gebhart/patrepeval huggingface dataset:
Measuring Binding of Protein to Gel-Bound Ligands Using Magnetic Levitation (2012)

This paper describes the use of magnetic levitation (MagLev) to measure the association of proteins and ligands. The method starts with diamagnetic gel beads that are functionalized covalently with small molecules (putative ligands). Binding of protein to the ligands within the bead causes a change in the density of the bead. When these beads are suspended in a paramagnetic aqueous buffer and placed between the poles of two NbFeB magnets with like poles facing, the changes in the density of the bead on binding of protein result in changes in the levitation height of the bead that can be used to quantify the amount of protein bound. This paper uses a reaction-diffusion model to examine the physical principles that determine the values of rate and equilibrium constants measured by this system, using the well-defined model system of carbonic anhydrase and aryl sulfonamides. By tuning the experimental protocol, the method is capable of quantifying either the concentration of protein in a solution, or the binding affinities of a protein to several resin-bound small molecules simultaneously. Since this method requires no electricity and only a single piece of inexpensive equipment, it may find use in situations where portability and low cost are important, such as in bioanalysis in resource-limited settings, point-of-care diagnosis, veterinary medicine, and plant pathology. It still has several practical disadvantages. Most notably, the method requires relatively long assay times and cannot be applied to large proteins (>70 kDa), including antibodies. The design and synthesis of beads with improved characteristics (e.g., larger pore size) has the potential to resolve these problems.
Identification of a Chemical Inhibitor of the Oncogenic Transcription Factor Forkhead Box M1 (2006)

The oncogenic transcription factor forkhead box M1 (FoxM1) is overexpressed in a number of different carcinomas, whereas its expression is turned off in terminally differentiated cells. For this reason, FoxM1 is an attractive target for therapeutic intervention in cancer treatment. As a first step toward realizing this goal, in this study, using a high-throughput, cell-based assay system, we screened for and isolated the antibiotic thiazole compound Siomycin A as an inhibitor of FoxM1. Interestingly, we observed that Siomycin A was able to down-regulate the transcriptional activity as well as the protein and mRNA abundance of FoxM1. Consequently, we found that the downstream target genes of FoxM1, such as Cdc25B, Survivin, and CENPB, were repressed. Also, we observed that consistent with earlier reports of FoxM1 inhibition, Siomycin A was able to reduce anchorage-independent growth of cells in soft agar. Furthermore, we found that Siomycin A was able to induce apoptosis selectively in transformed but not normal cells of the same origin. Taken together, our data suggest that FoxM1 inhibitor Siomycin A could represent a useful starting point for the development of anticancer therapeutics.
Cloning and expression of the ponB gene, encoding penicillin-binding protein 1B of Escherichia coli, in heterologous systems (1990)

A fragment from the ponB region of the Escherichia coli chromosome comprising the promoterless sequence encoding penicillin-binding protein 1B (PBP 1B) has been cloned in a broad-host-range expression vector under the control of the kanamycin resistance gene promoter present in the vector. The hybrid plasmid (pJP3) was used to transform appropriate strains of Salmonella typhimurium, Pseudomonas putida, and Pseudomonas aeruginosa. In all instances, the coding sequence was expressed in the heterologous hosts, yielding a product with electrophoretic mobility, protease accessibility, membrane location, and beta-lactam-binding properties identical to those of native PBP 1B in E. coli. These results indicated that PBP 1B of E. coli is compatible with the cytoplasmic membrane environment of unrelated bacterial species and support the idea that interspecific transfer of mutated alleles of genes coding for PBPs could potentially be an efficient spreading mechanism for intrinsic resistance to beta-lactams.
Phosphorylation of Eukaryotic Protein Synthesis Initiation Factor 4E at Ser-209 (1995)

Initiation factor 4E (eIF-4E) binds to the m7GTP-containing cap of eukaryotic mRNA and facilitates the entry of mRNA into the initiation cycle of protein synthesis. eIF-4E is a phosphoprotein, and the phosphorylated form binds to mRNA caps 3-4-fold more tightly than the nonphosphorylated form. A previous study indicated that the major phosphorylation site was Ser-53 (Rychlik, W., Russ, M. A., and Rhoads, R. E. (1987) J. Biol. Chem. 262, 10434-10437). In the present study, we synthesized the phosphopeptide expected to result from tryptic digestion of eIF-4E, O-phosphoseryllysine. Surprisingly, the tryptic and synthetic phosphopeptides did not comigrate electrophoretically. Accordingly, we redetermined the phosphorylation site by isolating a chymotryptic phosphopeptide on reverse phase high performance liquid chromatography. The peptide was sequenced by Edman degradation and corresponded to 198QSHADTATKSGSTTKNRF215. The site of phosphorylation was determined to be Ser-209 by four methods: the increase in the ratio of dehydroalanine to serine derivatives during Edman degradation, the release of 32P, the further digestion of the chymotryptic phosphopeptide with trypsin, Glu-C, and Asp-N, and site-directed mutagenesis of eIF-4E cDNA. The S209A variant was not phosphorylated in a rabbit reticulocyte lysate system, whereas the wild-type, S53A, and S207A variants were. This site falls within the consensus sequence for phosphorylation by protein kinase C.
Oligodeoxyribonucleotides Containing 4‐Aminobenzimidazole in Place of Adenine: Solid‐phase synthesis and base pairing (1995)

Abstract Oligonucleotides containing 4‐aminobenzimidazole 2′‐deoxyribofuranoside (1,3‐dideaza‐2′‐deoxyadenosine; c 1 c 3 A d , 1 ) were synthesized. For this purpose, various NH 2 ‐protecting groups were investigated, and the [(9 H ‐fluoren‐9‐yl)methoxy]carbonyl group was selected for phosphoramidite protection (→ 4c ). Apart from the phosphoramidite 3 , the phosphonate 2 was prepared. Compound 1 was incorporated in a homooligonuclectide as well as in oligomers containing naturally occurring nucleosides. The T m values and the thermodynamic data of various duplexes ( 11 · 10 , 17 · 10 , 18 · 10 ) containing 4‐aminobenzimidazole were determined. Although d[(c 1 c 3 A) 20 ] ( 11 ) does not form a Hoogsteen duplex with d(T 20 ) ( 10 ) as observed with d[(c 1 A) 20 ], it destabilizes the Watson ‐ Crick duplexes to a much smaller extent than it was expected from a bulged loop structure. Apparently, 4‐aminobenz‐imidazole interacts with regular nucleoside residues within a Watson ‐ Crick duplex structure, most likely by vertical stacking. According to the low basicity of the amino group, only weak H‐bonding is expected.
Die Entwicklung der transaktionskostenorientierten Controllingkonzeption (1998)

In diesem Kapitel wird die Konzeption des transaktionskostenorientierten Controlling entwickelt. Die Diskussion traditioneller Controllingauffassungen identifiziert die Anforderungen für die Weiterentwicklung des koordinationsorientierten Controlling. Danach wird das Führungssystem aus institutionenökonomischer Perspektive beleuchtet, bevor die Transaktionskosten als Kriterium für die Führungseffizienz eingeführt werden. Die Vorstellung der transaktionskostenorientierten Controllingkonzeption schließt mit einem Überblick über die Führungsteilsysteme als Objekt des Controlling.
Molecular cloning and expression of a fungal immunomodulatory protein, FIP-fve, from Flammulina velutipes. (1997)

FIP-fve, a fungal immunomodulatory protein, was isolated from the fruiting bodies of the edible mushroom, Flammulina velutipes. FIP-fve was shown to stimulate blast-forming activity of human peripheral blood lymphocytes and gene expression of interleukin-2, interferon-gamma and tumor necrosis factor-alpha. Repeated administration of FIP-fve to mice inhibits the Arthur and systemic anaphylaxis reactions. FIP-fve cDNA was cloned and sequenced, and the amino acid sequence of FIP-fve deduced from the nucleotide sequence is identical to that previously determined by protein sequencing. FIP-fve cDNA was amplified by polymerase chain reaction, ligated into the expression vector, pGEX-2T, and expressed in Escherichia coli as a fusion protein of glutathione S-transferase (GST) and FIP-fve. The GST-FIP-fve fusion protein was soluble, and the yield of recombinant FIP-fve was about 5 mg/L of induced culture. The recombinant FIP-fve was obtained by cleaving the GST-FIP-fve fusion protein with thrombin and purifing to homogeneity. The recombinant FIP-fve had about 50% of the immunomodulatory activity of the native FIP-fve.
Preparation of Pyridine-N-glucuronides of Tobacco-Specific Nitrosamines (2001)

Nicotine and cotinine are metabolized to pyridine-N-glucuronides in humans. This suggests that the analogous metabolites of the carcinogenic nicotine-related nitrosamines N'-nitrosonornicotine (NNN), 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) should also be formed in people exposed to these compounds via tobacco products. We describe the synthesis of the appropriate pyridine-N-glucuronides: pyridyl-N-beta-D-glucopyranuronosyl-N'-nitrosonornicotinium inner salt (NNN-N-Gluc, 8), 4-(methylnitrosamino)-1-(3-pyridyl-N-beta-D-glucopyranuronosyl)-1-butanonium inner salt (NNK-N-Gluc, 9), and 4-(methylnitrosamino)-1-(3-pyridyl-N-beta-D-glucopyranuronosyl)-1-butanolonium inner salt (NNAL-N-Gluc, 10). The starting material, methyl 2,3,4-tri-O-acetyl-1-bromo-1-deoxy-alpha-D-glucopyranuronate (1), is prepared in two steps from glucuronolactone. Reactions of 1 with racemic NNN (2), NNK (3), or racemic NNAL (4) are carried out with no solvent and the crude products are deprotected by treatment with base, giving the desired N-glucuronides 8-10 in 5-7% overall yield after HPLC purification. The N-glucuronides were characterized by (1)H NMR, including COSY and NOESY spectra, and by MS and MS/MS. NNN-N-Gluc exists as a 52:48 ratio of (E)- and (Z)-rotamers, which were partially separated by HPLC. This ratio was surprisingly similar to the (E):(Z) ratio for NNN itself suggesting hydrogen bonding of the (Z)-nitroso oxygen atom to the 2' '-hydroxyl group of the glucuronide moiety. Partial HPLC separations of the (E)- and (Z)-rotamers of NNK-N-Gluc and the (E)- and (Z)-rotamers as well as the (R)- and (S)-diastereomers of NNAL-N-Gluc were also achieved. The standards prepared in this study as well as the HPLC conditions developed for their separation will be important for analysis of these compounds in human urine.
Targeted hypoglossal nerve stimulation for the treatment of obstructive sleep apnea: Six‐month results (2016)

2b Laryngoscope, 126:2618-2623, 2016.
Polymeric human Fc-fusion proteins with modified effector functions (2011)

The success of Fc-fusion bio-therapeutics has spurred the development of other Fc-fusion products for treating and/or vaccinating against a range of diseases. We describe a method to modulate their function by converting them into well-defined stable polymers. This strategy resulted in cylindrical hexameric structures revealed by tapping mode atomic force microscopy (AFM). Polymeric Fc-fusions were significantly less immunogenic than their dimeric or monomeric counterparts, a result partly owing to their reduced ability to interact with critical Fc-receptors. However, in the absence of the fusion partner, polymeric IgG1-Fc molecules were capable of binding selectively to FcγRs, with significantly increased affinity owing to their increased valency, suggesting that these reagents may prove of immediate utility in the development of well-defined replacements for intravenous immunoglobulin (IVIG) therapy. Overall, these findings establish an effective IgG Fc-fusion based polymeric platform with which the therapeutic and vaccination applications of Fc-fusion immune-complexes can now be explored.
Azidothymidine and interferon-alpha in vitro effects on hematopoiesis: protective in vitro activity of IL-1 and GM-CSF. (1995)

Preclinical and clinical studies with an azidothymidine (AZT)/interferon-alpha (IFN-alpha) combination resulted in a marked and synergistic antiretroviral activity. The administration of the two drugs in HIV-seropositive patients affected with Kaposi's sarcoma, however, induced neutropenia, thrombocytopenia, and, in some cases, anemia. A possible means to improve the therapeutic index of AZT and/or IFN-alpha in AIDS patients could be the addition of hematopoietic growth factors. In vitro activity of cytokines on the hematotoxicity of the AZT-IFN-alpha association has not yet been studied. We have performed an in vitro study to evaluate the toxicity of AZT, IFN-alpha, or both on peripheral blood hematopoietic progenitors (CFU-GM and BFU-E) and to assess the activity of interleukin 1 (IL-1), granulocyte-macrophage colony-stimulating factor (GM-CSF), or both in modifying AZT-IFN-alpha hematotoxicity. Results indicate that AZT, IFN-alpha, and combinations of the two have a dose-dependent inhibitory effect on the in vitro growth of peripheral blood hematopoietic progenitors. Combinations of AZT and IFN-alpha inhibited CFU-GM and BFU-E proliferation in an additive manner. Neither IL-1 nor GM-CSF alone was able to induce a significant reduction of AZT-induced damage. Only the addition to the cultures of both cytokines partially curbed the antiproliferative activity of AZT at low dosages.
A case of SUDEP in a patient with Dravet syndrome with SCN1A mutation (2010)

A boy with a clinical history of pharmacologically resistant Dravet syndrome died suddenly after falling asleep. The autopsy concluded that the cause of death was sudden unexpected death in epilepsy (SUDEP). Postmortem molecular analysis of the SCN1A gene by multiplex ligation-dependent probe amplification (MLPA), high-resolution melting curve analysis (HRMCA), and sequencing revealed a frameshift duplication of adenosine at position 504. The incidence of this mutation is discussed as a potential cause of SUDEP.
Detection of herpes simplex virus type 1-encoded RNA by polymerase chain reaction: different pattern of viral RNA detection in latently infected murine trigeminal ganglia following in vitro or in vivo reactivation (1994)

Herpes simplex virus type 1 (HSV-1) establishes latent infection in the sensory ganglia. To investigate the process of reactivation from latency, we used the RNA polymerase chain reaction (RNA-PCR) to detect the expression of several HSV genes. BALB/c mice were inoculated in the anterior ocular chamber with HSV-1 strain KOS and the trigeminal ganglia were examined at least 8 weeks after inoculation. Latency-associated transcripts (LATs) were found in the latently infected ganglia and remained detectable 120 h after explantation. Besides LATs, we detected transcripts for infected cell protein 0 (ICP0) (Vmw110) 24 h after explantation, but RNAs encoding ICP4 (Vmw175), ICP27, thymidine kinase and VP16 (ICP25; Vmw65) remained undetectable for 120 h after explantation. Following in vivo reactivation of HSV-1 by administration of cyclophosphamide and dexamethasone, all viral transcripts including ICP0 RNA became detectable. The RNA-PCR enabled us to detect ICP0 RNA much earlier than has been previously reported in studies using the Northern blot technique and has laid a foundation for further study of viral and cellular transcripts during reactivation. Our results suggest that the process of reactivation of HSV-1 from trigeminal ganglia may be divided into at least two steps: (i) initiation of ICP0 gene transcription and (ii) detectable transcription of the other genes. The second step may be regulated in part by the host immune system, since cyclophosphamide and dexamethasone administration enabled the detection of several viral transcripts.
The role of T cell activation in anti-CD3 x antitumor bispecific antibody therapy. (1994)

Anti-CD3 x antitumor bispecific Ab can retarget T cell mediated lysis in an MHC-independent fashion and prevent tumor growth in animal models. Two bispecific Ab preparations that differ in the presence or absence of Fc were compared in the 38C13 immunocompetent murine lymphoma model to evaluate how functional Fc and T cell activation impact on response to bispecific Ab therapy. Bispecific (bs) IgG contained functional Fc and was purified from hybrid-hybridoma Ab product. Bsf(ab')2 lacked functional Fc, and was genetically constructed using the leucine zipper technique. In vitro, bsF(ab')2 induced tumor cell lysis by activated T cells more effectively than bsIgG. However, bsF(ab')2 failed to induce T cell activation in the absence of tumor cells, and did so more slowly than bsIgG when tumor cells were present. In vivo, bsIgG induced nonspecific T cell activation whereas bsF(ab')2 did not. In therapy experiments, bsIgG inhibited tumor growth in mice although a single dose of bsF(ab')2 had minimal antitumor effect. BsF(ab')2 was capable of preventing tumor growth and improving survival when mice were also treated with T cell activators (IL-2 or staphylococcal enterotoxin B), or given repeated bsF(ab')2 doses. We conclude that therapeutic response to bispecific Ab was not dependent on functional Fc, but did require T cell activation. The use of bifunctional constructs that lack functional Fc therefore allows for separate manipulation of T cell retargeting and T cell activation and deserves further evaluation as a potential immunotherapy for malignancy.
High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays (2009)

Abstract Background A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Results Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. Conclusion MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.
Dipole−Dipole Plasmon Interactions in Gold-on-Polystyrene Composites (2005)

Red-shifting of the optical absorption spectra of aggregates of gold nanoparticles by dipole-dipole interactions is of considerable interest, both for theoretical reasons and because the phenomenon can be potentially exploited in various applications. A convenient and practical way to control the effect is to assemble the aggregated ensemble of n gold nanoparticles on the outer surface of larger dielectric spheres. Here, we show by experiment and calculation how the spectra of these structures can be systematically morphed from that of isolated gold particles, through the regime of broad absorption dominated by particle-particle interactions, and finally to the limiting case of a continuous nanoshell. The experimental data were produced using the process of deposition-precipitation, which provides a facile method to decorate polystyrene microspheres with gold nanoparticles. There is no need for prior functionalization of the microsphere surface in our method of deposition-precipitation. Calculations were carried out using a code based on the discrete dipole approximation (DDA). The spectra were dominated by three effects. These were a peak absorption at about 540 nm produced by the conventional plasmon resonance of spherical gold nanoparticles, a broad absorption in the range 600-900 nm caused by diverse dipole-dipole interactions between particles, which strengthened as the number of attached gold particles increased and finally, when n was large, an absorption peak due to the onset of nanoshell-like resonances. The experimental spectra could be successfully fitted by spectra calculated using combinations of these effects.
Vibrational spectroscopy of the electronically excited state. 5. Time-resolved resonance Raman study of tris(bipyridine)ruthenium(II) and related complexes. Definitive evidence for the "localized" MLCT state (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVibrational spectroscopy of the electronically excited state. 5. Time-resolved resonance Raman study of tris(bipyridine)ruthenium(II) and related complexes. Definitive evidence for the "localized" MLCT statePaul G. Bradley, Nurit Kress, Boyce A. Hornberger, Richard F. Dallinger, and William H. WoodruffCite this: J. Am. Chem. Soc. 1981, 103, 25, 7441–7446Publication Date (Print):December 1, 1981Publication History Published online1 May 2002Published inissue 1 December 1981https://pubs.acs.org/doi/10.1021/ja00415a007https://doi.org/10.1021/ja00415a007research-articleACS PublicationsRequest reuse permissionsArticle Views2063Altmetric-Citations282LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The Alzheimer‐like phosphorylation of tau protein reduces microtubule binding and involves Ser‐Pro and Thr‐Pro motifs (1992)

Tau protein can be transformed into an Alzheimer-like state by phosphorylation with a kinase activity from brain [Biernat et al. (1992) EMBO J. 11, 1593-1597]. Here we show that the phosphorylation at Ser-Pro motifs strongly decreases tau's affinity for microtubules. The major reduction occurs during the first of the three main stages of phosphorylation. The data explain the lower stability of microtubules resulting from the pathological tau phosphorylation.