gebhart/patrepeval huggingface dataset:
Tubulin-Interactive Natural Products as Anticancer Agents (2009)

This review provides an overview of the discovery, structures, and biological activities of anticancer natural products that act by inhibiting or promoting the assembly of tubulin to microtubules. The emphasis is on providing recent information on those compounds in clinical use or in advanced clinical trials. The vinca alkaloids, the combretastatins, NPI-2358, the halichondrin B analogue eribulin, dolastatin 10, noscapine, hemiasterlin, and rhizoxin are discussed as tubulin polymerization inhibitors, while the taxanes and the epothilones are the major classes of tubulin polymerization promoters presented, with brief treatments of discodermolide, eleutherobin, and laulimalide. The challenges and future directions of tubulin-interactive natural products-based drug discovery programs are also discussed briefly.
Hypothesis: the ‘metabolic memory’, the new challenge of diabetes (2007)

Large randomized studies have established that early intensive glycaemic control reduces the risk of diabetic complications, both micro- and macrovascular. However, epidemiological and prospective data support a long-term influence of early metabolic control on clinical outcomes. This phenomenon has recently been defined as 'metabolic memory.' Potential mechanisms for propagating this 'memory' are the non-enzymatic glycation of cellular proteins and lipids, and an excess of cellular reactive oxygen and nitrogen species, in particular originated at the level of glycated-mitochondrial proteins, perhaps acting in concert with one another to maintain stress signalling. Furthermore, the emergence of this 'metabolic memory' suggests the need for very early aggressive treatment aiming to 'normalize' glycaemic control and the addition of agents which reduce cellular reactive species and glycation in order to minimize long-term diabetic complications.
Blockade of the Mitochondrial Permeability Transition Pore Diminishes Infarct Size in the Rat after Transient Middle Cerebral Artery Occlusion (1999)

The mitochondrial permeability transition pore is an inducer of cell death. During the reperfusion phase after cerebral ischemia, calcium accumulates in mitochondria, and a burst of free radical formation occurs, conditions that favor the activation of the mitochondrial permeability transition pore. Here the authors demonstrate that a blocker of the mitochondrial permeability transition pore, the nonimmunosuppressive cyclosporin A analogue N-methyl-Val-4-cyclosporin A (10 mg/kg intraperitoneally), administered during reperfusion and at 24 hours of reperfusion, diminishes infarct size in a rat model of transient focal ischemia of 2 hours' duration. The mitochondrial permeability transition pore may be an important target for drugs against stroke.
Survivin is expressed on CD40 stimulation and interfaces proliferation and apoptosis in B-cell chronic lymphocytic leukemia (2001)

Abstract In B-cell chronic lymphocytic leukemia (B-CLL), defective apoptosis causes the accumulation of mature CD5+ B cells in lymphoid organs, bone marrow (BM), and peripheral blood (PB). These cells are the progeny of a proliferating pool that feeds the accumulating compartment. The authors sought to determine which molecular mechanisms govern the proliferating pool, how they relate to apoptosis, and what the role is of the microenvironment. To begin to resolve these problems, the expression and modulation of the family of inhibitor of apoptosis proteins (IAPs) were investigated, with consideration given to the possibility that physiological stimuli, such as CD40 ligand (CD40L), available to B cells in the microenvironment, might modulate IAP expression. The in vitro data on mononuclear cells from PB or BM of 30 patients demonstrate that B-CLL cells on CD40 stimulation express Survivin and that Survivin is the only IAP whose expression is induced by CD40L. Through immunohistochemistry, in vivo Survivin expression in lymph node (LN) and BM biopsies was evaluated. In reactive LN, Survivin was detected only in highly proliferating germinal center cells. In LN from patients with B-CLL, Survivin was detected only in pseudofollicles. Pseudofollicle Survivin+ cells were actively proliferating and, in contrast to Survivin+ B cells found in normal GC, were Bcl-2+. In B-CLL BM biopsies, CD5+, Survivin+ cells were observed in clusters interspersed with T cells. These findings establish that Survivin controls the B-CLL proliferative pool interfacing apoptosis and that its expression may be modulated by microenvironmental stimuli.
Protein kinases that phosphorylate activated G protein‐coupled receptors (1995)

G protein-coupled receptor kinases (GRKs) are a family of serine/threonine protein kinases that specifically recognize agonist-occupied, activated G protein-coupled receptor proteins as substrates. Phosphorylation of an activated receptor by a GRK terminates signaling by that receptor, by initiating the uncoupling of the receptor from heterotrimeric G proteins. Six distinct mammalian GRKs are known, which differ in tissue distribution and in regulatory properties. The intracellular localization of GRKs to membrane-bound receptor substrates is the most important known regulatory feature of these enzymes. Rhodopsin kinase (GRK1) requires a post-translationally added farnesyl isoprenoid to bind to light-activated rhodopsin. The beta-adrenergic receptor kinases (GRK2 and GRK3) associate with heterotrimeric G protein beta gamma-subunits, released upon receptor activation of G proteins, for membrane anchorage. The recently-described GRKs 4, 5, and 6 comprise a distinct subgroup of GRKs. These kinases utilize distinct mechanisms for membrane localization, which are just beginning to be defined. All GRKs appear to play the same general cellular role of desensitizing activated G protein-coupled receptors, but utilize distinctly individual means to the same end.
Bioavailability and Pharmacokinetics of Magnesium After Administration of Magnesium Salts to Humans (2001)

Therapeutically, magnesium salts represent an important class of compounds and exhibit various pharmacologic actions. Examples of magnesium salts are ionic magnesium and magnesium citrate in nephrolithiasis, magnesium salicylate in rheumatoid arthritis, magnesium hydroxide as an antacid as well as a cathartic, and magnesium mandelate as urinary antiseptic. Various anions attached to the cation magnesium, such as oxide, chloride, gluconate, and lactate, affect the delivery of the amounts of elemental magnesium to the target site and thereby produce different pharmacodynamic effects. This review examines the bioavailability and pharmacokinetics of various magnesium salts and correlates pharmacodynamic action with the structure-activity relationship.
Site-Directed Mutagenesis Using Uracil-Containing Double-Stranded DNA Templates and DpnI Digestion (1999)

DpnI can cleave fully methylated parental DNA while leaving hemi-methylated DNA intact. Based on this observation, we developed a rapid site-directed mutagenesis method using uracil-containing, double-stranded (ds)DNA templates and DpnI digestion. A 38% mutation efficiency was achieved by DpnI treatment of the mutagenic strand-extension reaction, and it increased to 70%-91% when uracil-containing dsDNA templates were used. This method compares favorably to the most efficient current methods, but is simpler and does not require the use of single-stranded templates or phage vectors.
Picoliter Vials: A New Sample Handling Technique for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (1996)

Matrix-assisted laser desorption/ionization mass spectrometry (MALDIMS), introduced by Hillenkamp and Karas [, ], is becoming a valuable tool for biochemical and molecular biology research, especially with respect to mixture analysis and biological applications. The greatest analytical strength of MALDIMS is (1) its low detection limit, and (2) the high tolerance of the matrix to impurities.
Dietary status and impact of risperidone on nutritional balance in children with autism: A pilot study (2006)

These pilot data suggest that treatment with risperidone did not significantly affect the nutritional balance of this small group of children.
Prolonged Single-Agent Versus Combination Chemotherapy in Indolent Follicular Lymphomas: A Study of the Cancer and Leukemia Group B (2002)

There is no advantage to the initial use of the relatively intensive combination, CHOP-B, for patients with FSCL compared with the less toxic single agent, cyclophosphamide. However, in an unplanned subgroup analysis, patients with FML who received the combination experienced improved disease control and survival.
Muscle tremor as an input mechanism (2004)

We present the use of human physiological tremor, detected by a linear accelerometer, as a novel form of input for mobile devices. This allows the device to be aware if it is being held in a human hand, and in which posture. It also has security applications, as human tremor characteristics are individual. We describe two simple demonstrations of the use of tremor. One demo uses isometric muscle tremor as a proxy for a pressure sensor, and allows a user to ‘pump up ’ an onscreen balloon. The second demo simulates a mobile phone application, using muscle tremor to enable the device to be aware if it is currently held by human hand, and to stop ringing when picked up. Additional Keywords and Phrases: muscle tremor, accelerometer, input mechanism, pocket PC
Free fatty acids FFA a link between obesity and insulin resistance (1998)

Evidence, gained from human studies, is reviewed showing that elevation of plasma FFA levels produce peripheral and probably also hepatic insulin resistance in obese healthy and diabetic subjects. First, plasma FFA levels are elevated in most obese subjects. Second, physiological elevations of plasma FFA inhibit acutely as well as chronically insulin stimulated glucose uptake in a dose dependent fashion. Responsible for this inhibition is a FFA induced defect in insulin stimulated glucose transport and/or phosphorylation which develops after 3-4 hours of raising plasma FFA and a second defect, consisting of inhibition of glycogen synthase, the rate limiting enzyme of glycogen synthesis, which develops after 4-6 hours. FFA induced inhibition of fatty acid oxidation (Randle effect) does not affect insulin stimulated glucose uptake or glycogen synthesis and thus does not cause insulin resistance. Elevated plasma FFA levels also modestly increase insulin suppressed endogenous glucose production (EGP) although this effect has not been found by all investigators. The reasons why it has been difficult to demonstrate unequivocal effects of FFA on EGP include 1) the fact that FFA promote insulin secretion which counteracts its effect on EGP (FFA increase, while insulin decreases EGP); 2) the recognition that FFA induced increase in gluconeogenesis may be compensated by intrahepatic downregulation of EGP (i.e., by a decrease in glycogenolysis). The FFA induced insulin resistance is physiologically important during starvation by preserving carbohydrate for oxidation in the central nervous system and during pregnancy, where the well recognized accelerated starvation pattern provides carbohydrate for the growing fetus. In obesity, however, there is no need to spare carbohydrate and the FFA induced insulin resistance may result in type 2 diabetes and other cardiovascular risk factors.
Xenogeneic skin graft rejection is especially dependent on CD4+ T cells. (1989)

B6 mice were treated in vivo with anti-CD4, anti-CD8, or both anti-T cell antibodies together in an effort to prolong xenogeneic compared with allogeneic skin graft survival. Mice treated with anti-CD4 antibody showed prolonged survival of xenogeneic monkey or rabbit skin even after they had rejected whole MHC-disparate allogeneic mouse skin. Furthermore, the addition of cyclosporine was synergistic with the anti-CD4 antibody in prolonging graft survival. These results suggest that the cell-mediated response to xenogeneic antigens is especially dependent on CD4+ lymphocytes, a feature shared by the response to allogeneic minor histocompatibility antigens. In addition, the results suggest a possible approach to clinical immunosuppression for some forms of xenogeneic transplantation.
Multiplex real-time PCR for exhaustive detection of diarrhoeagenicEscherichia coli (2009)

This system makes epidemiological investigations for DEC sensitive and quick, and is a useful tool to clarify the source and routes of DEC.
The Macroglial Cells of the Rat Optic Nerve (1989)

The brain's default mode network consists of discrete, bilateral and symmetrical cortical areas, in the medial and lateral parietal, medial prefrontal, and medial and lateral temporal cortices of the human, nonhuman primate, cat, and rodent brains. Its ...Read More
The effect of γ‐irradiation on collagen molecules, isolated α‐chains, and crosslinked native fibers (1990)

This study shows how collagen molecules are readily damaged by gamma-radiation at dosages commonly used for sterilizing biomedical products. At 1 Mrad, while the reported effectiveness of the radiation at such a low dosage to completely sterilize a material is questionable, less damage was caused to the collagen peptide backbone. Above such dosage, however, significant damage was clearly demonstrated with collagen alone and collagen in a chemically crosslinked tissue matrix. The enzyme digestion study showed that the material exposed to a very high dosage of radiation resisted degradation by pronase. However, molecular weight analysis showed a significant number of peptide bonds being cleaved by the radiation which could cause considerable changes in the long-term characteristics of the material. Therefore, tissues exposed to high dosages of gamma-radiation should be tested for long term functional changes. We want to caution against the usage of the enzyme degradation assay as a universal test for all bioprosthetic derived from biological tissues.
Physical and functional structure of a yeast plasmid, pSB3, isolated fromZygosaccharomyces bisporus (1985)

The plasmid pSB3 of yeast Zygosacharomyces bisporus has been sequenced. It contains 6,615 base pairs, including a pair of inverted repeats (IR) consisting of 391 base pairs and 3 large open reading frames (ORF). One of the ORFs (A gene) participates in the recombination at the IRs and the other two (B and C genes) are necessary for the stable maintenance of this plasmid. The ARS sequence, which functions in a Saccharomyces cerevisiae host, was localized within 168 base pairs consisting of part of one of the IRs and a unique sequence contiguous to it. pSB3 can be maintained as stably in Z. rouxii as in the natural host Z.bisporus. In contrast, pSB3 is maintained fairly unstably in S.cerevisiae. The reason for this instability was found to be inefficient partitioning of pSB3 in S.cerevisiae. The molecular construction of pSB3 resembles that of 2-micron DNA, however, sequence homology at the DNA level was very poor.
Protective Effects of Aspirin against Acute Myocardial Infarction and Death in Men with Unstable Angina (1983)

We conducted a multicenter, double-blind, placebo-controlled randomized trial of aspirin treatment (324 mg in buffered solution daily) for 12 weeks in 1266 men with unstable angina (625 taking aspirin and 641 placebo). The principal end points were death and acute myocardial infarction diagnosed by the presence of creatine kinase MB or pathologic Q-wave changes on electrocardiograms. The incidence of death or acute myocardial infarction was 51 per cent lower in the aspirin group than in the placebo group: 31 patients (5.0 per cent) as compared with 65 (10.1 per cent); P = 0.0005. Nonfatal acute myocardial infarction was 51 per cent lower in the aspirin group: 21 patients (3.4 per cent) as compared with 44 (6.9 per cent); P = 0.005. The reduction in mortality in the aspirin group was also 51 per cent--10 patients (1.6 per cent) as compared with 21 (3.3 per cent)--although it was not statistically significant; P = 0.054. There was no difference in gastrointestinal symptoms or evidence of blood loss between the treatment and control groups. Our data show that aspirin has a protective effect against acute myocardial infarction in men with unstable angina, and they suggest a similar effect on mortality.
Homologous versus Heterologous Immune Responses to Norwalk‐Like Viruses among Crew Members after Acute Gastroenteritis Outbreaks on 2 US Navy Vessels (2003)

Host immune responses to human caliciviruses are difficult to study because of the lack of a clear definition of antigenic or serological types. This report describes antibody responses to several Norwalk-like viruses in large outbreaks of acute gastroenteritis on 2 US Navy ships. Enzyme immunoassays (EIAs) were used to measure antibody responses. To understand the antibody response to a homologous strain causing the outbreaks, the viral capsid gene of one isolate (C59) was expressed in baculovirus and included in the EIAs. Significantly greater seroresponses were detected in patients against the homologous strain than against the heterologous strains. Strains within genogroups reacted more strongly than did strains between genogroups. Significantly higher antibody titers against the outbreak strain were detected in acute serum samples from control subjects than in those from case patients. These results indicate that recombinant EIAs are useful for outbreak investigation and that the homologous antibody might be protective against reinfection.
An assessment of binary metallic glasses: correlations between structure, glass forming ability and stability (2010)

<title/>This manuscript explores the influence of atomic structure on glass forming ability and thermal stability in binary metallic glasses. A critical assessment gives literature data for 628 alloys from 175 binary glass systems. The atomic structure is quantified for each alloy using the efficient cluster packing model. Comparison of atomic structure with amorphous thickness and thermal stability gives the following major results. Binary glasses show a strong preference for discrete solute to solvent atomic radius ratios R*, which give efficient local atomic packing. Of 15 possible R* values, only five are common and only four represent the most stable glasses. The most stable binary glasses are also typically solute rich, with enough solute atoms to fill all the solute sites and roughly one-third of the solvent sites. This suggests that antisite defects, where solutes occupy solvent atom sites, are important in the glass forming ability of the most stable glasses. This stabilising effect results from an increase in the number of more stable solute-solvent bonds in solute rich glasses. Solute rich glasses also enable efficient global atomic packing. Together, these structural constraints represent only a narrow range of topologies and thus give a useful predictive tool for the exploration and discovery of new binary bulk metallic glasses (BMGs).
Acetylation of p53 Inhibits Its Ubiquitination by Mdm2 (2002)

In response to DNA damage, the activity of the p53 tumor suppressor is modulated by protein stabilization and post-translational modifications including acetylation. Interestingly, both acetylation and ubiquitination can modify the same lysine residues at the C terminus of p53, implicating a role of acetylation in the regulation of p53 stability. However, the direct effect of acetylation on Mdm2-mediated ubiquitination of p53 is still lacking because of technical difficulties. Here, we have developed a method to obtain pure acetylated p53 proteins from cells, and by using an in vitro purified system, we provide the direct evidence that acetylation of the C-terminal domain is sufficient to abrogate its ubiquitination by Mdm2. Importantly, even in the absence of DNA damage, acetylation of the p53 protein is capable of reducing the ubiquitination levels and extending its half-life in vivo. Moreover, we also show that acetylation of p53 can affect its ubiquitination through other mechanisms in addition to the site competition. This study has significant implications regarding a general mechanism by which protein acetylation modulates ubiquitination-dependent proteasome proteolysis.
Identification of Clinically Significant Tumor Antigens by Selecting Phage Antibody Library on Tumor Cells in Situ Using Laser Capture Microdissection (2006)

Much work has been done to develop tumor-targeting antibodies by selecting a phage antibody library on cancer cell lines. However, when tumor cells are removed from their natural environment, they may undergo genetic and epigenetic changes yielding different surface antigens than those seen in actual cases of cancer. We developed a strategy that allows selection of phage antibodies against tumor cells in situ on both fresh frozen and paraffin-embedded tissues using laser capture microdissection. By restricting antibody selection to binders of internalizing epitopes, we generated a panel of phage antibodies that target clinically represented prostate cancer antigens. We identified ALCAM/MEMD/CD166, a newly discovered prostate cancer marker, as the target for one of the selected antibodies, demonstrating the effectiveness of our approach. We further conjugated two single chain Fv fragments to liposomes and demonstrated that these nanotargeting devices were efficiently delivered to the interior of prostate cancer cells. The ability to deliver payload intracellularly and to recognize tumor cells in situ makes these antibodies attractive candidates for the development of targeted cancer therapeutics.
Dietary n-3 PUFA increases the apoptotic response to 1,2-dimethylhydrazine, reduces mitosis and suppresses the induction of carcinogenesis in the rat colon (1999)

The effect of dietary fish oil on colonic crypt cell apoptosis and proliferation was examined in male Wistar rats, 24 and 48 h after administration of 1,2-dimethylhydrazine (DMH), and its influence on the induction of aberrant crypt foci (ACF) in the distal colon was assessed. Rats (125-150 g) fed a high-fat semi-synthetic diet containing corn oil (CO) were given DMH (30 mg/kg body wt) or a sham injection of EDTA/NaCl. Animals were then fed either the CO diet or a diet in which fish oil (EPA 18.7%; DHA 8%) was substituted for corn oil. Subgroups of rats (n = 5) were killed after 24 and 48 h, and crypt cell apoptosis and proliferation were quantified by morphological criteria in isolated intact crypts from the mid and distal colon. Consumption of the fish oil diet (FO) was associated with increased apoptotic cell death (P < 0.001) and suppression of proliferation (P < 0.05) in colonic crypts both 24 and 48 h after DMH. In a second experiment, animals were given three injections of DMH or sham injections of carrier at weekly intervals. For 48 h after each injection animals were fed either the CO or FO diet, but otherwise maintained on the CO throughout. The number and crypt multiplicity of ACF in the distal colon were determined after 18 weeks, and animals given the FO diet for the 48 h period following carcinogen administration were found to have significantly fewer ACF than rats fed the CO diet (P < 0.05). The data demonstrate that the fatty acid composition of the diet is an important determinant in the induction of carcinogenesis by DMH. The proliferative and apoptotic response of the colonic crypt to carcinogen and fish oil, coupled with the reduced incidence of ACF, suggest n-3 PUFA can protect against the carcinogenic effects of DMH by mediating changes in the balance proliferation and cell death.