gebhart/patrepeval huggingface dataset:
Autocovariance-based MPC model mismatch estimation for SISO systems (2015)

Model predictive control (MPC) has become the de-facto standard for multivariable control in the process industries. MPC systems are able to handle complex dynamics, interactions and constraints, but are vulnerable to plant-model mismatch. The deviation of the process model from the plant is an inevitable phenomenon, caused by drifting equipment properties and process conditions. In this contribution, we introduce a novel autocovariance-based framework for estimating MPC plant-model mismatch from closed-loop operating data. Our initial results focus on SISO systems, where we begin by establishing an explicit relationship between the autocovariance of process input and output data, and the magnitude of the plant-model mismatch. We use this result to establish an optimization-based approach for solving the inverse problem, that is, computing plant-model mismatch from available data. We present a numerical study, where we demonstrate the excellent performance of the proposed framework.
Development and Application of an in Vivo Plant Peroxisome Import System (1995)

The purposes of this study are to develop an in vivo cell system that is suitable for the immunofluorescent detection of transiently expressed proteins targeted to plant peroxisomes and to determine whether a C-terminal serine-lysine-leucine (SKL) tripeptide, a consensus-targeting signal for mammalian peroxisomes, also targets proteins to plant peroxisomes. Protoplasts from mesophyll cells and from suspension-cultured cells initially were examined for their potential as an in vivo import system. Several were found suitable, but based on a combination of criteria, suspension-cultured tobacco (Nicotiana tabacum L. cv Bright Yellow 2) cells (TBY-2) were chosen. The tobacco cell extracts had catalase activity, and two polypeptides of approximately 55 and 57 kD specifically were detected on immunoblots with anti-cottonseed catalase immunoglobulins G as the probe. Indirect immunofluorescence microscopy with these immunoglobulins G revealed a punctate labeling pattern indicative of endogenous catalase localization within putative TBY-2 peroxisomes. The cells did not have to be completely converted to protoplasts for optimal microscopy; treatment with 0.1% (w/v) pectolyase for 2 h was sufficient. Microprojectile bombardment proved superior for transient transformation of the TBY-2 cells with plasmids encoding beta-glucuronidase, or chloramphenicol acetyltransferase (CAT), or CAT with an added C-terminal tripeptide (CAT-SKL). C-terminal SKL is a consensus, type 1, peroxisome targeting signal. Double indirect immunofluorescent labeling showed that CAT-SKL co-localized with endogenous catalase. Non-punctate, diffuse localization of CAT without SKL provided direct evidence that the C-terminal SKL tripeptide was necessary and sufficient for targeting of CAT to plant peroxisomes. These data demonstrate the effectiveness of this peroxisome targeting signal for plant cells.
Identification of Protein Targets of 4-Hydroxynonenal Using Click Chemistry for ex Vivo Biotinylation of Azido and Alkynyl Derivatives (2008)

Polyunsaturated fatty acids (PUFA) are primary targets of free radical damage during oxidative stress. Diffusible electrophilic alpha,beta-unsaturated aldehydes, such as 4-hydroxynonenal (HNE), have been shown to modify proteins that mediate cell signaling (e.g., IKK and Keap1) and alter gene expression pathways responsible for inducing antioxidant genes, heat shock proteins, and the DNA damage response. To fully understand cellular responses to HNE, it is important to determine its protein targets in an unbiased fashion. This requires a strategy for detecting and isolating HNE-modified proteins regardless of the nature of the chemical linkage between HNE and its targets. Azido or alkynyl derivatives of HNE were synthesized and demonstrated to be equivalent to HNE in their ability to induce heme oxygenase induction and induce apoptosis in colon cancer (RKO) cells. Cells exposed to the tagged HNE derivatives were lysed and exposed to reagents to effect Staudinger ligation or copper-catalyzed Huisgen 1,3 dipolar cycloaddition reaction (click chemistry) to conjugate HNE-adducted proteins with biotin for subsequent affinity purification. Both strategies yielded efficient biotinylation of tagged HNE-protein conjugates, but click chemistry was found to be superior for the recovery of biotinylated proteins from streptavidin-coated beads. Biotinylated proteins were detected in lysates from RKO cell incubations with azido-HNE at concentrations as low as 1 microM. These proteins were affinity purified with streptavidin beads, and proteomic analysis was performed by linear ion trap mass spectrometry. Proteomic analysis revealed a dose-dependent increase in labeled proteins with increased sequence coverage at higher concentrations. Several proteins involved in stress signaling (heat shock proteins 70 and 90 and the 78-kDa glucose-regulated protein) were selectively adducted by azido- and alkynyl-HNE. The use of azido and alkynyl derivatives in conjunction with click chemistry appears to be a valuable approach for the identification of the protein targets of HNE.
Controlled Solubility Phosphates--A Versatile Solution To Oilfield Scale Problems (1960)

Abstract Water flooding has focused attention on the problem of scale in producing wells. Four reasons why scale forms are discussed. A new theory which will help explain the severe scale build-up that occurs in many producing wells at the time of water breakthrough is presented. A recently developed family of scale preventives - the controlled solubility phosphates - are described chemically and physically. Factors which influence the performance of these unique phosphates in oilfield brines are evaluated in terms of laboratory test data. Case histories of producing wells treated with controlled solubility phosphates are summarized. The importance of bottom-hole temperature, the role of produced-fluid mineral characteristics and the value of knowing down-hole flow conditions are pointed out. Economic considerations well known to engineers and production men are used to compare the cost of conventional treatment and the cost of the new controlled solubility phosphate scale-prevention approach. Introduction General acceptance of the artificial water drive as a secondary producing mechanism for the recovery of oil has made many petroleum engineers and production men extremely "water conscious" during the last few years. Scale and corrosion problems of a type seldom encountered in primary production soon become evident as leases are placed under flood. In attempting to find solutions to these newly created problems, the oil industry has learned that standard municipal and industrial water-treatment practice is going to be of little value. The reason for this is that, until the oil industry started to emphasize water flooding and the conditioning of produced fluids, no one had ever attempted to make use of water of as poor quality as that now being handled by many secondary-recovery operators. The need for processing brines saturated with corrosive gases, scale-forming minerals and insidious microbiological growths has opened up a completely new field of water-conditioning technology. This paper deals with scale in oilfield brines. Factors which influence the formation of scale are discussed along with how petroleum engineers can get the most out of a unique family of chemicals which will effectively prevent scale.
Expansion of the genetic code: Site‐directed p‐fluoro‐phenylalanine incorporation in Escherichia coli (1998)

Site-directed incorporation of the amino acid analogue p-fluoro-phenylalanine (p-F-Phe) was achieved in Escherichia coli. A yeast suppressor tRNA(Phe)amber/phenylalanyl-tRNA synthetase pair was expressed in an analogue-resistant E. coli strain to direct analogue incorporation at a programmed amber stop codon in the DHFR marker protein. The programmed position was translated to 64-75% as p-F-Phe and the remainder as phenylalanine and lysine. Depending on the expression conditions, the p-F-Phe incorporation was 11-21-fold higher at the programmed position than the background incorporation at phenylalanine codons, showing high specificity of analogue incorporation. Protein expression yields of 8-12 mg/L of culture, corresponding to about two thirds of the expression level of the wild-type DHFR protein, are sufficient to provide fluorinated proteins suitable for 19F-NMR spectroscopy and other sample-intensive methods. The use of a nonessential "21st" tRNA/synthetase pair will permit incorporation of a wide range of analogues, once the synthetase specificity has been modified accordingly.
Epidermal Growth Factor-induced Association of the SHPTP2 Protein Tyrosine Phosphatase with a 115-kDa Phosphotyrosine Protein (1995)

Epidermal growth factor (EGF) stimulation of HepG2 and NIH 3T3 cells expressing high levels of the human EGF receptor (3T3/ER) resulted in the tyrosine phosphorylation of a 115-kDa protein that was co-immunoprecipitated with the Src homology 2 (SH2) domain containing protein tyrosine phosphatase, SHPTP2. In contrast, activation of the EGF receptor resulted in a relatively low level (< 1%) of the total SHPTP2 pool associated with the tyrosine-autophosphorylated EGF receptor itself. Similarly, quantitative immunoprecipitations also demonstrated that only trace amounts of the total EGF receptor pool were associated with SHPTP2. Further, activation of the EGF receptor did not result in any significant tyrosine phosphorylation of SHPTP2 and/or the association of the 115-kDa protein with Grb2. In comparison, activation of Jurkat cells with a T cell receptor agonist monoclonal antibody resulted in the co-immunoprecipitation of a 120-kDa tyrosine-phosphorylated protein with Grb2 and a 105-kDa protein with SHPTP2. Thus, these data have identified the 115- and 105-kDa proteins as the predominant SHPTP2-associated phosphotyrosine proteins in EGF- and T cell receptor-activated cells, respectively.
Keeping the Bugs at Bay (2006)

MEDICAL ENTOMOLOGYPublic health money gives a boost to the untidy science of crafting a better insect repellent. Researchers have uncovered possible new repellents in nature and in the lab, and a few have already made it to market. ([Read more][1].)

 [1]: http://www.sciencemag.org/cgi/content/full/313/5783/36
Tumor-targeted delivery of siRNA by non-viral vector: safe and effective cancer therapy (2008)

RNA interference technology has been developed as a potential therapeutic agent for many indications, including cancer. Silencing a specific oncogene in tumor cells brings about cell death both in vitro and in vivo. However, there is a great need for powerful delivery strategies to enhance the therapeutic effect of small interfering RNA (siRNA). This review summarizes different signaling pathways inhibited by siRNA and the advantages of targeted siRNA as a delivery system.
N-parallel filter bank equivalent to tree structure (1994)

This paper presents the equivalent polyphase implementations of an N-channel filter bank based on an s-level tree structured filter bank. The realization employs a cascade of the filter's polyphase components with distributed decimation followed by the NxN Hadamard matrix realizing a filter bank with real computations (real-valued filter coefficients) only, which is simple to realize.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Piezoelectric and electrostrictive polymeric actuator materials (2000)

Peizoelectric and electrostrictive polymers are widely used in many areas of electromechanical actuation and transduction. This paper summarizes the current status and recent works in this class of polymers. For the piezoelectric polymers, the electromechanical properties of poly(vinylidene fluoride-trifluoroethylene) copolymers (P(VDF-TrFE), which possess the best piezoelectric performance among the known piezopolymers, are presented. In order to improve the strain capability and other electromechanical properties, the large electrostrictive response and high electromechanical conversion efficient near a first order ferroelectric-paraelectric transition of P(VDF-TrFE) copolymer were exploited. It is shown that the copolymer, treated with high energy electron irradiation, exhibits high electrostrictive strains (-5% longitudinal strain under 150 MV/m and 3.5% transverse starin under 100 MV/m) with high strain energy density, high load capability and improved electromechanical coupling factor. For the comparison, the works related to the Maxwell stress induced strain response in soft polymers are also discussed.
Different restriction enzyme-generated sticky DNA ends can be joinedin vitro (1984)

We describe a simple method for joining the 5'-protruding, single-stranded DNA ends generated by restriction enzymes. The method allows ends with different sequences to be joined and prevents identical ends from being joined. This is accomplished by partially filling the single strands in a controlled reverse transcriptase reaction. Partial filling can create new single-stranded ends that can be ligated to different, partially filled ends. In almost all useful cases, partial filling simultaneously eliminates the self-complementarity of identical ends and thus prevents them from being joined by DNA ligase. Although all possible combinations of partially filled ends were not tested, the tests performed indicate that the method is fairly general. We demonstrate that ends of the same length can be ligated with useful efficiency if they are: 1) one nucleotide long and complementary; 2) two nucleotides long and complementary or have a mismatch (dA:dC) at one position; or 3) three nucleotides long and, in our test, have a dT:dC mismatch at the middle position.
Understanding the relationships between molecule structure and imprinting effect of two acetyl‐nitrogen heterocyclic compounds (2016)

The molecularly imprinted polymers (MIPs) for two structural analogs, 1,3,5-triacetyl-1,3,5-triazacyclohexane (TRAT) and 1,3,5,7-tetraacetyl-1,3,5,7-tetraazacyclooctane (TAT), have been synthesized respectively under the same conditions. The TAT-MIP showed excellent imprinting effect, whereas the TRAT-MIP did not. To understand the different imprinting effects of the MIPs prepared from these two templates, the geometric structures and energetic properties of complexes formed around TAT and TRAT were studied computationally. The results indicate that in liquid phase, for the complexes formed with TAT and its nearest neighbor molecules, the magnitude of the binding energy increases with the number of surrounding TAT, methacrylic acid, and acetonitrile (ACT), whereas for the cases of TRAT, the magnitude of the binding energy increases with the number of surrounding TRAT and trimethylolpropane trimethacrylate. The studied systems form stronger and thus more stable networks encapsulating TAT than with TRAT. ACT may also play an important role in the polymerization phase in stabilizing the shapes of the cavities that TATs reside in. We propose these as the major factors that affect the different imprinting effects of the two MIPs. Copyright © 2016 John Wiley & Sons, Ltd.
Enhancement of Fluorescence Yield of Rare-Earth Ions by Heavy Water (1963)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation John L. Kropp, Maurice W. Windsor; Enhancement of Fluorescence Yield of Rare‐Earth Ions by Heavy Water. J. Chem. Phys. 15 November 1963; 39 (10): 2769–2770. https://doi.org/10.1063/1.1734096 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioThe Journal of Chemical Physics Search Advanced Search |Citation Search
Improved Protein Hydrogen/Deuterium Exchange Mass Spectrometry Platform with Fully Automated Data Processing (2012)

Protein hydrogen/deuterium exchange (HDX) followed by protease digestion and mass spectrometric (MS) analysis is accepted as a standard method for studying protein conformation and conformational dynamics. In this article, an improved HDX MS platform with fully automated data processing is described. The platform significantly reduces systematic and random errors in the measurement by introducing two types of corrections in HDX data analysis. First, a mixture of short peptides with fast HDX rates is introduced as internal standards to adjust the variations in the extent of back exchange from run to run. Second, a designed unique peptide (PPPI) with slow intrinsic HDX rate is employed as another internal standard to reflect the possible differences in protein intrinsic HDX rates when protein conformations at different solution conditions are compared. HDX data processing is achieved with a comprehensive HDX model to simulate the deuterium labeling and back exchange process. The HDX model is implemented into the in-house developed software MassAnalyzer and enables fully unattended analysis of the entire protein HDX MS data set starting from ion detection and peptide identification to final processed HDX output, typically within 1 day. The final output of the automated data processing is a set (or the average) of the most possible protection factors for each backbone amide hydrogen. The utility of the HDX MS platform is demonstrated by exploring the conformational transition of a monoclonal antibody by increasing concentrations of guanidine.
Polyglutamine Diseases and Transport Problems (2005)

The expansion of CAG repeats encoding glutamine (polyQ) causes, to date, 9 late-onset progressive neurodegenerative disorders, including Huntington disease, spinobulbar muscular atrophy, dentatorubral-pallidoluysian atrophy, and spinocerebellar ataxias 1, 2, 3, 6, 7, and 17. Although many studies using both knockout and transgenic mouse models suggest that a toxic gain of function is central to neuronal dysfunction, the exact mechanisms of neurotoxic effects remain elusive. Protein aggregations within neurons seem to be a common manifestation in almost all polyQ diseases, and such accumulations are perhaps major triggers of cellular stress and neuronal death. Recent data lead to the tantalizing proposal that disruption of axonal transport pathways within long, narrow-caliber axons could lead to protein accumulations that can elicit neuronal death, ultimately causing a neuronal dysfunction pathway observed in polyQ expanded diseases. Perhaps perturbations in transport pathways are an early event involved in instigating polyQ disease pathology.
The effect of minor gastric surgery on gastric emptying in the rat (1991)

A new minimally invasive technique has recently been described which enables gastric emptying to be assessed on repeated occasions without the need for animal sacrifice. This technique has been applied to study the effect of a laparotomy or gastrotomy on gastric emptying in the rat. Groups of 10 animals underwent either a laparotomy or a gastrotomy, or were unoperated controls. Solid and liquid gastric emptying studies were performed preoperatively, and for two postoperative months. Emptying was unchanged in unoperated controls. Laparotomy animals showed delayed emptying of both solids and liquids, returning to normal by two months. Gastrotomy animals showed a similar delay in solid emptying, but liquid emptying was within the normal range postoperatively. It is concluded that minor abdominal surgery causes marked alteration in gastric emptying. The comparable emptying delay for patients is unknown, but this should be considered when patients are recovering from operation, and when interpreting postoperative gastric emptying studies.
Prediction of HIV Type 1 Subtype C Tropism by Genotypic Algorithms Built From Subtype B Viruses (2010)

Background: Genotypic predictions of HIV-1 tropism could simplify CCR5 antagonist usage. However, the genotypic algorithms built from subtype B viruses could be inadequate for non-B subtypes. We therefore performed paired genotypic and phenotypic determination of subtype C tropism. Methods: We studied 52 patients recruited in Malawi and 21 patients recruited in France. We directly sequenced the V3 env region and performed a recombinant virus phenotypic entry assay in parallel. Results: The Malawi patients had 29% of CXCR4-using subtype C viruses compared with only 5% in the patients from France. For detecting CXCR4-using subtype C viruses, the genotypic rule combining the amino acids at positions 11/25 and the net charge of V3 was 93.3% sensitive and 96.4% specific. The Geno2pheno tool was 86.7% sensitive and 89.1% specific. The WebPSSM tool with the SI/NSI matrix was 80% sensitive and 98.2% specific in its subtype B version and 93.3% sensitive and 81.8% specific in its subtype C version. Conclusions: The genotypic determinants of coreceptor usage for HIV-1 subtype C were mainly in V3 and were globally similar to those previously reported for subtype B viruses. The main genotypic algorithms built from subtype B viruses perform well when applied to subtype C viruses.
Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia (2012)

A previously unknown coronavirus was isolated from the sputum of a 60-year-old man who presented with acute pneumonia and subsequent renal failure with a fatal outcome in Saudi Arabia. The virus (called HCoV-EMC) replicated readily in cell culture, producing cytopathic effects of rounding, detachment, and syncytium formation. The virus represents a novel betacoronavirus species. The closest known relatives are bat coronaviruses HKU4 and HKU5. Here, the clinical data, virus isolation, and molecular identification are presented. The clinical picture was remarkably similar to that of the severe acute respiratory syndrome (SARS) outbreak in 2003 and reminds us that animal coronaviruses can cause severe disease in humans.
Ability of an avirulent mutant of Vibrio cholerae to colonize in the infant mouse upper bowel (1981)

Vibrio cholerae strain 3083 (biotype El Tor, serotype Ogawa) and Texas Star-SR (SR), a mutant derived from 3083 that produces the B (binding) but not the A (toxic) subunit of choleragen, were compared in their abilities to: (i) associate with the infant mouse upper bowel; (ii) survive and multiple there; and (iii) induce diarrhea. Vibrios labeled with 35SO4 were used to determine association with the upper bowel and ability to multiply. The parental strain associated significantly better than SR, although viable mutant cells were found in the infant mouse intestine 16 to 18 h after challenge. Addition of exogenous toxin enhanced the rate at which labeled SR (but not 3083) was cleared, further suggesting that SR associates less well with the upper bowel. Both SR and 3083 multiplied in the upper bowel but, due perhaps to slight net killing during the first 3 h and its more rapid rate of clearance, SR achieved a population size only 10% that of 3083 by 8 h postchallenge. Strain 3083 elicited diarrhea in infant mice but SR did not, even after 10 successive passages through the infant mouse intestine. Strain SR was slightly temperature sensitive at 37 and 40 degrees C. Its potential use as a live vaccine is discussed.