gebhart/patrepeval huggingface dataset:
Site specificity of casein kinase‐2 (TS) from rat liver cytosol (1986)

The factors determining the site recognition and phosphorylation by rat liver casein kinase‐2 (CK‐2) have been explored with a set of 14 related hexapeptides each including a single phosphorylatable amino acid and five acidic plus neutral residues. Such peptides are different from each other in the following features: (a) the nature of the phosphorylatable amino acid, if any; (b) its position relative to the critically required acidic residues; (c) the extension and (d) the structure of the acidic cluster. All of them were tested as substrates and/or competitive inhibitors of CK‐2, and their kinetic and inhibition constants were determined. The results suggest the following conclusions. (a) Under strictly comparable conditions Ser is by far preferred over Thr. Tyr not being affected at all. (b) In order to carry out its role of structural determinant the critical acidic cluster must be located on the C‐terminal side of the target residue, though not necessarily adjacent to it. (c) The affinity for the protein‐binding site, as deduced from K m and/or K i values, is largely dependent on the number of acidic residues but it is also significantly enhanced if a hydroxylic residue is located on their N‐terminal side. (d) An acidic residue at position +3 relative to serine plays an especially important role for triggering phosphorylation, the peptide Ser‐Glu‐Glu‐Ala‐Glu‐Glu having similar K m but negligible V max compared to Ser‐Glu‐Ala‐Glu‐Glu‐Glu and Ser‐Glu‐Glu‐Glu‐Ala‐Glu. These data provide a rationale for the substrate specificity of CK‐2 and will give a helpful insight into the structure of the protein‐binding site of this enzyme.
Deoxynucleic Guanidine/Peptide Nucleic Acid Chimeras:  Synthesis, Binding and Invasion Studies with DNA (2000)

A fully automated solid-phase synthetic procedure for incorporation of positively charged guanidinium linkages into otherwise neutral PNA sequences has been employed. These DNG/PNA chimeras form [(DNG/PNA)2·DNA] triplexes upon binding to single strand or duplex DNA (with accompanying D-loop for the latter). The [(DNG/PNA)2·DNA] triplexes of DNG/PNA T10, with DNA dA10, are more stable than DNA·DNA triplexes [(T10)2·dA10]. The binding of DNG/PNA chimera with guanidinium linkages on both ends, with single strand length-matched complementary DNA under thermal melt conditions and with longer double strand DNA under isothermal conditions is sequence specific. The association process of DNG/PNA chimera with single strand DNA and strand invasion of longer ds-DNA is faster than the association of PNA, with the same DNA targets, as evident by thermal hysteresis and gel retardation under isothermal conditions. The sequence specific and faster strand invasion of DNG/PNA may extend the potential utility of PNA in diagnostics, biomolecular probes, and antisense/antigene therapeutics.
Unexpected sarcolemmal complement membrane attack complex deposits on nonnecrotic muscle fibers in muscular dystrophies (1998)

Antibody-dependent complement-mediated muscle fiber injury is a hypothetical immune effector response in inflammatory muscle diseases. Moreover, a sarcolemmal alteration in muscular dystrophies might trigger antibody-independent activation of the alternative complement pathway. We therefore searched for C5b9 complement membrane attack complex (MAC), immunoglobulin (Ig)G, and IgM deposits on nonnecrotic muscle fibers in muscle specimens from 81 patients with inflammatory myopathies, 45 patients with muscular dystrophies, and 19 patients with necrotizing myopathies. Sarcolemmal MAC deposits were present on nonnecrotic fibers (C+ fibers) in only two unusual types of inflammatory myopathy. By contrast, seven of 17 facioscapulohumeral dystrophy, four of nine limb-girdle dystrophy, and three of six merosin (laminin-alpha-2)-positive congenital muscular dystrophy but none of the Becker or Duchenne dystrophy specimens harbored C+ fibers. None of the C+ fibers immunostained for IgG or IgM, and none failed to immunostain for CD59 or CD46-inhibitors of the complement cascade. Our findings do not support a role for antibody-dependent complement-mediated muscle fiber injury in the major inflammatory muscle diseases. The cause and pathogenetic significance of the C+ fibers in the different types of muscular dystrophies remains to be elucidated.
Gamma‐interferon production and quality in stoichiometric fed‐batch cultures of Chinese hamster ovary (CHO) cells under serum‐free conditions (1997)

The application of a stoichiometric medium design approach was studied in fed-batch cultivation of Chinese hamster ovary (CHO) cells. A serum-free medium containing a very low protein concentration (2 mg/L insulin) was developed. A supplemental medium was formulated according to the stoichiometric equation governing cell growth using cell composition obtained from hybridoma cells. Fed-batch culture was conducted in spinner flasks using the supplemental medium for feeding. Significant improvement in cell growth, by-product reduction, and Gamma-Interferon (IFN-γ) production was achieved as compared to a typical batch culture. Results indicate that the stoichiometric approach, originally developed for hybridoma cultures, is a fast and effective method for cell culture process design and improvement. The glycosylation of IFN-γ was monitored off-line during the culture process. The accumulative IFN-γ glycosylation efficiency was slightly improved as compared to that of the batch culture, due to the nutritional control through the stoichiometric feeding. Periodic glucose starvation was observed during the fed-batch culture as a result of the manual feeding. Pulse-chase radiolabeling assay shows that glucose starvation leads to a deteriorated IFN-γ glycosylation efficiency. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 577–582, 1997.
Toward Automated Holistic Beat Tracking, Music Analysis And Understanding. (2005)

Most music processing attempts to focus on one particular feature or structural element such as pitch, beat location, tempo, or genre. This hierarchical approach, in which music is separated into elements that are analyzed independently, is convenient for the scientific researcher, but is at odds with intuition about music perception. Music is interconnected at many levels, and the interplay of melody, harmony, and rhythm are important in perception. As a first step toward more holistic music analysis, music structure is used to constrain a beat tracking program. With structural information, the simple beat tracker, working with audio input, shows a large improvement. The implications of this work for other music analysis problems are discussed.
TLRs and innate immunity (2008)

One of the most fundamental questions in immunology pertains to the recognition of non-self, which for the most part means microbes. How do we initially realize that we have been inoculated with microbes, and how is the immune response ignited? Genetic studies have made important inroads into this question during the past decade, and we now know that in mammals, a relatively small number of receptors operate to detect signature molecules that herald infection. One or more of these signature molecules are displayed by almost all microbes. These receptors and the signals they initiate have been studied in depth by random germline mutagenesis and positional cloning (forward genetics). Herein is a concise description of what has been learned about the Toll-like receptors, which play an essential part in the perception of microbes and shape the complex host responses that occur during infection.
Inflammatory Bowel Disease (1996)

Drug induced pancreatitis EDITOR,-I have read with interest the article on drug induced pancreatitis by Lankisch
Group 13 Compounds Incorporating Salen Ligands (2000)

In a previous review it was predicted that "the reactivity of five-coordinate complexes would certainly be different than that of the four-coordinate derivatives". Structurally and spectroscopically, there is very little difference in the higher-coordinate compounds when compared to the four-coordinate derivatives. However, the prediction was remarkably accurate, if not a bit understated, for the reactivity of these compounds. There appears to be a tremendous potential in catalysis and synthesis for the five-coordinate derivatives, far more possibilities than exist for the lower-coordinate derivatives. Furthermore, the higher-coordinate derivatives are rarely air or moisture sensitive and, thus, may be handled under a wider range of conditions. Although reactions such as oxirane and lactide polymerizations are fairly well-known now with five- and six-coordinate aluminum compounds, the potential of these compounds has only begun to be developed. It is easy to imagine that these types of compounds will see wider use than the related transition-metal compounds.
Closing the Circadian Loop: CLOCK-Induced Transcription of Its Own Inhibitors per and tim (1998)

The circadian oscillator generates a rhythmic output with a period of about 24 hours. Despite extensive studies in several model systems, the biochemical mode of action has not yet been demonstrated for any of its components. Here, the Drosophila CLOCK protein was shown to induce transcription of the circadian rhythm genes period and timeless. dCLOCK functioned as a heterodimer with a Drosophila homolog of BMAL1. These proteins acted through an E-box sequence in the period promoter. The timeless promoter contains an 18-base pair element encompassing an E-box, which was sufficient to confer dCLOCK responsiveness to a reporter gene. PERIOD and TIMELESS proteins blocked dCLOCK's ability to transactivate their promoters via the E-box. Thus, dCLOCK drives expression of period and timeless, which in turn inhibit dCLOCK's activity and close the circadian loop.
Automated prediction and analysis of job interview performance: The role of what you say and how you say it (2015)

Ever wondered why you have been rejected from a job despite being a qualified candidate? What went wrong? In this paper, we provide a computational framework to quantify human behavior in the context of job interviews. We build a model by analyzing 138 recorded interview videos (total duration of 10.5 hours) of 69 internship-seeking students from Massachusetts Institute of Technology (MIT) as they spoke with professional career counselors. Our automated analysis includes facial expressions (e.g., smiles, head gestures), language (e.g., word counts, topic modeling), and prosodic information (e.g., pitch, intonation, pauses) of the interviewees. We derive the ground truth labels by averaging over the ratings of 9 independent judges. Our framework automatically predicts the ratings for interview traits such as excitement, friendliness, and engagement with correlation coefficients of 0.73 or higher, and quantifies the relative importance of prosody, language, and facial expressions. According to our framework, it is recommended to speak more fluently, use less filler words, speak as “we” (vs. “I”), use more unique words, and smile more.
Molecular characterization of the cai operon necessary for carnitine metabolism in Escherichia coii (1994)

The sequence encompassing the cai genes of Escherichia coli, which encode the carnitine pathway, has been determined. Apart from the already identified caiB gene coding for the carnitine dehydratase, five additional open reading frames were identified. They belong to the caiTABCDE operon, which was shown to be located at the first minute on the chromosome and transcribed during anaerobic growth in the presence of carnitine. The activity of carnitine dehydratase was dependent on the CRP regulatory protein and strongly enhanced in the absence of a functional H-NS protein, in relation to the consensus sequences detected in the promoter region of the cai operon. In vivo expression studies led to the synthesis of five polypeptides in addition to CaiB, with predicted molecular masses of 56,613 Da (CaiT), 42,564 Da (CaiA), 59,311 Da (CaiC), 32,329 Da (CaiD) and 21,930 Da (CaiE). Amino acid sequence similarity or enzymatic analysis supported the function assigned to each protein. CaiT was suggested to be the transport system for carnitine or betaines, CaiA an oxidoreduction enzyme, and CaiC a crotonobetaine/carnitine CoA ligase. CaiD bears strong homology with enoyl hydratases/isomerases. Overproduction of CaiE was shown to stimulate the carnitine racemase activity of the CaiD protein and to markedly increase the basal level of carnitine dehydratase activity. It is inferred that CaiE is an enzyme involved in the synthesis or the activation of the still unknown cofactor required for carnitine dehydratase and carnitine racemase activities. Taken together, these data suggest that the carnitine pathway in E. coli resembles that found in a strain situated between Agrobacterium and Rhizobium.
A Cleavage Enzyme-Cytometric Bead Array Provides Biochemical Profiling of Resistance Mutations in HIV-1 Gag and Protease (2011)

Most protease-substrate assays rely on short, synthetic peptide substrates consisting of native or modified cleavage sequences. These assays are inadequate for interrogating the contribution of native substrate structure distal to a cleavage site that influences enzymatic cleavage or for inhibitor screening of native substrates. Recent evidence from HIV-1 isolates obtained from individuals resistant to protease inhibitors has demonstrated that mutations distal to or surrounding the protease cleavage sites in the Gag substrate contribute to inhibitor resistance. We have developed a protease-substrate cleavage assay, termed the cleavage enzyme- cytometric bead array (CE-CBA), which relies on native domains of the Gag substrate containing embedded cleavage sites. The Gag substrate is expressed as a fluorescent reporter fusion protein, and substrate cleavage can be followed through the loss of fluorescence utilizing flow cytometry. The CE-CBA allows precise determination of alterations in protease catalytic efficiency (k(cat)/K(M)) imparted by protease inhibitor resistance mutations in protease and/or gag in cleavage or noncleavage site locations in the Gag substrate. We show that the CE-CBA platform can identify HIV-1 protease present in cellular extractions and facilitates the identification of small molecule inhibitors of protease or its substrate Gag. Moreover, the CE-CBA can be readily adapted to any enzyme-substrate pair and can be utilized to rapidly provide assessment of catalytic efficiency as well as systematically screen for inhibitors of enzymatic processing of substrate.
A probabilistic model for run-length coding of pictures (1959)

A first-order Markoff process representation for pictures is proposed in order to study the picture coding system known as run-length coding (differential-coordinate encoding). A lower bound for the saving in channel capacity is calculated on the basis of this model, and is compared with the results obtained by previous investigators. In addition, this representation is shown to yield an insight into the run-length coding system which might not otherwise be obtained. The application of this probabilistic model to an "elastic" system of run-length coding is also discussed.
ECG Paper Records Digitization through Image Processing Techniques (2012)

Electrocardiogram (ECG) is one of the most practiced methods to detect any abnormalities in heart function. ECG results are available as paper records. This leads to Archival and retrieval of patient's paper ECG records as a common practice for diagnosis of ailments. This process requires large storage space and extensive manual effort. This paper discusses method that involves processing of ECG paper records by an efficient and iterative set of digital image processing techniques for the conversion of ECG paper image data to time series digitized signal form, resulting in convenient storage and retrieval of ECG information. The method involves calculation of Heart rate, QRS Width and Stability (variation in R-R peaks) from the extracted signal. Comparison of the above calculated parameters with the manually calculated parameters shows an accuracy of 96.4%, hence proves the effectiveness of the process. This paper also proposes the development of fuzzy based ECG diagnosis system that assists the doctor in diagnosis.
Involvement of gut microbiota in the development of low-grade inflammation and type 2 diabetes associated with obesity (2012)

Obesity is associated with metabolic alterations related to glucose homeostasis and cardiovascular risk factors. These metabolic alterations are associated with low-grade inflammation that contributes to the onset of these diseases. We and others have provided evidence that gut microbiota participates in whole-body metabolism by affecting energy balance, glucose metabolism, and low-grade inflammation associated with obesity and related metabolic disorders. Recently, we defined gut microbiota-derived lipopolysaccharide (LPS) (and metabolic endotoxemia) as a factor involved in the onset and progression of inflammation and metabolic diseases. In this review, we discuss mechanisms involved in the development of metabolic endotoxemia such as the gut permeability. We also discuss our latest discoveries demonstrating a link between the gut microbiota, endocannabinoid system tone, leptin resistance, gut peptides (glucagon-like peptide-1 and -2), and metabolic features. Finally, we will introduce the role of the gut microbiota in specific dietary treatments (prebiotics and probiotics) and surgical interventions (gastric bypass).
LEFLUNOMIDE CONTROLS REJECTION IN HAMSTER TO RAT CARDIAC XENOGRAFTS (1994)

Leflunomide is an isoxazole derivative that has the ability to prevent acute rejection of cardiac, renal, and skin transplants in strongly rejecting rat models. Furthermore, leflunomide is able to interact synergistically with CsA to inhibit allograft rejection and also reverse ongoing allograft rejection. In vitro studies suggest that the mechanism of action of leflunomide is via an interruption of cytokine signaling in T cells. This study defines the ability of leflunomide to prevent and reverse rejection of concordant xenografts. One hundred nine adult Lewis rats in 13 groups received abdominal heterotopic cardiac transplants from Golden Syrian hamsters. The xenograft survived 3.9±0.3 days without treatment. When leflunomide was given at 2.5, 5, 10, 15, or 20 mg/kg by gavage daily, the cardiac xenograft survivals were 5.0±0.6, 8.0±3.0, 52.0±20.2, 76.5±21.14, and 58.9±28.1 days, respectively. The survival rates were 4.0±0 and 27.7±28.7 days when CsA was given at 10 and 20 mg/kg i.m., respectively. The combination of CsA at 10 mg/kg with leflunomide at 10 mg/kg or 5 mg/kg prolonged cardiac xenograft survival to 106.0±50.2 days and > 90 days, respectively. There were no observable side effects in the latter combination. Histologic studies of untreated graft hearts 4 days after transplantation revealed infarction of myocardium and severe RBC extravasation. In contrast, the rejected hamster hearts from long-term survivors showed massive mononuclear cell infiltration and myocardium fibrosis in contrast to the early rejected picture. Therapy with leflunomide begun on day 2 reversed these rejection responses by day 6. In addition, the increase in allospecific IgM titers observed on day 2 was reversed, and the allospecific IgM to IgG isotype switch that occurred in untreated animals was prevented by leflunomide. These observations demonstrate that leflunomide, at nontoxic doses, effectively controlled acute rejection of concordant xenografts and synergistic immunosuppressive effect was achieved with leflunomide and CsA.
Theoretical and experimental studies of ultrasound-modulated optical tomography in biological tissue (2000)

Ultrasound-modulated optical tomography in biological tissue was studied both theoretically and experimentally. An ultrasonic beam was focused into biological tissue samples to modulate the laser light passing through the ultrasonic beam inside the tissue. The ultrasound-modulated laser light reflects the local optical and mechanical properties in the ultrasonic beam and permits tomographic imaging of biological tissues by scanning. Parallel detection of the speckle field formed by the transmitted laser light was implemented with the source-synchronous-illumination lock-in technique to improve the signal-to-noise ratio. Two-dimensional images of biological tissues were successfully obtained experimentally with a laser beam at either normal or oblique incidence, which showed that ultrasound-modulated optical tomography depends on diffuse light rather than on ballistic light. Monte Carlo simulations showed that the modulation depth decreased much more slowly than the diffuse transmittance, which indicated the possibility that even thicker biological tissues can be imaged with this technique.
Monodisperse Multiwall Carbon Nanotubes Obtained with Ferritin as Catalyst (2002)

The iron-containing cores of ferritin were used as catalyst for the growth of patterned films of multiwall carbon nanotubes by chemical vapor deposition of C2H2 at 720 °C. The catalyst was delivered onto SiO2/Si substrates by microcontact printing and onto SiO/Cu transmission electron microscopy grids by dipping. The adjunction of Al(NO3)3·9H2O to ferritin has proven to be essential to prevent diffusion and coalescence of the catalyst particles and allows to produce monodisperse carbon nanotubes with an outer diameter of 5.2 ± 0.6 nm, which represents a significant improvement compared to existing solutions.
A Study Quantifying the Hand-to-Face Contact Rate and Its Potential Application to Predicting Respiratory Tract Infection (2008)

A substantial portion of human respiratory tract infection is thought to be transmitted via contaminated hand contact with the mouth, eyes, and/or nostrils. Thus, a key risk factor for infection transmission should be the rate of hand contact with these areas termed target facial membranes. A study was conducted in which 10 subjects were each videotaped for 3 hr while performing office-type work in isolation from other persons. The number of contacts to the eyes, nostrils, and lips was scored during subsequent viewing of the tapes. The total contacts per subject had sample mean x = 47 and sample standard deviation s = 34. The average total contact rate per hour was 15.7. The authors developed a relatively simple algebraic model for estimating the dose of pathogens transferred to target facial membranes during a defined exposure period. The model considers the rate of pathogen transfer to the hands via contact with contaminated environmental surfaces, and the rate of pathogen loss from the hands due to pathogen die-off and transfer from the hands to environmental surfaces and to target facial membranes during touching. The estimation of infection risk due to this dose also is discussed. A hypothetical but plausible example involving influenza A virus transmission is presented to illustrate the model.