gebhart/patrepeval huggingface dataset:
Protection of channel catfish, Ictalurus punctatus Rafmesque, against Ichthyophthirius multifiliis Fouquet by immunization (1980)

Channel catfish, Ictalurus punctatus Rafmesque, were immunized with ciliary and whole cell preparations of Ichthyophthirius multifiliis and subsequently challenged with I. multi‐filiis . Similar Telrahymena pyriformis preparations were used to determine if this heterologous immunization would elicit a protective immune response against I. mullifiliis infestation. Results indicate that T. pyriformis ciliary antigens provided the greatest degree of protection.
Biology of Ductal Carcinoma in Situ Classification Based on Biologic Potential (2006)

Incidence of ductal carcinoma in situ (DCIS) has increased significantly during the last decade, comprising almost 20% of all breast cancers diagnosed today. DCIS is composed of malignant breast duct epithelial cells that have clonally proliferated and accumulated within the mammary duct lumen. It comprises a group of heterogeneous tumors with varying biologic behavior rendering its classification and management challenging. By definition, DCIS does not invade through the basement membrane; it is a preinvasive malignancy and systemic disease is nonexistent. The basis of treatment is to prevent progression into an invasive cancer such as ductal carcinoma. Most current DCIS classification schemes do not predict its potential to progress to invasive disease. In this review the natural history of DCIS, as it relates to its biologic potential to progress to invasive disease, is summarized, and a broad classification system that may provide a guideline for patient management is proposed.
GENETIC SUSCEPTIBILITY TO SYSTEMIC LUPUS ERYTHEMATOSUS (1998)

Considerable evidence suggests that the development of systemic lupus erythematosus (SLE) has a strong genetic basis. Recent studies have emphasized that this disease, like other autoimmune diseases, is a complex genetic trait with contributions from major histocompatibility complex (MHC) genes and multiple non-MHC genes. Etiologic genes in these disorders determine susceptibility, and no particular gene is necessary or sufficient for disease expression. Studies of murine models of lupus have provided important insight into the immunopathogenesis of IgG autoantibody production and lupus nephritis, and genetic analyses of these mice overcome certain obstacles encountered when studying patients. Genome-wide linkage studies of different crosses have mapped the position of at least 12 non-MHC disease-susceptibility loci in the New Zealand hybrid model of lupus. Although the identity of the actual genes is currently unknown, recent studies have begun to characterize how these genetic contributions may function in the autoimmune process, especially in terms of their role in autoantibody production. Studies of MHC gene contributions in New Zealand mice have shown that heterozygosity for particular haplotypes greatly increases pathogenic autoantibody production and the incidence of severe nephritis. The mechanism for this effect appears to be genetically complex. Studies in human SLE have mostly focused on the association of disease with alleles of immunologically relevant genes, especially in the MHC. Associations with various complement component deficiencies and an allele of a particular Fc gamma receptor gene (FCGR2A) also have been described. In a diversion from previous association studies, a recent directed linkage analysis of sibpairs with SLE was based on mapping studies in murine lupus and may be an important step toward identifying a new disease-susceptibility gene in patients. Since the genes that predispose to autoimmunity are probably related to key events in pathogenesis, their identification in patients and murine models will almost certainly provide important insight into the breakdown of immunological self-tolerance and the cause of autoimmune disease.
gyrA Mutations in high-level fluoroquinolone-resistant clinical isolates of Escherichia coli (1996)

Double mutations in the quinolone resistance determining region of the gyrase A gene (gyrA) have recently been reported to be associated with high-level resistance to fluoroquinolones in clinical isolates of Escherichia coli. We examined the type and frequency of such mutations in a large number of clinical isolates that were obtained from ten different geographical locations and had been genotypically characterized by pulsed field gel electrophoresis (PFGE) of chromosomal DNA digests. Of 36 isolates with ofloxacin MICs > or = 4 mg/L that represented at least 24 distinct genotypes, 35 had double mutations at amino acid codons 83 and 87 of gyrA, while two isolates with ofloxacin MICs of 0.5 and 4 mg/L, respectively, each had a single mutation at codon 83. Mutations at codon Ser-83 were uniform, resulting in substitution by Leu. The additional mutations at amino acid codon 87 in the 35 double-mutants were diverse, resulting in Asp-87 substitutions by residues Asn (23 isolates), Gly (7 isolates), Tyr (4 isolates), or His (1 isolate) without a discernable correlation with fluoroquinolone MICs or with phenotypic resistance to chemically unrelated antibacterial agents. Maximal differences between MICs of double-mutants with the same amino acid substitution were eight-fold. The changes of amino acid residues at codon Asp-87 differed between individual patient isolates with the same genotype (and similar MICs), suggesting that the amino acid codon 87 mutations (and possibly the development of high-level fluoroquinolone resistance) might have occurred after the transmission and sharing of a precursor strain carrying the Ser-83-->Leu mutation.
Doxorubicin-induced congestive heart failure in adults (1985)

The prognosis of doxorubicin-induced congestive heart failure (CHF) is reported to be poor. To define the clinical course of doxorubicin-induced CHF, the authors reviewed their experience with 43 patients with this diagnosis. The median age of the total group was 55 years (range, 23-69); the median cumulative dose of doxorubicin was 450 mg/m2 (range, 200 mg/m2-1150 mg/m2). A majority of the patients had a diagnosis of breast cancer. The median survival of the whole group estimated by means of a Kaplan-Meier plot was 112 weeks. Twelve of 43 patients (28%) died of CHF, 7 of them (16%) because of fulminant failure in less than 8 weeks and the remaining 5 because of a more protracted course with recurrent episodes of cardiac decompensation. Twenty-five of the 43 patients (58%) achieved complete control of CHF. In the remaining 6 patients (14%), CHF had improved but was not completely controlled at the time of death, which was secondary to progressive tumor. Treatment consisted of standard therapy with digitalis and diuretics. Survival was significantly shorter in patients who presented with class IV dyspnea and in those who developed CHF less than 4 weeks after administration of the last dose of doxorubicin. The authors conclude that in a majority of patients, doxorubicin-induced CHF is easily treatable and frequently controlled with digitalis and diuretics.
A quantitative model of the security intrusion process based on attacker behavior (1997)

The paper is based on a conceptual framework in which security can be split into two generic types of characteristics, behavioral and preventive. Here, preventive security denotes the system's ability to protect itself from external attacks. One way to describe the preventive security of a system is in terms of its interaction with the alleged attacker, i.e., by describing the intrusion process. To our knowledge, very little is done to model this process in quantitative terms. Therefore, based on empirical data collected from intrusion experiments, we have worked out a hypothesis on typical attacker behavior. The hypothesis suggests that the attacking process can be split into three phases: the learning phase, the standard attack phase, and the innovative attack phase. The probability for successful attacks during the learning and innovative phases is expected to be small, although for different reasons. During the standard attack phase it is expected to be considerably higher. The collected data indicates that the breaches during the standard attack phase are statistically equivalent and that the times between breaches are exponentially distributed. This would actually imply that traditional methods for reliability modeling could be applicable.
Overview of the IGF-I System (2006)

• The IGF system is the major mediator of both intra-uterine and postnatal growth. • The IGF-I receptor appears to mediate the growth-promoting effects of both IGF-I and IGF-II. • The role of IGF binding proteins in mediating the growth-promoting actions of the IGFs is complex and remains incompletely understood.
ChemInform Abstract: Synthesis and Fungicidal Activity of Some 3,7‐Diaryl‐6‐cyanorhodanino(4,5‐b)pyridin‐5(4H)‐ones and 3‐Arylrhodanino(4,5‐b)furan‐6(5H)‐ones. (1990)

Abstract Compounds (V) possess a higher fungicidal activity than compounds (VII).
Ionic Liquids in Chemical Engineering (2010)

The development of engineering applications with ionic liquids stretches back to the mid-1990s when the first examples of continuous catalytic processes using ionic liquids and the first studies of ionic liquid-based extractions were published. Ever since, the use of ionic liquids has seen tremendous progress in many fields of chemistry and engineering, and the first commercial applications have been reported. The main driver for ionic liquid engineering applications is to make practical use of their unique property profiles, which are the result of a complex interplay of coulombic, hydrogen bonding and van der Waals interactions. Remarkably, many ionic liquid properties can be tuned in a wide range by structural modifications at their cation and anion. This review highlights specific examples of ionic liquid applications in catalysis and in separation technologies. Additionally, the application of ionic liquids as working fluids in process machines is introduced.
Bovine respiratory syncytial virus nucleocapsid protein: mRNA sequence analysis and expression from recombinant vaccinia virus vectors (1992)

The nucleotide sequence of the mRNA encoding the nucleocapsid (N) protein of bovine respiratory syncytial (BRS) virus, strain 391-2, was determined. Recombinant vectors containing a cDNA of the complete N gene were constructed, and expression of the N protein in eukaryotic cells was demonstrated using two different vector systems. The BRS virus N mRNA was 1197 nucleotides in length, exclusive of poly(A), and had a single major open reading frame that encoded a polypeptide of 391 amino acids with a calculated M(r) of 42.6K. The nucleotide and amino acid sequences of the BRS virus N gene were compared to those of human respiratory syncytial (HRS) virus strains A2 and 18537, and to BRS virus strain A51908. The level of nucleic acid identity between the N mRNA of BRS virus 391-2 and both HRS virus subtypes was 80 to 81%, whereas the identity between the two BRS virus strains was 97%. A 93 to 94% level of identity was observed between the deduced amino acid sequences of the N protein of BRS virus 391-2 and the corresponding sequences of the two HRS virus strains. The two BRS virus N proteins differed in amino acid sequence at only three positions. Recombinant BRS virus N protein was expressed using two different vector systems: in cells from a plasmid using the vaccinia virus/T7 polymerase expression system or from a recombinant vaccinia virus. N proteins synthesized by the two vector systems migrated with an electrophoretic mobility identical to that of authentic BRS virus N protein, and were precipitated by anti-BRS virus antibodies.
The synthesis of isotopically labelled glucosinolates for analysis and metabolic studies (2007)

Abstract Glucosinolates are dietary natural products with important cancer chemoprevention properties. The syntheses of a number of stable isotopically labelled ( 2 H, 13 C) glucosinolates, and their desulfo‐analogues, are described. These compounds are used as internal standards for analysis and for metabolic studies. Copyright © 2007 John Wiley &amp; Sons, Ltd.
Dietary flavone is a potent apoptosis inducer in human colon carcinoma cells. (2000)

Flavonoids are polyphenolic compounds that occur ubiquitously in plants. They are discussed to represent cancer preventive food components in a human diet that is rich in fruits and vegetables. To understand the molecular basis of the putative anticancer activity of flavonoids, we investigated whether and how the core structure of the flavones, 2-phenyl-4H-1-benzopyran-4-one (flavone) affects proliferation, differentiation, and apoptosis in HT-29 human colon cancer cells. Moreover, the effects of flavone in transformed epithelial cells were compared with those obtained in nontransformed primary mouse colonocytes. Proliferation, differentiation, and apoptosis in transformed as well as nontransformed colon cells were measured by fluorescence-based techniques. Apoptosis was also determined by changes in membrane permeability, FACScan analysis, and detection of DNA fragmentation. Semiquantitative reverse transcription PCR was performed to assess the effects of flavone on transcript levels. Flavone was found to reduce cell proliferation in HT-29 cells with an EC(50) value of 54.8 +/- 1.3 microM and to potently induce differentiation as well as apoptosis. The flavonoid proved to be a stronger apoptosis inducer than the clinically established antitumor agent camptothecin. The effects of flavone in HT-29 cells were associated with changed mRNA levels of cell-cycle- and apoptosis-related genes including cyclooxygenase-2 (COX-2), nuclear transcription factor kappaB (NF-kappaB), and bcl-X(L). Moreover, flavone, but not camptothecin, displayed a high selectivity for the induction of apoptosis and of growth inhibition only in the transformed colonocytes. In conclusion, the plant polyphenol flavone induces effectively programmed cell death, differentiation, and growth inhibition in transformed colonocytes by acting at the mRNA levels of genes involved in these processes. Because these genes play a crucial role in colon carcinogenesis, flavone may prove to be a potent new cytostatic compound with improved selectivity toward transformed cells.
Cytochrome C oxidase and chronic obstructive pulmonary disease (2008)

Cytoehrome Coxidase(COX)is a key oxidative enzyme because,as the terminal comDlex of the mitoehondrial electron transport chain,it catalyzes the oxidation of reduced cytochrome C by oxygen.Thus,a better understanding of the role of COX in chronic obstructive pulmonary disease(COPD)patients and pathogenesis of COPD can provide a more comprehensive knowledge of COPD.

Key words: 
Cytochrome C oxidase; Chronic obstructive pulmonary disease; 0xidative stress; Apoptosis
Tumor-Secreted LOXL2 Activates Fibroblasts through FAK Signaling (2013)

These findings reveal new insight into the mechanisms of fibroblast activation, a novel function of LOXL2, and further highlight the importance of generating LOXL2-targeted therapies for the prevention of tumor progression and metastasis.
Activated endothelial cells induce apoptosis in lymphoma cells (1997)

We have previously shown that the arrest or regression of mouse liver metastases formed by lacZ-transduced ESbL T lymphoma cells (ESbL-lacZ) is associated with the stimulation of nitric oxide (NO) production by liver endothelial cells in sis. Here we studied in vitro the NO-mediated cytotoxicity against ESbL-lacZ target cells using well-characterized bovine endothelial cells (BEG) as effector cells. It was found that the co-culture of BEC with human TNF-alpha caused an increase of NO synthesis which could be completely blocked by the treatment with inducible NO synthase (iNOS) inhibitor N-G-monomethyl-L-arginine (NMMA). Incubation of activated BEC with metastatic lymphoma cells led to the death of the latter cells as evidenced by staining with propidium iodide and FAGS analysis. This cytotoxicity was considerably reduced after pretreatment of BEC with NMMA. Cytotoxic effects were also demonstrated after incubation of tumor cells with NO donor glycerol trinitrate (GTN). Non-activated BEC were not able to produce NO and showed a substantially lower level of cytotoxicity. The anti-tumor cytotoxicity exerted by activated BEC includes the stimulation of apoptosis in metastatic lymphoma cells which is mediated to a large extent by NO. These data reveal a novel role of endothelial cells in the elimination of metastatic cells through the induction of programmed cell death.
An overview on the existing language models for prediction systems as writing assistant tools (2009)

The prediction task in national language processing means to guess the missing letter, word, phrase, or sentence that likely follow in a given segment of a text. Since 1980s many systems with different methods were developed for different languages. In this paper an overview of the existing prediction methods that have been used for more than two decades are described and a general classification of the approaches is presented. The three main categories of the classification are statistical modeling, knowledge-based modeling, and heuristic modeling (adaptive).
Rational Design of a Peptide Agonist That Interacts Selectively with the Orphan Receptor, Bombesin Receptor Subtype 3 (2001)

The orphan receptor, bombesin (Bn) receptor subtype 3 (BRS-3), shares high homology with bombesin receptors (neuromedin B receptor (NMB-R) and gastrin-releasing peptide receptor (GRP-R)). This receptor is widely distributed in the central nervous system and gastrointestinal tract; target disruption leads to obesity, diabetes, and hypertension, however, its role in physiological and pathological processes remain unknown due to lack of selective ligands or identification of its natural ligand. We have recently discovered (Mantey, S. A., Weber, H. C., Sainz, E., Akeson, M., Ryan, R. R. Pradhan, T. K., Searles, R. P., Spindel, E. R., Battey, J. F., Coy, D. H., and Jensen, R. T. (1997) J. Biol. Chem. 272, 26062-26071) that [d-Tyr(6),beta-Ala(11),Phe(13),Nle(14)]Bn-(6-14) has high affinity for BRS-3 and using this ligand showed BRS-3 has a unique pharmacology with high affinity for no known natural Bn peptides. However, use of this ligand is limited because it has high affinity for all known Bn receptors. In the present study we have attempted to identify BRS-3 selective ligands using a strategy of rational peptide design with the substitution of conformationally restricted amino acids into the prototype ligand [d-Tyr(6),beta-Ala(11),Phe(13),Nle(14)]Bn-(6-14) or its d-Phe(6) analogue. Each of the 22 peptides synthesized had binding affinities determined for hBRS-3, hGRPR, and hNMBR, and hBRS-3 selective ligands were tested for their ability to activate phospholipase C and increase inositol phosphates ([(3)H]inositol phosphate). Using this approach we have identified a number of BRS-3 selective ligands. These ligands functioned as receptor agonists and their binding affinities were reflected in their potencies for altering [(3)H]inositol phosphate. Two peptides with an (R)- or (S)-amino-3-phenylpropionic acid substitution for beta-Ala(11) in the prototype ligand had the highest selectivity for the hBRS-3 over the mammalian Bn receptors and did not interact with receptors for other gastrointestinal hormones/neurotransmitters. Molecular modeling demonstrated these two selective BRS-3 ligands had a unique conformation of the position 11 beta-amino acid. This selectivity was of sufficient magnitude that these should be useful in explaining the role of hBRS-3 activation in obesity, glucose homeostasis, hypertension, and other physiological or pathological processes.
Lipoic Acid Attenuates Inflammation via cAMP and Protein Kinase A Signaling (2010)

Oral administration of LA in vivo resulted in significant increases in cAMP concentration. The anti-inflammatory effects of LA are mediated in part by the cAMP/PKA signaling cascade. These novel findings enhance our understanding of the mechanisms of action of LA.
Comparison of the domain-level organization of starch hydrolases and related enzymes (1991)

Structure-prediction and hydrophobic-cluster analysis of several starch hydrolases and related enzymes indicated the organization of eleven domain types. Most enzymes possess a catalytic (beta/alpha)8-barrel and a smaller C-terminal domain as seen in crystal structures of alpha-amylase and cyclodextrin glucanotransferase. Some also have a starch-granule-binding domain. Enzymes breaking or forming endo-alpha-1,6 linkages contain domains N-terminal to the (beta/alpha)8-barrel.
Detection of Japanese encephalitis virus immunoglobulin M antibodies in serum by antibody capture radioimmunoassay (1982)

An assay for detecting human immunoglobulin M (IgM) antibodies to Japanese encephalitis (JE) virus was developed by using the antibody capture solid-phase radioimmunoassay approach (JE IgM ACRIAAA). Heavy-chain-specific goat antihuman IgM was first bound to the wells of a polyvinyl microtiter plate, and successive steps involved sequential binding of test sample IgM, acetone-extracted mouse brain JE antigen, and (125)I-labeled flavivirus hyperimmune human IgG. Among 20 patients hospitalized in Bangkok with clinical diagnoses of acute encephalitis, and with acute flavivirus infections proven by hemagglutination inhibition (HAI) serology, 16 had detectable (positive/negative [P/N] ratio, greater than 3.0) JE IgM ACRIA antibodies in the acute-phase serum specimen, and 19 had such antibodies in the convalescent-phase serum specimen. Convalescent patient sera regularly had higher P/N values than the corresponding acute-phase sera (mean +/- 1 standard deviation = 13.0 +/- 9.3 with acute-phase sera and 25.8 +/- 19.6 with convalescent-phase sera). JE virus-infected patients with HAI serological responses indicative of a primary flavivirus infection had higher JE IgM ACRI P/N responses than did those patients whose serological response indicated past exposure to other flaviviruses. None of 70 serum specimens from healthy Thai adults and children with serum JE HAI antibodies had detectable JE IgM ACRIA activity (P/N ratios all less than or equal to 3.0). Biological false-positives with low P/N ratios (range, 3 to 15) were found in sera from patients with acute or recent infections with flaviviruses other than JE virus but could be differentiated by the fact that these sera gave higher P/N ratios with homologous antigens than with JE virus. False-positive reactions with low P/N ratios (range, 3 to 6) due to serum rheumatoid factor activity were differentiated by testing with control antigen. The JE IgM ACRIA technique permits a rapid, accurate diagnosis of acute JE virus infections in both patients with and those without previous exposure to other flaviviruses.
Structure of the extracellular domains of the human interleukin-6 receptor α-chain (2002)

Dysregulated production of IL-6 and its receptor (IL-6R) are implicated in the pathogenesis of multiple myeloma, autoimmune diseases and prostate cancer. The IL-6R complex comprises two molecules each of IL-6, IL-6R, and the signaling molecule, gp130. Here, we report the x-ray structure (2.4 A) of the IL-6R ectodomains. The N-terminal strand of the Ig-like domain (D(1)) is disulfide-bonded to domain D(2), and domains D(2) and D(3), the cytokine-binding domain, are structurally similar to known cytokine-binding domains. The head-to-tail packing of two closely associated IL-6R molecules observed in the crystal may be representative of the configuration of the physiological dimer of IL-6R and provides new insight into the architecture of the IL-6R complex.