gebhart/patrepeval huggingface dataset:
Folic acid derived-P5779 mimetics regulate DAMP-mediated inflammation through disruption of HMGB1:TLR4:MD-2 axes (2018)

High mobility group box 1 (HMGB1) is a damage-associated molecular pattern (DAMP) protein that mediates inflammatory responses after infection or injury. Previously, we reported a peptide inhibitor of HMGB1 (P5779) that acts by directly interrupting HMGB1/MD-2 binding. Here, fingerprint similarity search and docking studies suggest folic acid derived-drugs function as P5779 mimetopes. Molecular dynamic (MD) simulation studies demonstrate that folic acid mimics the binding of P5779 at the TLR4 and MD-2 intersection. In surface plasmon resonance (SPR) studies, these drugs showed direct binding to TLR4/MD-2 but not HMGB1. Furthermore, these P5779 mimetopes inhibit HMGB1 and MD-2 binding and suppress HMGB1-induced TNF release in human macrophages in the nanomolar range. We assert from our findings that their demonstrated anti-inflammatory effects may be working through TLR4-dependent signaling.
The Adjuvant Effect of Pertussis Vaccine in Experimental Thyroiditis of the Rat (1969)

Single injections of rat thyroid extract with complete Freund adjuvant were not consistent in eliciting significant thyroid pathology in Lewis rats. Identical treatment accompanied by a simultaneous but separate injection of 100 billion killed pertussis organisms was consistently effective in inducing marked thyroid changes at an earlier time. Lewis rats developed thyroid lesions approximately 1 week earlier than Fischer 344 rats receiving the same treatment. Pertussis vaccine also seemed to increase the level of circulating autoantibodies to thyroid.
Evaluating the performance limitations of MPMD communication (1997)

The MPMD approach for parallel computing is attractive for programmers who seek fast development cycles, high code re-use, and modular programming, or whose applications exhibit irregular computation loads and communication patterns. RPC is widely adopted as the communication abstraction for crossing address space boundaries. However, the communication overheads of existing RPC-based systems are usually an order of magnitude higher than those found in highly tuned SPMD systems. This problem has thus far limited the appeal of high-level programming languages based on MPMD models in the parallel computing community. This paper investigates the fundamental limitations of MPMD communication using a case study of two parallel programming languages, Compositional C++ (CC++) and Split-C, that provide support for a global name space. To establish a common comparison basis, our implementation of CC++ was developed to use MRPC, a RPC system optimized for MPMD parallel computing and based on Active Messages. Basic RPC performance in CC++ is within a factor of two from those of Split-C and other messaging layers. CC++ applications perform within a factor of two to six from comparable Split-C versions, which represent an order of magnitude improvement over previous CC++ implementations. The results suggest that RPC-based communication can be used effectively in many high-performance MPMD parallel applications.
Cloning and expression of a widely distributed (type IV) adenylyl cyclase. (1991)

We have cloned and expressed a cDNA that encodes a widely distributed form of mammalian adenylyl cyclase (EC 4.6.1.1). Although those adenylyl cyclases described previously have a rather narrow tissue distribution, this enzyme (type IV) is apparently synthesized in a variety of peripheral tissues and in the central nervous system. The protein resembles the other adenylyl cyclases in its proposed structure. It most resembles the type II adenylyl cyclase described in the preceding paper [Feinstein, P. G., Schrader, K. A., Bakalyar, H. A., Tang, W.-J., Krupinski, J., Gilman, A. G. & Reed, R. R. (1991) Proc. Natl. Acad. Sci. USA 88, 10173-10177] in its amino acid sequence, lack of response to calmodulin, and synergistic activation by a combination of the Gs alpha subunit and the G-protein beta gamma subunit complex.
Evaluation of monoclonal antibody DF3 conjugated with ricin as a specific immunotoxin for in vitro purging of human bone marrow. (1990)

DF3 is an IgG1 monoclonal antibody (MAb) generated against a Mr 350,000-400,000 glycoprotein expressed by approximately 80% of human breast cancers. We have coupled MAb DF3 to ricin. Purification of the immunotoxin (DF3-IT) was obtained by affinity and size exclusion chromatography. DF3 antigen-positive breast cancer cell lines (ZR-75-1, BT-20, and MCF-7) and DF3 antigen-negative lung cancer cell lines (A549 and CALU6) were tested for cytotoxicity with metabolic labeling and clonogenic assays. The cells were exposed for 3 h to different concentrations of DF3-IT, MAb DF3, ricin, and a combination of unconjugated MAb DF3 and ricin. In the presence of 100 mM lactose, DF3-IT specifically inhibited protein synthesis of lines expressing DF3 antigen on their cell surface. Moreover, clonogenic survival experiments demonstrated that DF3-IT at a concentration of 1 x 10(-9) M specifically kills 2.6-2.8 log of ZR-75-1 and BT-20 cells and 1.6 log of MCF-7 cells. At the same concentration, nonspecific toxicity of DF3-IT resulted in a 30% reduction of bone marrow granulocyte and macrophage colony formation. In bone marrow-purging experiments, tumor cells were mixed with an excess of bone marrow cells and treated with DF3-IT or ricin. Tumor cell clonogenic survival assays demonstrated that the presence of bone marrow cells had no detectable effect on activity or specificity of the DF3-IT. These results thus indicate that MAb DF3 is an effective vehicle to specifically deliver toxins to cancer cells which express DF3 antigen on their surface and that DF3-IT may be useful for in vitro purging of bone marrow.
Sites for Antagonism on the N-Methyl-D-Aspartate Receptor Channel Complex (1991)

Heme oxygenases (HO) catabolize free heme, that is, iron (Fe) protoporphyrin (IX), into equimolar amounts of Fe2+, carbon monoxide (CO), and biliverdin. The stress-responsive HO-1 isoenzyme affords protection against programmed cell death. The mechanism ...Read More
Rapid Mutation of Spirulina platensis by a New Mutagenesis System of Atmospheric and Room Temperature Plasmas (ARTP) and Generation of a Mutant Library with Diverse Phenotypes (2013)

In this paper, we aimed to improve the carbohydrate productivity of Spirulina platensis by generating mutants with increased carbohydrate content and growth rate. ARTP was used as a new mutagenesis tool to generate a mutant library of S. platensis with diverse phenotypes. Protocol for rapid mutation of S. platensis by 60 s treatment with helium driven ARTP and high throughput screening method of the mutants using the 96-well microplate and microplate reader was established. A mutant library of 62 mutants was then constructed and ideal mutants were selected out. The characteristics of the mutants after the mutagenesis inclined to be stable after around 9(th) subculture, where the total mutation frequency and positive mutation frequency in terms of specific growth rate reached 45% and 25%, respectively. The mutants in mutant library showed diverse phenotypes in terms of cell growth rate, carbohydrate content and flocculation intensity. The positive mutation frequency in terms of cellular carbohydrate content with the increase by more than 20% percent than the wild strain was 32.3%. Compared with the wild strain, the representative mutants 3-A10 and 3-B2 showed 40.3% and 78.0% increase in carbohydrate content, respectively, while the mutant 4-B3 showed 10.5% increase in specific growth rate. The carbohydrate contents of the representative mutants were stable during different subcultures, indicating high genetic stability. ARTP was demonstrated to be an effective and non-GMO mutagenesis tool to generate the mutant library for multicellular microalgae.
Automatic Cloud I/O Configurator for I/O Intensive Parallel Applications (2014)

As the cloud platform becomes a promising alternative to traditional HPC (high performance computing) centers or in-house clusters, the I/O bottleneck problem is highlighted in this new environment, typically with top-of-the-line compute instances but sub-par communication and I/O facilities. It has been observed that changing the cloud I/O system configurations, such as choices of file systems, number of I/O servers and their placement strategies, etc., will lead to a considerable variation in the performance and cost efficiency of I/O intensive parallel applications. However, storage system configuration is tedious and error-prone to do manually, even for expert users, leading to solutions that are grossly over-provisioned (low cost inefficiency), substantially under-performing (poor performance) or, in the worst case, both. This paper proposes ACIC, a system which automatically searches for optimized I/O system configurations from many candidates for each individual application running on a given cloud platform. ACIC takes advantage of machine learning models to perform performance/cost predictions. To tackle the high-dimensional parameter exploration space, we enable affordable, reusable, and incremental training on cloud platforms, guided by the Plackett and Burman Matrices for experiment design. Our evaluation results with four representative parallel applications indicate that ACIC consistently identifies optimal or near-optimal configurations among a large group of candidate settings. The top ACIC-recommended configuration is capable of improving the applications' performance by a factor of up to 10.5 (3.1 on average), and cost saving of up to 89 percent (51 percent on average), compared with a commonly used baseline I/O configuration. In addition, we carried out a small-scale user study for one of the test applications, which found that ACIC consistently beat the user and even the application's developer, often by a significant margin, in selecting optimized configurations.
Irreversible encryption method by generation of polynomials (1996)

Patient follow up, within the framework of epidemiological studies, poses the problem of linking nominal files. An encryption method of identity is proposed to allow the linkage of medical information on the same patient while respecting the confidentiality of medical data. In contrast with most encryption algorithms, the proposed method is mathematically irreversible in response to the requirement of the French National Commission of Computerized Information Security which demands that the cryptosystem must not be decipherable even by the legitimate recipient. In order to prevent deciphering by frequency analysis, the proposed method introduces polynomial operations so that neither indication concerning the length of the string nor a possible repetition of characters can be obtained by code disclosure. The security of the system is reinforced by the use of two keys, the first one to be defined by the producers of information and the second one by the recipient so that nobody can decrypt the enciphered text.
Synthesis of a Novel Class of Polyhydroxyalkanoates in Arabidopsis Peroxisomes, and Their Use in Monitoring Short-Chain-Length Intermediates of β-Oxidation (2002)

The poly[(R)-3-hydroxyalkanoate] (PHA) synthase gene (phaC(Ac)) of Aeromonas caviae FA440 was modified by adding a peroxisome targeting signal encoding the last 10 amino acids at the carboxyl-terminal of spinach glycolate oxidase. The modified gene was introduced into Arabidopsis thaliana plants by Agrobacterium-mediated transformation. The transgenic Arabidopsis plant expressed the introduced gene and its protein, and it accumulated PHA in its tissues. Gas chromatography-mass spectrometry analysis demonstrated the accumulation of a novel type of PHA, poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-3-hydroxyhexanoate). This strongly suggests that short-chain-length (R)-3-hydroxyacyl-CoAs were generated from intermediates of peroxisomal beta-oxidation. It was revealed by using this transgenic plant that Tween-20 can activate peroxisomal beta-oxidation of short-chain-length fatty acids.
Pathogen and autoantigen homologous regions within the cystic fibrosis transmembrane conductance regulator (CFTR) protein suggest an autoimmune treatable component of cystic fibrosis (2011)

The cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel provides the glutathione and hypochlorous acid necessary for bactericidal/viricidal actions. CFTR mutations block these effects, diminishing pathogen defence and allowing extracellular pathogen accumulation, where antibody encounter is likely. KEGG pathway analysis of the CFTR interactome shows that CFTR is involved in pathogen entry pathways and immune defence as well as in pathways relevant to comorbid conditions (diabetes, cardiomyopathies and sexual organ development). Pseudomonas aeruginosa and Staphylococcus aureus infections decrease the lifespan of cystic fibrosis patients and Stenotrophomonas maltophilia colonization is increased. Autoantibodies, targeting myeloperoxidase, the bactericidal/permeability-increasing protein and calgranulin may further compromise pathogen defence. Short consensus sequences, within immunogenic extracellular regions of the CFTR protein, are homologous to proteins expressed by P. aeruginosa, S. aureus and S. maltophilia, and to several autoantigens, with a universal overlap between autoantigen/pathogen/CFTR consensi. Antibodies to pathogens are thus likely responsible for the creation of these autoantibodies, which, with pathogen antibodies, may target the CFTR protein acting as antagonists, further compromising its function. This creates a feedforward cycle, diminishing the function of the CFTR protein and increasing the probability of pathogen accumulation and antibody production at every turn. Interruption of this cycle by antibody adsorption or immunosuppressant therapy may be beneficial in cystic fibrosis.
Measurement of Differences in Timing and Sequence Between Two Ventricular Electrodes as a Means of Tachycardia Differentiation (1986)

The use of two ventricular sensing electrodes to determine electrical activation sequence could provide a method for differentiation of normal from abnormal rhythms by implantable antitachycardia devices. Simultaneous recordings from two ventricular sites were obtained during dual chamber pacemaker implantation (5/8 patients), cardioverter-defibrillator implantation (2/8 patients), or programmed electrical stimulation study (1/8 patients). Recordings were made in normal sinus rhythm (NSR) (5 beats each in 8/8 patients), during ventricular tachycardia (VT) (38 beats with 7 morphologies in 3 patients) and during premature ventricular contractions (PVCs) (20 beats with 8 morphologies in 6 patients). Leads were placed transvenously in the right ventricle in 6 patients, and epicardially on the left ventricle in two. Intervals between the intrinsic deflection of the two ventricular electrograms ranged from 0 to 91 ms (mean of 26 ms) during NSR, from 13 to 141 ms (mean of 66 ms) during VT, and from 10 to 72 ms (mean of 40 ms) during PVCs and were reproducible within each patient for each type of rhythm. In all patients, the difference in sequence and timing between the dual electrograms in NSR beats vs. ectopic beats allowed for the differentiation of normal and abnormal complexes. These differences in each patient ranged from 23 to 210 ms (mean of 81 ms) during VT and from 3 to 89 ms (mean of 44 ms) during PVCs. Fourteen of the 15 ectopic morphologies exhibited greater than 20 ms difference in timing compared to their corresponding NSR beats. Combined with the appropriate software, multiple ventricular leads may be used by antitachycardia devices to discriminate between normal and abnormal ventricular activity.
Modulation of Endoplasmic Reticulum Calcium Pump Expression during T Lymphocyte Activation (1997)

Calcium mobilization from intracellular storage organelles is a key component of the second messenger system inducing cell activation. Calcium transport ATPases associated with intracellular calcium storage organelles play a major role in controlling this process by accumulating calcium from the cytosol into intracellular calcium pools. In this study the modulation of the expression of the sarco-endoplasmic reticulum calcium transport ATPase (SERCA) isoenzymes has been studied in lymphocytes undergoing phorbol myristate acetate and ionomycin-induced activation. In several T lymphocyte cell lines a combined treatment by the two drugs resulted in an approximately 90% decrease of the expression of the calcium pump isoform recognized by the PLIM430 isoform-specific antibody, whereas the expression of the SERCA 2b isoform was increased approximately 2-fold. Phorbol ester or ionomycin applied separately was ineffective. In Jurkat T cells the down-modulation of expression of the SERCA isoform recognized by the PLIM430 antibody appeared concomitantly with the induction of interleukin-2 expression and could be inhibited by the immunosuppressant drug cyclosporine-A. These data indicate that T cell activation induces a selective and cyclosporine-A-sensitive modulation of the expression of the SERCA calcium pump isoforms. This reflects a profound reorganization of the calcium homeostasis of T cells undergoing activation and may open new avenues in the understanding of the plasticity of the calcium homeostasis of differentiating cells and in the pharmacological modulation of lymphocyte function.
Biomarker and cytologic abnormalities in women at high and low risk for breast cancer (1993)

Fine needle aspirates (FNA) from 106 high-risk women and 25 low-risk women were evaluated for overexpression of estrogen receptor (ER), epidermal growth factor receptor (EGFR), mutant p53, and HER-2/neu by immunocytochemistry, and for aneuploidy by image analysis. Aspirates were also classified cytologically as normal, apocrine metaplasia, epithelial hyperplasia (EH), or dysplasia. High-risk women were those with a first-degree relative with breast cancer (76%), precancerous breast disease (26%), prior cancer of the contralateral breast (9%), or multiple abnormalities (11%). Low-risk women had none of the above risk factors, nor a prior breast biopsy or clinical evidence of fibrocystic disease. The median 10-year Gail risk for the high-risk group was 4%, compared to 0.7% for the low-risk group. There were significant differences (p < 0.01) between high- and low-risk women in the prevalences of hyperplasia (55% versus 12%), dysplasia (19% versus 0%), aneuploidy (32% versus 0%), overexpressed EGFR (32% versus 4%), and overexpressed p53 (29% versus 4%). The prevalence of multiple biomarker abnormalities was also greater in high-risk than in low-risk women (28% versus 0%; p < 0.01). Four percent (4%) of FNAs from high-risk women with normal cytology, 29% of aspirates with hyperplastic cytology, and 60% of those with dysplasia were associated with two or more biomarker abnormalities. The differences in the prevalence of multiple biomarker abnormalities among various cytologic categories were statistically significant (p = 0.02, normal versus EH; p = 0.02, EH versus dysplasia; p < 0.01, normal versus dysplasia).(ABSTRACT TRUNCATED AT 250 WORDS)
Improved performance of an optically pumped FIR laser using metallic waveguide (1992)

In order to improve the overall output characteristics of far-infrared (FIR) lasers, recent development at UCLA has concentrated on the use of a metallic overmoded waveguide (smooth bore and corrugated) instead of a conventional smooth-bore dielectric waveguide. The metallic waveguide has substantially lower propagation losses, especially at frequencies below 500 GHz, and also supports the desired HE11 mode. Laboratory results show a substantial increase in output power using a corrugated metallic waveguide, with 37 mW being obtained at 1.22 mm using 13CH3F (isotopic methyl fluoride) while maintaining the same mode quality and polarization. This represents an improvement of 100% over a smooth-bore dielectric waveguide. Comparison of far-infrared output using the three types of waveguide will be made.
RIG-I Like Receptors in Antiviral Immunity and Therapeutic Applications (2011)

The RNA helicase family of RIG-I-like receptors (RLRs) is a key component of host defense mechanisms responsible for detecting viruses and triggering innate immune signaling cascades to control viral replication and dissemination. As cytoplasm-based sensors, RLRs recognize foreign RNA in the cell and activate a cascade of antiviral responses including the induction of type I interferons, inflammasome activation, and expression of proinflammatory cytokines and chemokines. This review provides a brief overview of RLR function, ligand interactions, and downstream signaling events with an expanded discussion on the therapeutic potential of targeting RLRs for immune stimulation and treatment of virus infection.
Antimicrobial Drug Susceptibility of Staphylococcus aureus Strains Isolated from Bovine and Ovine Mammary Glands (2003)

The activity of selected antimicrobial agents against Staphylococcus aureus was determined with the agar disk diffusion test to determine the diameter of the zone of inhibition and the E-test for determination of the minimal inhibitory concentration (MIC). The 92 S. aureus strains used in this study were isolated from bovine (n = 76) and ovine (n = 16) intramammary infections. Four antibiotics, which are frequently used in mastitis therapy were chosen: penicillin-G, ampicillin, kanamycin, and cephalexine. The fifth compound (oxacillin) was used to detect methicillin-resistant S. aureus, but no such strains could be found. According to the evaluation criteria, 65.2 (penicillin) to 93.5% (kanamycin, cephalexine) S. aureus strains were susceptible to the antibiotics tested. Ovine S. aureus strains reveal a lower resistance rate than bovine isolates. Comparison of the results of the two methods of susceptibility testing shows, with exception of penicillin and ampicillin, satisfactory agreement. Analyzing the results of the MIC endpoints and the zone diameter values, very major errors, according to the error rate bounded method of Metzler and DeHaan, occurred at an error rate of 3.3% for penicillin and 3.8% for ampicillin.
The Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI): A Completed Reference Database of Lung Nodules on CT Scans (2011)

The LIDC/IDRI Database is expected to provide an essential medical imaging research resource to spur CAD development, validation, and dissemination in clinical practice.
Benzimidazoles and congeneric tricyclic compounds (1980)

Benzimidazoles (P. N. Preston). Benzimidazole N-Oxides (D. M. Smith). Dihydroenzimidazoles, Benzimidazolones, Benzimidazolethiones and Related Compounds (D. M. Smith). Condensed Benzimidazoles of Type 5-6-5 (G. Tennant). Condensed Benzimidazoles of Type 6-6-5 (P. N. Preston and G. Tennant). Index.
Synthesis and properties of diastereoisomers of adenosine 5'-(O-1-thiotriphosphate) and adenosine 5'-(O-2-thiotriphosphate) (1976)

The chemical synthesis of adenosine 5'-(O-1-thiotriphosphate) (ATPalphaS) and adenosine 5'-(O-2-thiotriphosphate) (ATPbetaS) is described. Both exist as a pair of diastereomers, A and B. The isomers of ATPalphaS can be distinguished on the basis of their different reaction rates with myokinase as well as nucleoside diphosphate kinase. With both enzymes, isomer A reacts fast whereas isomer B reacts considerably more slowly. Phosphorylation of a mixture of isomers of ADPalphaS with pyruvate or acetate kinase yields ATPalphaS, isomer A, whereas the phosphoryl transfer with creatine or arginine kinase yields isomer B. The isomers of ATPbetaS differ in their reactivity with myosin. Isomer A is readily hydrolyzed, whereas isomer B is not. However, isomer B reacts faster with nucleoside diphosphate kinase and ADP than isomer A. Phosphoryl transfer with pyruvate kinase onto ADPbetaS yields ATPbetaS, isomer A, with acetate kinase, isomer B.