gebhart/patrepeval huggingface dataset:
The bHLH genes GLABRA3 (GL3) and ENHANCER OF GLABRA3(EGL3) specify epidermal cell fate in the Arabidopsis root (2003)

The position-dependent specification of the hair and non-hair cell types in the Arabidopsis root epidermis provides a simple model for the study of cell fate determination in plants. Several putative transcriptional regulators are known to influence this cell fate decision. Indirect evidence from studies with the maize R gene has been used to suggest that a bHLH transcription factor also participates in this process. We show that two Arabidopsis genes encoding bHLH proteins, GLABRA3 (GL3) and ENHANCER OF GLABRA3 (EGL3), act in a partially redundant manner to specify root epidermal cell fates. Plants homozygous for mutations in both genes fail to specify the non-hair cell type, whereas plants overexpressing either gene produce ectopic non-hair cells. We also find that these genes are required for appropriate transcription of the non-hair specification gene GL2 and the hair cell specification gene CPC, showing that GL3 and EGL3 influence both epidermal cell fates. Furthermore, we show that these bHLH proteins require a functional WER MYB protein for their action, and they physically interact with WER and CPC in the yeast two-hybrid assay. These results suggest a model in which GL3 and EGL3 act together with WER in the N cell position to promote the non-hair cell fate, whereas they interact with the incomplete MYB protein CPC in the H position, which blocks the non-hair pathway and leads to the hair cell fate.
Identification and removal of impediments to biocatalytic synthesis of aromatics from D-glucose: rate-limiting enzymes in the common pathway of aromatic amino acid biosynthesis (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIdentification and removal of impediments to biocatalytic synthesis of aromatics from D-glucose: rate-limiting enzymes in the common pathway of aromatic amino acid biosynthesisK. A. Dell and J. W. FrostCite this: J. Am. Chem. Soc. 1993, 115, 24, 11581–11589Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://doi.org/10.1021/ja00077a065Request reuse permissionsArticle Views627Altmetric-Citations78LEARN 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 (3 MB) Get e-Alertsclose Get e-Alerts
Characterization of Plasma Membrane Lipids and Luteinizing Hormone Receptors of Ovine Corpora Lutea during Luteolysis and Early Pregnancy1 (1988)

Lipid composition of plasma membranes from luteal cells was examined to determine whether changes in this organelle occur during regression and maintenance of the corpus luteum in nonpregnant (NP) and pregnant (P) ewes, respectively. Forty ewes were assigned to be killed on Day 13 or 15 of the estrous cycle (D13-NP and D15-NP) or pregnancy (D13-P and D15-P). Purification of luteal plasma membranes on discontinuous sucrose gradients yielded two fractions, designated F1 and F2, that exhibited the greatest enrichment of 5'-nucleotidase activity (five- and fourfold, respectively) over that of the homogenate. These fractions also yielded the lowest contamination by endoplasmic reticulum as represented by nicotinamide adenine dinucleotide phosphate (NADPH) cytochrome C reductase activity and mitochondrial membranes as indicated by succinate dehydrogenase activity. Predominant phospholipids identified in membranes obtained from all groups were phosphatidylcholine (PC, 48.9 +/- 0.6% of total phospholipid), phosphatidylethanolamine (PE, 33.3 +/- 0.4%), sphingomyelin (SPH, 9.7 +/- 0.3%), phosphatidylserine (PS, 3.5 +/- 0.2%), and phosphatidylinositol (PI, 4.0 +/- 0.5%). No changes in microgram phospholipid/mg membrane protein were observed for any luteal phospholipid on D13 and 15 of the estrous cycle or pregnancy. No significant changes in the relative percentages of major fatty acids present in PC (palmitic [16:0], oleic [18:1]), PE (stearic [18:0], 18:1 and arachidonic [20:4]), or PS (18:0, 18:1, docosatetraenoic [22:4]), nor in the ratios of unsaturated (U) to saturated (S) fatty acids in these phospholipids were observed. Significant differences in unsaturated fatty acids of chain length greater than 20 carbons present in minor quantities in PC, PE, and PS were detected between NP and P ewes as well as between days within reproductive stage. The profile of major fatty acids present in PI revealed decreases in 18:0 and 20:4 in D15-NP and increases in 22:4 and docosapentaenoic acid (22:5) in luteal membranes of both D13- and D15-NP ewes relative to the levels of these fatty acids in PI of corresponding groups of pregnant ewes. There was a general trend for 20:4 levels of PC and PI in membranes of D15-NP ewes to be inversely related to those of D15-P ewes. Collectively, these changes were reflected by an increased U:S fatty acid ratio in luteal membrane PI during the estrous cycle. Specific binding of [125I] iodo-human chorionic gonadotropin to luteal plasma membranes from NP and P ewes on D13 and 15 (6/group) revealed similar affinities and concentrations of unoccupied luteinizing hormone (LH) receptors.(ABSTRACT TRUNCATED AT 400 WORDS)
Secretion of a functional soluble form of neutral endopeptidase-24.11 from a baculovirus-infected insect cell line (1992)

Neutral endopeptidase (NEP; EC 3.4.24.11) is an integral membrane protein found at the plasma membrane of many cell types. A secreted form of NEP (sec-NEP) was recently obtained by transfection of COS-1 cells with a recombinant expression vector consisting of the cDNA encoding the signal peptide of pro-opiomelanocortin fused in-frame to the cDNA sequence of the complete ectodomain of rabbit NEP [Lemay, Waksman, Roques, Crine & Boileau (1989) J. Biol. Chem. 264, 15620-15623]. In order to produce large quantities of this enzyme for structural studies we have expressed this recombinant soluble form of NEP at high yields using a baculovirus/insect-cell system. A recombinant Autographa californica nuclear polyhedrosis-virus genome containing the sec-NEP sequence was used to infect host Spodoptera frugiperda Sf9 cells. Infected cells secreted an N-glycosylated soluble form of neutral endopeptidase which was enzymically active. The yield was about 80 nmol of enzyme/litre of culture. The soluble form of the recombinant enzyme purified by immunoaffinity showed the same catalytic properties as the wild-type enzyme extracted from the kidney brush-border membranes. Treatment of the recombinant enzyme with endo-beta-N-acetylglucosaminidase H showed, however, that invertebrate cells did not glycosylate the enzyme to the same extent as did mammalian cells. Our findings demonstrate that insect cells can be used as hosts for the production of the soluble form of neutral endopeptidase. We also conclude that neither a full complement of carbohydrate side chains nor the membrane anchor appear to be essential for the production and targeting to the cell surface of a fully functional enzyme in this expression system.
Mobile phone-based biosensing: An emerging “diagnostic and communication” technology (2016)

In this review we discuss recent developments on the use of mobile phones and similar devices for biosensing applications in which diagnostics and communications are coupled. Owing to the capabilities of mobile phones (their cameras, connectivity, portability, etc.) and to advances in biosensing, the coupling of these two technologies is enabling portable and user-friendly analytical devices. Any user can now perform quick, robust and easy (bio)assays anywhere and at any time. Among the most widely reported of such devices are paper-based platforms. Herein we provide an overview of a broad range of biosensing possibilities, from optical to electrochemical measurements; explore the various reported designs for adapters; and consider future opportunities for this technology in fields such as health diagnostics, safety & security, and environment monitoring.
A Maximum Likelihood Receiver for an Orthogonally Multiplexed QAM System (1984)

A maximum likelihood receiver for an orthogonally multiplexed QAM (OQAM) system has been derived based on the mathematical structure of an OQAM signal. The resulting receiver provides the minimum variance estimates of carrier and timing phases under the disturbance caused by not only Gaussian noise but also random data. It has also been proven that the carrier and timing joint control system is asymptotically stable almost everywhere in a state space. The equilibrium points are where the parallel synchronization over all subchannels in the OQAM system is established. Simulations have been carried out in order to verify the maximum likelihood receiver performances, where 9600 bit/s data are transmitted over 750-2450 Hz voiceband with 8×8 staggered QAM signal constellations. It has been shown that sufficient eye opening is obtained under 10 Hz carrier frequency offset and 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> timing frequency stability.
Ultralow resistance-area product of 0.4Ω(μm)2 and high magnetoresistance above 50% in CoFeB∕MgO∕CoFeB magnetic tunnel junctions (2006)

An ultralow resistance-area (RA) product of 0.4Ω(μm)2 was achieved in CoFeB∕MgO∕CoFeB magnetic tunnel junctions with a high magnetoresistance ratio of 57% at room temperature. Various growth conditions for polycrystalline MgO(001) tunneling barrier were optimized to improve the crystalline orientation of the MgO(001) layer, which resulted in a significant enhancement of magnetoresistance in an ultralow RA region below 1Ω(μm)2. Removal of residual H2O molecules from a growth chamber was especially effective in improving the crystalline orientation. The present achievements will enable the development of highly sensitive read heads for ultrahigh-density hard disk drives.
Mammalian Transgenesis by Intracytoplasmic Sperm Injection (1999)

Coinjection of unfertilized mouse oocytes with sperm heads and exogenous DNA encoding either a green fluorescent protein (GFP) or beta-galactosidase reporter produced 64 to 94 percent transgene-expressing embryos, reflecting DNA-sperm head association before coinjection. Nonselective transfer to surrogate mothers of embryos in the GFP series generated about 20 percent offspring expressing the integrated transgene. These data indicate that exogenous DNA can reproducibly be delivered into an oocyte by microinjected spermatozoa and suggest an adaptable method of transgenesis.
Characterization of lbpA, the structural gene for a lactoferrin receptor in Neisseria gonorrhoeae (1995)

Neisseria gonorrhoeae acquires iron (Fe) efficiently from lactoferrin (LF). A 103-kDa gonococcal outer membrane LF-binding protein (Lbp) was identified previously. We isolated the structural gene lbpA for Lbp1 by screening a gonococcal library for a clone that could repair an LF- receptor mutant. An mTnCm3 transposon insertion mutant of lbpA was unable to use LF-bound Fe for growth, unable to bind LF to whole cells, and unable to express Lbp1. The DNA sequence of lbpA predicted a protein that shared 94% identity with the meningococcal LF receptor protein, Lbp, and was closely related to Tbp1, one of the transferrin receptor proteins. Clinical isolates of gonococci are frequently unable to acquire Fe from LF, and LF- isolates do not have a functional LF receptor. The wild-type lbpA gene transformed most tested LF- clinical isolates to LF+, indicating that lbpA is defective in many clinical isolates.
Discrimination of refractory periodontitis subjects using clinical and laboratory parameters alone and in combination (1999)

The purpose of the present investigation was to use baseline clinical and laboratory parameters to distinguish subjects refractory to conventional periodontal therapy. Baseline clinical, microbial and host parameters were compared in 61 successfully-treated and 27 refractory subjects. Refractory subjects showed mean full-mouth attachment level (AL) loss and/or >3 sites with new AL loss >2.5 mm within 1 year after both scaling and root planing and surgery with systemic tetracycline. Successfully-treated subjects showed mean AL gain and no sites with new AL loss >2.5 mm after either regimen. Gingival redness, bleeding on probing, suppuration, supragingival plaque accumulation, pocket depth and AL were measured at 6 sites per tooth in each subject. The levels of 40 subgingival taxa were determined in subgingival plaque samples from up to 28 sites in each subject using checkerboard DNA-DNA hybridization. Serum antibody (Ab) to 85 subgingival species was determined using checkerboard immunoblotting. Levels of serum IgG2 and Gm23 allotype were measured using radial immunodiffusion; FcgammaRIIa and FcgammaRIIIb receptor haplotypes were determined using PCR and allele specific oligonucleotide probes. Odds ratios of a subject being refractory were determined by comparing measured parameters in the 2 subject groups using univariate and multivariate techniques. 17 of 151 clinical, microbial and immunological variables were significant using chi2 analysis after adjusting for multiple comparisons. For example, the odds ratios of a subject being refractory were 12.2, 5.4 and 6.9 if the subject had Ab >50 microg/ml to >9 species; S. constellatus counts >2.4% of the total DNA probe count or >2.1% of sites with AL >6 mm. The 17 significant predictor variables were used in logistic regression and discriminant analyses. Similar variables were selected using both analyses including the number of serum Ab to subgingival species >50 microg/ml, % S. constellatus in plaque samples and % sites with attachment loss >6 mm. In the logistic regression analysis model, the odds ratios associated with >9 species exhibiting >Ab 50 microg/ml, >2.1% of sites with AL >6 mm and >2.4% S. constellatus in plaque were 8.7, 6.8 and 2.4, respectively, after adjusting for other variables in the model. Discriminant analysis using these variables provided sensitivity, specificity, positive and negative predictive values of 0.66, 0.92, 0.80 and 0.85 respectively. Refractory periodontitis subjects could be distinguished using a subset of clinical, microbiological and immunological parameters.
Quantitative analysis of morphine from urine in drug abuse case (2004)

Objective To research the general pattern of gradual decrease of morphine content in a drug(heroin)users' urine when they stop using heroin. Method 182 drug(heroin)users' urine sample were continuously collected for 9 days after they stop using drug and morphine content in their urine were analysed by using radio-immunity. Results After they stop using heroin for 8 days, the morphine content in their urine decreased to 30ng/ml. Conclusion When dealing with a drug abuse case, the urine test for morphine content should be done within 8 days from the last time of using heroin.
Identification of the ubiD Gene on the Escherichia coli Chromosome (2000)

The open reading frame at 86.7 min on the Escherichia coli chromosome, "yigC," complemented a ubiD mutant strain, AN66, indicating that yigC is the ubiD gene. The gene product, a 497-amino-acid-residue protein, showed extensive homology to the UPF 00096 family of proteins in the Swiss-Prot database.
In vivo Antitumor Activity of MEK and Phosphatidylinositol 3-Kinase Inhibitors in Basal-Like Breast Cancer Models (2009)

Our studies suggest that single-agent MEK inhibition is a promising therapeutic modality for basal-like breast cancers with intact PTEN, and also provide a basis for rational combination of MEK and PI3K inhibitors in basal-like cancers with both intact and deleted PTEN.
Mitochondrial Signaling in Mammalian Cells Activated by Red and Near‐IR Radiation (2008)

Mitochondrial signaling is an information channel between the mitochondrial respiratory chain and the nucleus for the transduction signals regarding the functional state of the mitochondria. The present review examines the question whether radiation of visible and near-IR (IR-A) radiation can activate this retrograde-type cellular signaling pathway. Experimental data about modulation of elements of mitochondrial retrograde signaling by the irradiation (mitochondrial membrane potential DeltaPsi(m), reactive oxygen species ROS, Ca(2+), NO, pH(i), fission-fusion homeostasis of mitochondria) are reviewed. The terminal enzyme of the mitochondrial respiratory chain cytochrome c oxidase is considered as the photoacceptor. Functions of cytochrome c oxidase as a signal generator as well as a signal transducer in irradiated cells are outlined.
B7-1 Amplifies the Response to Interleukin-2-Secreting Tumor Vaccines In Vivo , but Fails to Induce a Response by Naive Cells In Vitro (1995)

Parental and interleukin-2 (IL-2)-secreting CMS5 tumor cells were transfected with the B7-1 costimulatory molecule to amplify anti-tumor responses. CMS5 cells transfected with B7-1 grew more slowly in vivo than did parental CMS5 cells. Moreover, tumor cells secreting levels of IL-2 too low to cause rejection alone were rejected following transfection with B7-1. To determine whether the expression of B7-1 enabled the tumor cells to activate T cells directly, their ability to stimulate in vitro functional responses by T cells was examined. We found that neither B7-1+ nor IL-2-secreting, B7-1+ CMS5 cells stimulated naive spleen cells to proliferate or to become cytotoxic. In contrast, restimulation of primed T cells by B7-1+ CMS5 cells resulted in stronger cytotoxicity responses than seen following restimulation by parental CMS5 cells. Lysis was even higher if the B7-1+ tumor cells also secreted IL-2. Our results suggest that the expression of costimulatory molecules can augment responses generated by vaccinating with IL-2-secreting tumor cells. Furthermore, they are consistent with the hypothesis that the initiation of an anti-tumor response by naive T cells may depend upon initial antigen presentation by another unidentified cell and that the major action of IL-2-secreting and/or B7-1+ tumor cell vaccines might be to potentiate the response of already primed cells.
Systemic Errors in Quantitative Polymerase Chain Reaction Titration of Self-Complementary Adeno-Associated Viral Vectors and Improved Alternative Methods (2012)

Self-complementary AAV (scAAV) vector genomes contain a covalently closed hairpin derived from a mutated inverted terminal repeat that connects the two monomer single-stranded genomes into a head-to-head or tail-to-tail dimer. We found that during quantitative PCR (qPCR) this structure inhibits the amplification of proximal amplicons and causes the systemic underreporting of copy number by as much as 10-fold. We show that cleavage of scAAV vector genomes with restriction endonuclease to liberate amplicons from the covalently closed terminal hairpin restores quantitative amplification, and we implement this procedure in a simple, modified qPCR titration method for scAAV vectors. In addition, we developed and present an AAV genome titration procedure based on gel electrophoresis that requires minimal sample processing and has low interassay variability, and as such is well suited for the rigorous quality control demands of clinical vector production facilities.
Growth of GeSi/Si strained-layer superlattices using limited reaction processing (1987)

SiGe/Si superlattices were grown using limited reaction processing. Each multilayer structure was fabricated in situ by changing the gas composition between high-temperature cycles. Commensurate SiGe alloy layers as thin as 15 nm were reproducibly deposited and were examined using transmission electron microscopy, sputtering Auger electron spectroscopy, and Rutherford backscattering. Si/SiGe interfaces are abrupt to within a few monolayers, establishing for the first time the use of a chemical vapor deposition technique to fabricate abrupt GeSi/Si-based heterostructures.
Imaging capabilities of synchrotron infrared microspectroscopy (2003)

It has become increasingly clear that synchrotron infrared micro-spectroscopy is an extremely valuable analysis tool when determining the chemical composition of biological and biomedical samples, at the diffraction-limited spatial resolution. Highly resolved infrared micro-spectroscopy, together with the high signal-to-noise level of the recorded spectra, is essential in generating chemical and statistical (multivariate) images. This is illustrated in the case of individual cell and hair section studies. Unprecedented chemical images of lipid distribution and secondary structure relative concentration have been achieved using the synchrotron source. A comparison with a Focal plane Array imaging system, on the same hair section, shows that, despite the fast imaging processing and improved quality achieved with the focal plane array detectors, spectral quality is markedly superior in the case of the synchrotron source. It is clear that the two approaches could be very complementary if combined on the same sample area, in a synchrotron facility.
Glowing optical fiber designs and parameters (1997)

Side-emitting optical fiber designs and main parameters have been studied. A simplified model to describe emission of the 'glowing' fiber is developed. Basic expressions for the emission parameters as functions of the input radiation intensity, distance along the fiber axis and scattering efficiency longitudinal distribution are given for several design modifications. The model assumptions have been checked experimentally by testing silica core side-glowing optical fiber samples.
Characterization of activated and normal mouse Mos gene in murine 3T3 cells. (1992)

We have characterized the mouse Mos proto-oncogene product, pp39Mos, in murine fibroblasts. When expressed in NIH3T3 cells under the influence of the long terminal repeat regulatory element from Moloney murine sarcoma virus [NIH(pTS-1) cells], the Mos protein was present in low levels and had a half-life of about 30 min. In extracts from NIH(pTS-1) cells, we detected additional forms of Mos protein that apparently arose from internal initiation codons (p24Mos and p29Mos) or from upstream non-AUG initiation codons (p42Mos and p44Mos). The Mos protein was found to exist in these cells as a phosphoprotein, pp39Mos, and, when immunoprecipitated with an antiserum specific for the Mos N-terminus [anti-Mos(6-24)], had autophosphorylating kinase activity. We found that anti-Mos(6-24) also detected non-Mos protein kinase activity and non-Mos phosphoproteins in addition to p39Mos. We present evidence, on both the RNA and protein levels, that non-transformed mouse 3T3 cells do not express endogenous Mos.