gebhart/patrepeval huggingface dataset:
History of Vaccines and Positioning of Current Trends (2001)

The history of vaccine development spans a relatively short period of time in comparison to the history of human civilization. However, monumental advances in the field of vaccines have been made in effort to combat infectious disease. These advances have led to a reduction, and in one case the complete eradication, of the burden of some infectious diseases of the world. Throughout the history of vaccine development, milestone discoveries can be identified that have shaped the field of vaccine development, as we know it. These milestones include the first official use of a vaccine by Edward Jenner, the attenuation principals observed by Pasteur, the development of cell culture for the propagation of viruses, and the production of first recombinant protein based vaccine for hepatitis B. As vaccine development progresses into the 21st century, it will be important to build on the experience and knowledge generated in the past, in an effort to surpass the limitations that currently hamper the development of new and more effective vaccine technologies. Presented here is an overview on the history of vaccine development and its influence on the positioning of current trends and future considerations.
Identification of N10-Substituted Phenoxazines as Potent and Specific Inhibitors of Akt Signaling (2005)

A series of 30 N10-substituted phenoxazines were synthesized and screened as potential inhibitors of Akt. In cellular assays at 5 mum, 17 compounds inhibited insulin-like growth factor 1 (IGF-I)-stimulated phosphorylation of Akt (Ser-473) by at least 50% but did not inhibit IGF-I-stimulated phosphorylation of Erk-1/2 (Thr-202/Tyr-204). Substitutions at the 2-position (Cl or CF3) did not alter inhibitory activity, whereas N10-substitutions with derivatives having acetyl (20B) or morpholino (12B) side chain lost activity compared with propyl or butyl substituents (7B and 14B). Inhibition of Akt phosphorylation was associated with the inhibition of IGF-I stimulation of the mammalian target of rapamycin phosphorylation (Ser-2448 and Ser-2481), phosphorylation of p70 S6 kinase (Thr-389), and ribosomal protein S6 (Ser-235/236) in Rh1, Rh18, and Rh30 cell lines. The two most potent compounds 10-[4'-(N-diethylamino)butyl]-2-chlorophenoxazine (10B) and 10-[4'-[(beta-hydroxyethyl)piperazino]butyl]-2-chlorophenoxazine (15B) (in vitro, IC50 approximately 1-2 microM) were studied further. Inhibition of Akt phosphorylation correlated with inhibition of its kinase activity as determined in vitro after immunoprecipitation. Akt inhibitory phenoxazines did not inhibit the activity of recombinant phosphatidylinositol 3'-kinase, PDK1, or SGK1 but potently inhibited the kinase activity of recombinant Akt and Akt deltaPH, a mutant lacking the pleckstrin homology domain. Akt inhibitory phenoxazines blocked IGF-I-stimulated nuclear translocation of Akt in Rh1 cells and suppressed growth of Rh1, Rh18, and Rh30 cells (IC50 2-5 microM), whereas "inactive" derivatives were > or = 10-fold less potent inhibitors of cell growth. In contrast to rapamycin analogs, Akt inhibitory phenoxazines induced significant levels of apoptosis under serum-containing culture conditions at concentrations of agent consistent with Akt inhibition. Thus, the cellular responses to phenoxazine inhibitors of Akt appear qualitatively different from the rapamycin analogs. Modeling studies suggest inhibitory phenoxazines may bind in the ATP-binding site, although ATP competition studies were unable to distinguish between competitive and noncompetitive inhibition.
F plasmid CcdB killer protein ccdB gene mutants coding for non‐cytotoxic proteins which retain their regulatory functions (1995)

The ccd locus of the F plasmid codes for two gene products, CcdA and CcdB, which contribute to the plasmid's high stability by post-segregational killing of plasmid-free bacteria. Like the quinolones, the CcdB protein is a poison of the DNA-topoisomerase II complexes, while CcdA acts as an antidote against CcdB. In addition to these poison-antipoison properties, the CcdA and CcdB proteins act together at transcription level to repress their own synthesis. In this work, we have isolated, in vivo, and characterized several non-killer CcdB mutants. All missense mutations which inactivate CcdB killer activity are located in the region coding for the last three C-terminal residues. However, the resulting mutant CcdB proteins retain their autoregulatory properties. We conclude that the last three C-terminal residues of CcdB play a key role in poisoning but are not involved in repressor formation.
Hydrogen sulphide is a mediator of carrageenan‐induced hindpaw oedema in the rat (2005)

Hydrogen sulphide (H(2)S) is a naturally occurring gas, with potent vasodilator activity. In this report, we identify a role for H(2)S in carrageenan-induced hindpaw oedema in the rat. Intraplantar injection of carrageenan (150 microl, 2% (w v(-1))) resulted in an increase in hindpaw H(2)S synthesising enzyme activity and increased myeloperoxidase (MPO) activity. Pretreatment (i.p. 60 min before carrageenan) with DL-propargylglycine (PAG, 25-75 mg kg(-1)), an inhibitor of the H(2)S synthesising enzyme cystathionine-gamma-lyase (CSE), significantly reduced carrageenan-induced hindpaw oedema in a dose-dependent manner (e.g. increase in hindpaw weight at 3 h, saline: 0.12+/-0.017 g; carrageenan, 1.39+/-0.037 g; PAG, 50 mg kg(-1), 1.11+/-0.06 g, n=10) and MPO activity (fold increase) in the hindpaw (saline: 1.0+/-0.12; carrageenan, 2.92+/-0.45 g; PAG, 50 mg kg(-1), 1.1+/-0.22, n=10); PAG (50 mg kg(-1)) also inhibited H(2)S synthesising enzyme activity (nmol microg DNA(-1)) in the hindpaw in a dose-dependent manner (saline, 0.46+/-0.05; carrageenan, 0.71+/-0.08 g; PAG, 50 mg kg(-1), 0.17+/-0.05, n=10).
Reversal of isoprenaline-induced cardiac remodeling by rutaecarpine via stimulation of calcitonin gene-related peptide production (2010)

Dysfunction of capsaicin-sensitive sensory nerves is involved in cardiac remodeling, and rutaecarpine has been shown to exert a beneficial effect on cardiac function through activating the sensory nerves. This study was conducted to explore the potential inhibitory effect of rutaecarpine on cardiac remodeling and the underlying mechanisms. A rat cardiac remodeling model was established by injection of isoprenaline (5 mg/kg per day, s.c.) for 10 days. Rutaecarpine (10 or 40 mg/kg, i.g.) was coadministrated with isoprenaline to evaluate the effect of rutaecarpine on cardiac remodeling. After echocardiographic analysis was performed, blood samples were collected to quantify calcitonin gene-related peptide (CGRP), dorsal root ganglia were isolated for examining CGRP mRNA expression, and the hearts were weighed and saved for evaluating the parameters related to apoptosis and hypertrophy. Isoprenaline significantly increased the ratio of left ventricle weight to body weight, the cross-sectional area of cardiomyocytes, cardiac apoptosis, and collagen deposition concomitantly with decreased CGRP production, which were reversed by rutaecarpine treatment. The beneficial effects of rutaecarpine were attenuated by pretreatment with capsaicin, which selectively depleted CGRP. These results suggest that rutaecarpine was able to reverse isoprenaline-induced cardiac remodeling through stimulating CGRP production.
Insulitis in transgenic mice expressing tumor necrosis factor beta (lymphotoxin) in the pancreas. (1992)

Tumor necrosis factor beta (TNF-beta) (lymphotoxin) may play an important role in the immune response and pathologic inflammatory diseases. Insulitis is an important early step in the development of insulin-dependent diabetes mellitus. To understand better the role of TNF-beta in the regulation of inflammation and type 1 diabetes, we produced transgenic mice in which the murine TNF-beta gene was regulated by the rat insulin II promoter. The transgene was expressed in the pancreas, kidney, and skin of transgenic mice. The expression of TNF-beta in the pancreas of transgenic mice resulted in a leukocytic inflammatory infiltrate consisting primarily of B220+ IgM+ B cells and CD4+ and CD8+ T cells. The insulitis is reminiscent of the early stages of diabetes, though the mice did not progress to diabetes.
Cloning of BY55, a Novel Ig Superfamily Member Expressed on NK Cells, CTL, and Intestinal Intraepithelial Lymphocytes (1998)

Expression of the BY55 protein has been shown to be tightly associated with NK and CD8+ T lymphocytes with cytolytic effector activity. To determine the function of this protein, we molecularly cloned BY55 cDNA. The cDNA sequence predicts a cysteine-rich, glycosylphosphatidylinositol-anchored protein of 181 amino acids with a single Ig-like domain weakly homologous to killer inhibitory receptors. Reduction and carboxyamidomethylation of immunoprecipitated BY55 gave a band of 27 kDa, whereas reduction alone led to an 80-kDa species, suggesting that BY55 is a tightly disulfide-linked multimer. RNA blot analysis revealed BY55 mRNAs of 1.5 and 1.6 kb whose expression was highly restricted to NK and T cells. BY55 was expressed on the CD56dim, CD16+ subset of NK cells, which have high cytolytic activity, but was not expressed and was not induced on the CD56bright, CD16-subset of NK cells, a subset with high proliferative, but low cytolytic, capacity. In human tissues, BY55 mRNA was expressed only in spleen, PBL, and small intestine (in gut lymphocytes). BY55 was expressed on all intestinal intraepithelial lymphocytes, which were predominantly CD3+TCRalpha/beta+CD4-CD8+CD11b+CD28-CD45RO+C D56-CD101+CD103+ (alphaEbeta7 integrin). In addition, BY55 was expressed on most CD8+CD28- peripheral blood T cells. These phenotypic relationships suggest that CD8+CD28+ precursor CTL may terminally differentiate into CD8+CD28-BY55+ effector CTL and that some of the peripheral blood CD8+CD28- subset may represent recirculation from mucosal epithelial immune sites.
Antiviral Cytotoxic T Lymphocyte Induction and Vaccination (1988)

In developing vaccines to counteract viral infections, it is important to produce reagents that engender the type of immune response best suited to provide protection and avoid immunopathology. Recovery from infection is the principal role of T cell immunity, and cells that recognize virus-infected cells (cytotoxic T lymphocytes) and kill them--often before new virus is replicated--represent a crucial component of the recovery process. The cytotoxic T lymphocytes are particularly important in situations where the load of infection is high. In this review the cells and mediators, as well as the viral and host cell antigens involved in antiviral induction of cytotoxic T lymphocytes, are discussed. Particular attention is paid to the importance of the intracellular pathway of processing taken by viral antigens and the outcome in terms of the recognition of cytotoxic T lymphocytes. The new types of vaccines--especially subunits, antiidiotypes, and recombinant viral vectors--are discussed in terms of their likely effectiveness at inducing cytotoxic T lymphocytes.
Alterations in intestinal transport of oxalate in disease states. (1995)

Normally, absorption of oxalate from dietary sources can occur in all segments of the intestinal tract. However, alterations in both the magnitude and direction of oxalate fluxes across the intestine can occur in disease states. In enteric hyperoxaluria, enhanced absorption of oxalate by the large intestine is caused by increased permeability of a shunt conductance induced by malabsorbed bile salts and fatty acids. In this condition, the contribution of a paracellular passive flux of oxalate moving along its electrochemical gradient will predominate when intraluminal concentrations of free oxalate are high. In contrast, in chronic renal failure, secretion of oxalate can occur across both small and large intestine thereby facilitating extrarenal elimination with subsequent degradation by mucosal substrate-specific microorganisms. Clearly, in recent studies of oxalate transport, the intestine has emerged with an integral role in mass balance of oxalate in health and disease.
PERP, a host tetraspanning membrane protein, is required forSalmonella‐induced inflammation (2014)

Salmonella enterica Typhimurium induces intestinal inflammation through the activity of type III secreted effector (T3SE) proteins. Our prior results indicate that the secretion of the T3SE SipA and the ability of SipA to induce epithelial cell responses that lead to induction of polymorphonuclear transepithelial migration are not coupled to its direct delivery into epithelial cells from Salmonella. We therefore tested the hypothesis that SipA interacts with a membrane protein located at the apical surface of intestinal epithelial cells. Employing a split ubiquitin yeast-two-hybrid screen, we identified the tetraspanning membrane protein, p53 effector related to PMP-22 (PERP), as a SipA binding partner. SipA and PERP appear to have intersecting activities as we found PERP to be involved in proinflammatory pathways shown to be regulated by SipA. In sum, our studies reveal a critical role for PERP in the pathogenesis of S. Typhimurium, and for the first time demonstrate that SipA, a T3SE protein, can engage a host protein at the epithelial surface.
Identification of KIF5B-RET and GOPC-ROS1 Fusions in Lung Adenocarcinomas through a Comprehensive mRNA-Based Screen for Tyrosine Kinase Fusions (2012)

The KIF5B-RET fusion defines an additional subset of lung cancer with a potentially targetable driver oncogene enriched in never smokers with "pan-negative" lung adenocarcinomas. We also report in lung cancer the GOPC-ROS1 fusion originally discovered and characterized in a glioma cell line.
Kir4.1 Potassium Channel Subunit Is Crucial for Oligodendrocyte Development andIn VivoMyelination (2001)

To understand the cellular and in vivo functions of specific K(+) channels in glia, we have studied mice with a null mutation in the weakly inwardly rectifying K(+) channel subunit Kir4.1. Kir4.1-/- mice display marked motor impairment, and the cellular basis is hypomyelination in the spinal cord, accompanied by severe spongiform vacuolation, axonal swellings, and degeneration. Immunostaining in the spinal cord of wild-type mice up to postnatal day 18 reveals that Kir4.1 is expressed in myelin-synthesizing oligodendrocytes, but probably not in neurons or glial fibrillary acidic protein-positive (GFAP-positive) astrocytes. Cultured oligodendrocytes from developing spinal cord of Kir4.1-/- mice lack most of the wild-type K(+) conductance, have depolarized membrane potentials, and display immature morphology. By contrast, cultured neurons from spinal cord of Kir4.1-/- mice have normal physiological characteristics. We conclude that Kir4.1 forms the major K(+) conductance of oligodendrocytes and is therefore crucial for myelination. The Kir4.1 knock-out mouse is one of the few CNS dysmyelinating or demyelinating phenotypes that does not involve a gene directly involved in the structure, synthesis, degradation, or immune response to myelin. Therefore, this mouse shows how an ion channel mutation could contribute to the polygenic demyelinating diseases.
High-Resolution Diffusion and Relaxation Edited One- and Two-Dimensional 1H NMR Spectroscopy of Biological Fluids (1996)

A new approach to the characterization of biomolecules in whole biological fluids is presented based on simplification of 1H NMR spectra by utilizing differences in molecular diffusion coefficients alone and combinations of relaxation and diffusion parameters. New NMR pulse sequences incorporating both spectral editing features together with solvent water resonance elimination are presented. The methods are exemplified using whole human blood plasma, and it is shown that it is possible to obtain NMR spectra of the slowly diffusing species (generally large molecules) by diffusion editing, the slowly relaxing species (generally small molecules) by spin relaxation editing, or spectra showing any range of molecular mobility using a combination of the two methods. The diffusion-based editing methods are also applicable to the selection of resonances in two-dimensional NMR spectroscopy of biofluids, and we show this for the first time by the production of 1H-1H diffusion-edited TOCSY spectra of human blood plasma where the resonance intensities are weighted according to the molecular diffusion coefficient. In this case, by measuring a diffusion-edited 1H-1H TOCSY NMR spectrum of plasma, it is possible to obtain signals from only the macromolecular components, and this may be of benefit in the analysis of blood lipoproteins. In complex biofluids, the combination of diffusion and relaxation editing brings about considerable spectral simplification leading to an easier resonance assignment process. We also demonstrate the production of 1H NMR spectra with intensities corresponding to diffusion coefficient rather than number of protons, and this opens up new possibilities for pattern recognition classification of samples based on altered molecular mobility features of biofluid components.
Electric-field-induced aggregation in dilute colloidal suspensions (1990)

Electric-field-induced chain formation in dilute, non-aqueous suspensions of sterically stabilized, 1 µm poly(methyl methacrylate)(PMMA) latices are investigated. Optical microscopy and digital image analysis provide the chain-length distribution. We find that the particles carry a charge sufficient to inhibit field-induced aggregation. Equilibrium predictions of chain aggregation incorporating a screened Coulombic repulsion and field-induced dipole attraction agree well with experimental observations near the onset of aggregation; chain formation becomes diffusion limited above the threshold field strength.
Empowering developers to estimate app energy consumption (2012)

Battery life is a critical performance and user experience metric on mobile devices. However, it is difficult for app developers to measure the energy used by their apps, and to explore how energy use might change with conditions that vary outside of the developer's control such as network congestion, choice of mobile operator, and user settings for screen brightness. We present an energy emulation tool that allows developers to estimate the energy use for their mobile apps on their development workstation itself. The proposed techniques scale the emulated resources including the processing speed and network characteristics to match the app behavior to that on a real mobile device. We also enable exploring multiple operating conditions that the developers cannot easily reproduce in their lab. The estimation of energy relies on power models for various components, and we also add new power models for components not modeled in prior works such as AMOLED displays. We also present a prototype implementation of this tool and evaluate it through comparisons with real device energy measurements.
Sorbent Cost and Performance in CO2 Capture Systems (2004)

Power plants are prime candidates to apply CO2 capture for final storage as a mitigation option for climate change. Many CO2 capture concepts make use of a sorption−desorption cycle to separate CO2 from flue gas or O2 from air. These include commercial absorption processes, as well as processes using new sorbent formulations, adsorption, and high-temperature chemical looping cycles for CO2 and O2. All of these new processes must confront the large scale of carbon flows typical in a power plant. In this work, a common mass balance for all of these processes is used to define a parameter that highlights the minimum sorbent performance required to keep sorbent makeup costs at an acceptable level. A well-established reference system for which reliable commercial data exist (absorption with monoethanolamine, MEA) is used as a technoeconomic baseline to show that some of the sorbents being proposed in the open literature might need to be tested under laboratory conditions for tens of thousands of sorption−desorption cycles before they can be further considered as viable options for CO2 capture from power plants.
Genetic Analyses of Proteolysis, Hemoglobin Binding, and Hemagglutination of Porphyromonas gingivalis (1999)

Porphyromonas gingivalis produces arginine-specific cysteine proteinase (Arg-gingipain, RGP) and lysine-specific cysteine proteinase (Lys-gingipain, KGP) in the extracellular and cell-associated forms. Two separate genes (rgpA and rgpB) and a single gene (kgp) have been found to encode RGP and KGP, respectively. We constructed rgpA rgpB kgp triple mutants by homologous recombination with cloned rgp and kgp DNA interrupted by drug resistance gene markers. The triple mutants showed no RGP or KGP activity in either cell extracts or culture supernatants. The culture supernatants of the triple mutants grown in a rich medium had no proteolytic activity toward bovine serum albumin or gelatin derived from human type I collagen. Moreover, the mutants did not grow in a defined medium containing bovine serum albumin as the sole carbon/energy source. These results indicate that the proteolytic activity of P. gingivalis toward bovine serum albumin and gelatin derived from human type I collagen appears to be attributable to RGP and KGP. The hemagglutinin gene hagA of P. gingivalis possesses the adhesin domain regions responsible for hemagglutination and hemoglobin binding that are also located in the C-terminal regions of rgpA and kgp. A rgpA kgp hagA triple mutant constructed in this study exhibited no hemagglutination using sheep erythrocytes or hemoglobin binding activity, as determined by a solid-phase binding assay with horseradish peroxidase-conjugated human hemoglobin, indicating that the adhesin domains seem to be particularly important for P. gingivalis cells to agglutinate erythrocytes and bind hemoglobin, leading to heme acquisition.
Cardiovascular risk factors in confirmed prediabetic individuals. Does the clock for coronary heart disease start ticking before the onset of clinical diabetes? (1990)

Although type II diabetes is associated with both microvascular and macrovascular complications, duration of diabetes and severity of glycemia are strongly associated only with the former. Since prediabetic individuals are hyperinsulinemia, and since hyperinsulinemia may be a cardiovascular risk factor, we hypothesized that prediabetic individuals might have an atherogenic pattern of risk factors even before the onset of clinical diabetes, thereby explaining the relative lack of an association of macrovascular complications with either glycemic severity or disease duration. We documented the cardiovascular risk factor status of 614 initially nondiabetic Mexican Americans who later participated in an 8-year follow-up of the San Antonio Heart Study, a population-based study of diabetes and cardiovascular disease. Individuals who were nondiabetic at the time of baseline examination, but who subsequently developed type II diabetes (ie, confirmed prediabetic subjects, n = 43), had higher levels of total and low-density lipoprotein cholesterol, triglyceride, fasting glucose and insulin, 2-hour glucose, body mass index, and blood pressure, and lower levels of high-density lipoprotein cholesterol than subjects who remained nondiabetic (n = 571). Most of these differences persisted after adjustment for obesity and/or level of glycemia, but were abolished after adjustment for fasting insulin concentration. When subjects with impaired glucose tolerance at baseline (n = 106) were eliminated, the more atherogenic pattern of cardiovascular risk factors was still evident (and statistically significant) among initially normoglycemic prediabetic subjects. These results indicate that prediabetic subjects have an atherogenic pattern of risk factors (possibly caused by obesity, hyperglycemia, and especially hyperinsulinemia), which may be present for many years and may contribute to the risk of macrovascular disease as much as the duration of clinical diabetes itself.