations was transdermally extracted, collected, and measured. The absolute error in the volume measurement of the transdermally extracted “ISF analog” was less than 0.05 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\mu\hbox{L}$</tex></formula> . The microfluidic system makes it possible to realize the clinical application of continuous glucose monitoring based on ISF transdermal extraction technology. <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\hfill$</tex></formula> [2011-0329]
A novel antibiotic free plasmid selection system: Advances in safe and efficient DNA therapy (2007)

The presence of antibiotic resistance genes in the delivered plasmids is one of the drawbacks of modern gene therapy and DNA vaccine applications. Here, we describe a strategy that allows for plasmid selection in bacterial hosts, without the requirement of any selection marker. Several bacterial strains were modified, so that the plasmid's replicational inhibitor RNA I could suppress the translation of a growth essential gene by RNA-RNA antisense reaction. An essential gene (murA) was modified such that a repressor protein (tetR) would hamper its expression. Only in the presence of plasmid and, hence, RNA I, was tetR turned down and murA expressed. Different commercially available plasmids could be selected by various modified Escherichia coli strains. We further designed a minimalistic plasmid devoid of any selection marker. All of the clones (n=6) examined, when the modified strain JM109-murselect was used for selection, contained plasmids. Thus, we have designed bacterial host strains that for the first time serve to select and maintain plasmids without the use of any selection marker or other additional sequence on the plasmid. Consequently, such plasmids may not only be safer, but due to their decreased size, advantages for the manufacturer and higher transfection efficiencies are anticipated.
Identification of the polypeptides of the major light‐harvesting complex of photosystem II (LHCII) with their genes in tomato (1992)

Using an improved SDS-PAGE system, the polypeptides of the major chlorophyll a/b light-harvesting complex of PSII (LHCII) from tomato leaves were resolved into five polypeptide bands. All the polypeptides were matched with the genes encoding them by comparing amino acid sequences of tryptic peptides with gene sequences. The two major LHCII bands (usually comigrating as a '27 kDa' polypeptide) were encoded by cab1 and cab3 (Type I LHCII) genes. A third strong band of about 25 kDa was encoded by cab4 (Type II) genes. Polypeptides from two minor bands of 23-24 kDa were not N-terminally blocked; their N-terminal sequences showed they were Type III LHCII proteins. One complete cDNA clone and several incomplete clones for Type III polypeptides were sequenced. Combined with the peptide sequences, the results indicate that there are at least four different Type III genes in tomato, encoding four almost identical polypeptides. Thus, all the LHCII CAB polypeptides have been identified, and each type of LHCII polypeptide is encoded by distinct gene or genes in tomato.
Effect of pretreatment on PET films and its application for flexible amorphous silicon solar cells (2009)

We proposed a low cost solution of flexible amorphous silicon solar cells on Polyethylene terephthalate(PET) polymer substrates deposited at low temperatures. PET films were firstly annealed both in the air and in vacuum at different temperatures, and the properties of PET films after annealing were evaluated. Then PET films were exposed to glow discharge Argon plasma in a standard PECVD system to improve their surface properties. The relationship between glow discharge parameters and the energy of Ar plasma were investigated by OES. After Ar plasma treatment, not only the surface morphology of PET but also the adhesion of the solar cell thin films to the PET substrates were improved. Finally, single junction a-Si solar cells with a p-i-n superstrate type were fabricated on PET/ITO substrates at low temperature of Ts=125°C, and an initial efficiency of 4.8% was obtained.