gebhart/patrepeval huggingface dataset:
Synthesis, purification, and active site mutagenesis of recombinant porcine pepsinogen (1989)

In order to carry out studies on structure and function relationships of porcine pepsinogen using site-directed mutagenesis approaches, the cDNA of this zymogen was cloned, sequenced, expressed in Escherichia coli, and the protein refolded, and purified to homogeneity. Porcine pepsinogen cDNA, obtained from a lambda gt10 cDNA library of porcine stomach contains 1364 base pairs. It contains leader, pro, and pepsin regions of 14, 44, and 326 residues, respectively. In addition, it also contains 5'- and 3'-untranslated regions. Four differences are present between the sequence deduced from the cDNA and the pepsinogen sequence determined previously by protein chemistry methods. Residues P19 (in the pro region) and 263 are asparagines in the cDNA sequence instead of aspartic acids. Isoleucine 230 is not present in the cDNA sequence and residue 242 is a tyrosine in the cDNA instead of an aspartic acid. Porcine pepsinogen cDNA was placed under the control of a tac promoter in a plasmid and expressed in E. coli. The synthesis of pepsinogen was optimized to about 50 mg/liter of culture. The recombinant (r-) pepsinogen, which was insoluble, was recovered by centrifugation, washed, dissolved in 6 M urea in Tris-HCl, pH 8, and refolded by rapid dilution. r-pepsinogen was purified to homogeneity after chromatography on Sephacryl S-300 and fast protein liquid chromatography on a monoQ column. r-pepsinogen contains an additional methionine residue at the NH2 terminus as compared to native (n-) pepsinogen. However, r- and n-pepsinogens are indistinguishable in their intramolecular activation constants. After activation, r- and n-pepsins have the same NH2-terminal sequences as well as Km values. Based on these data, r-pepsinogen was judged suitable for mutagenesis studies. A mutant pepsinogen (D32A) with the active site aspartic acid changed to an alanine was produced and purified. D32A-pepsinogen did not convert to pepsin in acid solution but it bound to pepstatin with an apparent KD of about 5 x 10(-10) M. D32A-pepsinogen possesses no detectable proteolytic activity. These results indicate that (i) intramolecular pepsinogen activation is accomplished by the pepsin active site, and (ii) unlike subtilisin (Carter, P., and Wells, J. A. (1988) Nature 332, 564-568), the active site mutant of pepsin is not enzymically active.
Comparison of botulinum neurotoxin type A formulations in Asia (2018)

Although Botulax and Nabota had more neurotoxin than Xeomin in an equivalent volume, they contained greater amounts of inactive neurotoxin. In addition, although Meditoxin and Relatox had slightly more neurotoxin than Xeomin, both contained greater amounts of inactive neurotoxin.
Heterogenization of Homogeneous Catalysts in Metal–Organic Frameworks via Cation Exchange (2013)

This paper describes the heterogenization of single-site transition-metal catalysts in metal-organic frameworks (MOFs) via cation exchange. A variety of cationic complexes of Pd, Fe, Ir, Rh, and Ru have been incorporated into ZJU-28, and the new materials have been characterized by optical microscopy, inductively coupled plasma optical emission spectroscopy, and powder X-ray diffraction. MOF-supported [Rh(dppe)(COD)]BF4 catalyzes the hydrogenation of 1-octene to n-octane. The activity of this supported catalyst compares favorably to its homogeneous counterpart, and it can be recycled at least four times. Overall, this work provides a new and general approach for supporting transition-metal catalysts in MOFs.
Invasion and MMP expression profile in desmoid tumours (2004)

Desmoid tumours are locally invasive soft tissue tumours in which beta-catenin mediated TCF-dependent transcription is activated. The role of soluble factors secreted by the myofibroblastic desmoid tumour, which could stimulate tumour invasiveness, was investigated. Using collagen gel invasion assays, the presence of factors stimulating invasion in desmoid conditioned media (CM) could be established. Since matrix metalloproteinases (MMPs) have been implicated in the process of tumoral invasion, the expression levels of the MMP family members were evaluated. Quantitative reverse transcription-PCR was used to determine the expression levels of MMP1, MMP2, MMP3, MMP7, MMP11, MMP12, MMP13, MMP14 and the inhibitors TIMP1, TIMP2 and TIMP3. Besides overexpression of MMP7, a known TCF-dependent target gene, a striking upregulation of the expression levels of MMP1, MMP3, MMP11, MMP12 and MMP13 in desmoid tumours, compared to unaffected fibroblasts from the same patients, was found. Treating the CM of desmoids with a synthetic and a physiologic MMP inhibitor reduced the invasion-stimulating capacity of the desmoid CM by approximately 50%. These results suggest the involvement of soluble factors, released by the desmoid cells, in stimulating invasion and implicate the MMPs as facilitators of invasion.
Prolate Spheroidal Wave Functions, Fourier Analysis and Uncertainty - I (1961)

A complete set of bandlimited functions is described which possesses the curious property of being orthogonal over a given finite interval as well as over (− ∞, ∞). Properties of the functions are derived and several applications to the representation of signals are made.
Production of Poly(3-Hydroxybutyrate- co -3-Hydroxyhexanoate) from Plant Oil by Engineered Ralstonia eutropha Strains (2011)

The polyhydroxyalkanoate (PHA) copolymer poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) [P(HB-co-HHx)] has been shown to have potential to serve as a commercial bioplastic. Synthesis of P(HB-co-HHx) from plant oil has been demonstrated with recombinant Ralstonia eutropha strains expressing heterologous PHA synthases capable of incorporating HB and HHx into the polymer. With these strains, however, short-chain-length fatty acids had to be included in the medium to generate PHA with high HHx content. Our group has engineered two R. eutropha strains that accumulate high levels of P(HB-co-HHx) with significant HHx content directly from palm oil, one of the world's most abundant plant oils. The strains express a newly characterized PHA synthase gene from the bacterium Rhodococcus aetherivorans I24. Expression of an enoyl coenzyme A (enoyl-CoA) hydratase gene (phaJ) from Pseudomonas aeruginosa was shown to increase PHA accumulation. Furthermore, varying the activity of acetoacetyl-CoA reductase (encoded by phaB) altered the level of HHx in the polymer. The strains with the highest PHA titers utilized plasmids for recombinant gene expression, so an R. eutropha plasmid stability system was developed. In this system, the essential pyrroline-5-carboxylate reductase gene proC was deleted from strain genomes and expressed from a plasmid, making the plasmid necessary for growth in minimal media. This study resulted in two engineered strains for production of P(HB-co-HHx) from palm oil. In palm oil fermentations, one strain accumulated 71% of its cell dry weight as PHA with 17 mol% HHx, while the other strain accumulated 66% of its cell dry weight as PHA with 30 mol% HHx.
Prebiotic Effect Of Fructo-Oligosaccharide Supplemented Term Infant Formula at Two Concentrations Compared with Unsupplemented Formula and Human Milk (2005)

Background: Human milk components, including oligosaccharides, affect the gastrointestinal flora of infants. Previous studies in adults have demonstrated that fructo-oligosaccharides increase potentially beneficial fecal bacteria, including bifidobacteria. The purpose of this study was to determine the prebiotic effect of infant formula supplemented with fructo-oligosaccharides. Methods: Healthy term infants 2 to 6 weeks of age were enrolled in a 5-week, prospective, randomized, crossover, single-site study with a nonrandomized human milk comparator group. Washout weeks preceded and followed a week of feeding with fructo-oligosaccharide-supplemented formula (1.5 or 3.0 g/L). Stool specimens were quantitatively cultured weekly for bacteroides, lactobacilli, bifidobacteria, clostridia and enterococci and were tested for Clostridium difficile toxin. Results: Seventy-two of 87 infants completed the trial; 58 were formula fed and 14 were human milk fed. Mean counts of bifidobacteria and lactobacilli were similar in all groups at entry and no group experienced a significant change in counts with fructo-oligosaccharide supplementation. After 7 days of fructo-oligosaccharide supplementation the bifidobacteria counts were greater in the 1.5 g/L fructo-oligosaccharide formula group than in the human milk fed or 3.0 g/L fructo-oligosaccharide formula groups. Formula-fed infants had higher counts of enterococci and bacteroides before fructo-oligosaccharide supplementation, and these counts did not change after supplementation. Clostridium counts increased 7 days after supplementation in the 1.5 g/L fructo-oligosaccharide formula group (P = 0.0356). No human milk fed infants had C. difficile toxin in stools. Fructo-oligosaccharide (3.0 g/L) supplementation resulted in more frequent and significantly softer stools. Conclusions: Infant formula supplemented with 1.5 or 3.0 g/L fructo-oligosaccharides was safe but had minimal effect on fecal flora and C. difficile toxin.
Solvothermal Synthesis of Nanoporous Polymer Chalk for Painting Superhydrophobic Surfaces (2011)

Reported here is a facile synthesis of nanoporous polymer chalk for painting superhydrophobic surfaces. Taking this nanoporous polymer as a media, superhydrophobicity is rapidly imparted onto three typical kinds of substrates, including paper, transparent polydimethylsiloxane (PDMS), and finger skin. Quantitative characterization showed that the adhesion between the water droplet and polymer-coated substrates decreased significantly compared to that on the original surface, further indicating the effective wetting mode transformation. The nanoporous polymer coating would open a new door for facile, rapid, safe, and larger scale fabrication of superhydrophobic surfaces on general substrates.
Efficient, numerically stabilized rank-one eigenstructure updating (signal processing) (1990)

Rank-one eigenvalue decomposition (EVD) updating is well suited to the problem of tracking time-varying subspaces. Previously published rank-one EVD updating algorithms suffer from a linear buildup of roundoff error, which makes them impractical for a large number of recursive updates. In the present work, the authors develop a numerical stabilization technique, which eliminates the error buildup problem in a computationally efficient manner and makes the rank-one EVD update a practical numerical tool for online computation. A simplified eigenvalue iteration is also given. It reduces the complexity of the algorithm somewhat as well as the computation time. Simulations are presented to illustrate numerical performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Real-Time PCR Quantitation of Clostridia in Feces of Autistic Children (2004)

Based on the hypothesis that intestinal clostridia play a role in late-onset autism, we have been characterizing clostridia from stools of autistic and control children. We applied the TaqMan real-time PCR procedure to detect and quantitate three Clostridium clusters and one Clostridium species, C. bolteae, in stool specimens. Group- and species-specific primers targeting the 16S rRNA genes were designed, and specificity of the primers was confirmed with DNA from related bacterial strains. In this procedure, a linear relationship exists between the threshold cycle (CT) fluorescence value and the number of bacterial cells (CFU). The assay showed high sensitivity: as few as 2 cells of members of cluster I, 6 cells of cluster XI, 4 cells of cluster XIVab, and 0.6 cell of C. bolteae could be detected per PCR. Analysis of the real-time PCR data indicated that the cell count differences between autistic and control children for C. bolteae and the following Clostridium groups were statistically significant: mean counts of C. bolteae and clusters I and XI in autistic children were 46-fold (P = 0.01), 9.0-fold (P = 0.014), and 3.5-fold (P = 0.004) greater than those in control children, respectively, but not for cluster XIVab (2.6 x 10(8) CFU/g in autistic children and 4.8 x 10(8) CFU/g in controls; respectively). More subjects need to be studied. The assay is a rapid and reliable method, and it should have great potential for quantitation of other bacteria in the intestinal tract.
Antisweet Natural products. VII. Hodulosides I, II, III, IV, and V from the Leaves of Hovenia dulcis THUNB. (1992)

From the fresh leaves of Hovenia dulcis THUNB., five new dammarane glycosides named hodulosides I-V (1-5)were isolated besides the khown saponins hovenoside I (6), saponins C2, (7), E (8) and H (9) and jujuboside B (10).Their structures were determined on the basis of chemical and spectral evidence. Further nuclear magnetic resonance spectral analysis of neohesperidosyl moieties of 1 led to the conclusion that the reported shifts of C2 and C3 of the glucosyl part in neohesperidose should be revised. All of the compounds (1-10) showed antisweet activities.
Modem Transmission of Data for 3-D Fracture Modelling (1993)

ABSTRACT Hydraulic fracturing treatments require measurement of numerous parameters including surface rates and pressures to quantify the fluids, proppant and additives being utilized. Computers are used to acquire data for the purpose of calculating bottomhole pressure, compiling quality control data, generating diagnostic plots and, on occasion, for modelling fracture geometry in real-time. In the recent past, modems have been routinely utilized in conjunction with cellular phone systems to transmit field monitored data to a remote office. More recently, this data has been used at the remote site to perform 3-D fracture modelling for design verification and adjustment. A description of the data transmission technology is presented and a discussion of the related cost and reliability made. A field example Is provided which involves the use of realtime 3-D analysis at the remote location. Remote transmission of data offers a major benefit to operators by providing the ability to monitor treatments and communicate requests or queries over the phone during the execution of a job. Since reports and pertinent job information are immediately available at the remote location, it is possible to perform more sophisticated real-time analyses at a lower cost. In the past, remote transmission of data has not been practical due to the related cost and technological difficulties. Recent advances in technology, such as the wide availability of cellular phone coverage, however, have made it both cost effective and reliable. Although the frequency of "noise" and lost connections is typically low, these problems can be handled by implementing an error correction/recovery scheme. This technique ensures a continuous flow of information.
Novel approach to quantitative polymerase chain reaction using real-time detection: Application to the detection of gene amplification in breast cancer (1998)

Gene amplification is a common event in the progression of human cancers, and amplified oncogenes have been shown to have diagnostic, prognostic and therapeutic relevance. A kinetic quantitative polymerase-chain-reaction (PCR) method, based on fluorescent TaqMan methodology and a new instrument (ABI Prism 7700 Sequence Detection System) capable of measuring fluorescence in real-time, was used to quantify gene amplification in tumor DNA. Reactions are characterized by the point during cycling when PCR amplification is still in the exponential phase, rather than the amount of PCR product accumulated after a fixed number of cycles. None of the reaction components is limited during the exponential phase, meaning that values are highly reproducible in reactions starting with the same copy number. This greatly improves the precision of DNA quantification. Moreover, real-time PCR does not require post-PCR sample handling, thereby preventing potential PCR-product carry-over contamination; it possesses a wide dynamic range of quantification and results in much faster and higher sample throughput. The real-time PCR method, was used to develop and validate a simple and rapid assay for the detection and quantification of the 3 most frequently amplified genes (myc, ccndl and erbB2) in breast tumors. Extra copies of myc, ccndl and erbB2 were observed in 10, 23 and 15%, respectively, of 108 breast-tumor DNA; the largest observed numbers of gene copies were 4.6, 18.6 and 15.1, respectively. These results correlated well with those of Southern blotting. The use of this new semi-automated technique will make molecular analysis of human cancers simpler and more reliable, and should find broad applications in clinical and research settings.
The CRISPR-Cas system of Streptococcus pyogenes: function and applications (2016)

Many Streptococcus pyogenes strains harbor CRISPR-Cas loci that encode for the RNA-guided nuclease Cas9. Due to the use of this nuclease in genome editing, there has been a great deal of focus on the study of CRISPR-Cas immunity in these organisms, and as a result the S. pyogenes CRISPR-Cas9 system is one of the most studied and better understood of these systems. In this chapter, we review how the Cas9 nuclease mediates anti-phage immunity and how it can be repurposed for the genetic engineering of human cells and other eukaryotic organisms.
Isolation and Characterization of acetate kinase and phosphotransacetylase mutants of Escherichia coli and Salmonella typhimurium (1980)

Mutations in the ack (acetate kinase) and pta (phosphotransacetylase) genes in Salmonella typhimurium were characterized and determined to be analogous to those of previously described Escherichia coli mutants. We established that in both bacterial species these genes were cotransducible with the neighboring histidine transport operon and were distally located relative to purF. pta mutants were sensitive to the dye alizarin yellow and were unable to grow on medium containing inositol as a carbon source. We selected mutants of both species with deletions covering both the ack and the pta genes; some deletions extended into the histidine transport operon.
Prevalence, phenotype and architecture of developmental disorders caused by de novo mutation: The Deciphering Developmental Disorders Study (2016)

Abstract Individuals with severe, undiagnosed developmental disorders (DDs) are enriched for damaging de novo mutations (DNMs) in developmentally important genes. We exome sequenced 4,293 families with individuals with DDs, and meta-analysed these data with published data on 3,287 individuals with similar disorders. We show that the most significant factors influencing the diagnostic yield of de novo mutations are the sex of the affected individual, the relatedness of their parents and the age of both father and mother. We identified 94 genes enriched for damaging de novo mutation at genome-wide significance (P &lt; 7 × 10 −7 ), including 14 genes for which compelling data for causation was previously lacking. We have characterised the phenotypic diversity among these genetic disorders. We demonstrate that, at current cost differentials, exome sequencing has much greater power than genome sequencing for novel gene discovery in genetically heterogeneous disorders. We estimate that 42% of our cohort carry pathogenic DNMs (single nucleotide variants and indels) in coding sequences, with approximately half operating by a loss-of-function mechanism, and the remainder resulting in altered-function (e.g. activating, dominant negative). We established that most haplo insufficient developmental disorders have already been identified, but that many altered-function disorders remain to be discovered. Extrapolating from the DDD cohort to the general population, we estimate that developmental disorders caused by DNMs have an average birth prevalence of 1 in 213 to 1 in 448 (0.22-0.47% of live births), depending on parental age. Abbreviations PTV Protein-Truncating Variant DNM De Novo Mutation DD Developmental Disorder DDD Deciphering Developmental Disorders study
Electrodeposition of Nickel‐Iron Alloys: I . Effect of Agitation (1989)

Agitation effects on electrodeposition have been systematically investigated using a rotating ring‐disk electrode. Alloy compositions and bath current efficiencies have been shown to vary widely over the range of plating current densities and rotation speeds used. An analysis of partial currents as a function of electrode potential has shown that the Fe deposition reaction is mass‐transport controlled at sufficient cathodic potentials, and that the diffusivity of the Fe2+ ion is the same for both the reduction to Fe0 and the oxidation to Fe3+. In agreement with the observations of Dahms and Croll, the Ni deposition reaction is inhibited when Fe is codeposited. This inhibition effect, manifest as a cathodic shift in the Ni polarization curve, increases in magnitude with increased agitation. The dependence of Ni inhibition on agitation is seen only under conditions at which Fe deposition is mass‐transfer influenced, which suggests that Ni inhibition is primarily dependent on the flux of Fe2+ to the electrode surface. The rate of hydrogen evolution during deposition shows the same dependence on potential and agitation as it does in a Ni2+‐ and Fe2+‐free bath on a substrate.
An Unexpected Synthesis of 7,8-Polymethyleneimidazo-1,3,2-diazaphosphorines – Heteroanalogues of Mercaptopurine Derivatives (1995)

A new synthesis of 7,8-polymethyleneimidazodiazaphosphorines, involving the interaction of cyclic 1-carbamoylmethyl-2-cyanamidines with phosphorus pentasulfide in the presence of pyridine, is described.
High Avidity Antigen-Specific CTL Identified by CD8-Independent Tetramer Staining (2003)

Tetrameric MHC/peptide complexes are important tools for enumerating, phenotyping, and rapidly cloning Ag-specific T cells. It remains however unclear whether they can reliably distinguish between high and low avidity T cell clones. In this report, tetramers with mutated CD8 binding site selectively stain higher avidity human and murine CTL capable of recognizing physiological levels of Ag. Furthermore, we demonstrate that CD8 binding significantly enhances the avidity as well as the stability of interactions between CTL and cognate tetramers. The use of CD8-null tetramers to identify high avidity CTL provides a tool to compare vaccination strategies for their ability to enhance the frequency of high avidity CTL. Using this technique, we show that DNA priming and vaccinia boosting of HHD A2 transgenic mice fail to selectively expand large numbers of high avidity NY-ESO-1(157-165)-specific CTL, possibly due to the large amounts of antigenic peptide delivered by the vaccinia virus. Furthermore, development of a protocol for rapid identification of high avidity human and murine T cells using tetramers with impaired CD8 binding provides an opportunity not only to monitor expansion of high avidity T cell responses ex vivo, but also to sort high avidity CTL clones for adoptive T cell transfer therapy.
Imiquimod is a strong inhibitor of tumor cell‐induced angiogenesis (2004)

Antiangiogenic effect of imiquimod was found to be mediated by IL-18, probably through promoting production of INFgamma, the most important inhibitor of angiogenesis.
MPEG-4 Audio Lossless Coding (2004)

Lossless coding will become the latest extension of the MPEG-4 audio standard. The lossless audio codec of the Technical University of Berlin was chosen as reference model for MPEG-4 Audio Lossless Coding (ALS). The MPEG-4 ALS encoder is based on linear prediction, which enables high compression even with moderate complexity, while the corresponding decoder is straightforward. The paper describes the basic elements of the codec as well as some additional features, gives compression results, and points out envisaged applications.