gebhart/patrepeval huggingface dataset:
Polymyxin and Related Peptide Antibiotics (1977)

The general mechanism for the antibiotic activities of the polymyxins and octapeptins has been elucidated by research using a broad range of experimental techniques. However, this phenomenon has not been described in detailed molecular terms, and this must be one of the major goals for future research in this area. Since 1947, when polymyxin was first isolated, there have been tremendous advances in our knowledge of membrane structure. The application of biophysical technology such as NMR, ESR, fluorescence spectroscopy, differential scanning calorimetry, and electron microscopy has been particularly valuable for studying model and biological membrane structures. It is these techniques which will provide a detailed molecular mechanism for the effects of these peptide antibiotics on membrane structure. In addition, the large number of antibiotic derivatives available should be exploited more extensively for structure-function correlations. The ultimate goal is to correlate the biological properties of these peptides with their effects on the physical properties of membranes and to rationalize these events in terms of lipid-peptide interactions.
Anti-PSCA mAbs inhibit tumor growth and metastasis formation and prolong the survival of mice bearing human prostate cancer xenografts (2001)

Prostate stem-cell antigen (PSCA) is a cell-surface antigen expressed in normal prostate and overexpressed in prostate cancer tissues. PSCA expression is detected in over 80% of patients with local disease, and elevated levels of PSCA are correlated with increased tumor stage, grade, and androgen independence, including high expression in bone metastases. We evaluated the therapeutic efficacy of anti-PSCA mAbs in human prostate cancer xenograft mouse models by using the androgen-dependent LAPC-9 xenograft and the androgen-independent recombinant cell line PC3-PSCA. Two different anti-PSCA mAbs, 1G8 (IgG1kappa) and 3C5 (IgG2akappa), inhibited formation of s.c. and orthotopic xenograft tumors in a dose-dependent manner. Furthermore, administration of anti-PSCA mAbs led to retardation of established orthotopic tumor growth and inhibition of metastasis to distant sites, resulting in a significant prolongation in the survival of tumor-bearing mice. These studies suggest PSCA as an attractive target for immunotherapy and demonstrate the therapeutic potential of anti-PSCA mAbs for the treatment of local and metastatic prostate cancer.
A simple procedure for isolation of cloning vectors and endogenous plasmids from viridans group streptococci and Staphylococcus aureus (1996)

Isolation of plasmid DNA from viridans group streptococci is difficult, and preparations are often heavily contaminated with chromosomal DNA. We developed a simple protocol to isolate pure plasmid DNA for use in different molecular techniques, including automated sequencing. The protocol is also applicable for plasmid isolation from Staphylococcus aureus. In addition, the protocol allows isolation of pure endogenous plasmids from streptococci and S. aureus.
Purification and characterization of calcitonin receptors in rat kidney membranes by covalent cross‐linking techniques (1986)

We have characterized the binding parameters of renal receptors (Scatchard analysis revealed the presence of two binding sites: site I, Ka1 = 1.29 X 10(9) M-1, number of binding sites = 9.9 X 10(6)/micrograms protein; site II, Ka2 = 0.93 X 10(8) M-1, number of binding sites = 4.27 X 10(8)/micrograms protein) and studied the effect of solubilization. The high-affinity sites are preserved during affinity chromatography and the process results in a 6080-fold purification of those sites. The lower-affinity sites are also preserved but the overall purification factor is about 40% lower than that obtained using molecular sieving. The purification of the renal calcitonin receptor by molecular sieving (Sephacryl S-200) is accompanied by total loss of the high-affinity site; however, the low-affinity site is enriched over 1642-fold. Binding parameters were obtained for the purified fractions. Synthetic salmon calcitonin was also bound to renal membranes using the bifunctional reagent disuccinimidyl suberate and photo-affinity cross-linking using hydroxysuccinimidyl azidobenzonate reagent. Cross-linked receptor eluted in the same volume as solubilized membranes specifically binding salmon calcitonin (S-200 chromatography). Sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis of purified fractions showed several protein bands with apparent molecular masses ranging from 18 000 Da to 100 000 Da in the presence or absence of a reducing agent (2-mercaptoethanol). Autoradiography of polyacrylamide gels of cross-linked calcitonin receptor showed only three protein bands specifically binding salmon calcitonin. Their molecular masses were 70 000 Da, 40 000 Da and 33 000 Da respectively. The 40 000-Da molecule represents a major band (47% total binding species). This suggests that these three proteins are the principal components of the calcitonin receptor and that S-S bonds are not involved in the assembly of the receptor subunits.
Immunostimulatory DNA as a vaccine adjuvant (2007)

Immunostimulatory DNA containing unmethylated CpG motifs is recognized by Toll-like receptor 9, resulting in the activation of innate immune responses that subsequently amplify the adaptive-immune response. Advances in the characterization of Toll-like receptor 9 signaling have identified immunostimulatory sequences (ISS) with distinct biological activities. Numerous animal models have demonstrated that synthetic ISS are effective adjuvants that enhance both humoral and cellular immune responses in diverse indications, ranging from infectious disease to cancer and allergy. An added benefit supporting the use of ISS as a vaccine adjuvant is that the specific activation of a pathway critical to the regulation of the immune response results in minimal toxicity. To date, clinical testing has largely affirmed the potency and safety of ISS-adjuvanted vaccines.
Regiocontrolled Synthesis of Carbocycle-Fused Indoles via Arylation of Silyl Enol Ethers with o-Nitrophenylphenyliodonium Fluoride (1999)

[formula: see text] A new, regiocontrolled synthesis of carbocycle-fused indoles has been developed. The two-step procedure involves first the regiospecific arylation of silyl enol ethers with o-nitrophenylphenyliodonium fluoride (1). Reduction of the nitro group on the aromatic ring with TiCl3 followed by spontaneous condensation of the aniline with the ketone then affords the indole products.
Electronic structure of metalloporphyrins. 1. Experimental electron density distribution of (meso-tetraphenylporphinato)cobalt(II) (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectronic structure of metalloporphyrins. 1. Experimental electron density distribution of (meso-tetraphenylporphinato)cobalt(II)Edwin D. StevensCite this: J. Am. Chem. Soc. 1981, 103, 17, 5087–5095Publication Date (Print):August 1, 1981Publication History Published online1 May 2002Published inissue 1 August 1981https://pubs.acs.org/doi/10.1021/ja00407a023https://doi.org/10.1021/ja00407a023research-articleACS PublicationsRequest reuse permissionsArticle Views315Altmetric-Citations39LEARN 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 (1)»Supporting Information Supporting Information Get e-Alerts
Molecular engineering: applications to the clinical laboratory (1993)

Advances in cellular and molecular biology methods have led to the molecular engineering of novel human biomolecules, some of which have been successfully applied to the documentation of clinical laboratory assays. Here I describe the use of engineered chimeric antibodies in the clinical immunology laboratory in three principal applications: (a) as reference proteins to document the specificity of clinical assay reagents, be used as reagent-grade purified antigens, and facilitate the epitope mapping of antibody reagents; (b) as calibration proteins to assign mass/volume estimates to proposed antibody standards; and (c) as interference proteins to study the effects of naturally occurring autoantibodies on the accuracy and sensitivity of current clinical assays. The model recombinant proteins used for these illustrations are chimeric antibodies with a defined V-region specificity for one of two haptens (nitrophenyl or dansyl) and C-region domains covering a spectrum of human isotypes. I also describe a panel of mutant human IgG1-4 anti-dansyl chimeric antibodies that have been genetically engineered with swapped, deleted, or point-mutated wild-type C-region exons and used as specialized reagents for mapping the epitopes to which clinically used human IgG-specific monoclonal antibodies bind. Finally, the use of a recombinant human IgG1 anti-human IgE Fc chimeric antibody to simulate human IgG anti-IgE autoantibody interference in assays of total serum IgE is investigated.
Melanoma growth stimulatory activity enhances the phosphorylation of the class II interleukin-8 receptor in non-hematopoietic cells. (1994)

The class II IL-8 receptor (IL-8R) binds both melanoma growth stimulatory activity (MGSA) and IL-8 with high affinity. Reverse transcriptase polymerase chain reaction demonstrates that the class II IL-8R mRNA, which has previously been detected only in cells of hematopoietic lineage, is also expressed in non-hematopoietic cell types shown to respond to MGSA or IL-8. To study the signaling mechanism by MGSA through the class II IL-8R in non-hematopoietic cells, this receptor was overexpressed in the 3ASubE human placental and the 293 human kidney cell lines. Membrane preparations of the class II IL-8R expressing 3ASubE transfectants exhibited a 2.3 +/- 0.2-fold increase in GTP gamma 35S binding, which was sensitive to pertussis toxin, in response to MGSA treatment (0.2 microM). This MGSA response was not observed in cells transfected with the parental expression vector. In vivo phosphorylation studies demonstrated that the class II IL-8R was basally phosphorylated in the untreated transfectants, and MGSA (5 nM) treatment markedly enhanced the phosphorylation of this receptor. The MGSA-induced receptor phosphorylation was both time and concentration dependent and could be mimicked by treatment with the calcium ionophore A23187. Phosphoamino acid analysis indicated that the MGSA-induced receptor phosphorylation was on serine residue(s), suggesting that a serine kinase is activated in response to MGSA binding to the class II IL-8R in non-hematopoietic cells.
Janus Kinases Affect Thrombopoietin Receptor Cell Surface Localization and Stability (2005)

The thrombopoietin receptor (TpoR) regulates hematopoietic stem cell renewal, megakaryocyte differentiation, and platelet formation. TpoR signals by activating Janus kinases JAK2 and Tyk2. Here we show that, in addition to signaling downstream from the activated TpoR, JAK2 and Tyk2 strongly promote cell surface localization and enhance total protein levels of the TpoR. This effect is caused by stabilization of the mature endoglycosidase H-resistant form of the receptor. Confocal microscopy indicates that TpoR colocalizes partially with recycling transferrin in Ba/F3 cells. The interaction with JAK2 or Tyk2 appears to protect the receptor from proteasome degradation. Sequences encompassing Box1 and Box2 regions of the receptor cytosolic domain and an intact JAK2 or Tyk2 FERM domain are required for these effects. We discuss the relevance of our results to the reported defects of TpoR processing in myeloproliferative diseases and to the mechanisms of Tpo signaling and clearance via the TpoR.
Effect of pH and Light on Aggregation and Conformation of an IgG1 mAb (2012)

During the purification process, monoclonal antibodies may be exposed to parts of UV-C (200 to 290 nm), UV-B (290 to 320 nm) and visible light (400 to 760 nm) under a variety of buffer and pH conditions. Together, these conditions can promote both chemical and physical degradation which may result in conformational changes. To examine this possibility, an IgG1 mAb at pH 3.5, 5, and 8 was exposed to UV light at multiple protein concentrations. Exposure to 302 nm light resulted in a pH-dependent formation of high molecular weight species where the degree of oligomerization increased with increasing pH. Characterization by SDS-PAGE under reducing and nonreducing conditions and size exclusion MALS revealed that the predominant species were nonreducible dimeric, trimeric and higher order oligomeric species which occurred through processes other than intermolecular disulfide bond formation. Biophysical characterization by differential scanning calorimetry demonstrated an overall loss of heat capacity suggesting a loss of conformational integrity with light exposure. A decrease in tryptophan fluorescence was paralleled by a significant decrease in the transition temperature measured during heat-induced unfolding following light exposure, also suggesting a significant change in conformational integrity. The observations by fluorescence spectroscopy coincided with pH-dependent changes in the alterations of secondary structure characterized by Fourier transform infrared spectroscopy and far-UV circular dichroism with the most acidic pH showing the greatest degree of change in the β-sheet structure. Exposure to UV light resulted in aggregation with pH-dependent yields decreasing in the order 8.0 > 5.0 > 3.5, while the opposite trend was observed for conformational changes, with pH-dependent extents decreasing in the following order 3.5 > 5.0 > 8.0. These pH-dependent trends suggest that different strategies will be required to stabilize the protein against these modifications during processing.
Cytokines as adjuvants for vaccines: antigen-specific responses differ from polyclonal responses (1995)

The use of cytokines in the administration of vaccines has a unique value in obtaining the appropriate immune response and in ensuring a protective outcome. Earlier studies indicating that cytokines can influence the generation of a particular antibody isotype may represent an oversimplification of a more complex problem. Several studies discussed in this review show that the effect of a given cytokine on the immune response depends on whether one examines the antigen-specific response or the polyclonal response (i.e., total serum immunoglobulins). Further, a balanced regulation of immune responsiveness is important in maintaining homeostasis of the immune system. Consequently, for any vaccine that uses cytokines to boost the response, due consideration must be given to these important variables.
Meta-analysis in asymmetric catalysis. Influence of chelate geometry on the roles of PN chelating ligands (2013)

All X-ray structures of PN ligands forming 6-ring metal complex chelates have been retrieved from the CDS database, and those lacking chelate chirality filtered out. Many of the remainder fit naturally into four main families (PPFA, FcPhox, Phox and Quinap), which have been widely applied to asymmetric catalysis in diverse ways. It is known through experimental observation that certain of these ligand structures are more effective for specific classes of reaction but there has been little by way of explanation for their divergent behaviour. In this paper we examine the wide variation of conformations within individual families of PN complexes in the solid state, establish common features, and make cross-correlations with their effectiveness in specific catalytic asymmetric reactions. The extent of rigidity in the chelate varies widely and yet flexible complexes may be extremely effective in asymmetric catalysis. These observations emphasise the importance of induced fit between reactants and catalyst and militate against over-reliance on rigid lock-and-key models.
G Protein α Subunits Activate Tubulin GTPase and Modulate Microtubule Polymerization Dynamics (1999)

G proteins serve many functions involving the transfer of signals from cell surface receptors to intracellular effector molecules. Considerable evidence suggests that there is an interaction between G proteins and the cytoskeleton. In this report, G protein alpha subunits Gi1alpha, Gsalpha, and Goalpha are shown to activate the GTPase activity of tubulin, inhibit microtubule assembly, and accelerate microtubule dynamics. Gialpha inhibited polymerization of tubulin-GTP into microtubules by 80-90% in the absence of exogenous GTP. Addition of exogenous GTP, but not guanylylimidodiphosphate, which is resistant to hydrolysis, overcame the inhibition. Analysis of the dynamics of individual microtubules by video microscopy demonstrated that Gi1alpha increases the catastrophe frequency, the frequency of transition from growth to shortening. Thus, Galpha may play a role in modulating microtubule dynamic instability, providing a mechanism for the modification of the cytoskeleton by extracellular signals.
Chitosan-based thermosensitive hydrogel as a promising ocular drug delivery system: Preparation, characterization, andin vivoevaluation (2011)

The purpose of this study was to evaluate the feasibility of in situ thermosensitive hydrogel based on chitosan in combination with disodium α-d-Glucose 1-phosphate (DGP) for ocular drug delivery system. Aqueous solution of chitosan/DGP underwent sol-gel transition as temperature increased which was flowing sol at room temperature and then turned into non-flowing hydrogel at physiological temperature. The properties of gels were characterized regarding gelation time, gelation temperature, and morphology. The sol-to-gel phase transition behaviors were affected by the concentrations of chitosan, DGP and the model drug levocetirizine dihydrochloride (LD). The developed hydrogel presented a characteristic of a rapid release at the initial period followed by a sustained release and remarkably enhanced the cornea penetration of LD. The results of ocular irritation demonstrated the excellent ocular tolerance of the hydrogel. The ocular residence time for the hydrogel was significantly prolonged compared with eye drops. The drug-loaded hydrogel produced more effective anti-allergic conjunctivitis effects compared with LD aqueous solution. These results showed that the chitosan/DGP thermosensitive hydrogel could be used as an ideal ocular drug delivery system in terms of the suitable sol-gel transition temperature, mild pH environment in the hydrogel as well as the organic solvent free.
Future basic science directions into mechanisms of neuropathic pain. (2004)

The aim of this article is to outline mechanisms underlying generation and maintenance of pain arising from trauma to peripheral nerve fibers and to present an overview of our recent studies of animal models of peripheral neuropathic pain and pain of temporomandibular disorders (TMD). The former model was induced by placing a polyethylene cuff around the sciatic nerve of the Sprague-Dawley rat and the TMD model was induced by injection of complete Freund's adjuvant into the rat's temporomandibular joint. In cuff-implanted rats, ongoing activity of dorsal horn neurons was greater than in controls, the cutaneous receptive field size of the neurons was greater, and both noxious and innocuous mechanical stimuli to the receptive field elicited an excitatory response during stimulation but also a marked afterdischarge that lasted up to 30 minutes; this afterdischarge was never observed in control rats in response to innocuous stimulation. The model of TMD was characterized by joint space narrowing, bone remodeling, infiltration of immune cells, loss in the range of jaw opening, and signs of nociception. Alterations in the neural substrate of nociception in animal models, and therefore also possibly in humans, appear to include changes in peripheral as well as central neurons. In the periphery, changes include alterations in the phenotype and central projections of large-diameter sensory nerve fibers. At the level of the trigeminal brainstem and spinal cord, there appear to be several types of change. One type is an increased efficacy of synaptic transmission onto second-order neurons. Another type of change is a reduction in inhibitory mechanisms, including a shift of gamma-amino butyric acid (GABAA) receptor activation to excitation. There is a need for further studies to focus on mechanisms for either the generation or the maintenance, or both, of neuropathic pain.
Genetic Analysis of DNA Excreted in Urine: A New Approach for Detecting Specific Genomic DNA Sequences from Cells Dying in an Organism (2000)

The data suggest that the kidney barrier in rodents and humans is permeable to DNA molecules large enough to be analyzed by standard genetic methodologies.
Triple-stage pentaquadrupole (QqQqQ) mass spectrometry and ion/molecule reactions (1997)

The general concepts, advantages, and applications of pentaquadrupole mass spectrometry and of a variety of pentaquadrupole multidimensional triple-stage (MS3) scans as applied to the study of gas-phase ion/molecule reactions are reviewed. An overview is presented of the development and the present stage of triple-stage pentaquadrupole mass spectrometry, and examples of successful applications of “QqQqQ-MS” in revealing, elucidating, and helping to consolidate new classes of gas-phase ion/molecule reactions are summarized. The variety of features and advantages that make pentaquadrupoles most suitable laboratories for studies of ion/molecule reactions, and the exceptional gains in chemical information and selectivity of QqQqQ-MS are also discussed. © 1997 John Wiley & Sons, Inc., Mass Spectrom Rev 16(3), 113–144, 1997
Route-Based Control of Hybrid Electric Vehicles (2008)

&lt;div class="htmlview paragraph"&gt;Today's hybrid electric vehicle (HEV) controls do not necessarily provide maximum fuel savings over all drive cycles. An approach that employs route-based control could improve HEV efficiency at potentially minimal additional cost. This paper evaluates a range of route-based control approaches and identifies look-ahead strategies (using input from “on-the-fly” route predictions) as an area meriting further analysis. A novel implementation approach is developed and discussed, and a comparison with simulation results using an optimized general control setting indicates that fuel savings of approximately 2% to 4% can be obtained with route-based control. Given the increasing prevalence of GPS systems in vehicles, this advance has the potential to provide considerable aggregate fuel savings if applied across the entire national fleet. For instance, a 3% across-the-board reduction in HEV fuel use would save nearly 6.5 million gallons of fuel annually in the United States. These estimated savings will increase further as HEVs achieve greater market penetration.&lt;/div&gt;
Hydrogels: their future, Part I. (1998)

A multitude of new materials with diverse properties can be made from poly(ethylene oxide). Part I of this two-part article described the range of biomaterial syntheses, properties and applications that can be obtained. The production of a novel class of responsive hydrogels for transducing and sensing applications is reviewed in Part II.