gebhart/patrepeval huggingface dataset:
Binding of the transcription factor EBP-80 mediates the methylation response of an intracisternal A-particle long terminal repeat promoter. (1991)

Intracisternal A-particle (IAP) expression in mouse cells has been correlated with hypomethylation of HhaI and HpaII sites in proviral long terminal repeats (LTRs). In a previous study, in vitro methylation of three HhaI sites in the U3 region of the LTR from the cloned genomic IAP element, MIA14, was shown to inhibit promoter activity in vivo. In this study, we found by site-directed mutagenesis that the two more downstream HhaI sites within this LTR were responsible for the methylation effects on promoter activity in vivo; methylation of the other (5') HhaI site, which lies within a putative SP1 binding domain, did not affect promoter activity. Methylation of the HhaI sites also inhibited promoter activity of the LTR in a cell-free transcription system. Exonuclease III footprinting demonstrated methylation-induced changes in protein binding over the region encompassing the downstream HhaI site, designated the Enh2 domain. The protein that interacts specifically with this domain, EBP-80, was characterized in a previous study (M. Falzon and E. L. Kuff, J. Biol. Chem. 264:21915-21922, 1989). We show here that the presence of methylcytosine in the HhaI site within the Enh2 domain inhibited binding of EBP-80 in vitro. The methylated MIA14 LTR construct was much less responsive to added EBP-80 in an in vitro transcription system than was the unmethylated construct. These data suggest that CpG methylation within the Enh2 domain may exert its effect on transcription in vivo by altering the interaction between EBP-80 and its cognate DNA sequence.
Fungicides: QoI fungicides (2006)

Quinone outside inhibitor (QoI) fungicides include three fungicide families, the well-known family of strobilurins and two new families, represented by fenamidone and famoxadone. QoI fungicides approved for, or in review for, use on field crops in Iowa include strobilurins azoxystrobin, pyraclostrobin and trifloxystrobin, and famoxadone. These fungicides are used on cereal grains, corn, and soybean as well as many other crops in Iowa, such as fruit trees, small fruit, vegetables, and turf.
Dual Fluorescent In Situ Hybridization and Immunohistochemical Detection with Tyramide Signal Amplification (2000)

To understand the biological relationships among various molecules, it is necessary to define the cellular expression patterns of multiple genes and gene products. Relatively simple methods for performing multi-label immunohistochemical detection are available. However, there is a paucity of techniques for dual immunohistochemical (IHC) and mRNA in situ hybridization (ISH) detection. The recent development of improved non-radioactive detection systems and simplified ISH protocols has prompted us to develop a tyramide signal amplification method for sequential multi-label fluorescent ISH and IHC detection in either frozen or paraffin-embedded tissue sections. We used this method to examine the relationship between glial cell line-derived neurotrophic factor receptor α2 (GFRα2) mRNA expression and IHC localization of its co-receptor Ret in the trigeminal ganglion of postnatal Day 0 mice. We found that approximately 70% of Ret-immunoreactive neurons possessed GFRα2 mRNA and virtually all GFRα2-expressing neurons contained Ret-immunoreactive protein. Finally, we used paraformaldehyde-fixed, paraffin-embedded sections and a monoclonal antibody against neuron-specific nuclear antigen (NeuN) to demonstrate the neuronal specificity of GFRα2 mRNA expression in adult mouse brain. This multi-labeling technique should be applicable to a wide variety of tissues, antibodies, and probes, providing a relatively rapid and simple means to compare mRNA and protein localization.
The Effect of Lactobacillus rhamnosus on Enterohemorrhagic Escherichia coli Infection of Human Intestinal Cells In Vitro (2003)

There are many examples of probiotic effects of various lactic bacteria on enteropathogens. In this study, Lactobacillus strains (L. rhamnosus, L. gasseri, L. casei and L. plantarum) were tested in an in vitro model of enterohemorrhagic Escherichia coli (EHEC) infection of a human colon epithelial cell line, C2BBe1. While the adhesion and colonization of EHEC was not affected by any of the lactobacillus strains tested, the internalization of EHEC into the cell line was markedly suppressed by L. rhamnosus, though not by others. Concerning the possible mechanisms, the viabilities of EHEC and host cell were not affected by the presence of L. rhamnosus. Simple competitions at certain receptors were unlikely because the suppressive effect on EHEC internalization was strictly dependent on viable L. rhamnosus and could not be observed with the conditioned medium or killed L. rhamnosus. The fact that L. rhamnosus showed outstanding potential for adhering to the colon epithelial cell line, compared with other strains, suggested that an avid interaction between L. rhamnosus and the host cell might be modulating intra-cellular events responsible for the internalization of EHEC.
Time trends in the prevalence of human papillomavirus infections in archival Papanicolaou smears: Analysis by cytology, DNA hybridization, and polymerase chain reaction (1990)

A retrospective study was undertaken to determine the prevalence of human papillomavirus (HPV) infections in routine Papanicolaou (Pap) smears collected by general practitioners from Western Australian women in each of the years 1972, 1982, and 1987. HPV infection was detected by cytology, dot-blot hybridization, or polymerase chain reaction (PCR). It was found that the prevalence of HPV infection remained unchanged over the 15 year study period, was independent of age, and was associated with normal cytology at a rate far greater than previously recognized. Indeed, the prevalence of cervical intraepithelial neoplasia (CIN) lesions, as detected by cytology, was 3.0% in 1972 and 3.8% in 1982 and 1987. The prevalence of HPV infection, detected as koilocytosis or parakeratosis, was 6.5%, 6.8%, and 5.3% in smears collected in 1972, 1982, and 1987, respectively, from 1,800 women. In 237 cytologically normal smears reprocessed for HPV-DNA studies, the prevalence of HPV 16 was determined to be 15.6%, 11.2%, and 17.8% in 1972, 1982, and 1987, respectively, as determined by dot-blot hybridization. However, the PCR detected HPV 16 in an additional 55.5%, 62.9%, and 57.0% of cytologically normal and dot-blot negative smears. The prevalence of HPV 16 infection in cytologically normal smears was estimated to be 71.0%, 74.1%, and 74.8% in 1972, 1982, and 1987, respectively, by combining the HPV 16 dot-blot and PCR-positive results. The high prevalence of HPV 16 in cytologically normal Pap smears suggests that infection with HPV 16, as detected by PCR amplification, does not place women in a high-risk category for cervical cancer.(ABSTRACT TRUNCATED AT 250 WORDS)
Suppression of the heterotrimeric G protein causes abnormal morphology, including dwarfism, in rice (1999)

Transgenic rice containing an antisense cDNA for the alpha subunit of rice heterotrimeric G protein produced little or no mRNA for the subunit and exhibited abnormal morphology, including dwarf traits and the setting of small seeds. In normal rice, the mRNA for the alpha subunit was abundant in the internodes and florets, the tissues closely related to abnormality in the dwarf transformants. The position of the alpha-subunit gene was mapped on rice chromosome 5 by mapping with the restriction fragment length polymorphism. The position was closely linked to the locus of a rice dwarf mutant, Daikoku dwarf (d-1), which is known to exhibit abnormal phenotypes similar to those of the transformants that suppressed the endogenous mRNA for the alpha subunit by antisense technology. Analysis of the cDNAs for the alpha subunits of five alleles of Daikoku dwarf (d-1), ID-1, DK22, DKT-1, DKT-2, and CM1361-1, showed that these dwarf mutants had mutated in the coding region of the alpha-subunit gene. These results show that the G protein functions in the formation of normal internodes and seeds in rice.
Immunotherapy for Drug‐Refractory Mucosal Leishmaniasis (2006)

These data support the concept that vaccine therapy with a defined antigen combination, used with standard chemotherapy, is a safe and effective approach to treat drug-refractory ML.
Hunter syndrome: isolation of an iduronate-2-sulfatase cDNA clone and analysis of patient DNA. (1990)

Iduronate 2-sulfatase (IDS, EC 3.1.6.13) is required for the lysosomal degradation of heparan sulfate and dermatan sulfate. Mutations causing IDS deficiency in humans result in the lysosomal storage of these glycosaminoglycans and Hunter syndrome, an X chromosome-linked disease. We have isolated and sequenced a 2.3-kilobase cDNA clone coding for the entire sequence of human IDS. Analysis of the deduced 550-amino acid IDS precursor sequence indicates that IDS has a 25-amino acid amino-terminal signal sequence, followed by 8 amino acids that are removed from the proprotein. An internal proteolytic cleavage occurs to produce the mature IDS present in human liver shown to contain a 42-kDa polypeptide N-terminal to a 14-kDa polypeptide. The IDS sequence has strong sequence homology with other sulfatases (such as sea urchin arylsulfatase, human arylsulfatases A, B, and C, and human glucosamine 6-sulfatase), suggesting that the sulfatases comprise an evolutionarily related family of genes that arose by gene duplication and divergent evolution. The arylsulfatases have a greater homology with each other than with the non-arylsulfatases (IDS and glucosamine 6-sulfatase). The IDS cDNA detected RNA species of 5.7, 5.4, 2.1, and 1.4 kilobases in human placental RNA and revealed structural alterations and gross deletions of the IDS gene in many of the clinically severe Hunter syndrome patients studied.
Biosynthesis of vitamin B6: incorporation of D-1-deoxyxylulose (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBiosynthesis of vitamin B6: incorporation of D-1-deoxyxyluloseRobert E. Hill, Brian G. Sayer, and Ian D. SpenserCite this: J. Am. Chem. Soc. 1989, 111, 5, 1916–1917Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March 1989https://pubs.acs.org/doi/10.1021/ja00187a076https://doi.org/10.1021/ja00187a076research-articleACS PublicationsRequest reuse permissionsArticle Views160Altmetric-Citations71LEARN 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 Get e-Alerts
Two-Dimensional Streptavidin Crystals on Giant Lipid Bilayer Vesicles (2002)

Streptavidin was crystallized on giant bilayer vesicles (20−60 μm) in sucrose solution at various pH values. The streptavidin-coated vesicles exhibited unique roughened spherical and prolate ellipsoidal shapes, illustrating resistance to curvature of the two-dimensional crystals. Studies indicated that the spheroids and prolate ellipsoids correspond to different crystal morphologies. Through confocal microscopy, the various crystal morphologies on vesicle surfaces were observed under different solution conditions. Unlike two-dimensional (2D) streptavidin crystals grown in ionic buffer that assume the P1, P2, and C222 lattices at pH 4, 5.5, and 7, respectively (Wang et al. Langmuir 1999, 15, 1541), crystals grown in sucrose with no added salt show only the lowest density C222 lattice due to strong electrostatic interactions.
Tyrosine phosphorylation of the LDL receptor‐related protein (LRP) and activation of the ERK pathway are required for connective tissue growth factor to potentiate myofibroblast differentiation (2004)

Renal myofibroblasts play a crucial role in the accumulation of excess extracellular matrix during renal fibrosis. Both transforming growth factor-beta1 (TGFbeta1) and connective tissue growth factor (CTGF) are important profibrotic growth factors, which interact in the pathogenesis of fibrosis. In this study, we demonstrate that CTGF alone has no influence on myofibroblast transformation and fibronectin secretion in kidney interstitial fibroblasts, whereas incubation of CTGF in combination with TGFbeta1 enhanced TGFbeta1 responses, including myofibroblast activation, de novo expression of alpha-SMA, and extracellular accumulation of fibronectin. CTGF induced tryrosine phosphorylation of the cytoplasmic domain of the low-density lipoprotein receptor-associated protein (LRP) in fibroblasts, and the LRP-antagonist, receptor-associated protein (RAP) inhibited CTGF-induced tryrosine phosphorylation of LRP. Inhibition of LRP signaling reduced CTGF-mediated synergistic induction of alpha-SMA protein. Furthermore, the potentiating action of CTGF was neither dependent on modulation of TGFbeta1-induced Smad2 phosphorylation and its association with Smad4, nor did it result from nuclear accumulation of activated Smad2. When TGFbeta1-pretreated fibroblasts were incubated with CTGF, activation of ERK1/2 MAPK signaling was observed. Inhibition of ERK activation by the MEK1 inhibitor PD98059 was associated with a reduction of CTGF-promoted alpha-SMA protein expression. Our in vitro studies provide evidence that CTGF potentiates TGFbeta1-mediated myofibroblast differentiation and activates differentiated myofibroblasts.
1-alpha,25-Dihydroxyvitamin D3 (1,25(OH)(2)D(3)) hampers the maturation of fully active immature dendritic cells from monocytes (2001)

Our data confirm earlier reports showing that 1,25(OH)(2)D(3) hampers the maturation of fully active immunostimulatory major histocompatibility complex (MHC) class II+, CD1a+, CD80+ DCs from monocytes. Our data supplement the data from other reports by showing that the expression of CD86 was upregulated in 1,25(OH)(2)D(3)-differentiated DCs, whilst the capacity for IL-10 production remained high. Collectively, these data are in line with earlier descriptions of suppressive activities of this steroid-like hormone with respect to the stimulation of cell-mediated immunity.
A Species-Specific Repetitive Sequence in Mycobacterium leprae DNA (1989)

A 2.2-kilobase Mycobacterium leprae DNA insert fragment from a recombinant genomic library (pYA1065) was found to hybridize to at least 19 fragments of chromosomal M. leprae DNA by Southern hybridizations. The probe hybridized to identical fragments of chromosomal DNA from four M. leprae isolates (two from patients with leprosy, one from a naturally infected armadillo, and one from a naturally infected Mangabey monkey) whether the chromosomal DNA was digested with BamHI, BstEII, PstI, or SacI. The pYA1065 probe is specific for M. leprae; it did not hybridize to chromosomal DNA from 14 cultivable slow- and fast-growing mycobacterial species. Dot-blot hybridizations between pYA1065 and purified M. leprae chromosomal DNA indicate that the probe can detect DNA equivalent to 4 x 10(3) M. leprae cells in a spot. The probe can also hybridize to DNA in M. leprae cells spotted on a filter from homogenized skin biopsy specimens from patients with lepromatous leprosy.
Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications (2010)

With an intensifying need for microbial cell factories that produce a wide array of target compounds, whole genome high-throughput sequencing and annotation for SNP detection can aid in better reducing and defining the metabolic landscape. This work demonstrates direct correlations between genotype and phenotype that provides clear and high-probability of success metabolic engineering targets. The genome sequence, annotation, and a SNP viewer of CEN.PK113-7D are deposited at http://www.sysbio.se/cenpk.
Atomic resolution in lensless low-energy electron holography (1991)

With the low-energy-electron projection microscope it has been possible to image the lattice of thin gold films with atomic resolution. A theory modeling the coherent point source as the origin of a spherical wave is capable of describing both the Gabor-type holograms as well as the automatically resolved lattice images of the gold films.
Electric Coiled Tubing Drilling: A Smarter CT Drilling System (1999)

Abstract The paper describes the ongoing development of an electrically powered bottom hole assembly for use in coiled tubing drilling (CTD) applications. Electric coiled tubing drilling (E-CTD) offers many distinct advantages over conventional CTD which are considered in more depth within the paper. These may be summarised to include: Drive power provided independent of fluid flowHigh tolerance of energised drilling fluids–ideal for underbalanced drilling–ideal for subsea drilling applicationsHigh temperature operationFlexible control of electric power with instantaneous feedback for closed loop drilling and optimisation of drilling efficiencyMotor operation is scalable. The same drive may be used for auxiliary actuation, e.g. orientation, active traction and formation testing.Real-time transmission of data to surface using power cableExtended longevity of motorReduced vibration (affects gyro placement, reliability of other equipment, eg NMR magnets)Reversible direction of rotation (passive or active traction capabilities) It is these advantages that have driven the development of the electric BHA in a European Drilling Engineers Association [DEA(E)] joint industry project. This paper reviews prototype bottom hole assemblies from phases 1 and 2 of the project. Surface components, the electrical transmission system and its consequences for an integrated drilling package are also considered. Phase 2 of the project, currently ongoing, has delivered a purpose-built, electric downhole motor (EDM) design suitable for drilling a 3.75" hole. This motor is currently being incorporated into an electric BHA which incorporates pressure, temperature and vibration sensors. The proposed test program is reviewed with some earlier results presented from phase 1 for illustrative purposes. The ultimate goal of this project is to integrate the electric motor into a ‘smart’, closed-loop drilling system. It is envisaged that, based upon feedback from near-bit sensors, such a system would be able to automatically adjust drilling parameters to optimise drilling performance. The paper concludes that not only is electric coiled tubing drilling a practical and effective alternative to conventional CTD, but that the system delivers many additional benefits.
De Novo Design, Synthesis, and Characterization of Quinoproteins (2006)

Quinones and quinoproteins are essential redox components and enzymes in biological systems. Here, we report the de novo design, synthesis, and properties of model four-alpha-helix bundle quinoproteins. The proteins were designed and constructed from three different helices with 21 or 22 amino acid residues by chemoselective ligation to a cyclic decapeptide template. A free cysteine unit is placed at the hydrophobic core of the protein for binding of ubiquinone-0 and menaquinone-0 through a thioether bond. The quinoproteins with molecular weights of 11-12 kDa were characterized by electrospray ionization mass spectrometry, UV/Vis spectroscopy, size-exclusion chromatography, circular dichroism measurements, (1)H NMR spectroscopy, cyclic voltammetry, and redox-induced FTIR difference spectroscopy. The midpoint redox potentials at pH 8 in aqueous solution E(m,8) of thioether conjugates with N-acetyl cysteine methyl ester were 89 mV and -63 mV and with a synthetic protein 229 mV and 249 mV versus standard hydrogen electrode (SHE) for ubiquinone-0 and menaquinone-0, respectively. Detailed redox-induced FTIR difference spectroscopic studies of the model compounds and quinoproteins show the special resonance features for C=O bands at 1656-1660 and 1655-1665 cm(-1) due to the sulfur substitution to ubiquinone-0 and menaquinone-0, respectively. The construction of model quinoproteins represents a significant step toward more complex artificial redox systems.
An Ion‐Induced Low‐Oil‐Adhesion Organic/Inorganic Hybrid Film for Stable Superoleophobicity in Seawater (2012)

Superoleophobicity under seawater: An ion-induced low-oil-adhesion film with underwater superoleophobicity is prepared by a typical layer-by-layer (LBL) method. Under an artificial marine environment with high ion-strength, the prepared polyelectrolytes/AuNPs hybrid film becomes rougher and possesses a higher water ratio, which in turn endows the film with superoleophobicity and low underwater oil adhesion. The as-prepared film shows excellent environmental stability in artificial seawater. This study provides a new strategy for controlling the self-cleaning property and accelerating the development of stable underwater superoleophobic films.
Comparison of AWGs and Echelle Gratings for Wavelength Division Multiplexing on Silicon-on-Insulator (2014)

We compare the performance (insertion loss and crosstalk) of silicon-based arrayed waveguide gratings (AWGs) and echelle gratings for different channel spacings. For high-resolution de/multiplexer (DWDM) applications, AWGs are the better choice, whereas echelle gratings perform well for low-resolution de/multiplexer (CWDM) applications. Alternatively, for low-resolution de/multiplexer applications, the conventional box-shaped silicon AWG can be modified by an S-shaped AWG. We report crosstalk as low as -27 dB for regular AWGs, whereas in the S-shaped AWGs, the crosstalk is better than -19 dB, with an insertion loss below -2 dB. The crosstalk of the echelle gratings varies between -19 and -23 dB, with insertion loss below -2 dB.
An economy for flow control in computer networks (1989)

A flow control mechanism based on an economic model of optimum decentralized decision making is presented. The virtual circuits (VCs) of the network are considered as economic agents competing for link capacity resources. Each VC is equipped with a preference relation defining its individual throughput-delay goals. The work makes three contributions to the study of flow control protocols. First, it presents fully decentralized flow control algorithms that allocate capacity to reflect both, varying priorities among VCs as well as their preferences and needs. Second, it establishes that the flow control algorithms result in Pareto-optimal allocation of capacities. This implies that the algorithms accomplish optimally fair allocation of resources given the set priorities and preferences. Third, experimental evidence is provided that the algorithms converge rapidly.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A data collection system for gathering electrical impedance measurements from the human breast (1987)

A data collection system for gathering electrical impedance measurements from the human breast is described. The system consists of 16 electrodes which are held in a ring that encompasses the breast. The system, which is battery operated, is controlled by a microprocessor enabling computer control of electrode selection and storage of data.