gebhart/patrepeval huggingface dataset:
Kappa B-specific DNA binding proteins are differentially inhibited by enhancer mutations and biological oxidation. (1991)

Kappa B (kappa B) enhancer binding proteins isolated from the nuclei of activated human T cells produce two distinct nucleoprotein complexes when incubated with the kappa B element from the interleukin-2 receptor-alpha (IL-2R alpha) gene. These two DNA-protein complexes are composed of at least four host proteins (p50, p55, p75, p85), each of which shares structural similarity with the v-rel oncogene product. Nuclear expression of these proteins is induced with distinctly biphasic kinetics following phorbol ester activation of T cells (p55/p75 early and p50/p85 late). DNA-protein crosslinking studies have revealed that the more rapidly migrating B2 complex contains both p50 and p55 while the more slowly migrating B1 complex is composed of p50, p55, p75, and p85. Site-directed mutagenesis of the wild-type IL-2R alpha kappa B enhancer (GGGGAATCTCCC) has revealed that the binding of p50 and p55 (B2 complex) is particularly sensitive to alteration of the 5' triplet of deoxyguanosine residues. In contrast, formation of the B1 complex, reflecting the binding of p75 and p85, critically depends upon the more 3' sequences of this enhancer element. DNA binding by all four of these Rel-related factors is blocked by selective chemical modification of lysine and arginine residues, suggesting that both of these basic amino acids are required for binding to the kappa B element. Similarly, covalent modification of free sulfhydryl groups with diamide (reversible) or N-ethylmaleimide (irreversible) results in a complete loss of DNA binding activity. In contrast, mild oxidation with glucose oxidase selectively inhibits p75 and p85 binding while not blocking p50 and p55 interactions. These findings suggest that reduced cysteine thiols play an important role in the DNA binding activity of this family of Rel-related transcription factors.
Cancer Pain Management (2000)

A revision of the Agency for Health Care Policy and Research Cancer Pain Guidelines is currently underway. The management of pain in cancer patients should include more frequent reassessment of both analgesia and side effects to ensure optimal cancer pain relief.
Localization in disordered superconducting wires with broken spin-rotation symmetry (2005)

Localization and delocalization of noninteracting quasiparticle states in a superconducting wire are reconsidered, for the cases in which spin-rotation symmetry is absent, and time-reversal symmetry is either broken or unbroken; these are referred to as symmetry classes BD and DIII, respectively. We show that, if a continuum limit is taken to obtain a Fokker-Planck (FP) equation for the transfer matrix, as in some previous work, then when there are more than two scattering channels, all terms that break a certain symmetry are lost. It was already known that the resulting FP equation exhibits critical behavior. The additional symmetry is not required by the definition of the symmetry classes; terms that break it arise from non-Gaussian probability distributions, and may be kept in a generalized FP equation. We show that they lead to localization in a long wire. When the wire has more than two scattering channels, these terms are irrelevant at the short distance (diffusive or ballistic) fixed point, but as they are relevant at the long-distance critical fixed point, they are termed dangerously irrelevant. We confirm the results in a supersymmetry approach for class BD, where the additional terms correspond to jumps between the two components of the sigma model target space. We consider the effect of random $\ensuremath{\pi}$ fluxes, which prevent the system localizing. We show that in one dimension the transitions in these two symmetry classes, and also those in the three chiral symmetry classes, all lie in the same universality class.
Multiple types of chimeric germ-line Ig heavy chain transcripts in human B cells: evidence for trans-splicing of human Ig RNA (1996)

Germ-line transcripts from Ig heavy chain loci precede the occurrence of isotype switching and are thought to play an important though still controversial role in Ig class switching. In this study, we employed a reverse transcriptase-PCR approach to detect human chimeric Ig germ-line mRNA transcripts. Multiple types of chimeric Ig germ-line transcripts (Imu-Cepsilon, Iepsilon-Cmu, Imu-Cgamma4, Igamma-Cmu, Igamma-Cepsilon, Iepsilon-Cgamma, and Igamma4-Calpha1 transcripts) were readily detected in human B cells stimulated with IL-4 alone. Sequence analysis revealed that all of these chimeric Ig germ-line transcripts represented the I exons from one Ig locus spliced to the CH exons from another locus by using consensus sequences for splicing donor and acceptor sites, indicating that they were generated through splicing machinery. In the case of stimulation of human resting B cells with IL-4 alone, the chimeric Ig germ-line transcripts are likely derived from a trans-splicing mechanism, as the extensive searching did not find evidence that Ig class-switch recombination had occurred, which alternatively could give rise to chimeric Ig mRNA by mechanisms other than trans-splicing. Similarly, an EBV-transformed gamma2 rearranged B cell line, GM1500, which produces IgG2 and contains both gamma2 productive and epsilon germ-line transcripts, also expressed chimeric germ-line RNA (Iepsilon-Cgamma2) and epsilon-productive transcripts (VDJ-Cepsilon). This line had no further sequential Sgamma2-Sepsilon rearrangements, providing evidence that the productive VDJ-Cepsilon mRNA was derived from a transcriptionally active unrearranged epsilon gene locus by trans-splicing. Taken together, these results provide possible evidence that trans-splicing of germ-line Ig RNA transcripts occurs in human B cells.
Monoclonal Antibody E-13 (M-810) to Human Cytomegalovirus Recognizes an Epitope Encoded by Exon 2 of the Major Immediate Early Gene (1992)

Monoclonal antibody (MAb) E-13 to human cytomegalovirus is used widely for diagnostic and fundamental studies, and has been shown to be directed against an immediate early (IE) protein(s). To determine which viral antigen is detected by MAb E-13, four subfragments from the open reading frame encoded by exons 2, 3 or 4 of IE-1 were cloned in the bacterial expression vector pROS. The resulting fusion proteins contained amino acids 77 to 491 encoded by mainly exon 4, amino acids 25 to 78 encoded by exon 3, amino acids 1 to 85 encoded by exons 2 and 3, and amino acids 1 to 24 encoded by exon 2. The reactivity of MAb E-13 with the fusion proteins was assayed by Western blotting. MAb E-13 was shown to react exclusively with proteins encoded by exon 2 and therefore recognizes IE proteins which contain the N-terminal amino acid sequence encoded by exon 2, namely the major 72K IE protein, the 82K to 86K IE-2 protein and the 52K to 55K IE-2 protein. MAb E-13 can be used to detect both IE-1- and IE-2-encoded proteins, which share the polypeptide encoded by exon 2.
Endothelial cell-matrix interactions: in vitro models of angiogenesis. (1986)

Free accessAbstractFirst published January 1986Endothelial cell-matrix interactions: in vitro models of angiogenesis.J A Madri and B M PrattView all authors and affiliationsVolume 34, Issue 1https://doi.org/10.1177/34.1.2416801
Prime riflessioni sulle società di gestione del risparmio (1998)

In recent years, a growing interest had arisen in hormonal factors in salivary glands. We have investigated the changes in the content of an insulin-like immunoreactive (ILI) compound in the submandibular salivary glands of Sprague Dawley rats during physiological aging, in the range 15 days-27 months. The amount of ILI in the submandibular glands of young adult rats was found to be doubled in the post-natal period until the age of puberty and was maintained in senescence. No significant correlation was found between age-dependent variations in ILI levels of submandibular salivary glands and circulating insulin concentrations, further supporting previous indications that ILI is being synthesized in situ. It is possible that ILI could exert paracrine effects within the glands, as regards the development of other glandular structures during the first months of life, as well as the preservation of glandular function in senescent animals as well.
Impaired immune responses in streptozotocin-induced type I diabetes in mice. Involvement of high glucose (2008)

Summary Diabetes is widely believed to predispose to serious infections. However, the mechanisms linking diabetes and immunosuppression are not well defined. One potential mediator of the altered defence mechanisms is hyperglycaemia. It has been identified as the main factor contributing to the development of diseases associated with diabetes mellitus. In this study we analyse the immune response in diabetes and the direct effect of hyperglycaemia on T and B lymphocyte reactivity. Diabetes induced an early decrease in IgG levels in the secondary response. However, both primary responses against a T-cell-dependent or independent antigen were affected after 6 months of diabetes induction. T- and B- cell proliferation was only decreased at this time. To gain insight into the potential mechanisms involved, we evaluated the influence of hyperglycaemia over the immune response. Pre-incubation of lymph node and spleen cells in a high glucose (HG) containing medium led to a significant time- and dose-dependent decrease in T- and B-cell proliferation. This effect was associated with the presence of HG-derived supernatants. Still viable cells after HG exposition were able to improve their proliferative response when cultured with the mitogen in a fresh standard medium. HG diminished cell viability, increased apoptosis and induced oxidative stress in lymphocytes. These results indicate that HG concentrations can directly affect lymphoid cell growth. An increase in oxidative stress would be implicated in this deleterious effect. The possibility that prolonged exposure to pathologically HG concentrations would result in the immunosuppressive state observed in diabetes is also discussed.
Inhibitors of mammalian target of rapamycin as novel antitumor agents: from bench to clinic. (2002)

Rapamycin and its derivatives, CCI-779 and RAD-001, inhibit the mammalian target of rapamycin (mTOR), downregulating translation of specific mRNAs required for cell cycle progression from G1 to S phase. Preclinically, mTOR inhibitors potently suppress growth and proliferation of numerous tumor cell lines in culture or when grown in mice as xenografts. CCI-779 and RAD-001 are being developed as antitumor drugs and are undergoing clinical trials. Clinically, CCI-779 has shown evidence of antitumor activity but induced relatively mild side effects in patients. Here we discuss potential antitumor mechanisms and resistance mechanisms of mTOR inhibitors, and summarize the current status of these compounds as novel antitumor agents.
Modeling Opportunities in Comparative Oncology for Drug Development (2010)

Successful development of novel cancer drugs depends on well-reasoned scientific drug discovery, rigorous preclinical development, and carefully conceived clinical trials. Failure in any of these steps contributes to poor rates of approval for new drugs to treat cancer. As technological and scientific advances have opened the door to a variety of novel approaches to cancer drug discovery and development, preclinical models that can answer questions about the activity and safety of novel therapies are increasingly necessary. The advance of a drug to clinical trials based on information from preclinical models presupposes that the models convey informative data for future use in human patients with cancer. The study of novel cancer drugs using in vitro models is highly controllable, reproducible, relatively inexpensive, and linked to high throughput. However, these models fail to reproduce many of the complex features of human cancer. Mouse models address some of these limitations but have important biological differences from human cancer. The integration of studies using pet dogs with spontaneously occurring tumors as models in the development path can answer questions not adequately addressed in conventional models and is therefore gaining attention and interest in drug development communities. The study of novel cancer drugs in dogs with naturally occurring tumors allows drug assessment in a cancer that shares many fundamental features with the human cancer condition, and thus provides an opportunity to answer questions that inform the cancer drug development path in ways not possible in more conventional models.
Microwave‐Assisted Synthesis under Continuous‐Flow Conditions (2007)

Abstract Microwave‐assisted chemistry is about to change the art and practice of synthesis performed in many academic and industrial laboratories. One of the major drawbacks of this enabling technology is the difficulty associated with scale‐up. Because of the limited penetration depth of microwaves into absorbing media, the solution to scale‐up lies in continuous‐flow processing. In this review we summarize the current state of the art in this field and present an overview on published examples of microwave‐assisted synthesis using continuous‐flow and stop‐flow processing in custom‐built or commercially available microwave reactors. magnified image
XQuery: An XML query language (2002)

The World Wide Web Consortium has convened a working group to design a query language for Extensible Markup Language (XML) data sources. This new query language, called XQuery, is still evolving and has been described in a series of drafts published by the working group. XQuery is a functional language comprised of several kinds of expressions that can be nested and composed with full generality. It is based on the type system of XML Schema and is designed to be compatible with other XML-related standards. This paper explains the need for an XML query language, provides a tutorial overview of XQuery, and includes several examples of its use.
A 38-kD Mycobacterium tuberculosis antigen associated with infection. Its isolation and serologic evaluation. (1989)

To identify antigens that could be specifically associated with tuberculosis infection, the antibody response to Mycobacterium tuberculosis antigens of patients with pulmonary tuberculosis and of healthy individuals were compared by immunoblot. In healthy individuals, serum antibodies were found in the majority of cases. Bands of 60 and 32-31 kilodaltons (kD) were the antigens more frequently recognized by antibodies of normal sera (55.8 and 64.7%, respectively). In patients with pulmonary tuberculosis, the number and intensity of the developed antigen bands were much higher than in normal individuals. Antigens reacting preferentially with tuberculosis sera were also identified. Furthermore, a unique disease-associated protein antigen of 38 kD was found to react with 57% of patients' sera but with none of the controls. This antigen was isolated by elution from nitrocellulose membranes and tested as an ELISA reagent in the serodiagnosis of pulmonary tuberculosis. A specificity of 0.96 and sensitivity of 0.68 were obtained.
The Effect of Charge and Ionic Strength on the Viscosity of Ribonuclease. (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Effect of Charge and Ionic Strength on the Viscosity of Ribonuclease.John G. Buzzell and Charles TanfordCite this: J. Phys. Chem. 1956, 60, 9, 1204–1207Publication Date (Print):September 1, 1956Publication History Published online1 May 2002Published inissue 1 September 1956https://doi.org/10.1021/j150543a014RIGHTS & PERMISSIONSArticle Views277Altmetric-Citations76LEARN 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 (486 KB) Get e-Alerts
Subunit structure of thrombin-activated porcine factor VIII (1989)

Factor VIII (fVIII) is synthesized as a single chain having a domainal sequence A1-A2-B-A3-C1-C2. Analysis of the proteolyic cleavage of fVIII by thrombin by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) identifies three fragments designated fVIIIA1, fVIIIA2, and fVIIIA3-C1-C2 with fragment(s) derived from the B domain being difficult to visualize. The appearance of these fragments is associated with the development of coagulant activity, but the activity is labile without further apparent proteolysis. In this study, porcine fVIII was reacted with thrombin until peak coagulant activity was obtained and then subjected to cation-exchange (Mono S) high-pressure liquid chromatography. Coagulant activity was recovered in a single peak that contained all three fragments and was stable for weeks at 20 degrees C in 0.65 M NaCl/0.01 M His-HCl/0.005 M CaCl2 at pH 6.0. Analytical ultracentrifugation of activated fVIII was done to test whether all three fragments were associated. The apparent molecular weight of activated fVIII from equilibrium sedimentation increased from 148,000 to 161,000 as the loading concentration was increased from 0.06 to 0.16 mg/mL. This agrees well with the summed apparent molecular weights of fVIIIA1, fVIIIA2, and fVIIIA3-C1-C2 calculated from SDS-PAGE analysis (148,000) or from the amino acid sequence of human fVIII (159,000). This establishes the major species in the preparation as a fVIIIA1/A2/A3-C1-C2 heterotrimer and additionally indicates either weak self-association of the trimer and/or incomplete association of the individual subunits to form the trimer. Velocity sedimentation of activated fViii revealed a single boundry (S020,w = 7.2 S).(ABSTRACT TRUNCATED AT 250 WORDS)
Complete Genome Sequence of Pseudomonas denitrificans ATCC 13867 (2013)

Pseudomonas denitrificans ATCC 13867, a Gram-negative facultative anaerobic bacterium, is known to produce vitamin B12 under aerobic conditions. This paper reports the annotated whole-genome sequence of the circular chromosome of this organism.
Differential expression of p53 and p21 in low grade cervical squamous intraepithelial lesions infected with low, intermediate, and high risk human papillomaviruses (2000)

The authors' data suggest that low, intermediate, and high risk HPVs have different effects on p53 and p21 protein expression, and that the induction of numeric chromosomal abnormalities by intermediate/high risk HPVs may be related to altered expression of p53.
Natural genetic exchange between Haemophilus and Neisseria : Intergeneric transfer of chromosomal genes between major human pathogens (1998)

Members of the bacterial families Haemophilus and Neisseria, important human pathogens that commonly colonize the nasopharynx, are naturally competent for DNA uptake from their environment. In each genus this process is discriminant in favor of its own and against foreign DNA through sequence specificity of DNA receptors. The Haemophilus DNA uptake apparatus binds a 29-bp oligonucleotide domain containing a highly conserved 9-bp core sequence, whereas the neisserial apparatus binds a 10-bp motif. Each motif ("uptake sequence", US) is highly over-represented in the chromosome of the corresponding genus, particularly concentrated with core sequences in inverted pairs forming gene terminators. Two Haemophilus core USs were unexpectedly found forming the terminator of sodC in Neisseria meningitidis (meningococcus), and sequence analysis strongly suggests that this virulence gene, located next to IS1106, arose through horizontal transfer from Haemophilus. By using USs as search strings in a computer-based analysis of genome sequence, it was established that while USs of the "wrong" genus do not occur commonly in Neisseria or Haemophilus, where they do they are highly likely to flag domains of chromosomal DNA that have been transferred from Haemophilus. Three independent domains of Haemophilus-like DNA were found in the meningococcal chromosome, associated respectively with the virulence gene sodC, the bio gene cluster, and an unidentified orf. This report identifies intergenerically transferred DNA and its source in bacteria, and further identifies transformation with heterologous chromosomal DNA as a way of establishing potentially important chromosomal mosaicism in these pathogenic bacteria.
Structural aspects of the hydrolysis of titanium tetraethoxide (1955)

D. C. Bradley, R. Gaze and W. Wardlaw, J. Chem. Soc., 1955, 3977 DOI: 10.1039/JR9550003977
Intein harbouring large tandem repeats in replicative DNA helicase of Trichodesmium erythraeum (2003)

Protein splicing inteins can be small as approximately 130 aa or up to approximately 600 aa when harbouring an endonuclease domain. Here we report the identification and characterization of an unusually large intein, 1650 aa long and the largest of known inteins, encoded by the replicative DNA helicase gene dnaB of the oceanic N2-fixing cyanobacterium Trichodesmium erythraeum. This Ter DnaB-1 intein co-exists with a 177-aa mini-intein in the same host protein and harbours large tandem repeats in which an 84-aa sequence is repeated 16 times. Comparison between this tandem repeats and the recently reported tandem repeats of Ter DnaE-1 intein revealed differences and similarities. The two tandem repeats, residing in different inteins of different host proteins, differ by 50% in size and have little sequence similarity. Tandem repeats in the Ter DnaB-1 intein were required for the protein splicing activity when tested in Escherichia coli, in contrast to tandem repeats of the Ter DnaE-1 intein that inhibited protein splicing. On the other hand, tandem repeats of both inteins are located in the same corresponding region of the intein sequence and have the same number of repeating units. These suggest that the two tandem repeats could be related but have diverged greatly in size, sequence and effect on protein splicing. Alternatively, they could have independent origins but evolved certain similarities because of common constraints in structure and maintenance.
Investigation on Effect of Rainfall on Performance of Soil-Reinforced Regtaining Wall (2003)

This paper presents the two field walls that demonstrate the effect of rainfall on the performance of soil-reinforced retaining wall. A field test wall constructed in Geotechnical Experimental Site at Sungkyunkwan University has been monitored for more than 8 months to study the long-term behavior of soil-reinforced retaining wall. The measured data showed a good correlation between rainfall and wall movement after wall completion. A case of failed soil-reinforced retaining wall also is presented to highlight the effect of rainfall on the performance of soil-reinforced retaining wall. Implications of the findings are discussed.