gebhart/patrepeval huggingface dataset:
Intracellular pH Distribution in Saccharomyces cerevisiae Cell Populations, Analyzed by Flow Cytometry (2005)

Intracellular pH has an important role in the maintenance of the normal functions of yeast cells. The ability of the cell to maintain this pH homeostasis also in response to environmental changes has gained more and more interest in both basic and applied research. In this study we describe a protocol which allows the rapid determination of the intracellular pH of Saccharomyces cerevisiae cells. The method is based on flow cytometry and employs the pH-dependent fluorescent probe carboxy SNARF-4F. The protocol attempts to minimize the perturbation of the system under study, thus leading to accurate information about the physiological state of the single cell. Moreover, statistical analysis performed on major factors that may influence the final determination supported the validity of the optimized protocol. The protocol was used to investigate the effect of external pH on S. cerevisiae cells incubated in buffer. The results obtained showed that stationary cells are better able than exponentially grown cells to maintain their intracellular pH homeostasis independently of external pH changes. Furthermore, analysis of the intracellular pH distribution within the cell populations highlighted the presence of subpopulations characterized by different intracellular pH values. Notably, a different behavior was observed for exponentially grown and stationary cells in terms of the appearance and development of these subpopulations as a response to a changing external pH.
Diblock Copolymers Based on Dihydroxyacetone and Ethylene Glycol:  Synthesis, Characterization, and Nanoparticle Formulation (2006)

Polymeric biomaterials have played an integral role in tissue engineering, biomedical devices, and targeted drug delivery. Block copolymers are especially important because their physical and chemical properties can be controlled by adjusting the ratio, size, and type of constituting blocks. Herein, the synthesis and characterization of diblock copolymers composed of poly(ethylene glycol) and a polycarbonate based on the metabolic intermediate, dihydroxyacetone, are reported. The length of the dihydroxyacetone-based block was controlled by adjusting the reactant feed ratios and initiator injection conditions. Intermediates and final products were characterized via 1H NMR, GPC, DSC, TGA, and diffusion-ordered NMR spectroscopy. The dihydroxyacetone-based hompolymer is insoluble in water and most organic solvents, but is hydrophilic in nature. This, coupled with poly(ethylene glycol)'s solubility characteristics, allows the block copolymer to form nanoparticles in aqueous and organic anti-solvents. Dynamic light scattering and TEM results indicated the formation of spherical nanoparticles.
Effect of epidermal growth factor on enterocyte brush-border surface area (1993)

The effect of acute in vivo epidermal growth factor (EGF) exposure on intestinal absorptive surface area was examined in blind jejunal loops in New Zealand White rabbits (500-900 g). Brush-border surface area was assessed by electron microscopy at 30 and 120 min, and total surface area was assessed by the fluorophore 1-[4-(trimethylamino)phenyl)]-6-phenylhexatriene (TMA-DPH) at 10 and 60 min after EGF exposure. Mucosa obtained at 120 min was also used for morphometrics and analysis of membrane composition and fluidity. Brush-border surface area was significantly increased in EGF-treated tissue after 30 (42%) and 120 min (60%). Total absorptive surface area measured by TMA-DPH was increased more than twofold after 10 and 60 min EGF exposure. The increase in absorptive surface area was abolished by pretreatment with intravenous verapamil. Mucosal morphometrics and membrane sucrase activity, total phospholipids, cholesterol content, cholesterol-to-phospholipid ratio, phospholipid species (wt%), phospholipid fatty acid composition, and fluidity did not differ between control and EGF-treated tissue. These findings indicate that EGF can rapidly increase brush-border surface area by a mechanism that appears to be due to a redistribution of existing performed microvillus plasma membrane.
Smoking Increases the Risk of Panic (2003)

In young adults, prospective analyses revealed a fairly unique and specific, unidirectional relationship between prior smoking and increased risk for subsequent panic attacks/disorder. However, we could not exclude the existence of a second, less frequent, reverse pathway of prior panic and secondary nicotine dependence.
Transformation of a Leu−Mutant ofRhizopus niveuswith theleuAGene ofMucor circinelloides (1992)

Journal Article Transformation of a Leu− Mutant of Rhizopus niveus with the leuA Gene of Mucor circinelloides Get access Chung Ming Liou, Chung Ming Liou Department of Agricultural Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113, Japan Search for other works by this author on: Oxford Academic Google Scholar Koji Yanai, Koji Yanai Department of Agricultural Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113, Japan Search for other works by this author on: Oxford Academic Google Scholar Hiroyuki Horiuchi, Hiroyuki Horiuchi Department of Agricultural Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113, Japan Search for other works by this author on: Oxford Academic Google Scholar Masamichi Takagi Masamichi Takagi Department of Agricultural Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113, Japan Search for other works by this author on: Oxford Academic Google Scholar Bioscience, Biotechnology, and Biochemistry, Volume 56, Issue 9, 1 January 1992, Pages 1503–1504, https://doi.org/10.1271/bbb.56.1503 Published: 01 January 1992 Article history Published: 01 January 1992 Received: 07 April 1992
Learning probabilistic networks (1999)

A probabilistic network is a graphical model that encodes probabilistic relationships between variables of interest. Such a model records qualitative influences between variables in addition to the numerical parameters of the probability distribution. As such it provides an ideal form for combining prior knowledge, which might be limited solely to experience of the influences between some of the variables of interest, and data. In this paper, we first show how data can be used to revise initial estimates of the parameters of a model. We then progress to showing how the structure of the model can be revised as data is obtained. Techniques for learning with incomplete data are also covered. In order to make the paper as self contained as possible, we start with an introduction to probability theory and probabilistic graphical models. The paper concludes with a short discussion on how these techniques can be applied to the problem of learning causal relationships between variables in a domain of interest.
Palladium‐Catalyzed Hydroxylation of Aryl Halides under Ambient Conditions (2009)

Turning down the heat: The first room temperature Pd-catalyzed synthesis of phenols from aryl bromides and chlorides is presented. Stoichiometric studies of Pd-mediated hydroxylation of aryl halides employing a bulky imidazolyl-phosphine ligand and the novel palladium precursor [Pd(cod)(CH2SiMe3)2] led to development of efficient catalytic synthesis of phenols under ambient conditions (see scheme; Ad=adamantyl, cod=1,5-cyclooctadiene). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
High-κ gate dielectrics: Current status and materials properties considerations (2001)

Many materials systems are currently under consideration as potential replacements for SiO2 as the gate dielectric material for sub-0.1 μm complementary metal–oxide–semiconductor (CMOS) technology. A systematic consideration of the required properties of gate dielectrics indicates that the key guidelines for selecting an alternative gate dielectric are (a) permittivity, band gap, and band alignment to silicon, (b) thermodynamic stability, (c) film morphology, (d) interface quality, (e) compatibility with the current or expected materials to be used in processing for CMOS devices, (f) process compatibility, and (g) reliability. Many dielectrics appear favorable in some of these areas, but very few materials are promising with respect to all of these guidelines. A review of current work and literature in the area of alternate gate dielectrics is given. Based on reported results and fundamental considerations, the pseudobinary materials systems offer large flexibility and show the most promise toward successful integration into the expected processing conditions for future CMOS technologies, especially due to their tendency to form at interfaces with Si (e.g. silicates). These pseudobinary systems also thereby enable the use of other high-κ materials by serving as an interfacial high-κ layer. While work is ongoing, much research is still required, as it is clear that any material which is to replace SiO2 as the gate dielectric faces a formidable challenge. The requirements for process integration compatibility are remarkably demanding, and any serious candidates will emerge only through continued, intensive investigation.
Activation of p300 Histone Acetyltransferase by Small Molecules Altering Enzyme Structure:  Probed by Surface-Enhanced Raman Spectroscopy (2007)

Reversible acetylation of nucleosomal histones and nonhistone proteins play pivotal roles in the regulation of all the DNA templated phenomenon. Dysfunction of the enzymes involved in the acetylation/deacetylation leads to several diseases. Therefore, these enzymes are the targets for new generation therapeutics. Here, we report the synthesis of trifluoromethyl phenyl benzamides and their effect on histone acetyltransferase (HAT) activity of p300. One of these benzamides, CTPB (N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide), was discovered as a potent activator of the p300 HAT activity. We have found that pentadecyl hydrocarbon chain of CTPB is required to activate the HAT only under certain context. Furthermore, our results show that the relative position of -CF3 and -Cl in CTB (N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide) is also very critical for the activation. Surface-enhanced Raman spectroscopy (SERS) of p300 and the HAT activator complexes evidently suggest that the activation of HAT activity is achieved by the alteration of p300 structure. Therefore, apart from elucidating the chemical basis for small molecule mediated activation of p300, this report also describes, for the first time, Raman spectroscopic analysis of the complexes of histone-modifying enzymes and their modulators, which may be highly useful for therapeutic applications.
A Novel Viral System for Generating Antigen-Specific T Cells (2005)

Dendritic cell (DC)-based vaccines are increasingly used for the treatment of patients with malignancies. Although these vaccines are typically safe, consistent and lasting generation of tumor-specific immunity has been rarely demonstrated. Improved methods for delivering tumor Ags to DCs and approaches for overcoming tolerance or immune suppression to self-Ags are critical for improving immunotherapy. Viral vectors may address both of these issues, as they can be used to deliver intact tumor Ags to DCs, and have been shown to inhibit the suppression mediated by CD4+CD25+ regulatory T cells. We have evaluated the potential use of Venezuelan equine encephalitis virus replicon particles (VRPs) for in vitro Ag delivery to human monocyte-derived DCs. VRPs efficiently transduced immature human DCs in vitro, with approximately 50% of immature DCs expressing a vector-driven Ag at 12 h postinfection. VRP infection of immature DCs was superior to TNF-alpha treatment at inducing phenotypic maturation of DCs, and was comparable to LPS stimulation. Additionally, VRP-infected DC cultures secreted substantial amounts of the proinflammatory cytokines IL-6, TNF-alpha, and IFN-alpha. Finally, DCs transduced with a VRP encoding the influenza matrix protein (FMP) stimulated 50% greater expansion of FMP-specific CD8+ CTL when compared with TNF-alpha-matured DCs pulsed with an HLA-A*0201-restricted FMP peptide. Thus, VRPs can be used to deliver Ags to DCs resulting in potent stimulation of Ag-specific CTL. These findings provide the rationale for future studies evaluating the efficacy of VRP-transduced DCs for tumor immunotherapy.
Formation of pentosidine during nonenzymatic browning of proteins by glucose. Identification of glucose and other carbohydrates as possible precursors of pentosidine in vivo (1991)

A fluorescent compound has been detected in proteins browned during Maillard reactions with glucose in vitro and shown to be identical to pentosidine, a pentose-derived fluorescent cross-link formed between arginine and lysine residues in collagen (Sell, D. R., and Monnier, V. M. (1989) J. Biol. Chem. 264, 21597-21602). Pentosidine was the major fluorophore formed during nonenzymatic browning of ribonuclease and lysozyme by glucose, but accounted for less than 1% of non-disulfide cross-links in protein dimers formed during the reaction. Pentosidine was formed in greatest yields in reactions of pentoses with lysine and arginine in model systems but was also formed from glucose, fructose, ascorbate, Amadori compounds, 3-deoxyglucosone, and other sugars. Pentosidine was not formed from peroxidized polyunsaturated fatty acids or malondialdehyde. Its formation from carbohydrates was inhibited under nitrogen or anaerobic conditions and by aminoguanidine, an inhibitor of advanced glycation and browning reactions. Pentosidine was detected in human lens proteins, where its concentration increased gradually with age, but it did not exceed trace concentrations (less than or equal to 5 mumol/mol lysine), even in the 80-year-old lens. Although its precise carbohydrate source in vivo is uncertain and it is present in only trace concentrations in tissue proteins, pentosidine appears to be a useful biomarker for assessing cumulative damage to proteins by nonenzymatic browning reactions with carbohydrates.
Cyclopamine and Hedgehog Signaling: Chemistry, Biology, Medical Perspectives (2010)

When Odysseus left the devastated city of Troy after ten years of siege he could not foresee the perils he still had to face. The encounter with the cyclops, a giant with only one eye placed in the middle of its forehead, was doubtlessly one of the creepiest and most dangerous of his adventures. In the end, Odysseus could only escape with the help of a sheep. Whether Homers cyclops was inspired by the observation of terribly malformed neonates remains speculative. However, when sheep herders in Idaho in the middle of the 20th century faced an increasing number of cyclops-like sheep in their herds, a unique cascade of chemical, biological, and medicinal discoveries was initiated. This Minireview tells this story and shows its impact on modern biomedical research.
Transcription factor AP-4 contains multiple dimerization domains that regulate dimer specificity. (1990)

Enhancer binding protein AP-4 is a transcription factor that activates both viral and cellular genes by binding to the symmetrical DNA sequence, CAGCTG. Here, we report the molecular cloning and characterization of human AP-4 cDNAs. The deduced amino acid sequence reveals that AP-4 is a helix-loop-helix (HLH) protein. Like other members of this family, the AP-4 HLH motif and the adjacent basic domain are necessary and sufficient to confer site-specific DNA binding. However, unlike other HLH proteins, AP-4 also contains two additional protein dimerization motifs consisting of leucine repeat elements LR1 and LR2. The analysis of various deletion and point mutants for their ability to dimerize in the presence or absence of DNA reveals several unusual features. Although the HLH basic region is sufficient for DNA recognition and binding, dimer formation between different truncated versions of AP-4 in solution requires an intact LR1 or LR2 domain. AP-4 is unable to form heterodimers with other helix-loop-helix family members such as the immunoglobulin enhancer binding factor, E12. In contrast, an AP-4 derivative, delta C222, which lacks LR1 and LR2 but retains an intact HLH, can form heterodimers with E12. Moreover, AP-4 molecules containing LR2 or LR1 are unable to form mixed dimers with carboxy-terminally truncated AP-4 molecules such as delta C222, but retain the ability to form complexes with longer versions of AP-4 that contain LR1 and/or LR2. Our findings strongly suggest that AP-4 contains multiple protein-protein interfaces that function to promote homodimer formation and restrict heterocomplexes. These findings provide a mechanism by which different members of the helix-loop-helix family of transcription factors can form functional dimers in a specific fashion with their appropriate partners to control transcriptional networks during cellular differentiation.
New Insights into Inflammatory Bowel Disease Pathophysiology: Paving the Way for Novel Therapeutic Targets (2008)

The etiopathogenesis of Crohn's disease (CD) and ulcerative Colitis (UC), the two major forms of inflammatory bowel disease (IBD), is still unknown. Although the exact cause and mechanisms of both IBD have yet to be completely understood, it is widely accepted that both CD and UC result from an inappropriate immune response that occurs in genetically susceptible individuals as the result of a complex interaction among environmental factors, microbial factors, and the intestinal immune system. In the last few years a tremendous advance in knowledge of the mechanisms underlying intestinal inflammation in IBD has been achieved, leading to new therapeutic targets and novel drugs. These new therapeutic weapons have been specifically designed to selective shut down intestinal inflammation at different levels. Aim of this review is to summarize the recent advances in IBD pathophysiology and the new therapeutic targets and drugs that are changing the IBD clinical management.
The induction of apoptosis by chemotherapeutic agents occurs in all phases of the cell cycle. (1992)

A1.1 T-cell hybridoma cells exposed to either actinomycin D (1 microgram/ml), camptothecin (200 ng/ml) or aphidicolin (10 micrograms/ml) for 16 hrs at 37 degrees C die via apoptosis. The cell death was independent of RNA synthesis, in contrast to previous data reported for other forms of apoptosis in murine lymphocyte cells and their derived lines. Each of the three agents described appeared to induce death in all phases of the cell cycle in asynchronously proliferating cells. G1 cells appeared to be more susceptible to the effects of camptothecin and contrasts with other reports which detail its selectivity for S and G2 phase cells. This might indicate that cells are progressing into S phase before dying or, alternatively, cells may indeed be dying in G1. When elutriated synchronised cells were exposed to each of the three cytotoxic agents cell death occurred in all phases of the cell cycle. In view of the fact that G1 and S phase cells did not cycle to any appreciable extent during drug exposure, it was likely that ensuing death, occurred specifically from these phases. G2/M cells, however, moved rapidly into G1 in the presence of each drug, thus making it difficult to determine whether G2/M cells were capable of undergoing drug-induced apoptosis. To overcome this problem, nocodazole (50 ng/ml) was used to block asynchronous cells in M phase. When these cells were exposed to actinomycin D, aphidicolin or camptothecin, cell death ensued via apoptosis.
Formulation of the Optimal Latin Hypercube Design of Experiments Using a Permutation Genetic Algorithm (2004)

The choice of location of the evaluation points is important in response surface generation, especially when the evaluations are expensive. Space-filling designs can be used to specify the points so that as much of the design space is sampled as possible with the minimum number of response evaluations. One popular technique is the optimal Latin hypercube design of experiments. However, its generation is non-trivial, time consuming and is – but for the simplest problems – infeasible to carry out by enumeration. Therefore, solving this problem requires an optimization technique to search the design space. As the problem is discrete, it is ideally suited to the use of discrete optimization techniques such as genetic algorithms. This paper describes a method for generating optimal latin hypercubes using a permutation genetic algorithm and compares it with a standard binary genetic algorithm. The objective of the optimization is based on minimizing a function that is analogous the potential energy of the system of material points. The developed method offers considerable improvements over previous solutions; it generates better solutions and the computational effort in reaching those solutions is significantly reduced.
The Biology of Normal and Neoplastic Stem Cells in CML (1993)

Chronic myeloid leukemia (CML) has long served as a prototype malignancy for basic as well as clinical studies aimed at developing curative cancer treatment protocols. Well established features of chronic phase CML are its origin in a pluripotent stem cell, a now well defined molecular genetic basis involving the creation of a BCR-ABL fusion gene and evidence of resultant abnormalities in the mechanisms that normally control primitive hemopoietic cell proliferation. We have recently shown how the long-term marrow culture system can be adapted to quantitate and characterize a very primitive cell type in normal blood and marrow samples, as well as their normal and leukemic counterparts in patients with CML. This system has also been used to dissect mechanisms of normal progenitor regulation and to identify specific anomalies affecting leukemic (CML) progenitors. Our studies show that cells detected by their ability to initiate long-term cultures (LTC) of leukemic cells (i.e., CML LTC-initiating cells or LTC-IC) are differently distributed between marrow and blood by comparison to LTC-IC in normal individuals and, although functionally similar in terms of the number and differentiation types of clonogenic cells they produce, CML LTC-IC exhibit defective self-maintenance. Phenotypically these primitive leukemic cells are heterogeneous; the majority display features of activated/proliferating cells but a significant proportion do not. We have also documented heterogeneity in primitive CML cell responses to two factors that specifically and reversibly arrest the cycling of primitive normal hemopoietic cells; i.e., TGF-beta and MIP-1 alpha, to which CML cells are normally responsive and abnormally unresponsive, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)