gebhart/patrepeval huggingface dataset:
Substrate Specificity of the Integral Membrane Protease OmpT Determined by Spatially Addressed Peptide Libraries (2001)

Escherichia coli outer membrane protease T (OmpT) is an endopeptidase that specifically cleaves between two consecutive basic residues. In this study we have investigated the substrate specificity of OmpT using spatially addressed SPOT peptide libraries. The peptide acetyl-Dap(dnp)-Ala-Arg/Arg-Ala-Lys(Abz)-Gly was synthesized directly onto cellulose membrane. The peptide contained the aminobenzoyl (Abz) fluorophore, which was internally quenched by the dinitrophenyl (dnp) moiety. Treatment of the SPOT membrane with the small, water-soluble protease trypsin resulted in highly fluorescent peptide SPOTs. However, no peptide cleavage was observed after incubation with detergent-solubilized OmpT, a macromolecular complex with an estimated molecular mass of 180 kDa. This problem could be solved by the introduction of a long, polar polyoxyethylene glycol linker between the membrane support and the peptide. Peptide libraries for the P(2), P(1), P(1)', and P(2)' positions in the substrate were screened with OmpT, and peptides of positive SPOTs were resynthesized and subjected to kinetic measurements in solution. The best substrate Abz-Ala-Lys-Lys-Ala-Dap(dnp)-Gly had a turnover number k(cat) of 40 s(-)(1), which is 12-fold higher than the starting substrate. Peptides containing an acidic residue at P(2) or P(2)' were not substrates for OmpT, suggesting that long-range electrostatic interactions are important for the formation of the enzyme-substrate complex. OmpT was highly selective toward L-amino acids at P(1) but was less so at P(1)' where a peptide with D-Arg at P(1)' was a competitive inhibitor (K(i) of 19 microM). An affinity chromatography resin based on these findings was developed, which allowed for the one-step purification of OmpT from a bacterial lysate. The implications of the determined consensus substrate sequence (Arg/Lys)/(Arg/Lys)-Ala for the proposed biological function of OmpT in defense against antimicrobial peptides are discussed.
Homeostasis as Regulated by Activated Macrophage. III. Protective Effect of LPSw(Lipopolysaccharide(LPS) of Wheat Flour) on Gastric Ulcer in Mice as Compared with Those of Other LPS from Various Sources. (1992)

Protective effect of lipopolysaccharide (LPS) from various sources on gastric ulcer has been examined in mice using parenteral as well as oral route. Ulcer is induced by indomethacin, stress or alcohol. LPS was prepared from 6 species of bacteria (Escherichia coli, Pantoea agglomerans, Serratia ficaria, Enterobacter cloacae, Bordetella pertussis, Alcaligenes faecalis) and from wheat flour. When administered intravenously, LPS of Pantoea agglomerans was the most effective among other LPS examined. Lipopolysaccharide of wheat flour (LPSw) showed a significantly protective effect by the oral route, especially when given ad libitum in drinking water to mice.
Expression and Purification of the Light Chain of Botulinum Neurotoxin A: A Single Mutation Abolishes Its Cleavage of SNAP-25 and Neurotoxicity after Reconstitution with the Heavy Chain (1995)

Botulinum neurotoxin type A (BoNT/A) selectively and irreversibly inhibits acetylcholine release from peripheral nerve endings. While the toxin's heavy (H) chain contributes to neuronal binding and internalization, its light (L) chain is a Zn(2+)-dependent endoprotease that intracellularly cleaves synaptosomal-associated protein of M(r) = 25 kDa (SNAP-25). For research and clinical exploitation of this uniquely-acting neurotoxin, recombinant wild-type L chain was produced together with a mutant in which His227 in the Zn(2+)-binding motif was substituted by Tyr. The PCR-amplified wild-type and mutant L chain genes were cloned, fused to the gene for maltose-binding protein, and expressed at high levels in Escherichia coli. The soluble fusion proteins were purified using amylose affinity chromatography, and, after factor Xa cleavage, the free L chains were isolated. The wild-type was shown to proteolyze SNAP-25 at a rate approaching that of the native chain while the mutant was inactive. Reconstitution of the pure wild-type L chain with native homogeneous H chain yielded a disulfide-linked dichain form that inhibited neuromuscular transmission in vitro and produced the symptoms of botulism in vivo. After reconstitution with the H chain, the Tyr227 mutant L chain failed to show any neuroparalytic activity in either of these assays. This methodology allows, for the first time, routine preparation of recombinant forms of the L chain that are needed to decipher the molecular details of its interaction with substrate and, thereby, assist the design of effective inhibitors.(ABSTRACT TRUNCATED AT 250 WORDS)
Crystal Structure of Leucotoxin S Component (2004)

Staphylococcal leucocidins and gamma-hemolysins (leucotoxins) are bi-component toxins that form lytic transmembrane pores. Their cytotoxic activities require the synergistic association of a class S component and a class F component, produced as water-soluble monomers that form hetero-oligomeric membrane-associated complexes. Strains that produce the Panton-Valentine leucocidin are clinically associated with cutaneous lesions and community-acquired pneumonia. In a previous study, we determined the crystal structure of the F monomer from the Panton-Valentine leucocidin. To derive information on the second component of the leucotoxins, the x-ray structure of the S protein from the Panton-Valentine leucocidin was solved to 2.0 angstrom resolution using a tetragonal crystal form that contains eight molecules in the asymmetric unit. The structure demonstrates the different conformation of the domain involved in membrane contacts and illustrates sequence and tertiary structure variabilities of the pore-forming leucotoxins. Mutagenesis studies at a key surface residue (Thr-28) further support the important role played by these microheterogeneities for the assembly of the bipartite leucotoxins.
Autocrine growth of Epstein-Barr virus-positive gastric carcinoma cells mediated by an Epstein-Barr virus-encoded small RNA. (2003)

Although 5-10% of gastric carcinoma (GC) cases worldwide are associated with EBV, a human herpesvirus, it is still not clear what the precise contribution of the virus is to the pathogenesis of EBV-positive GC. Here we report that EBV infection induces expression of insulin-like growth factor 1 (IGF-I) in the GC-derived EBV-negative cell line NU-GC-3 and that the secreted IGF-I acts as an autocrine growth factor. Transfection of individual EBV latent genes into NU-GC-3 cells revealed that the EBV-encoded small RNA (EBER) was responsible for IGF-I expression. Addition of recombinant IGF-I accelerated growth of NU-GC-3 cells, whereas growth of the EBV-converted NU-GC-3 cells was blocked by treatment with an anti-IGF-I antibody. These results suggest that IGF-I induced by EBER acts as an autocrine growth factor for EBV-positive GC. These findings seem to be operative in vivo, as EBV-positive GC biopsies consistently express IGF-I, whereas EBV-negative GC biopsies do not. EBER is invariably expressed in EBV-associated malignancies including GC. The present findings strongly suggest that EBV directly affects the pathogenesis of EBV-positive GC and underline the importance of RNA molecules on cell growth regulation.
Research and Development at Universities: Worldwide Change in Petroleum Engineering (2012)

The fundamental properties of hydrocarbons and the basics of drilling will always remain the same. Nevertheless, innovation in petroleum engineering by researchers at universities around the world is changing the face of oil and gas drilling and production in the 21st century. In addition to traditional approaches, technologies for enhanced production from mature fields; production methods for unconventional resources such as tight gas, methane hydrate, and heavy oil; and experimental nanotechnology applications today are critical and increasingly are a part of petroleum engineering research and technology development. Schulich School of Engineering, University of Calgary, Canada The upstream research at Schulich’s Department of Chemical and Petroleum Engineering concentrates on improving the exploitation of Canadian unconventional oil and gas resources such as heavy oil and bitumen, and tight gas formations. The department has a dozen research teams, said professor Brij Maini. The In Situ Combustion Research Group specializes in laboratory and numerical simulation studies of the in-situ combustion of heavy oils, and high-pressure air injection in light oil reservoirs. The faculty’s EnCana/Paleontological Society of Canadian Institute of Mining, Metallurgy, and Petroleum Endowed Chair heads the department’s joint industry project studying the geomechanics of shale gas. The CMG Foundation Chair in Reservoir Simulation is developing fast and reliable reservoir simulators for the recovery of oil, gas, and coal. The NSERC Industrial Research Chair in Heavy Oil Properties and Processing is researching the properties and phase behavior of heavy oil and solvents. Schulich’s SHARP (Solvent/Heat Assisted Recovery Processes) consortium is supported by 11 local and international companies. The improved heavy oil science and technology group is studying various aspects of heavy oil recovery technology, including cold heavy oil production with sand, and solvent-based recovery processes and steam additives for steam injection-based processes.
Anti-Sticking Effect of Organic Dielectric Formed by Electrodeposition in Microelectromechanical-System Structures (2005)

In microelectromechanical-system (MEMS) structures, selective encapsulation with an organic dielectric using electrodeposition can prevent sticking. Selective electrodeposition characteristics were investigated on a gold surface using sulfonium cations with epoxy groups as a source material. We observed an incubation period in the initial stage of the deposition. X-ray photoelectron spectroscopy revealed that the cause of the incubation period is the removal of oxygen adsorbed on the gold surface. Applying this technique to the encapsulation of MEMS structures confirmed the anti-sticking effect between an actuator and a gold electrode selectively coated with an organic dielectric.
Expression of two isoforms of the third sarco/endoplasmic reticulum Ca2+ATPase (SERCA3) in platelets. Possible recognition of the SERCA3b isoform by the PL/IM430 monoclonal antibody1 (1998)

Human platelets express several sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) isoenzymes: SERCA2b of 100 kDa apparent molecular mass and two distinct enzymes of 97 kDa, one of them identified as being the SERCA3a isoform. The molecular identity of the third enzyme specifically recognized by the PL/IM430 monoclonal antibody has remained elusive. First, the study of the 3'-end part of platelet SERCA3 mRNA, by means of RT-PCR amplification using sets of primers covering the N-3 to N (ultimate) exons of the human SERCA3 sequence, revealed the presence of two distinct mRNA sequences, SERCA3a and a longer variant. Second, this additional sequence was identified as SERCA3b and found to refer to the insertion of a new exon of 73 bp, located at bp 349 from the beginning of the intronic sequence, linking the penultimate (N-1) exon to the last exon (N) of the human SERCA3 gene. Third, a relationship between the expression of this SERCA3b mRNA and the PL/ IM430 recognizable SERCA protein was observed. SERCA3b mRNA was found to be absent in epithelial HeLa cells not recognized by the PL/IM430 antibody and the expression of this SERCA3b RNA species correlated with that of the SERCA protein recognized by PL/IM430 which was down-modulated in the platelet precursor megakaryocytic CHRF 288-11 cell line as well as upon in vitro lymphocyte activation. Taken together, these results strongly support the notion of the presence of the SERCA3b protein in human cells by showing SERCA3b mRNA in platelets and the fact that the protein corresponding to this mRNA species is very likely the 97 kDa protein recognized by the PL/IM430 antibody.
Recombinant soluble tumor necrosis factor receptor (p80) fusion protein: toxicity and dose finding trial in refractory rheumatoid arthritis. (1996)

This initial experience with rhTNFR:Fc fusion protein in RA justifies further evaluation of this agent in a larger placebo controlled trial.
Effects of dextran-bound inhibitors on carbonic anhydrase activity in isolated rat lungs (1986)

Effects of macromolecular Prontosil-dextran inhibitors (PD) on carbonic anhydrase (CA) activity in isolated rat lungs were studied. Isolated lungs were perfused with Krebs-Ringer bicarbonate (KRB) solutions containing no inhibitor, PD 100,000 (mol wt 100,000), PD 5,000 (mol wt 5,000), or low-molecular-weight inhibitors (Prontosil or acetazolamide). The time course of effluent perfusate pH equilibration was measured in a stop-flow pH electrode apparatus. Pulmonary CO2 excretion (Vco2) was monitored by continuously recording expired CO2 concentration. The lungs were ventilated with room air and perfused at 37 degrees C with KRB prebubbled with 5% CO2- 20% O2- 75% N2. The results obtained show that both the low-molecular-weight inhibitors and PD's caused postcapillary pH disequilibria (delta pH) in effluent perfusate. However, only acetazolamide and Prontosil caused a reduction in Vco2. These results suggest that there is an intravascular CA, presumably associated with endothelial cell membranes, that is accessible to all inhibitors used and is responsible in part for equilibration of the CO2- HCO3- -H+ reactions in the perfusate but, under the conditions used, does not affect CO2 excretion; and there is an extravascular (possibly intracellular) CA that can be inhibited by low-molecular-weight inhibitors, is primarily responsible for enhanced CO2 transfer across the alveolar-capillary barrier (perhaps via facilitation of CO2 diffusion), and is in part responsible for pH equilibration.
A utility framework for the automatic generation of audio-visual skims (2002)

In this paper, we present a novel algorithm for generating audio-visual skims from computable scenes. Skims are useful for browsing digital libraries, and for on-demand summaries in set-top boxes. A computable scene is a chunk of data that exhibits consistencies with respect to chromaticity, lighting and sound. There are three key aspects to our approach: (a) visual complexity and grammar, (b) robust audio segmentation and (c) an utility model for skim generation. We define a measure of visual complexity of a shot, and map complexity to the minimum time for comprehending the shot. Then, we analyze the underlying visual grammar, since it makes the shot sequence meaningful. We segment the audio data into four classes, and then detect significant phrases in the speech segments. The utility functions are defined in terms of complexity and duration of the segment. The target skim is created using a general constrained utility maximization procedure that maximizes the information content and the coherence of the resulting skim. The objective function is constrained due to multimedia synchronization constraints, visual syntax and by penalty functions on audio and video segments. The user study results indicate that the optimal skims show statistically significant differences with other skims with compression rates up to 90%.
Vero cell technology for rapid development of inactivated whole virus vaccines for emerging viral diseases (2017)

Rapid development and production of vaccines against emerging diseases requires well established, validated, robust technologies to allow industrial scale production and accelerated licensure of products. Areas covered: A versatile Vero cell platform has been developed and utilized to deliver a wide range of candidate and licensed vaccines against emerging viral diseases. This platform builds on the 35 years' experience and safety record with inactivated whole virus vaccines such as polio vaccine. The current platform has been optimized to include a novel double inactivation procedure in order to ensure a highly robust inactivation procedure for novel emerging viruses. The utility of this platform in rapidly developing inactivated whole virus vaccines against pandemic (-like) influenza viruses and other emerging viruses such as West Nile, Chikungunya, Ross River and SARS is reviewed. The potential of the platform for development of vaccines against other emerging viruses such as Zika virus is described. Expert commentary: Use of this platform can substantially accelerate process development and facilitate licensure because of the substantial existing data set available for the cell matrix. However, programs to provide vaccines against emerging diseases must allow alternative clinical development paths to licensure, without the requirement to carry out large scale field efficacy studies.
Active specific immunotherapy with polyvalent melanoma cell vaccine for patients with in‐transit melanoma metastases (1999)

BACKGROUND This study was conducted to document the rate, duration, and type of objective response to active specific immunotherapy with a polyvalent melanoma cell vaccine (PMCV) for patients with in-transit melanoma metastases and to identify any acute or chronic toxic effects of PMCV treatment. METHODS An analysis was conducted of all in-transit melanoma patients seen at the John Wayne Cancer Institute in Santa Monica, California, during the period 1985–1997 who were enrolled in prospective PMCV protocols in the absence of other therapies with possible antitumor activity (n = 54). Clinical response to PMCV was assessed by standard criteria. Survival curves were estimated by the Kaplan–Meier method. Toxicity was graded according to the Eastern Cooperative Oncology Group standard. RESULTS PMCV produced a 17% (9 of 54 patients) objective response rate with a 13% rate (7 of 54 patients) of complete remission (CR). The median duration of CR was >22 months. Complete response lasting more than 1 year was observed in 4 patients (7.2%); 1 patient remained in remission over 9 years. Median survival was >53 months (i.e., not reached) for responders, 42 months for nonresponders, and 53 months overall. Salvage interventions allowed reinduction with PMCV in 23 of 25 patients, who subsequently remained clinically free of disease for a median of 14 months. Overall toxicity was mild, easily tolerable, and did not significantly change the quality of life. There were no toxic deaths. CONCLUSIONS PMCV can cause objective complete regression of measurable in-transit metastatic melanoma with minimal toxicity, and may prolong patients' median survival. Cancer 1999;85:2160–9. © 1999 American Cancer Society.
Electronic Imaging in Neuroscience (2002)

This unit is intended to aid the neuroscientist in understanding the basics of image detectors and selecting a suitable camera for various neuroscience research applications. A procedure is described for evaluating cameras in the laboratory.
A Combinatorial Approach Toward DNA Recognition (1991)

A combinatorial approach has been used to identify individual RNA molecules from a large population of sequences that bind a 16-base pair homopurine-homopyrimidine DNA sequence through triple-helix formation. Fourteen of the seventeen clones selected contained stretches of pyrimidines highly homologous to the target DNA sequence (T.AT and C+.GC). In addition, these RNA molecules contained hairpin loops, interior loops, and nonstandard base triplets [C+(or C).AT, U.GC, G.GC, and A.AT] at various positions. Affinity cleavage experiments confirmed the ability of selected sequences to bind specifically to the target DNA. Systematic variation in both the target DNA sequence and buffer components should provide increased insight into the molecular interactions required for triple-helix-mediated recognition of natural DNA.
A Cineradiographic Study of Breast Feeding (1958)

Cineradiographic films were taken of 41 mothers breast feeding; the mother's nipple and areola were coated with a paste of barium sulphate in lanoline. Our conclusions are:— 1. The nipple is sucked to the back of the baby's mouth and a teat is formed from the mother's breast. 2. When the jaw is raised this teat is compressed between the upper gum and the tip of the tongue resting on the lower gum. The tongue is applied to the lower surface of the teat from before backwards, pressing it against the hard palate: the teat is reduced to approximately half its former width. As the tongue moves towards the posterior edge of the hard palate the teat shortens and becomes thicker. 3. When the jaw is lowered the teat is again sucked to the back of the mouth and restored to its previous size. 4. Each cycle of jaw and tongue movement takes place in approximately 1·5 seconds. The pharyngeal cavity becomes airless and the larynx closed every time the upward movement of the tongue against the teat and hard palate is completed. 5. These movements are analogous to those seen in bottle feeding: they suggest that the contents of the ducts or cisterns of the teat are expressed into the mouth. 6. The influence of suction upon the flow of milk from the teat has not been established. It is considered that suction may be exerted during the phase of compression of the teat as the tongue is simultaneously lowered behind the teat. 7. It is suggested that the teat is formed from the nipple and the adjacent areola and underlying tissues.
The Streptomyces Genome Contains Multiple Pseudo- attB Sites for the φC31-Encoded Site-Specific Recombination System (2002)

The integrase from the Streptomyces phage (phi)C31 is a member of the serine recombinase family of site-specific recombinases and is fundamentally different from that of lambda or its relatives. Moreover, (phi)C31 int/attP is used widely as an essential component of integration vectors (such as pSET152) employed in the genetic analysis of Streptomyces species. phiC31 or integrating plasmids containing int/attP have been shown previously to integrate at a locus, attB, in the chromosome. The DNA sequences of the attB sites of various Streptomyces species revealed nonconserved positions. In particular, the crossover site was narrowed to the sequence 5'TT present in both attP and attB. Strains of Streptomyces coelicolor and S. lividans were constructed with a deletion of the attB site ((Delta)attB), and pSET152 was introduced into these strains by conjugation. Thus, secondary or pseudo-attB sites were identified by Southern blotting and after rescue of plasmids containing DNA flanking the insertion sites from the chromosome. The sequences of the integration sites had similarity to those of attB. Analysis of the insertions of pSET152 into both attB(+) and (Delta)attB strains indicated that this plasmid can integrate at several loci via independent recombination events within a transconjugant.