gebhart/patrepeval huggingface dataset:
Differences between the promoting activities of the peroxisome proliferator WY-14,643 and phenobarbital in rat liver. (1989)

In order to characterize the promoting activity of the peroxisome proliferator [4-chloro-6-(2,3-xylidino)-2-pyrimidinylthio]acetic acid (WY-14,463), male F344 rats which received a single 150-mg/kg dose of diethylnitrosamine (DEN) were fed 0.1% WY-14,643 or 0.05% phenobarbital in the diet for 11, 22, or 54 wk. WY-14,643 promoted the development of ATPase-deficient foci but not GGTase-positive or G6Pase-deficient foci, in contrast to phenobarbital which promoted development of foci detected by all three markers. The mode of promotion of ATPase-deficient foci by WY-14,643 was distinctly different from that of phenobarbital. WY-14,643 primarily increased mean volume of foci at 11 and 22 wk, while phenobarbital primarily increased the numerical density of foci at these time points. At 54 wk, the yield of hepatic neoplasms per liver was higher in rats fed WY-14,643 than in rats fed phenobarbital. To evaluate the possibility that the promotional activity of WY-14,643 was more effective at a later stage in hepatocarcinogenesis, rats receiving a dose of DEN and then phenobarbital in the diet for 11 wk were changed to a diet containing WY-14,643 for an additional 11 or 43 wk. However, WY-14,643 feeding from wk 11 to 22 caused a reduction in volume density of ATPase-deficient foci relative to the volume density of foci at 11 wk. In addition, feeding WY-14,643 from wk 11 to 54 caused similar yields of hepatic neoplasms whether or not phenobarbital was fed for the initial 11 wk. WY-14,643 induced hepatic peroxisome proliferation as indicated by palmitoyl CoA oxidase activity regardless of prior treatment with DEN and/or phenobarbital. The yield of neoplasms in rats not receiving DEN was greater in rats fed WY-14,643 for wk 11 to 54 than in rats fed WY-14,643 for wk 1 to 54. In summary, the peroxisome proliferator WY-14,643 was a more efficient promoter of hepatocarcinogenesis in DEN-initiated rats than phenobarbital. The promotional activity of WY-14,643, when evaluated by stereological analysis and by changing promoters, is distinct from that of phenobarbital, perhaps suggesting different cellular and/or molecular mechanisms of promotion. Understanding the role of promotion by WY-14,643 and other peroxisome proliferators may be important in understanding the mechanism of their hepatocarcinogenicity.
Phase, phase, phase (2002)

I have been trying for some time now to write about phase. Sounds easy enough, but the more I think about it, the less easy it gets. I think I know why. Phase is one of those technical terms that has way too many meanings attached to it. Sheriff's dictionary gives four primary definitions of the word, and no less than 20 more derivative definitions.
Intermittent chemotherapy can retain the therapeutic potential of anti‐CD137 antibody during the late tumor‐bearing state (2014)

Immunomodulating monoclonal antibodies (mAb) can evoke antitumor T-cell responses, which are attenuated by regulatory T cells (Treg) and myeloid-derived suppressor cells (MDSC). Treatment with cyclophosphamide (CP) and gemcitabine (GEM) can mitigate the immunosuppression by Treg and MDSC, respectively. In the current study, we examined the antitumor effects of a combination of local injection with anti-CD137 mAb and intermittent low-dose chemotherapy using CP and GEM in subcutaneously established CT26 colon carcinoma. Although a significant antitumor effect was observed when local anti-CD137 mAb therapy (5 μg) was started early in the tumor-bearing stage (day 10), no therapeutic efficacy was observed when the mAb therapy was started at a later tumor-bearing stage (day 17). Analyses of the tumor-infiltrating immune cells revealed that the number of Gr-1(high/low) CD11b(+) MDSC started to increase 13 days after tumor inoculation, whereas injection with low-dose (50 mg/kg) CP and GEM mitigated this increase. In addition, although intermittent injections with low-dose CP and GEM on days 10 and 18 suppressed tumor growth significantly, additional local injections of anti-CD137 mAb on days 19, 21, and 23 further augmented the therapeutic efficacy. Cytotoxic T lymphocytes reactive to CT26 and a tumor antigen peptide were induced successfully from the spleen cells of tumor-cured or tumor-stable mice. In a bilateral tumor inoculation model, this combination therapy achieved systemic therapeutic effects and suppressed the growth of mAb-untreated tumors. These results suggest that intermittent immunochemotherapy using CP and GEM could retain the therapeutic potential of anti-CD137 mAb that is normally impaired during the late tumor-bearing stage.
Genetic alterations and changes in expression of histone demethylases in prostate cancer (2010)

As no genetic alterations and only very modest expression changes were found, it is unlikely that LSD1, JHDM2A, or GASC1 play a major role in the progression of PC.
Construction of a Plasmid Carrying both CTP Synthetase and a Fused Gene Formed from Cholinephosphate Cytidylyltransferase and Choline Kinase Genes and Its Application to Industrial CDP-Choline Production: Enzymatic Production of CDP-Choline from Orotic Acid (Part II) (1997)

A new method for enzymatic production of cytidine diphosphate choline (CDP-choline) from orotic acid and choline chloride was developed. To establish an industrial manufacturing process, we constructed a plasmid, pCKG55, which simultaneously expressed in Escherichia coli the three following enzymes; CTP synthetase (encoded by the pyrG gene from E. coli), cholinephosphate cytidylyltransferase (encoded by the CCT gene from Saccharomyces cerevisiae), and choline kinase (encoded by the CKI gene from S. cerevisiae). CCT and CKI genes on pCKG55 were designed to be expressed as a single CCT/CKI fused protein. This CCT/CKI fused protein retained both activities and the thermal stability of its cholinephosphate cytidylyltransferase activity was nearly the same as the native CCT enzyme. Corynebacterium ammoniagenes KY13505 and E. coli MM294/pCKG55 were cultured in 5-liter jar fermentor independently. Equal volumes of each broth were mixed in a 2-liter jar fermentor, and then the enzymatic reaction was done using 47 mM orotic acid and 60 mM choline chloride as substrates. After 23 h of the reaction at 32 degrees C, 21.5 mM (11 g/liter) of CDP-choline was accumulated.
QUMA: quantification tool for methylation analysis (2008)

Bisulfite sequencing, a standard method for DNA methylation profile analysis, is widely used in basic and clinical studies. This method is limited, however, by the time-consuming data analysis processes required to obtain accurate DNA methylation profiles from the raw sequence output of the DNA sequencer, and by the fact that quality checking of the results can be influenced by a researcher's bias. We have developed an interactive and easy-to-use web-based tool, QUMA (quantification tool for methylation analysis), for the bisulfite sequencing analysis of CpG methylation. QUMA includes most of the data-processing functions necessary for the analysis of bisulfite sequences. It also provides a platform for consistent quality control of the analysis. The QUMA web server is available at http://quma.cdb.riken.jp/.
Hypochloremia and Diuretic Resistance in Heart Failure (2016)

URL: http://www.clinicaltrials.gov. Unique identifier: NCT02031354.
Characterization of an Interaction between Functionalized Carbon Nanotubes and an Enzyme (2003)

Carbon nanotubes (CNTs) did not exhibit strong interactions with Biliverdin IX beta reductase enzyme (BVRB) in water. With the use of noncovalent functionalization by the surfactant Triton X-100, the surfaces of the CNTs were changed from hydrophobic to hydrophilic. The hydrophilic surface of the CNT-Triton conjugate interacts with the hydrophilic surface of BVRB, thus creating a water-soluble complex. Results from ultracentrifugation through a sucrose gradient and gel electrophoresis show the presence of the enzyme. Raman spectroscopy confirmed that the enzyme indeed interacts with CNT-Triton conjugates.
An ELISA for the Serodiagnosis of Tuberculosis Using a 30,000-Da Native Antigen of Mycobacterium tuberculosis (1990)

An ELISA was established for the measurement of IgG antibody in human serum to the 30,000-Da native antigen of Mycobacterium tuberculosis and evaluated for its utility in the diagnosis of tuberculosis at the Instituto Nacional de Enfermedades Respiratorias in Mexico City. The test had a sensitivity of 70% in patients with sputum-positive active pulmonary tuberculosis and a specificity in control subjects of 100%. The accuracy of positive prediction was 100% and of negative prediction 93% for patients with pulmonary tuberculosis at this institute. Less favorable test characteristics were obtained for patients with miliary and pleural tuberculosis, in which the test had sensitivities of 22% and 14%. These results offer the promise of an accurate serodiagnostic test for pulmonary tuberculosis using readily obtained reagents.
Involvement of chymase-mediated angiotensin II generation in blood pressure regulation (2004)

Angiotensin I–converting enzyme (ACE) inhibitors are thought to lower blood pressure in hypertensive patients, mainly by decreasing angiotensin II (Ang II) formation. Chymase, a human mast cell protease, has recently been proposed to play a role in blood pressure regulation because of its Ang II–forming activity. Here we show that the predominant chymase mRNA species in the mouse aorta are those for types 4 and 5 isoforms, and that both are efficient Ang II–forming enzymes. Evaluation of ACE-dependent and ACE-independent Ang II–forming pathways in mast cell–deficient (Kitw/Kitw-v) mice and their mast cell–sufficient littermate (MC+/+) controls revealed that, in contrast to the latter, Kitw/Kitw-v mice fail to express chymase mRNAs in the vasculature and have almost no ACE-independent Ang II–forming activity in either isolated blood vessels or homogenates. Moreover, in MC+/+ but not in Kitw/Kitw-v mice, a contribution of ACE-independent Ang II generation to blood pressure regulation was evident by a 1.6-fold greater maximal reduction in mean arterial pressure with acute ACE inhibition plus AT1 receptor blockade than with ACE inhibition alone. Thus, mast cells are the source of the vascular ACE-independent pathway, and the antihypertensive benefit of combining ACE inhibitor therapy with AT1 receptor antagonist therapy is most likely due to negation of chymase-catalyzed Ang II generation.
A prospective randomized study of megestrol acetate and ibuprofen in gastrointestinal cancer patients with weight loss (1999)

The use of megestrol acetate in the treatment of weight loss in gastrointestinal cancer patients has been disappointing. The aim of the present study was to compare the combination of megestrol acetate and placebo with megestrol acetate and ibuprofen in the treatment of weight loss in such patients. At baseline, 4-6 weeks and 12 weeks, patients underwent measurements of anthropometry, concentrations of albumin and C-reactive protein and assessment of appetite, performance status and quality of life using EuroQol-EQ-5D and EORTC QLQ-C30. Thirty-eight and 35 patients (median weight loss 18%) were randomized to megestrol acetate/placebo or megestrol acetate/ibuprofen, respectively, for 12 weeks. Forty-six (63%) of patients failed to complete the 12-week assessment. Of those evaluable at 12 weeks, there was a decrease in weight (median 2.8 kg) in the megestrol acetate/placebo group compared with an increase (median 2.3 kg) in the megestrol acetate/ibuprofen group (P<0.001). There was also an improvement in the EuroQol-EQ-5D quality of life scores of the latter group (P<0.05). The combination of megestrol acetate/ibuprofen appeared to reverse weight loss and appeared to improve quality of life in patients with advanced gastrointestinal cancer. Further trials of this novel regimen in weight-losing patients with hormone-insensitive cancers are warranted.
Rapid Engineering of the Geldanamycin Biosynthesis Pathway by Red/ET Recombination and Gene Complementation (2005)

Genetic manipulation of antibiotic producers, such as Streptomyces species, is a rational approach to improve the properties of biologically active molecules. However, this can be a slow and sometimes problematic process. Red/ET recombination in an Escherichia coli host has permitted rapid and more versatile engineering of geldanamycin biosynthetic genes in a complementation plasmid, which can then be readily transferred into the Streptomyces host from which the corresponding wild type gene(s) has been removed. With this rapid Red/ET recombination and gene complementation approach, efficient gene disruptions and gene replacements in the geldanamycin biosynthetic gene cluster have been successfully achieved. As an example, we describe here the creation of a ketoreductase 6 null mutation in an E. coli high-copy-number plasmid carrying gdmA2A3 from Streptomyces hygroscopicus NRRL3602 and the subsequent complementation of a gdmA2A3 deletion host with this plasmid to generate a novel geldanamycin analog.
A quantum bit commitment scheme provably unbreakable by both parties (2002)

We describe a complete protocol for bit commitment based on the transmission of polarized photons. We show that under the laws of quantum physics, this protocol cannot be cheated by either party except with exponentially small probability (exponential in the running time needed to implement the honest protocol). A more thorough analysis is required to adjust all the constants used in this paper to get the best performance from our construction. Better performances may probably be achieved by using a third conjugate transmission-reception basis of circular polarization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antifibrotic Effects of the Dual CCR2/CCR5 Antagonist Cenicriviroc in Animal Models of Liver and Kidney Fibrosis (2016)

CVC displayed potent anti-inflammatory and antifibrotic activity in a range of animal fibrosis models, supporting human testing for fibrotic diseases. Further experimental studies are needed to clarify the underlying mechanisms of CVC's antifibrotic effects. A Phase 2b study in adults with NASH and liver fibrosis is fully enrolled (CENTAUR Study 652-2-203; NCT02217475).
MicroRNA and Colorectal Cancer (2009)

MicroRNAs are small 19 to 22 nucleotide sequences of RNA that participate in the regulation of cell differentiation, cell cycle progression, and apoptosis. MicroRNAs act much like small interfering RNA, annealing with RISC, to cleave messenger RNA, and microRNAs exert translational inhibition that is incompletely understood. They are important factors in tumorigenesis and have been the subject of research in many types of cancers, including colon cancer. MicroRNAs may be abnormally down-regulated or up-regulated in colon-cancer tissue. Artificial dysregulation of certain microRNAs will trigger tumorigenesis or apoptosis depending on which microRNA is manipulated. Although the natural mechanisms for the dysregulation of microRNAs is still largely unknown, one theory tested in colon cancers proposes that DNA hypermethylation leads to down-regulation of certain microRNAs. Specific microRNA expression patterns help characterize specific cancers and may be used as a prognostication factor and in following patient response to 5-fluorouracil chemotherapy. This article reviews the existing literature pertaining to the study of microRNA in colorectal cancer.
Interaction of Antistasin-Related Peptides with Factor Xa: Identification of a Core Inhibitory Sequence (1994)

Antistasin, isolated from the Mexican leech, is a 119 amino acid protein which is a selective and potent inhibitor of coagulation Factor Xa. Previous studies indicated that an arginine residue located at position 34 of the inhibitor was cleaved by Factor Xa during the inhibition reaction. To evaluate this residue as the reactive site of antistasin, and to define shorter fragments of antistasin displaying Factor Xa-inhibitory activity, a series of peptides were synthesized corresponding to amino acids 27-49 of the inhibitor. The most potent peptide synthesized was a disulfide-bridged, 19 amino acid peptide, ATS29-47, which inhibited Factor Xa with a Ki = 35 nM, and increased plasma clotting times by over 4-fold at a concentration of 33 uM. Reduction or sulfation of the cysteine residues in ATS29-47 reduced Factor Xa inhibitory activity by over 95%. Peptides as short as seven residues corresponding to position 33-39 of antistasin displayed Factor Xa inhibitory activity. The peptides did not inhibit thrombin or trypsin at concentrations 1000-fold higher than used in Factor Xa assays. The shortest peptide displaying anticoagulant activity in human plasma was the disulfide-bridged peptide, D-Arg-Cys-Arg-Val-His-Cys-Pro, which increased clotting times by 50% at micromolar concentrations. These results demonstrate that antistasin-related peptide sequences can serve as model structures for the development of novel, low molecular weight anticoagulants.
Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria (2008)

The H-NS nucleoid-associated DNA-binding protein is an important global repressor of transcription in Gram-negative bacteria. Recently, H-NS has been implicated in the process of xenogeneic silencing, where it represses the transcription of foreign genes acquired by horizontal transfer. This raises interesting questions about the integration of the horizontally acquired genes into the existing gene regulatory networks of the microbe. In particular, how do bacteria derepress silenced genes in order to benefit from their expression without compromising competitive fitness through doing so inappropriately? This article reviews current knowledge about the derepression of genes that are transcriptionally silenced by H-NS. It describes a variety of anti-silencing mechanisms involving (i) protein-independent processes that operate at the level of local DNA structure, (ii) DNA-binding proteins such as Ler, LeuO, RovA, SlyA, VirB, and proteins related to AraC, and (iii) modulatory mechanisms in which H-NS forms heteromeric protein-protein complexes with full-length or partial paralogues such as StpA, Sfh, Hha, YdgT, YmoA or H-NST. The picture that emerges is one of apparently ad hoc solutions to the problem of H-NS-mediated silencing, suggesting that microbes are capable of evolving anti-silencing methods based on the redeployment of existing regulatory proteins rather than employing dedicated, bespoke antagonists. There is also evidence that in a number of cases more sophisticated regulatory processes have been superimposed on these rather simple anti-silencing mechanisms, broadening the range of environmental signals to which H-NS-repressed genes respond.
Mucosal immunodeficiency in smokers, and in patients with epithelial head and neck tumours. (1990)

Cigarette smoking influences the risk of orogastrointestinal disease in both protective (ulcerative colitis), and inductive (squamous tumours of the head, neck and oesophagus) roles. In order to study the effects of smoking on mucosal immunity, salivary immunoglobulins were measured in pure parotid saliva from groups of healthy non-smokers, smokers, and exsmokers and from patients with epithelial head and neck tumours, both untreated and after radiotherapy. Of the healthy individuals, smokers had significantly lower salivary IgA and higher IgM concentrations than did non-smokers. The effect on IgA was dose related, and reversible after cessation of smoking. Likewise, in patients with head and neck tumours (the majority being smokers), salivary IgA concentration was reduced and IgM increased when compared with non-smoking controls. Results were similar before and after radiotherapy. This study provides evidence of the effects of smoking on mucosal immunity as evaluated by parotid salivary immunoglobulins. Further studies of the influence of smoking on secretory immunity are indicated.
The Submandibular Gland: A Key Organ in the Neuro-Immuno-Regulatory Network? (1995)

The evidence for the integration of the submandibular gland (SMG) into the neuroimmunoregulatory network has been reviewed. In laboratory rodents, factors extracted from the SMG were shown to stimulate lymphocyte proliferation, to affect the weight of the thymus, spleen and lymph nodes and to induce immunosuppression in several in vivo animal models. The SMG produces significant quantities of nerve growth factor (NGF), epidermal growth factor (EGF), transforming growth factor-beta and kallikreins, which are secreted into the saliva and affect immune and mucosal tissues and nerve endings in the gastrointestinal tract. These factors play a role in regulating mucosal immuno/inflammatory response and in regeneration and healing. The major salivary glands also produce antimicrobial proteins and secretory IgA antibodies which are essential factors in mucosal host defense. SMG-derived NGF, EGF and glandular kallikrein are delivered into the bloodstream where they may act as important systemic immunoregulators and also have major regulatory influences on the central neuroendocrine system. There is evidence to indicate that EGF is involved in the regulation of gonadal function. Growth hormone, prolactin, androgens, thyroid hormone and corticosteroids regulate protein synthesis in the SMG, whereas secretory activity is regulated by sympathetic (alpha- and beta-adrenergic) parasympathetic (muscarinic) and peptidergic (substance P and vasoactive intestinal peptide) nerve fibers. Fluid and electrolyte secretion is promoted by parasympathetic, whereas protein secretion is stimulated by sympathetic nerve impulses. Steroid hormones and cytokines (interleukin-1 alpha, -beta, tumor necrosis factor, interferon-gamma) have a major regulatory influence on protein secretion, including the secretion of immunoglobulin into the saliva. The SMG interacts with the mucosal and systemic compartments of the immune system, with the central and peripheral nervous systems, with the pituitary gland, and with peripheral endocrine organs. These interactions enable the SMG to exert regulatory influences on immune/inflammatory reactions in the gastrointestinal tract, in the lungs, and possibly elsewhere. It is suggested that these functions make this gland a key regulatory organ in the neuroimmunoregulatory network. Evidence is increasing that the major salivary glands fulfill similar functions in other species, including humans.
Characterization of cell lines established from merkel‐cell (“small‐cell”) carcinoma of the skin (1993)

Six cell lines have been established from different biopsies of the rare small-cell skin cancer of neuro-endocrine origin known as Merkel-cell carcinoma (MCC). These were established from metastatic lesions and have now been in culture for periods varying from 1 to 3 years. All lines grow as suspension cultures and exhibit typical MCC cytological features of small round cells with little cytoplasm, round nuclei and tight junctions. There was variation in the number and size of nucleoli and dense-core granules. We present details of their immunohistochemistry and growth characteristics in culture. The latter were similar to small-cell lung-cancer (SCLC) lines and can be subdivided, by their appearance, into type I, type II and type III in the same way as SCLC lines. This classification may be of significance for the prognosis and management of MCC.