gebhart/patrepeval huggingface dataset:
Isolation of chromosomal mutations that affect carotenoid production inEscherichia coli: mutations alter copy number of ColE1-type plasmids (2004)

Chromosomal mutants were isolated in &lt;it&gt;Escherichia coli&lt;/it&gt; that altered carotenoid production from transformed carotenoid biosynthesis genes on a pACYC-derived plasmid (pPCB15). The mutations were mapped by sequencing. One group of mutations appeared to affect the cell metabolism without changing the copy number of the carotenoid synthesis plasmid. The other group of mutations either increased or decreased the copy number of the pPCB15 plasmid as determined by real-time PCR. The copy number change in most mutants was likely specific for ColE1-type plasmids for which copy number is controlled by a small antisense RNA. This collection of host strains would be useful for fine tuning expression of proteins and adjusting production of desired molecules without recloning to different vectors.
Synthesis of Some Heterocyclic Sulfones Related to Quinolinol (1993)

It is well known that pyrazolone derivatives possess antifungal and antibacterial activities. Pyrazole and isoxazole derivatives are widely used in medicinal chemistry. In continuation of our work on the synthesis of heterocycles containing the quinoline moiety we synthesized different heterocyclic sulfones related to quinolinol.
A chronology of interpolation: from ancient astronomy to modern signal and image processing (2002)

This paper presents a chronological overview of the developments in interpolation theory, from the earliest times to the present date. It brings out the connections between the results obtained in different ages, thereby putting the techniques currently used in signal and image processing into historical perspective. A summary of the insights and recommendations that follow from relatively recent theoretical as well as experimental studies concludes the presentation.
Idiopathic small dense osseous lesions of extremities (1999)

We report 12 cases (eight in feet and four in hands) of idiopathic small dense osseous lesions involving the distal extremities with follow-up of at least five years. The lesion shows cortical and endosteal thickening parallel to the long axis of the involved bone without concomitant soft tissue or bone abnormality. Long term follow- up demonstrates the radiographic stability of the lesion and its lack of activity with radionuclide imaging. Differential diagnosis are discussed. (author abstract)
Application of Volterra series to intermodulation distortion analysis of transistor feedback amplifiers (1970)

This paper analyzes the intermodulation distortion of a solid-state feedback amplifier. Each transistor of the amplifier has been represented by a frequency-dependent model incorporating four nonlinearities. The Volterra series is used as the analysis tool. The primary motivation for this study is that intermodulation distortion is a critical problem in high-frequency long-haul solidstate systems. A computer program that calculates the amplifier intermodulation distortion has been developed. This program can be used to select the optimum bias point of each stage, optimum interstage and feedback networks, and optimum load and source impedances. Good correlation between calculated and measured results was obtained. The closed-form expressions derived show that the feedback is fully effective in reducing the open-loop second-order distortion and that the feedback may not significantly reduce the open-loop third-order distortion, if the "second-order interaction" phenomenon is dominant. The second-order interaction is explained in detail in this paper.
Sequence Properties of the 1,2-Diacylglycerol 3-Glucosyltransferase from Acholeplasma laidlawiiMembranes (2001)

Synthesis of the nonbilayer-prone alpha-monoglucosyldiacylglycerol (MGlcDAG) is crucial for bilayer packing properties and the lipid surface charge density in the membrane of Acholeplasma laidlawii. The gene for the responsible, membrane-bound glucosyltransferase (alMGS) (EC ) was sequenced and functionally cloned in Escherichia coli, yielding MGlcDAG in the recombinants. Similar amino acid sequences were encoded in the genomes of several Gram-positive bacteria (especially pathogens), thermophiles, archaea, and a few eukaryotes. All of these contained the typical EX(7)E catalytic motif of the CAZy family 4 of alpha-glycosyltransferases. The synthesis of MGlcDAG by a close sequence analog from Streptococcus pneumoniae (spMGS) was verified by polymerase chain reaction cloning, corroborating a connection between sequence and functional similarity for these proteins. However, alMGS and spMGS varied in dependence on anionic phospholipid activators phosphatidylglycerol and cardiolipin, suggesting certain regulatory differences. Fold predictions strongly indicated a similarity for alMGS (and spMGS) with the two-domain structure of the E. coli MurG cell envelope glycosyltransferase and several amphipathic membrane-binding segments in various proteins. On the basis of this structure, the alMGS sequence charge distribution, and anionic phospholipid dependence, a model for the bilayer surface binding and activity is proposed for this regulatory enzyme.
New Methods for Stereoselective Synthesis of α-Alkylidene-γ-butyrolactones Using Monoanion of O-Ethyl S-(Tetrahydro-2-oxo-3-furanyl) Thiocarbonate and Dianion of α-Mercapto-γ-butyrolactone (1980)

Abstract The lithium enolates of O-ethyl S-(tetrahydro-2-oxo-3-furanyl) dithiocarbonate and thiocarbonate were found to be efficient reagents for the stereoselective synthesis of α-alkylidene-γ-butyrolactones from carbonyl compounds. The dianion of α-mercapto-γ-butyrolactone was successfully generated by treatment of α-mercapto-γ-butyrolactone with 2.2 equivalents of lithium diisopropylamide in the presence of N,N,N′,N′-tetramethylethylenediamine at −78°C in THF. The dianion thus formed has been utilized for the efficient and stereoselective synthesis of α-alkylidene-γ-butyrolactones from carbonyl compounds.
Bovine Oocyte Cytoplasm Supports Development of Embryos Produced by Nuclear Transfer of Somatic Cell Nuclei from Various Mammalian Species1 (1999)

The transfer of nuclei from one cell to another provides a powerful tool for studying the interactions between the cytoplasm of one cell and the nucleus of another. This study was designed to examine the ability of the bovine metaphase oocyte cytoplasm to support mitotic cell cycles under the direction of differentiated somatic cell nuclei of various mammalian species. Skin fibroblast cells from cows, sheep, pigs, monkeys, and rats were used as sources of donor nuclei. Nuclear transfer units produced by fusion of enucleated bovine oocytes and individual fibroblasts from all species examined underwent transition to interphase accompanied by nuclear swelling, further progression through the cell cycle, and completion of the first mitosis. Regardless of the species of donor fibroblasts used, some cleaving units progressed further and developed to advanced stages, as evidenced by continuation of cell proliferation and formation of a blastocoele cavity at the time appropriate for the donor fibroblast species. Although no pregnancies have been carried to term after transfer of embryos into surrogate animals, these observations suggest that mechanisms regulating early embryonic development may be conserved among mammalian species and that bovine oocyte cytoplasm can support the introduced differentiated nucleus regardless of chromosome number, species, or age of the donor fibroblast.
Novel Unsupervised Feature Filtering of Biological Data (2006)

We apply our methods to different benchmarks. In each case we evaluate the success of clustering the data in the selected feature spaces, by measuring Jaccard scores with respect to known classifications. We demonstrate that feature filtering according to CE outperforms the variance method and gene-shaving. There are cases where the analysis, based on a small set of selected features, outperforms the best score reported when all information was used. Our method calls for an optimal size of the relevant feature set. This turns out to be just a few percents of the number of genes in the two Leukemia datasets that we have analyzed. Moreover, the most favored selected genes turn out to have significant GO enrichment in relevant cellular processes.
Characterization of an equine herpesvirus type 1 gene encoding a glycoprotein (gp13) with homology to herpes simplex virus glycoprotein C (1988)

The molecular structure of the equine herpesvirus type 1 (EHV-1) gene encoding glycoprotein 13 (gp13) was analyzed. The gene is contained within a 1.8-kilobase AccI-EcoRI restriction fragment mapping at map coordinates 0.136 to 0.148 in the UL region of the EHV-1 genome and is transcribed from right to left. Determination of the nucleotide sequence of the DNA fragment revealed a complete transcriptional unit composed of typical regulatory promoter elements upstream to a long open reading frame (1,404 base pairs) that encoded a 468-amino-acid primary translation product of 51 kilodaltons. The predicted protein has the characteristic features of a membrane-spanning protein: an N-terminal signal sequence, a hydrophobic membrane anchor region, a charged C-terminal cytoplasmic tail, and an exterior domain with nine potential N-glycosylation sites. The EHV-1 DNA sequences expressed in lambda gt11 as gp13 epitopes were present in the open reading frame. Amino acid sequences composing a major antigenic site, recognized by 35% of a panel of 42 anti-gp13 monoclonal antibodies, were identified in the N-terminal surface domain of the deduced gp13 molecule. Comparison of the EHV-1 gp13 DNA sequence with that encoding glycoproteins of other alphaherpesviruses revealed no detectable homology. However, a search for homology at the amino acid level showed regions of significant sequence similarity between the amino acids of the carboxy half of EHV-1 gp13 and those of the same region of gC-like glycoproteins of herpes simplex virus (gC-1 and gC-2), pseudorabies herpesvirus (gIII), and varicella-zoster virus (gp66). The sequences of the N-terminal portion of gp13, by contrast, were much less conserved. The results of these studies indicate that EHV-1 gp13 is the structural homolog of herpes simplex virus glycoprotein C and further suggest that the epitope-containing N-terminal amino acid sequences of the herpesvirus gC-like glycoproteins have undergone more extensive evolutionary divergence than the C-terminal sequences.
NKG2D Receptor and Its Ligands in Host Defense (2015)

NKG2D is an activating receptor expressed on the surface of natural killer (NK) cells, CD8(+) T cells, and subsets of CD4(+) T cells, invariant NKT cells (iNKT), and γδ T cells. In humans, NKG2D transmits signals by its association with the DAP10 adapter subunit, and in mice alternatively spliced isoforms transmit signals either using DAP10 or DAP12 adapter subunits. Although NKG2D is encoded by a highly conserved gene (KLRK1) with limited polymorphism, the receptor recognizes an extensive repertoire of ligands, encoded by at least eight genes in humans (MICA, MICB, RAET1E, RAET1G, RAET1H, RAET1I, RAET1L, and RAET1N), some with extensive allelic polymorphism. Expression of the NKG2D ligands is tightly regulated at the level of transcription, translation, and posttranslation. In general, healthy adult tissues do not express NKG2D glycoproteins on the cell surface, but these ligands can be induced by hyperproliferation and transformation, as well as when cells are infected by pathogens. Thus, the NKG2D pathway serves as a mechanism for the immune system to detect and eliminate cells that have undergone "stress." Viruses and tumor cells have devised numerous strategies to evade detection by the NKG2D surveillance system, and diversification of the NKG2D ligand genes likely has been driven by selective pressures imposed by pathogens. NKG2D provides an attractive target for therapeutics in the treatment of infectious diseases, cancer, and autoimmune diseases.
A Secreted PTEN Phosphatase That Enters Cells to Alter Signaling and Survival (2013)

Phosphatase and tensin homolog on chromosome ten (PTEN) is a tumor suppressor and an antagonist of the phosphoinositide-3 kinase (PI3K) pathway. We identified a 576-amino acid translational variant of PTEN, termed PTEN-Long, that arises from an alternative translation start site 519 base pairs upstream of the ATG initiation sequence, adding 173 N-terminal amino acids to the normal PTEN open reading frame. PTEN-Long is a membrane-permeable lipid phosphatase that is secreted from cells and can enter other cells. As an exogenous agent, PTEN-Long antagonized PI3K signaling and induced tumor cell death in vitro and in vivo. By providing a means to restore a functional tumor-suppressor protein to tumor cells, PTEN-Long may have therapeutic uses.
Replication of an rRNA Gene Origin Plasmid in the Tetrahymena thermophila Macronucleus is Prevented by Transcription through the Origin from an RNA Polymerase I Promoter (1995)

In the somatic macronucleus of the ciliate Tetrahymena thermophila, the palindromic rRNA gene (rDNA) minichromosome is replicated from an origin near the center of the molecule in the 5' nontranscribed spacer. The replication of this rDNA minichromosome is under both cell cycle and copy number control. We addressed the effect on origin function of transcription through this origin region. A construct containing a pair of 1.9-kb tandem direct repeats of the rDNA origin region, containing the origin plus a mutated (+G), but not a wild type, rRNA promoter, is initially maintained in macronuclei as an episome. Late, linear and circular replicons with long arrays of tandem repeats accumulate (W.-J. Pan and E. H. Blackburn, Nucleic Acids Res, in press). We present direct evidence that the +G mutation inactivates this rRNA promoter. It lacks the footprint seen on the wild-type promoter and produces no detectable in vivo transcript. Independent evidence that the failure to maintain wild-type 1.9-kb repeats was caused by transcription through the origin came from placing a short DNA segment containing the rRNA gene transcriptional termination region immediately downstream of the wild-type rRNA promoter. Insertion of this terminator sequence in the correct, but not the inverted, orientation restored plasmid maintenance. Hence, origin function was restored by inactivating the rRNA promoter through the +G mutation or causing termination before transcripts from a wild-type promoter reached the origin region. We propose that transcription by RNA polymerase I through the rDNA origin inhibits replication by preventing replication factors from assembling at the origin.
Small-Molecule Inhibitors of Wnt Signaling Pathway: Towards Novel Anticancer Therapeutics (2015)

Focusing on recent developments, we reviewed the small-molecule inhibitors targeting various components of Wnt signaling pathways and the progress from the discovery of lead compounds to highly potent inhibitors with significant therapeutic potential.
The alpha form of human tryptase is the predominant type present in blood at baseline in normal subjects and is elevated in those with systemic mastocytosis. (1995)

Tryptase, a protease produced by all mast cells, was evaluated as a clinical marker of systemic mastocytosis. Two sandwich immunoassays were evaluated, one which used the mAb G5 for capture, the other which used B12 for capture. The B12 capture assay measured both recombinant alpha- and beta-tryptase, whereas the G5 capture assay measured primarily recombinant beta-tryptase. G5 binds with low affinity to both recombinant alpha-tryptase and tryptase in blood from normal and nonacute mastocytosis subjects, and binds with high affinity to recombinant beta-tryptase, tryptase in serum during anaphylaxis, and tryptase stored in mast cell secretory granules. B12 recognizes all of these forms of tryptase with high affinity. As reported previously, during systemic anaphylaxis in patients without known mastocytosis, the ratio of B12- to G5-measured tryptase was always < 5 and approached unity (Schwartz L.B., T.R. Bradford, C. Rouse, A.-M. Irani, G. Rasp, J.K. Van der Zwan and P.-W.G. Van der Linden, J. Clin. Immunol. 14:190-204). In this report, most mastocytosis patients with systemic disease have B12-measured tryptase levels that are elevated (> 20 ng/ml) and are at least 10-fold greater than the corresponding G5-measured tryptase level. Most of those subjects with B12-measured tryptase levels of < 20 ng/ml had only cutaneous manifestations. The B12 assay for alpha-tryptase and beta-tryptase, particularly when performed in conjunction with the G5 assay for beta-tryptase, provides a more precise measure of mast cell involvement than currently available assessments, a promising potential screening test for systemic mastocytosis and may provide an improved means to follow disease progression and response to therapy.
Mechanism of inhibition of trypanothione reductase and glutathione reductase by trivalent organic arsenicals (1994)

The dithiol trypanothione, novel to trypanosomatids and analogous to glutathione in mammalian systems, has been shown to interact with anti-trypanocidal trivalent arsenical drugs forming a stable adduct, MelT. This adduct is a competitive inhibitor of the flavoprotein trypanothione reductase, responsible for maintaining intracellular trypanothione in the reduced form. Since trypanothione reductase and the analogous glutathione reductase both contain catalytically active sulphydryl groups we have examined the ability of several arsenicals to differentially inhibit these enzymes. Melarsen oxide [p-(4,6-diamino-s-triazin-2-yl)aminophenylarsenoxide] potently inhibits both enzymes in two stages, the first being essentially complete within 1 min, the second being time dependent, exhibiting saturable pseudo-first-order kinetics with kinact of 14.3 x 10(-4) s-1 and 1.06 x 10(-4) s-1 and Ki of 17.2 microM and 9.6 microM for trypanothione reductase and glutathione reductase, respectively. Inhibition requires prior reduction of the enzyme by NADPH and can be reversed by excess dithiols or prevented by MelT in the case of trypanothione reductase. In both cases a time-dependent loss of the characteristic charge-transfer absorbance band at 530 nm is observed upon addition of arsenical to pre-reduced enzyme, which with excess NADPH leads to a spectrum resembling the EH4 form and is accompanied by an increased ability to reduce molecular oxygen. A model for inhibition is proposed where, first, free arsenical and previously reduced enzyme immediately establish an equilibrium with an inactive monothioarsane enzyme-inhibitor complex involving the interchange cysteine distal to the FAD; second, a subsequent rearrangement about the sulphur-arsenic bond leads to the binding of the arsenical to the charge-transfer cysteine, proximal to the FAD, forming a more stable dithioarsane complex. Molecular modelling suggests that the differences in kinetic behaviour of the two enzymes can be attributed to structural features of their respective disulphide-binding sites. Incubation of reduced trypanothione reductase with excess dihydrotrypanothione and melarsen oxide prevents direct inhibition of the enzyme, suggesting that dihydrotrypanothione acts as a protectant in vivo, preventing the direct modification of trypanothione reductase by sequestering the arsenical as MelT.
Connective Tissue Growth Factor Induces Apoptosis in Human Breast Cancer Cell Line MCF-7 (1999)

Connective tissue growth factor (CTGF) is a member of an emerging CCN gene family that is implicated in various diseases associated with fibro-proliferative disorder including scleroderma and atherosclerosis. The function of CTGF in human cancer is largely unknown. We now show that CTGF induces apoptosis in the human breast cancer cell line MCF-7. CTGF mRNA was completely absent in MCF-7 but strongly induced by treatment with transforming growth factor beta (TGF-beta). TGF-beta by itself induced apoptosis in MCF-7, and this effect was reversed by co-treatment with CTGF antisense oligonucleotide. Overexpression of CTGF gene in transiently transfected MCF-7 cells significantly augmented apoptosis. Moreover, recombinant CTGF protein significantly enhanced apoptosis in MCF-7 cells as evaluated by DNA fragmentation, Tdt-mediated dUTP biotin nick end-labeling staining, flow cytometry analysis, and nuclear staining using Hoechst 33258. Finally, recombinant CTGF showed no effect on Bax protein expression but significantly reduced Bcl2 protein expression. Taken together, these results suggest that CTGF is a major inducer of apoptosis in the human breast cancer cell line MCF-7 and that TGF-beta-induced apoptosis in MCF-7 cells is mediated, in part, by CTGF.
Analysis of low density codes and improved designs using irregular graphs (1998)

We introduce a new set of probabilistic analysis tools based on the analysis of And-Or trees with random inputs. These tools provide a unifying, intuitive, and powerful framework for carrying out the analysis of several previously studied random processes of interest, includingrandom loss-resilient codes, solving random k-SAT formula using the pure literal rule, and thegreedy algorithm for matchings in random graphs. In addition, these tools allow generalizations of these problems not previously analyzed to be analyzed in a straightforward manner. We illustrate our methodology on the three problems listed above
High‐Contrast Paramagnetic Fluorescent Mesoporous Silica Nanorods as a Multifunctional Cell‐Imaging Probe (2008)

A real contrast: Multifunctional fluorescent and paramagnetic mesoporous silica nanorods can be used to label both phagocytic and nonphagocytotic cells. The cells can be detected simultaneously by a fluorescence technique and the T1- or T2-weighted modes of magnetic resonance imaging (see picture). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2296/2008/z700457_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.