gebhart/patrepeval huggingface dataset:
Characterization of genetically inactivated pertussis toxin mutants: candidates for a new vaccine against whooping cough (1990)

the introduction of two amino acid substitutions within the enzymatically active subunit S1 of pertussis toxin (PT) abolishes its ADP-ribosyltransferase activity and toxicity on CHO cells (Pizza et al., Science 246:497-500, 1989). These genetically inactivated molecules are also devoid of other in vivo adverse reactions typical of PT, such as induction of leukocytosis, potentiation of anaphylaxis, stimulation of insulin secretion, and histamine sensitivity. However, the mutant PT molecules are indistinguishable from wild-type PT in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and maintain all the physical and chemical properties of PT, including affinity for toxin-neutralizing poly- and monoclonal antibodies. Either alone or stabilized with formaldehyde, PT mutants are able to induce high levels of neutralizing antibodies and to protect mice in a dose-dependent fashion against intracerebral challenge with virulent B. pertussis. These results clearly show that these genetically inactivated PT molecules are nontoxic but still immunogenic and justify their development as a component of a new, safer acellular vaccine against whooping cough.
Accuracy Evaluation of Intra-Oral Optical Impressions: A Novel Approach (2019)

Objective: To compare the accuracy (trueness and precision) of optical and conventional impressions in-vivo. Materials and Methods: Five study participants were consented and enrolled. For each participant, optical (CEREC Omnicam; Dentsply Sirona, Charlotte, USA ) and conventional (vinylsiloxanether; Identium, Kettenbach, Huntington Beach, USA ) impressions of a custom-made intra-oral Co-Cr alloy reference appliance fitted to the mandibular arch were obtained. 3D digital models were created for stone models obtained from the conventional impression group and for the reference appliances using a validated high accuracy reference scanner (Infinite focus standard; Alicona Corporation, Bartlett, USA). For the optical impression group, 3D digital models were obtained directly from the intraoral scans. Total mean trueness of each impression system was calculated by superimposing the 3D models and averaging the mean absolute deviations of the impression replicates from their 3D reference model for each participant followed by averaging the obtained values across all participants. Total mean precision for each impression system was calculated by superimposing the 3D models and averaging the mean absolute deviations between all the impression replicates for each participant (10 pairs) followed by averaging the obtained values across all participants. Data were analyzed using repeated measures ANOVA at a 0.05 significance level. Results: Optical impressions had significantly lower mean trueness and precision (46.2 ± 11.4 µm and 61.1 ± 4.9 µm, respectively) than those for conventional impressions (17.0 ± 6.6 µm and 16.9 ± 5.8 µm, respectively), suggesting higher accuracy for conventional impressions. Conclusion: Within the limitations of this study, full-arch (first molar-first molar) optical impressions are less accurate than conventional impressions, but might exhibit enough accuracy for quadrant impressions.
Production and purification of recombinant human interleukin‐5 from yeast and baculovirus expression systems (1991)

A cDNA for human interleukin-5 (hIL-5) was created from the hIL-5 gene using site-directed mutagenesis to splice out the introns in vitro. This cDNA was expressed in yeast and baculovirus systems, utilizing in both cases an in-frame fusion to the pre sequence of the alpha-mating-type factor to direct secretion. The highest level of production was achieved from Sf9 cells using a baculovirus vector in serum-containing medium (2.7 mg/l), whereas in serum-free medium ten times less hIL-5 was produced. In the yeast system much lower levels of hIL-5 were produced (12.5 micrograms/l). Recombinant hIL-5 was purified to homogeneity from serum-free baculovirus cultures. The rhIL-5 consisted of a 30-kDa homodimer linked by disulfide bridging. The purified recombinant protein had a specific activity on murine BCL1 cells of 1.5 x 10(4) U/mg, of 3 x 10(5) U/mg in the murine eosinophil differentiation factor assay, and 2.4 x 10(7) U/mg in a human peripheral eosinophil maintenance assay.
Angiosuppressive and angiostimulatory effects exerted by synthetic partial sequences of endostatin. (2003)

In view of these results, which show strikingly distinct profiles of endostatin fragments, we propose that the amino acid sequence of endostatin contains both angiosuppressive and angiostimulatory domains.
CXCR4 nanobodies (VHH-based single variable domains) potently inhibit chemotaxis and HIV-1 replication and mobilize stem cells (2010)

The important family of G protein-coupled receptors has so far not been targeted very successfully with conventional monoclonal antibodies. Here we report the isolation and characterization of functional VHH-based immunoglobulin single variable domains (or nanobodies) against the chemokine receptor CXCR4. Two highly selective monovalent nanobodies, 238D2 and 238D4, were obtained using a time-efficient whole cell immunization, phage display, and counterselection method. The highly selective VHH-based immunoglobulin single variable domains competitively inhibited the CXCR4-mediated signaling and antagonized the chemoattractant effect of the CXCR4 ligand CXCL12. Epitope mapping showed that the two nanobodies bind to distinct but partially overlapping sites in the extracellular loops. Short peptide linkage of 238D2 with 238D4 resulted in significantly increased affinity for CXCR4 and picomolar activity in antichemotactic assays. Interestingly, the monovalent nanobodies behaved as neutral antagonists, whereas the biparatopic nanobodies acted as inverse agonists at the constitutively active CXCR4-N3.35A. The CXCR4 nanobodies displayed strong antiretroviral activity against T cell-tropic and dual-tropic HIV-1 strains. Moreover, the biparatopic nanobody effectively mobilized CD34-positive stem cells in cynomolgus monkeys. Thus, the nanobody platform may be highly effective at generating extremely potent and selective G protein-coupled receptor modulators.
Recombinant proteins for genetic disease (1999)

The era of molecular biology has led to the development of powerful tools capable of generating therapeutics for genetic disorders. Although there is much current emphasis placed on the development of 'gene therapy' for human disease, developments in the production and availability of recombinant proteins are likely to have a more substantial impact on genetic disease in the short term. The clinical evaluation of recombinant or purified proteins serves as an initial 'proof of principle' of gene-based therapies and thus should expedite advances in this area. Current examples include the use of bovine adenosine deaminase for a form of severe combined immune deficiency (SCID) (Hilman BC, Sorensen RU. Management options: SCIDS with adenosine deaminase deficiency. Ann Allergy 72: 1994: 395-403) and glucocerebrosidase for Gaucher disease (Niederau C, vom Dahl S, Haussinger D. First long-term results of imiglucerase therapy of type 1 Gaucher disease. Eur J Med Res 1998: 3: 25-30). The success of these two enzyme replacement regimes in human clinical trials has been a main impetus for the development of gene-based therapies for these disorders. The 'molecularization of medicine' has led to a more thorough understanding of the molecular basis of disease and disease pathogenesis. The availability of recombinant proteins and the development of appropriate delivery systems will result in more widespread use of these agents. Protein engineering will generate agents with novel functions as is already witnessed with the generation of fusion proteins. This review will highlight advances in the use of recombinant proteins for genetic disease and future potential uses of recombinant proteins.
Cell‐free production of transducible transcription factors for nuclear reprogramming (2009)

Ectopic expression of a defined set of transcription factors chosen from Oct3/4, Sox2, c-Myc, Klf4, Nanog, and Lin28 can directly reprogram somatic cells to pluripotency. These reprogrammed cells are referred to as induced pluripotent stem cells (iPSCs). To date, iPSCs have been successfully generated using lentiviruses, retroviruses, adenoviruses, plasmids, transposons, and recombinant proteins. Nucleic acid-based approaches raise concerns about genomic instability. In contrast, a protein-based approach for iPSC generation can avoid DNA integration concerns as well as provide greater control over the concentration, timing, and sequence of transcription factor stimulation. Researchers recently demonstrated that polyarginine peptide conjugation can deliver recombinant protein reprogramming factor (RF) cargoes into cells and reprogram somatic cells into iPSCs. However, the protein-based approach requires a significant amount of protein for the reprogramming process. Producing fusion RFs in the large amounts required for this approach using traditional heterologous in vivo production methods is difficult and cumbersome since toxicity, product aggregation, and proteolysis by endogenous proteases limit yields. In this work, we show that cell-free protein synthesis (CFPS) is a viable option for producing soluble and functional transducible transcription factors for nuclear reprogramming. We used an E. coli-based CFPS system to express the above set of six human RFs as fusion proteins, each with a nona-arginine (R9) protein transduction domain. Using the flexibility offered by the CFPS platform, we successfully addressed proteolysis and protein solubility problems to produce full-length and soluble R9-RF fusions. We subsequently showed that R9-Oct3/4, R9-Sox2, and R9-Nanog exhibit cognate DNA-binding activities, R9-Nanog translocates across the plasma and nuclear membranes, and R9-Sox2 exerts transcriptional activity on a known downstream gene target.
Isolation of Rhizobium loti Strain-Specific DNA Sequences by Subtraction Hybridization (1988)

Mixed-phase (heterogeneous) and single-phase (homogeneous) DNA subtraction-hybridization methods were used to isolate specific DNA probes for closely related Rhizobium loti strains. In the heterogeneous method, DNA from the prospective probe strain was repeatedly hybridized to a mixture of DNA from cross-hybridizing strains (subtracter DNA) which was immobilized on an epoxy-activated cellulose matrix. Probe strain sequences which shared homology with the matrix-bound subtracter DNA hybridized to it, leaving unique probe strain sequences in the mobile phase. In the homogeneous method, probe strain sequences were hybridized in solution to biotinylated, mercurated subtracter DNA. Biotinylated, mercurated subtracer DNA and probe strain sequences hybridized to it were removed by two-step affinity chromatography on streptavidin-agarose and thiol-Sepharose. The specificity of the sequences remaining after subtraction hybridization by both methods was assessed and compared by colony hybridization with R. loti strains. Both methods allowed the rapid isolation of strain-specific DNA fragments which were suitable for use as probes.
An Extremely Active Solid Acid Catalyst, Nafion Resin/Silica Composite, for the Friedel−Crafts Benzylation of Benzene and p-Xylene with Benzyl Alcohol (1997)

Nafion resin, a recently developed Nafion resin/silica composite, and triflic acid are very effective catalysts for the Friedel−Crafts benzylation of benzene (at 80 °C) and p-xylene (at 100 °C) with p-methylbenzyl alcohol under ambient pressure. The composite is nearly 2 orders of magnitude more active than plain Nafion resin beads and even more active than the strong triflic acid based on the same amount of acid groups in the catalysts. The commercial Amberlyst-15 resin catalyst and p-toluenesulfonic acid (p-TSA) are inactive catalysts. Flowing nitrogen through the reactor to carry out the byproduct water was found to be very beneficial for driving the benzylation reaction to completion.
A Case of Autoimmune Progesterone Dermatitis Misdiagnosed as Allergic Contact Dermatitis (2011)

Autoimmune progesterone dermatitis is a rare autoimmune response to endogenous progesterone that usually occurs in fertile females. Cutaneous or mucosal lesions develop cyclically during the luteal phase of the menstrual cycle when progesterone levels are elevated. Symptoms usually start 3-10 days before menstruation and resolve 1-2 days after menstruation ceases. We report the case of a 48-year-old woman with intermittent eczematous skin lesions of the legs, forearms, and buttocks. She was diagnosed with allergic contact dermatitis, and topical steroids were prescribed. Her skin eruptions waxed and waned for 6 years and were associated with her menstrual cycle. We performed an intradermal test using progesterone, which was positive, and prescribed gonadotropin-releasing hormone analogues monthly for 3 months. The patient's skin lesions improved, confirming the diagnosis. Autoimmune progesterone dermatitis should be included in the differential diagnosis of recurrent eczema that is refractory to treatment in women of child-bearing age.
Micelles based on AB block copolymers of poly(ethylene oxide) and poly(.beta.-benzyl L-aspartate) (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMicelles based on AB block copolymers of poly(ethylene oxide) and poly(.beta.-benzyl L-aspartate)G. Kwon, M. Naito, M. Yokoyama, T. Okano, Y. Sakurai, and K. KataokaCite this: Langmuir 1993, 9, 4, 945–949Publication Date (Print):April 1, 1993Publication History Published online1 May 2002Published inissue 1 April 1993https://pubs.acs.org/doi/10.1021/la00028a012https://doi.org/10.1021/la00028a012research-articleACS PublicationsRequest reuse permissionsArticle Views1782Altmetric-Citations369LEARN 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 87-kDa protein, a major specific substrate for protein kinase C: purification from bovine brain and characterization. (1987)

The 87-kDa protein, a major specific substrate for protein kinase C, has been purified 500-fold to apparent homogeneity from bovine forebrain supernatant. The purification procedure included batch adsorption to DE-52 (DEAE-cellulose), (NH4)2SO4 precipitation, and chromatography on DEAE-Sephacel, Bio-Gel HTP (hydroxylapatite), Sephacryl S-400, and fast protein liquid chromatography ProRPC. The amino acid composition was notable for its high proportion of alanine (28.6 mol%) and its enrichment in glutamate/glutamine (18.1 mol%), glycine (12.6 mol%), and proline (11.3 mol%). The partial specific volume was 0.702 ml/g; the Stokes radius and sedimentation coefficient were 85 A and 2.11 S, respectively. Although the relative molecular mass of the protein on NaDodSO4/8% PAGE was 87-90 kDa, the molecular mass as determined from the above values was 68 kDa. The frictional ratio was 3.2, and the axial ratio was 60, indicating that the 87-kDa protein is an extremely elongated monomer. The purified 87-kDa protein was phosphorylated by purified protein kinase C to a stoichiometry of 2.2 mol of 32P per mol of 87-kDa protein (calculated using a value of 68 kDa for the molecular mass). Phosphorylation was exclusively on serine residues.
Mechanical and Electrical Responses of the Squid Giant Axon to Simple Elongation (1993)

There is a limited amount of information available on the mechanical and functional response of the nervous system to loading. While deformation of cerebral, spinal, or peripheral nerve tissue can have particularly severe consequences, most research in this area has concentrated on either demonstrating in-vivo functional changes and disclosing the effected anatomical pathways, or describing material deformations of the composite structure. Although such studies have successfully produced repeatable traumas, they have not addressed the mechanisms of these mechanically induced injuries. Therefore, a single cell model is required in order to gain further understanding of this complex phenomena. An isolated squid giant axon was subjected to controlled uniaxial loading and its mechanical and physiological responses were monitored with an instrument specifically designed for these experiments. These results determined that the mechanical properties of the isolated axon are similar to those of other soft tissues, and include features such as a nonlinear load-deflection curve and a hysteresis loop upon unloading. The mechanical response was modeled with the quasi-linear viscoelastic theory (Fung, 1972). The physiological response of the axon to quasi-static loading was a small reversible hyperpolarization; however, as the rate of loading was increased, the axon depolarized and the magnitude and the time needed to recover to the original resting potential increased in a nonlinear fashion. At elongations greater than twenty percent an irreversible injury occurs and the membrane potential does not completely recover to baseline.
Effect of monophosphoryl lipid A on host resistance to bacterial infection (1986)

The ability of monophosphoryl lipid A (MPLA) to enhance nonspecific host resistance to bacterial infections was studied. Mice were treated with MPLA prior to intraperitoneal challenge with Escherichia coli or Staphylococcus epidermidis. Animals received additional MPLA for 2 days postinfection, and survival rates were determined. Ten micrograms of MPLA per mouse significantly improved the survival of animals infected with either bacterial species. Dose-response studies showed significant MPLA-induced protection at doses of 6 micrograms/kg against E. coli challenge and 60 micrograms/kg against S. epidermidis challenge.
THE EFFECTIVENESS OF AUDITORY SIDE- AND FORWARD-COLLISION AVOIDANCE WARNINGS IN WINTER DRIVING CONDITIONS (2003)

Because the snowplow operator's tasks are predominately visual, warnings presented visually may interfere with critical tasks. Auditory warnings could reduce visual load if they are meaningful, effectively signal danger, and are not annoying. We conducted a driving simulation experiment and a field test to investigate using auditory icons as side- and forward-collision avoidance warnings. Participants in the experiment drove on simulated snow-covered roads in 105-meter (344 feet) visibility conditions. Analysis of data from 28 participants showed the side-collision avoidance warnings were equally effective; lane change response times were approximately 1.1 seconds for both a single- and double-beep car horn warning, although participants said the double-beep warning sounded more urgent. Analysis of the forward-collision avoidance warning data, obtained from 32 participants, showed the mean response time with a warning consisting of two bursts of screeching-tire sounds was significantly faster than with a single screech warning, with both warnings significantly faster than the mean time obtained when no warning was given. The poorest collision outcomes occurred with no warning. Outcomes were better with the single-screech warning, and better still with the double-screech warning (which the participants said sounded more urgent than the single-beep warning). In the field test, six of seven snowplow operators preferred the double-beep side-collision warning. We recommend an auditory icon sounding like the double-beep of a car horn be used as a side-collision avoidance warning and an auditory icon sounding like two successive bursts of screeching tires should be used as a forward-collision avoidance warning.
Co-Complexes of MASP-1 and MASP-2 Associated with the Soluble Pattern-Recognition Molecules Drive Lectin Pathway Activation in a Manner Inhibitable by MAp44 (2013)

The lectin pathway of complement is an integral component of innate immunity. It is activated upon binding of mannan-binding lectin (MBL) or ficolins (H-, L-, and M-ficolin) to suitable ligand patterns on microorganisms. MBL and ficolins are polydisperse homo-oligomeric molecules, found in complexes with MBL-associated serine proteases (MASP-1, -2, and -3) and MBL-associated proteins (MAp19 and MAp44). This scenario is far more complex than the well-defined activation complex of the classical pathway, C1qC1r(2)C1s(2), and the composition of the activating complexes of the lectin pathway is ill defined. We and other investigators recently demonstrated that both MASP-1 and MASP-2 are crucial to lectin pathway activation. MASP-1 transactivates MASP-2 and, although MASP-1 also cleaves C2, MASP-2 cleaves both C4 and C2, allowing formation of the C3 convertase, C4bC2a. Juxtaposition of MASP-1 and MASP-2 during activation must be required for transactivation. We previously presented a possible scenario, which parallels that of the classical pathway, in which MASP-1 and MASP-2 are found together in the same MBL or ficolin complex. In this study, we demonstrate that, although MASPs do not directly form heterodimers, the addition of MBL or ficolins allows the formation of MASP-1-MASP-2 co-complexes. We find that such co-complexes have a functional role in activating complement and are present in serum at varying levels, impacting on the degree of complement activation. This raises the novel possibility that MAp44 may inhibit complement, not simply by brute force displacement of MASP-2 from MBL or ficolins, but by disruption of co-complexes, hence impairing transactivation. We present support for this contention.
Molecular evolutionary genetics of the cattle-adapted serovar Salmonella dublin (1992)

An electrophoretic analysis of allelic variation at 24 enzyme loci among 170 isolates of the serovar Salmonella dublin (serotype 1,9,12[Vi]:g,p:-) identified three electrophoretic types (Du 1, Du 3, and Du 4), marking three closely related clones, one of which (Du 1) is globally distributed and was represented by 95% of the randomly selected isolates. All but 1 of 114 nonmotile isolates of serotype 1,9,12:-:- recovered from cattle and swine in the United States were genotypically Du 1. The virulence capsular polysaccharide (Vi antigen) is confined to clone Du 3, which apparently is limited in distribution to France and Great Britain. For all 29 isolates of Du 3, positive signals were detected when genomic DNA was hybridized with a probe specific for the ViaB region, which contains the structurally determinant genes for the Vi antigen; and 23 of these isolates had been serologically typed as Vi positive. In contrast, all 30 isolates of Du 1 tested with the ViaB probe were negative. These findings strongly suggest that the ViaB genes were recently acquired by S. dublin via horizontal transfer and additive recombination. The clones of S. dublin are closely similar to the globally predominant clone (En 1) of Salmonella enteritidis (serotype 1,9,12:g,m:-) in both multilocus enzyme genotype and nucleotide sequence of the fliC gene encoding phase 1 flagellin. Comparative sequencing of fliC has revealed the molecular genetic basis for expression of the p and m flagellar epitopes by which these serovars are distinguished in the Kauffmann-White serological scheme of classification.