gebhart/patrepeval huggingface dataset:
Role of the Agrobacterium tumefaciens VirD2 Protein in T-DNA Transfer and Integration (1998)

VirD2 is one of the key Agrobacterium tumefaciens proteins involved in T-DNA processing and transfer. In addition to its endonuclease domain, VirD2 contains a bipartite C-terminal nuclear localization sequence (NLS) and a conserved region called omega that is important for virulence. Previous results from our laboratory indicated that the C-terminal, bipartite NLS and the omega region are not essential for nuclear uptake of T-DNA, and further suggested that the omega domain may be required for efficient integration of T-DNA into the plant genome. In this study, we took two approaches to investigate the importance of the omega domain in T-DNA integration. Using the first approach, we constructed a T-DNA binary vector containing a promoterless gusA-intron gene just inside the right T-DNA border. The expression of beta-glucuronidase (GUS) activity in plant cells transformed by this T-DNA would indicate that the T-DNA integrated downstream of a plant promoter. Approximately 0.4% of the tobacco cell clusters infected by a wild-type A. tumefaciens strain harboring this vector stained blue with 5-bromo-4-chloro-3-indolyl beta-D-glucuronic acid (X-gluc). However, using an omega-mutant A. tumefaciens strain harboring the same binary vector, we did not detect any blue staining. Using the second approach, we directly demonstrated that more T-DNA is integrated into high-molecular-weight plant DNA after infection of Arabidopsis thaliana cells with a wild-type A. tumefaciens strain than with a strain containing a VirD2 omega deletion/substitution. Taken together, these data indicate that the VirD2 omega domain is important for efficient T-DNA integration. To determine whether the use of the T-DNA right border is altered in those few tumors generated by A. tumefaciens strains harboring the omega mutation, we analyzed DNA extracted from these tumors. Our data indicate that the right border was used to integrate the T-DNA in a similar manner regardless of whether the VirD2 protein encoded by the inciting A. tumefaciens was wild-type or contained an omega mutation. In addition, a mutant VirD2 protein lacking the omega domain was as least as active in cleaving a T-DNA border in vitro as was the wild-type protein. Finally, we investigated the role of various amino acids of the omega and bipartite NLS domains in the targeting of a GUS-VirD2 fusion protein to the nucleus of electroporated tobacco protoplasts. Deletion of the omega domain, or mutation of the 10-amino-acid region between the two components of the bipartite NLS, had little effect upon the nuclear targeting of the GUS-VirD2 fusion protein. Mutation of both components of the NLS reduced, but did not eliminate, targeting of the fusion protein to the nucleus.
Visible photoluminescence from nanocrystalline Ge formed by H2 reduction of Si0.6Ge0.4O2 (1993)

Samples of nanocrystalline Ge embedded in SiO2 that display visible photoluminescence were synthesized from chemical vapor deposition-grown Si0.6Ge0.4 in a two step process of hydrothermal oxidation using steam at 25 MPa and 475 °C followed by annealing at 750 °C in flowing forming gas (80/20:N2/H2). A broad photoluminescence band, peaked at 2.14 eV (580 nm) with a full width at half maximum of 0.3 eV, was observed in samples that were annealed at 750 °C in flowing forming gas for 10, 30, and 60 min. As-oxidized (i.e., unprecipitated) samples show no photoluminescence peak when excited under identical conditions.
Synthesis of Superconducting Y-Ba-Cu-O Powder by the Spray Drying Method (1988)

Raw materials for sintering of superconductor were synthesized by the spray drying method. Three kinds of atomized solutions were used: (1) solution of Ba-, Y- and Cu-nitrates, (2) its ammoniacal alkaline solution and (3) slurry made by the mixing of Ba-, Y-, Cu-nitrates solution diluted by the water-ethanol solvents with oxalic acid solution. Resulting powders were calcined up to 900°C. They formed perovskite structure at 850°C ((1), (2)) and 800°C ((3)). Calcinated powders from (1) and (2) showed strongly aggregated or cortinuous structure with many pores, whereas that from (3) was flocculated structure and homogeneity in the mass and each particles. In conclusion, (3) was optimum method to produce the raw materials for sintering of superconductor.
Multiple-dose pharmacokinetics of ceftibuten in healthy volunteers (1995)

The pharmacokinetics of ceftibuten, a new cephalosporin antibiotic, and its conversion product, ceftibutentrans, were studied in healthy male volunteers following daily oral administration of a 400-mg capsule for 7 days. Mean concentrations of ceftibuten in plasma obtained on day 5 were similar to those obtained on day 7. Analysis of variance indicated that the concentrations in plasma on days 5 and 7 were at steady state. The mean accumulation factor was 1.14 for day 5 and 1.13 for day 7. The half-life (2.4 h) was independent of the duration of drug administration, and the mean maximum concentration of drug in plasma was 18 to 19 micrograms/ml. Urinary excretion was the major elimination route for ceftibuten, by which 57 to 59% of the drug was excreted unchanged over a 24-h period. The amounts of ceftibuten-trans in plasma and urine were low.
A Novel Protective Prion Protein Variant that Colocalizes with Kuru Exposure (2009)

The 127V polymorphism is an acquired prion disease resistance factor selected during the kuru epidemic, rather than a pathogenic mutation that could have triggered the kuru epidemic. Variants at codons 127 and 129 of PRNP demonstrate the population genetic response to an epidemic of prion disease and represent a powerful episode of recent selection in humans.
The differentiation of snoring mechanisms using sound analysis (1996)

Ten subjects known to suffer from heavy snoring but not obstructive sleep apnoea were studied using the technique of sleep nasendoscopy. The mechanism of snoring was noted for each and sound recordings of the snoring noise were made. Six subjects were observed to snore using their soft palate only, three snored using only their tongue base and one snored using a combination of palate and tongue base. The sound recordings were subjected to computer analysis of waveform and frequency. Palatal flutter snoring and tongue base snoring appear to have distinct waveform and frequency patterns which allows them to be differentiated from each other.
Posttranslational processing of secretory component in the rat jejunum by a brush border metalloprotease. (1986)

Secretory component (SC) is a glycoprotein that mediates the transcellular transport of polymeric immunoglobulins into external secretions. SC is synthesized and inserted into the plasma membrane of epithelial cells and hepatocytes as a transmembrane protein, where it serves as a receptor for polymeric immunoglobulins. SC is posttranslationally cleaved to a soluble protein before secretion into external fluids. In the rat jejunum, we observed that the molecular weights of both the major membrane and soluble forms of SC were 10,000-20,000 smaller than the comparable hepatic forms of the glycoprotein. We therefore set out to determine the reason for the differences in size of SC between these two tissues. The smaller size of jejunal SC was not due to the action of pancreatic proteases or differential glycosylation but was due to proteolysis by a jejunal brush border protease. The protease was characterized as a metalloprotease, with a pH optimum of approximately 5. It is present in jejunal, ileal, and renal tubular brush borders as an integral membrane constituent. When the protease was inhibited in vivo, conversion of jejunal secretory component to the smaller size was partially prevented. Thus, in the rat jejunum, SC undergoes two posttranslational proteolytic events: conversion of membrane secretory component to the soluble form and conversion of soluble SC to a smaller size by a previously undescribed brush border protease.
Catalytic conversion of simple haloporphyrins into alkyl-, aryl-, pyridyl-, and vinyl-substituted porphyrins (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalytic conversion of simple haloporphyrins into alkyl-, aryl-, pyridyl-, and vinyl-substituted porphyrinsStephen G. DiMagno, Victor S. Y. Lin, and Michael J. TherienCite this: J. Am. Chem. Soc. 1993, 115, 6, 2513–2515Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/ja00059a060https://doi.org/10.1021/ja00059a060research-articleACS PublicationsRequest reuse permissionsArticle Views950Altmetric-Citations133LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Age of Onset as a Discriminator Between Alcoholic Subtypes in a Treatment‐Seeking Outpatient Population (2000)

Subtyping alcoholics may provide a more accurate guide as to the course and character of the disease. Classifications of different ages of onset of problem drinking have so far resulted in categorical inconsistencies. In the past, hospital-based alcoholics have over-represented those most severely ill, and comprehensive evaluations of psychopathology for discriminating between alcoholic subtypes have been infrequent. In a heterogeneous treatment-seeking, outpatient, alcoholic population, we tested the hypothesis that age of onset represents a continuum of disease, and that greater severity of psychopathology is associated with lower ages of onset. Using a standard questionnaire, 253 male and female treatment-seeking alcoholics were stratified according to specific ages of onset: a) < 20 years; b) 20-25 years, and c) > 25 years. These age of onset groups were compared on alcohol severity and craving, family history, childhood behavior, personality, hostility, overt aggression, mood, and social functioning. Symptom severity and age of onset were negatively correlated, and the 20-25-year onset group usually had intermediate scores. The < 20 year onset group was characterized by greater severity of alcohol-related problems, family history, childhood behavioral problems, craving, hostility, antisocial traits, mood disturbance, and poor social functioning. Alcoholics with an earlier age of onset have relatively greater psychopathology than those of later onset. While the preponderance of psychopathology among those in the < 20-year onset group could be conceptualized as a clinical "subtype," such a characterization would not define an entirely homogeneous category. Yet, this clinical characterization would be clinically important if specific age of onset levels were found to be differentially sensitive to pharmacological and/or psychological treatments.
Tuning ITAM multiplicity on T cell receptors can control potency and selectivity to ligand density (2018)

The T cell antigen receptor (TCR) recognizes peptides from pathogenic proteins bound in the major histocompatibility complex (MHC). To convert this binding event into downstream signaling, the TCR complex contains immunoreceptor tyrosine-based activation motifs (ITAMs) that act as docking sites for the cytoplasmic tyrosine kinase ZAP-70. Unique among antigen receptors, the TCR complex uses 10 ITAMs to transduce peptide-MHC binding to the cell interior. Using synthetic, drug-inducible receptor-ligand pairs, it was found that greater ITAM multiplicity primarily enhanced the efficiency with which ligand binding was converted into an intracellular signal. This manifested as an increase in the fraction of cells that became activated in response to antigen, and a more synchronous initiation of TCR-proximal signaling, rather than direct amplification of the intracellular signals. Exploiting these findings, the potency and selectivity of chimeric antigen receptors targeted against cancer were substantially enhanced by modulating the number of encoded ITAMs.
Biosynthesis and Incorporation into Protein of Norleucine by Escherichia coli (1989)

The methionine analog norleucine was produced during the synthesis of bovine somatotropin by Escherichia coli strain W3110G containing the recombinant plasmid pBGH1. Norleucine was generated by the leucine biosynthetic pathway from pyruvate or alpha-ketobutyrate in place of alpha-ketoisovalerate as the initial substrate. The intracellular level of norleucine was high enough to permit the analog to compete successfully with methionine for incorporation into protein. Two ways were found to prevent either the formation of norleucine or its incorporation into protein. The endogenous synthesis of norleucine was eliminated by deleting the leucine operon. The addition of sufficient methionine or 2-hydroxy-4-methylthiobutanoic acid, a precursor of methionine, to the culture medium prevented any norleucine from being incorporated into protein.
Preparation and performance of bispecific F(ab' gamma)2 antibody containing thioether-linked Fab' gamma fragments. (1987)

A simple and efficient method is described for the production of pure bispecific F(ab' gamma)2 heterodimers, in which the individual antibody Fab' gamma fragments are joined via a stable thioether linkage. Hybrid molecules were constructed from both mouse monoclonal and rabbit polyclonal antibodies with equal efficiency, in the combinations mouse-rabbit and mouse-mouse. Peptic F(ab' gamma)2 fragments from the two chosen antibodies were first reduced to provide Fab' gamma SH. The SH groups on one of the Fab' gamma SH partners were then fully alkylated with o-phenylenedi-maleimide to provide free maleimide groups. Finally the two preparations, Fab' gamma mal and Fab' gamma SH, combined under conditions which allowed cross-linking of the maleimide and SH groups and avoided reoxidation of SH groups. The major product isolated from the reaction mixture after chromatography was always the F(ab' gamma)2 heterodimer (50 to 70%), other products being unreacted Fab' gamma and trace amounts of putative F(ab' gamma)3. Immunochemical analysis revealed that the thioether-linked F(ab' gamma)2 molecules were essentially all heterodimers, most of which had been joined via their Fd chains. The dual specificity of F(ab' gamma)2 heterodimers was tested functionally in three systems: 1) the combination (anti-idiotype + anti-phycoerythrin) linked L2C cells to the fluorochrome phycoerythrin, allowing fluorescence analysis; 2) the combination (anti-idiotype + anti-saporin) linked L2C cells to the ribosome-inactivating protein saporin, and transformed a subtoxic dose of saporin into a highly toxic mixture which prevented further protein synthesis by L2C cells; and 3) the combination of anti-idiotype with 3G8 (antibody to the Fc gamma receptor CD16) subjected L2C cells to cytotoxic attack by human mononuclear effectors.
In Vitro Recombination and Mutagenesis by Overlap Extension PCR (2003)

The polymerase chain reaction (PCR) (,) is now a fundamental tool of molecular biology. Although PCR provides the basis for a variety of sensitive analytical techniques, it can also be used in a synthetic capacity to generate large quantities of specific DNA fragments. The alteration of amplified DNA sequences is also possible, since synthetic oligonucleotide primers become incorporated into the final PCR product. Although the 3′ ends of these primers must match the target DNA sequence, the 5′ ends may contain modifications. Sequence modifications in the primers will therefore be present in the ends of the amplified DNA fragment, offering a straightforward, although limited, ability to introduce site-directed mutations during PCR.
Photophysical Processes of Merocyanine 540 in Solutions and in Organized Media (1999)

Photophysical processes of merocyanine 540 (MC540) are studied using picosecond time-resolved emission spectroscopy. The nonradiative rate of MC540 increases from 0.32 × 109 s-1 in dioxane to 8.73 × 109 s-1 in water, i.e., nearly 27 times. This is attributed to the decrease in the barrier of photoisomerization with increase in polarity and the consequent increase in the rate of photoisomerization for MC540. The polarity-dependent isomerization is also shown to be the cause for the observed increase in emission intensity and lifetime of MC540 in aerosol-OT microemulsions and aqueous bovine serum albumin solutions.
The human VASA gene is specifically expressed in the germ cell lineage (2000)

To understand the origins and function of the human germ cell lineage and to identify germ cell-specific markers we have isolated a human ortholog of the Drosophila gene vasa. The gene was mapped to human chromosome 5q (near the centromere) by radiation hybrid mapping. We show by Northern analysis of fetal and adult tissues that expression of the human VASA gene is restricted to the ovary and testis and is undetectable in somatic tissues. We generated polyclonal antibodies that bind to the VASA protein in formalin-fixed, paraffin-embedded tissue and characterized VASA protein expression in human germ cells at various stages of development. The VASA protein is cytoplasmic and expressed in migratory primordial germ cells in the region of the gonadal ridge. VASA protein is present in fetal and adult gonadal germ cells in both males and females and is most abundant in spermatocytes and mature oocytes. The gene we have isolated is thus a highly specific marker of germ cells and should be useful for studies of human germ cell determination and function.
Nitric oxide as a mediator of delayed pharmacological (A1 receptor triggered) preconditioning; is eNOS masquerading as iNOS? (2002)

This is the first study to demonstrate a role for eNOS in delayed A(1) receptor triggered (pharmacological) preconditioning, potentially representing a new pharmacological target for protecting the ischemic heart.
Cod glycopeptide with picomolar affinity to galectin-3 suppresses T-cell apoptosis and prostate cancer metastasis (2013)

Cancer metastasis and immune suppression are critical issues in cancer therapy. Here, we show that a β-galactoside-binding lectin [galectin-3 (gal3)] that recognizes the Thomsen-Friedenreich disaccharide (TFD, Galβ1,3GalNAc) present on the surface of most cancer cells is involved in promoting angiogenesis, tumor-endothelial cell adhesion, and metastasis of prostate cancer cells, as well as evading immune surveillance through killing of activated T cells. To block gal3-mediated interactions, we purified a glycopeptide from cod (designated TFD100) that binds gal3 with picomolar affinity. TFD100 blocks gal3-mediated angiogenesis, tumor-endothelial cell interactions, and metastasis of prostate cancer cells in mice at nanomolar levels. Moreover, apoptosis of activated T cells induced by either recombinant gal3 or prostate cancer patient serum-associated gal3 was inhibited at nanomolar concentration of TFD100. Because the gal3-TFD interaction is a key factor driving metastasis in most epithelial cancers, this high-affinity TFD100 should be a promising antimetastatic agent for the treatment of various cancers, including prostate adenocarcinoma.
Effect of Carbohydrates on the Pharmacokinetics of Human Interferon-γ (1993)

Human interferon-gamma (IFN-gamma) has two N-linked glycosylation sites at positions 25 and 97 of the 143-amino-acid-long secretory form. To study the role of glycan residues in the pharmacokinetics of IFN-gamma, we produced recombinant IFN-gamma molecules lacking either one or both of the glycosylation sites (Asn mutated to Gln) by baculovirus expression in insect cells. In addition, we produced the fully glycosylated forms both in insect cells and in human leukocyte cultures. Two million units of each IFN were injected intravenously or intramuscularly into rabbits. The glycosylated IFN-gamma molecules from the insect cells were rapidly eliminated from the blood. This is probably due to the fact that their oligosaccharides are of a high mannose type that are rapidly taken up by the liver. The unglycosylated IFN-gamma persisted longer in the blood than the glycosylated recombinant forms. However, the natural IFN-gamma exhibited the longest survival in the blood. The results emphasize the importance of the carbohydrate groups in human IFN-gamma to its pharmacokinetic properties.
Evaluation of the use of the luciferase-reporter-gene system for gene-regulation studies involving cyclic AMP-elevating agents (1995)

The effects of cyclic AMP (cAMP)-elevating agents on the activity of cis-acting gene promoter sequences are frequently studied using the luciferase-reporter-gene system. The aim of the present study was to assess whether cAMP-elevating agents induce any changes in the level of luciferase activity independently of a transcriptional activation of promoter elements. Chloramphenicol acteyltransferase (CAT) and luciferase reporter genes under the control of the same promoter elements were transiently expressed in primary cultures of human vascular smooth-muscle cells. Transfected cells were treated with a cell-permeable and non-hydrolysable cAMP analogue, 2'-O-monobutyryl-8-bromo cAMP, or with the cAMP-elevating agents forskolin and prostaglandin E1 (PGE1). Forskolin and PGE1 induced a significant increase in the level of luciferase activity, but had no effect on CAT activity. Conclusions based solely on the use of the luciferase-reporter-gene system in studies involving promoter activation by cAMP-elevating agents could therefore be misleading.
Relative stability of parallel- and anti-parallel-stranded duplex DNA (1988)

We have recently shown that DNA containing homopolymeric A-T base pairs can form a parallel-stranded intramolecular duplex [van de Sande et al. (1988) Science (Washington, D.C.) 241, 551-557]. In the present paper, we demonstrate that parallel-stranded DNA can also be formed in unconstrained bimolecular DNA of appropriate sequence homology. Three deoxyoligonucleotides, a 21-mer [dCCCATATATATTTTTTTTCCC], a ps-15-mer [dTATATATAAAAAAAA], and an aps-15-mer [dAAAAAAAATATATAT], have been synthesized. Annealing of 21-mer and aps-15-mer results in the formation of a conventional antiparallel duplex (aps); however, the combination of 21-mer and ps-15-mer forms a duplex in which the two strands are in a parallel orientation (ps). The parallel-stranded structure was established from the following criteria: (i) The parallel-stranded structure shows a 1:1 stoichiometry of the constituent strands. (ii) Gel electrophoretic mobility of the ps and aps duplexes are similar under native conditions. (iii) Spectroscopic properties of the ps duplex are characteristics for a base-paired structure but are different from the aps structure. (iv) Both duplexes undergo a thermally induced helix to coil transition; however, the melting temperature for the ps duplex is 22 degrees C lower. (v) The minor groove binding drug Hoechst 33258 shows a reduced affinity for the ps compared to the aps duplex. (vi) The parallel-stranded duplex is not a substrate for DNA Escherichia coli polymerase I (Klenow fragment) or AMV reverse transcriptase. Parallel-stranded DNA can exist under normal solution conditions, but competition experiments show it to be thermodynamically less favorable than the conventional antiparallel form.