gebhart/patrepeval huggingface dataset:
Apoptosis as a Mechanism of Tissue Injury in Liver Allograft Rejection (1998)

Recent studies suggest that apoptosis is an important mechanism of cell death in the rejection of liver allografts and that infiltrating host lymphocytes mediate this process. The first section of this chapter addresses the cells and molecules that initiate the immune response following transplantation of a liver allograft. The recognition of donor alloantigens by infiltrating host lymphocytes stimulates a cascade of immune events which culminate in development of the effector cells that mediate tissue damage. Studies which demonstrate that apoptosis of hepatocytes and bile duct cells accompany allograft rejection are detailed in the second section of this chapter. The final section discusses the potential pathways which lead to apoptosis in liver allograft rejection. The contributions of the granule-exocytosis pathway, the Fas-mediated pathway, and cytokines to the induction of apoptosis in liver allografts are discussed. In addition, the concept that alloreactive graft infiltrating cells are deleted by apoptosis is presented. A further understanding of the mechanisms involved in apoptosis will lead to unique approaches toward the goal of achieving allograft tolerance.
Oxidative DNA Damage in Prostate Cancer Patients Consuming Tomato Sauce-Based Entrees as a Whole-Food Intervention (2001)

These data indicate a possible role for a tomato sauce constituent, possibly lycopene, in the treatment of prostate cancer and warrant further testing with a larger sample of patients, including a control group.
Manganese(III) Biliverdin IX Dimethyl Ester:  A Powerful Catalytic Scavenger of Superoxide Employing the Mn(III)/Mn(IV) Redox Couple (2001)

A manganese(III) complex of biliverdin IX dimethyl ester, (MnIIIBVDME)2, was prepared and characterized by elemental analysis, UV/vis spectroscopy, cyclic voltammetry, chronocoulometry, electrospray mass spectrometry, freezing-point depression, magnetic susceptibility, and catalytic dismuting of superoxide anion (O2.-). In a dimeric conformation each trivalent manganese is bound to four pyrrolic nitrogens of one biliverdin dimethyl ester molecule and to the enolic oxygen of another molecule. This type of coordination stabilizes the +4 metal oxidation state, whereby the +3/+4 redox cycling of the manganese in aqueous medium was found to be at E1/2 = +0.45 V vs NHE. This potential allows the Mn(III)/Mn(IV) couple to efficiently catalyze the dismutation of O2.- with the catalytic rate constant of kcat = 5.0 x 10(7) M-1 s-1 (concentration calculated per manganese) obtained by cytochrome c assay at pH 7.8 and 25 degrees C. The fifth coordination site of the manganese is occupied by an enolic oxygen, which precludes binding of NO., thus enhancing the specificity of the metal center toward O2.-. For the same reason the (MnIIIBVDME)2 is resistant to attack by H2O2. The compound also proved to be an efficient SOD mimic in vivo, facilitating the aerobic growth of SOD-deficient Escherichia coli.
Preclinical and clinical studies of anticancer agent‐incorporating polymer micelles (2009)

The size of anticancer agent-incorporating micelles can be controlled within the diameter range of 20-100 nm to ensure that they do not penetrate normal vessel walls. With this development, it is expected that the incidence of drug-induced side-effects may be decreased owing to the reduced drug distribution in normal tissue. Micelle systems can also evade non-specific capture by the reticuloendothelial system because the outer shell of a micelle is covered with polyethylene glycol. Consequently, a polymer micelle carrier can be delivered selectively to a tumor by utilizing the enhanced permeability and retention effect. Moreover, a water-insoluble drug can be incorporated into polymer micelles. Presently, several anticancer agent-incorporating micelle carrier systems are under preclinical and clinical evaluation. Furthermore, nucleic acid-incorporating micelle carrier systems are also being developed.
Interaction of Two Phagocytic Host Defense Systems (2010)

Phagocytosis of foreign pathogens by cells of the immune system is a vitally important function of innate immunity. The phagocytic response is initiated when ligands on the surface of invading microorganisms come in contact with receptors on the surface of phagocytic cells such as neutrophils, monocytes/macrophages, and dendritic cells. The complement receptor CR3 (CD11b/CD18, Mac-1) mediates the phagocytosis of complement protein (C3bi)-coated particles. Fcγ receptors (FcγRs) bind IgG-opsonized particles and provide a mechanism for immune clearance and phagocytosis of IgG-coated particles. We have observed that stimulation of FcγRs modulates CR3-mediated phagocytosis and that FcγRIIA and FcγRI exert opposite (stimulatory and inhibitory) effects. We have also determined that an intact FcγR immunoreceptor tyrosine-based activation motif is required for these effects, and we have investigated the involvement of downstream effectors. The ability to up-regulate or down-regulate CR3 signaling has important implications for therapeutics in disorders involving the host defense system.
Homogeneous Datasets of Triple Negative Breast Cancers Enable the Identification of Novel Prognostic and Predictive Signatures (2011)

Using two distinct false discovery rate thresholds, 25% and <3.5%, a larger (n = 264 probesets) and a smaller (n = 26 probesets) prognostic gene sets were identified and used as prognostic predictors. Most of these genes were positively associated with poor prognosis and correlated to metagenes for inflammation and angiogenesis. No correlation to other previously published prognostic signatures (recurrence score, genomic grade index, 70-gene signature, wound response signature, 7-gene immune response module, stroma derived prognostic predictor, and a medullary like signature) was observed. In multivariate analyses in the validation cohort the two signatures showed hazard ratios of 4.03 (95% confidence interval [CI] 1.71-9.48; P = 0.001) and 4.08 (95% CI 1.79-9.28; P = 0.001), respectively. The 10-year event-free survival was 70% for the good risk and 20% for the high risk group. The 26-gene signatures had modest predictive value (AUC = 0.588) to predict response to neoadjuvant chemotherapy, however, the combination of a B-cell metagene with the prognostic signatures increased its response predictive value. We identified a 264-gene prognostic signature for TNBC which is unrelated to previously known prognostic signatures.
Comparison of API ZYM system with API AN-Ident, API 20A, Minitek Anaerobe II, and RapID-ANA systems for identification of Clostridium difficile (1988)

The API ZYM system was compared with four anaerobe identification systems for the definitive identification of Clostridium difficile by using 88 cultures of C. difficile grown on Mueller-Hinton blood agar medium. The API ZYM system yielded a distinct and consistent enzyme profile for all test strains, whereas the sensitivities of the other systems in identifying C. difficile ranged from 78 to 96% (AN-Ident, 77.9%; RapID-ANA, 88.6%; Minitek Anaerobe II, 90.9%; and API 20A, 95.5%). The API ZYM system is highly reliable in identifying C. difficile accurately, is rapid, and is relatively simple to use.
REGENERATION OF FUNCTIONAL BLADDER SUBSTITUTES USING LARGE SEGMENT ACELLULAR MATRIX ALLOGRAFTS IN A PORCINE MODEL (2000)

We present evidence that large patch bladder acellular matrix allograft implantation is technically feasible and may prove to be a viable surgical alternative to bladder augmentation with intestinal segments. Its advantages may include the potential for complete and functional regeneration of a bladder substitute.
Essentials of Medicinal Chemistry (1988)

Basic Considerations Development of Drugs Theoretical Aspects of Drug Action PSYCHOPHARMACOLOGICAL AGENTS: Central Nervous System Depressants Central Nervous System Stimulants Psychopharmacologicals Respiratory Tract Drugs PHARMACODYNAMIC AGENTS: Peripheral Nervous System Drugs Drugs Acting at Synaptic and Neuroeffector Junctional Sites Smooth Muscle Active Drugs Histamine and Antihistamines Cardiovascular Drugs Blood and Hemopoietic System Drugs Gastrointestinal Tract Drugs Locally Acting Drugs CHEMOTHERAPEUTIC DRUGS: Anti- Infective Agents Cytostatics DRUGS FOR METABOLIC DISEASES AND ENDOCRINE FUNCTION: Drugs for Metabolism and Nutrition Water and Mineral Metabolism Drugs VITAMINS AND HORMONES: Vitamins Hormones MISCELLANEOUS AGENTS: Diverse Agents.
Nature, Position, and Frequency of Mutations Made in a Single Cycle of HIV-1 Replication (2010)

There is considerable HIV-1 variation in patients. The extent of the variation is due to the high rate of viral replication, the high viral load, and the errors made during viral replication. Mutations can arise from errors made either by host DNA-dependent RNA polymerase II or by HIV-1 reverse transcriptase (RT), but the relative contributions of these two enzymes to the mutation rate are unknown. In addition, mutations in RT can affect its fidelity, but the effect of mutations in RT on the nature of the mutations that arise in vivo is poorly understood. We have developed an efficient system, based on existing technology, to analyze the mutations that arise in an HIV-1 vector in a single cycle of replication. A lacZalpha reporter gene is used to identify viral DNAs that contain mutations which are analyzed by DNA sequencing. The forward mutation rate in this system is 1.4 x 10(-5) mutations/bp/cycle, equivalent to the retroviral average. This rate is about 3-fold lower than previously reported for HIV-1 in vivo and is much lower than what has been reported for purified HIV-1 RT in vitro. Although the mutation rate was not affected by the orientation of lacZalpha, the sites favored for mutations (hot spots) in lacZalpha depended on which strand of lacZalpha was present in the viral RNA. The pattern of hot spots seen in lacZalpha in vivo did not match any of the published data obtained when purified RT was used to copy lacZalpha in vitro.
Genetic regulation of fatty acid synthetase expression in adipose tissue: overtranscription of the gene in genetically obese rats. (1992)

We have investigated the molecular mechanism of the overactivity of fatty acid synthetase (FAS) in adipose tissue from the genetically obese Zucker rat. Purified FAS from lean and obese rat adipose tissues displayed kinetics constants, molecular weight, and immunological properties that were identical. Western blot analysis revealed that FAS overactivity in obese versus lean rat adipose tissue was paralleled by a proportionate increase in FAS mass, i.e., 4-fold increase in suckling normoinsulinemic 16-day-old pups and 25-fold in weaned hyperinsulinemic 30-day-old rats. The determination of absolute FAS mass disclosed that FAS was quantitatively a major protein in obese rat adipose tissue accounting for 13% of cytosolic proteins versus 2% in lean rat at 30 days of age. FAS hyperabundance could be ascribed to an increased relative rate of FAS synthesis that was 6-fold higher in obese than in lean rat adipose tissue. Northern blot analysis demonstrated that FAS mRNA levels in obese rats were increased 4- and 14-fold over those of lean rats at 16 and 30 days of age, respectively, in very close proportion to the 3- and 15-fold increases in FAS gene transcription rates revealed by nuclear run-on assays. Southern analysis of genomic DNA did not allow for detecting amplification or any major structural changes in the FAS gene. It is concluded that FAS overactivity, shown here to be a life-long and general feature of all adipose tissue sites in the obese rat, arises primarily from FAS gene overtranscription.
Uracil analogues of the acyclonucleoside 9-[[2-hydroxy-1-(hydroxymethyl)ethoxy]- methyl]guanine (BIOLF-62) (1984)

A series of substituted uracil analogues of the antiviral agent 9-[[2-hydroxy-1(hydroxymethyl)ethoxy]methyl]guanine (BIOLF-62) has been synthesized and characterized. The uracil analogues show little activity against herpesviruses.
Role of phosphatidylinositol 3′-kinase/AKT pathway in diffuse large B-cell lymphoma survival (2006)

Phosphatidylinositol 3'-kinase (PI3K) is a key player in cell-growth signaling in a number of lymphoid malignancies, but its role in diffuse large B-cell lymphoma (DLBCL) has not been fully elucidated. Therefore, we investigated the role of the PI3K/AKT pathway in a panel of 5 DLBCL cell lines and 100 clinical samples. Inhibition of PI3K by a specific inhibitor, LY294002, induced apoptosis in SUDHL4, SUDHL5, and SUDHL10 (LY-sensitive) cells, whereas SUDHL8 and OCI-LY19 (LY-resistant) cells were refractory to LY294002-induced apoptosis. AKT was phosphorylated in 5 of 5 DLBCL cell lines and inhibition of PI3K caused dephosphorylation/inactivation of constitutively active AKT, FOXO transcription factor, and GSK3 in LY-sensitive cell lines. In addition, there was a decrease in the expression level of inhibitory apoptotic protein, XIAP, in the DLBCL cell lines sensitive to LY294002 after treatment. However, no effect was observed in XIAP protein levels in the resistant DLBCL cell lines following LY294002 treatment. Finally, using immunohistochemistry, p-AKT was detected in 52% of DLBCL tumors tested. Furthermore, in univariate analysis, high p-AKT expression was associated with short survival. In multivariate analysis, this correlation was no longer significant. Altogether, these results suggest that the PI3K/AKT pathway may be a potential target for therapeutic intervention in DLBCL.
Self-assembly of microscopic chiplets at a liquid–liquid–solid interface forming a flexible segmented monocrystalline solar cell (2010)

This paper introduces a method for self-assembling and electrically connecting small (20-60 micrometer) semiconductor chiplets at predetermined locations on flexible substrates with high speed (62500 chips/45 s), accuracy (0.9 micrometer, 0.14 degrees), and yield (> 98%). The process takes place at the triple interface between silicone oil, water, and a penetrating solder-patterned substrate. The assembly is driven by a stepwise reduction of interfacial free energy where chips are first collected and preoriented at an oil-water interface before they assemble on a solder-patterned substrate that is pulled through the interface. Patterned transfer occurs in a progressing linear front as the liquid layers recede. The process eliminates the dependency on gravity and sedimentation of prior methods, thereby extending the minimal chip size to the sub-100 micrometer scale. It provides a new route for the field of printable electronics to enable the integration of microscopic high performance inorganic semiconductors on foreign substrates with the freedom to choose target location, pitch, and integration density. As an example we demonstrate a fault-tolerant segmented flexible monocrystalline silicon solar cell, reducing the amount of Si that is used when compared to conventional rigid cells.
A Population-Based Experimental Model for Protein Evolution: Effects of Mutation Rate and Selection Stringency on Evolutionary Outcomes (2013)

Protein evolution is a critical component of organismal evolution and a valuable method for the generation of useful molecules in the laboratory. Few studies, however, have experimentally characterized how fundamental parameters influence protein evolution outcomes over long evolutionary trajectories or multiple replicates. In this work, we applied phage-assisted continuous evolution (PACE) as an experimental platform to study evolving protein populations over hundreds of rounds of evolution. We varied evolutionary conditions as T7 RNA polymerase evolved to recognize the T3 promoter DNA sequence and characterized how specific combinations of both mutation rate and selection stringency reproducibly result in different evolutionary outcomes. We observed significant and dramatic increases in the activity of the evolved RNA polymerase variants on the desired target promoter after selection for 96 h, confirming positive selection occurred under all conditions. We used high-throughput sequencing to quantitatively define convergent genetic solutions, including mutational "signatures" and nonsignature mutations that map to specific regions of protein sequence. These findings illuminate key determinants of evolutionary outcomes, inform the design of future protein evolution experiments, and demonstrate the value of PACE as a method for studying protein evolution.
Riddles in the Dark (1988)

Before we start I'd like to make a disclaimer. I think I'm not really ready for this Guest of Honour speech business. I haven't made a great study of the phenomenon but I do remember a little, and I know you're supposed to start, first thing, by being modest about your achievements — a few throw away lines about the awards and the film rights 'n all that. Well, I don't happen to have a great deal to be modest about, in a genre to which I've contributed one published story and two books, only one of which anyone has read. So although as a good socialist I thoroughly approve — it's like one of those Utopian stories where everybody has to take their turn at being President, for half an hour or so a year — I don't think you ought to expect too much. In the circumstances it's going to be a bit difficult for me to spend forty-five minutes discussing my hoover (that's oeuvre. It's an American expression meaning all of your writing that you'll own to in public) and dwelling lovingly on the highspots in my career … my nights with the famous 'n all that. But I'll do my best. What I'm going to be talking about mainly is a relationship — because I'm a girl and that's what girls are into isn't it, relationships, not rocketships — my relationship, tangential or antagonistic or whatever, with science fiction.KeywordsScience FictionSanitary TowelScience Fiction WriterEternal HappinessAmerican ExpressionThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Polynitroxyl Albumin Reduces Infarct Size in Transient Focal Cerebral Ischemia in the Rat: Potential Mechanisms Studied by Magnetic Resonance Imaging (1998)

Nitroxide free radicals are known to protect cells from oxidative damage. Diffusion-weighted and perfusion-weighted magnetic resonance imaging was used to evaluate the effects of polynitroxyl albumin (PNA) in a middle cerebral artery intraluminal suture model of transient focal cerebral ischemia in the rat. Three groups of Sprague-Dawley rats were investigated: (1) PNA (N=6), (2) human serum albumin (N =6), and (3) saline (N=7). The middle cerebral artery was occluded for 2 hours. Treatment was started 30 minutes after induction of ischemia. A total dose of 1% body weight (volume/weight) of PNA (23.5 mg/dL protein and 110 mmol/L nitroxide), albumin (23.5 mg/dL), or saline was injected intravenously at three time points: 0.5% at 0.5 hours, 0.25% at 2 hours (i.e., just before reperfusion), and 0.25% at 4 hours after occlusion. Six sets of diffusion- and perfusion-weighted magnetic resonance images were acquired throughout the 2 hours of ischemia and the 2 hours of reperfusion. The rats were killed at 24 hours, and the brains were stained with 2,3,5-triphenyltetrazolium chloride (TTC). Diffusion-weighted imaging showed that the growth of the ischemic lesion was suppressed in the PNA-treated group. The 4 hours diffusion-weighted imaging--derived hemispheric lesion volume in the PNA-treated group (25%+/-9%) was significantly smaller than that in the saline-treated (43%+/-13%; P=0.016) or albumin-treated groups (38%+/-6%; P=0.017). A larger difference was observed for the 24-hour TTC-derived lesion volumes in the PNA (8%+/-7%), saline (35%+/-8%; P < 0.001), and albumin (31%+/-6%; P < 0.001) groups. Perfusion-weighted imaging demonstrated a marked improvement in cerebral perfusion in the PNA-treated group during ischemia and reperfusion. In conclusion, treatment with PNA results in an improvement in perfusion and a reduction of infarct volume in a model of transient focal cerebral ischemia in the rat.
Adult human aortic smooth muscle cells in culture produce active TGF-beta (1993)

Vascular smooth muscle cells (VSMC) from adult human aortas proliferated in culture in response to fetal calf serum (FCS) with a population doubling time of 70-85 h compared with 35 +/- 5 h for VSMC derived from adult rat aortas. Medium conditioned on cultures prepared from aortas from three different donors and mixed 1:1 with fresh Dulbecco's modified Eagle's medium plus 20% FCS [human conditioned medium (HCM)] reduced the rate of proliferation of rat VSMC by 46 +/- 6% (n = 3) after 48 h compared with cells in fresh medium. HCM did not reduce the proportion (> 65%) of rat VSMC that entered DNA synthesis but delayed entry into mitosis by at least 18 h. This effect was similar to previous observations of the action of transforming growth factor-beta (TGF-beta) on rat VSMC (G. K. Owens, A. A. Geisterfer, Y. W. Yang, and A. Komoriya. J. Cell Biol. 107: 771-780, 1988). A TGF-beta assay using DNA synthesis in mink lung epithelial cells confirmed that human, but not rat, VSMC in culture secrete active TGF-beta. Addition of a neutralizing antibody to TGF-beta to human VSMC in the presence of 20% FCS decreased the population doubling time from 74 +/- 3 to 46 +/- 6 h (n = 3). These observations demonstrate that the long population doubling time of human VSMC is due to the production of active TGF-beta and to an inhibitory autocrine loop.
Moderators and Mediators of Behavioral Treatment for Headache (2005)

Although work has been done establishing the efficacy of behavioral treatments for headache, almost no work has been done using appropriate methodology to evaluate what types of patients in which settings (termed "moderators") are likely to benefit from treatment and what treatment components account for treatment response (termed "mediators"). The current article provides an overview of moderators and mediators and their assessment and analysis as they pertain to clinical trials. The article also discusses the need for moderator and mediator hypotheses to be theory driven. A brief consideration of potential moderators and mediators of behavioral treatment for headache is then presented. The article concludes with a discussion of methodological issues to be addressed when conducting moderator and mediator analysis for behavioral treatment for headache.
Separation of Bovine Spermatozoa by Density on Water Insoluble Newtonian Gels and Their Use for Insemination (1982)

Bovine spermatozoa were separated into different density subpopulations utilizing water insoluble hydrocarbon and silicone gels of defined specific gravity. Sperm density profiles were generated for 13 bulls. The separations were found to be repeatable and characteristic of the bull examined. Considerable density variation among animals was demonstrated. Analysis of the separated spermatozoa, before and after freezing, demonstrated that good motility and acrosomal integrity of spermatozoa were maintained. When the least dense fraction of spermatozoa was used for insemination, conception rates were similar to those obtained routinely by artificial insemination with unfractionated spermatozoa. Therefore, this system may be useful in separating spermatozoa of various densities and for removing extraneous matter from semen. However, the sex ratio, among 51 60-day-old fetuses recovered from heifers inseminated with the lowest density fraction of spermatozoa, was 26 males:25 females.