gebhart/patrepeval huggingface dataset:
In-vitro schedule-dependent interaction between oxaliplatin and 5-fluorouracil in human gastric cancer cell lines (2006)

In order to define the most effective combination schedule of oxaliplatin (L-OHP) and 5-fluorouracil (5-FU), we investigated the in vitro interaction between these drugs in a panel of four human gastric adenocarcinoma cell lines (MKN-1, NUGC-3, NUGC-5 and AZ-521). Cytotoxic activity was determined by the WST-1 assay. Different schedules of the two drugs were compared and evaluated for synergism, additivity or antagonism with a quantitative method based on the median-effect principle of Chou and Talalay. Cell cycle perturbation and apoptosis were evaluated by flow cytometry. Simultaneous and sequential treatments of L-OHP followed by 5-FU exhibited synergistic effects in all four cell lines, whereas the reverse sequence yielded a clear antagonism. 5-FU exclusively arrested cells at the G0/G1 phase, and L-OHP at the G0/G1 and G2/M phases. Apoptosis was most prominent when cells were treated simultaneously or in a sequence of L-OHP followed by 5-FU, producing apoptosis in the majority of treated cells (55.5-61.5%). In contrast, the reverse sequence yielded only 20% induction of apoptosis, the rate being not significantly different from those induced by each drug singly. Moreover, this sequence dependence was further confirmed by the experiment which compared the total number of NUGC-3 cells 7 days after these combination schedules. These findings suggest that the interaction of 5-FU and L-OHP could be highly schedule dependent, with the most efficacious interaction observed in simultaneous combination and that 5-FU followed by L-OHP would not be recommended in clinical trials for patients with advanced gastric cancer.
Mimicry of Host-Defense Peptides by Unnatural Oligomers:  Antimicrobial β-Peptides (2002)

We have designed beta-amino acid oligomers that are helical, cationic, and amphiphilic with the intention of mimicking the biological activity of amphiphilic, cationic alpha-helical antimicrobial peptides found in nature (e.g., magainins). We have previously identified a 17-residue beta-peptide (called beta-17) with antibiotic activity similar to that of a magainin derivative against four bacterial species, including two clinical isolates that are resistant to common antibiotics. This beta-peptide displays very low hemolytic activity against human red blood cells, which indicates selectivity for bacterial cells over mammalian cells. Here we examine some of the factors important for activity in this class of beta-peptides. An amphiphilic helix is necessary, because a nonamphiphilic isomer proved to be inactive. The ratio of cationic to hydrophobic residues is also important. Active beta-peptides induce the leakage of beta-galactosidase from treated Bacillus subtilis cells, as do alpha-helical antibiotic peptides, and this similarity suggests that the beta-peptide mode of action involves disruption of microbial membranes. This class of beta-peptides is not degraded by proteases, which bodes well for biological applications.
Free-Standing Layer-by-Layer Assembled Films of Magnetite Nanoparticles (2000)

A new technique for preparation of free-standing ultrathin films is presented. These films were made by layer-by-layer (LBL) deposition process, which is utilized for coatings on solid substrates and colloids. A film composed of alternating layers of magnetite nanoparticles and poly(diallyldimethylammonium bromide) was assembled on cellulose acetate, which was subsequently dissolved in acetone. From the suspended state, the LBL film can be transferred onto any solid or porous support. The strength of the film was observed to significantly increase when every other layer of magnetite was replaced with a layer of alumosilicate sheets serving as a molecular framework for the assembly.
Performance evaluation of a general traffic control framework in ATM networks (1999)

This paper presents a general traffic control framework for Asynchronous Transfer Mode (ATM) networks with its performance evaluation. The proposed traffic control scheme can incorporate all the recently considered ATM service classes including Constant Bit Rate (CBR), real time Variable Bit Rate (rtVBR), non-real time Variable Bit Rate (nrVBR), Available Bit Rate (ABR) and Unspecified Bit Rate (UBR) services. The control is based on a complete buffer partitioning architecture and on the associated buffer scheduling rule with adaptive weighting functions. We present, the formulation of the traffic control as an optimization problem in a 3-dimensional Quality of Service (QoS) state space. A solution approach based on dynamic programming is also suggested. A comprehensive performance evaluation of the method has been performed based on simulations and results are presented with several examples. The QoS dependence on CBR load, VBR load, VBR burstiness, UBR load are investigated and results are demonstrated with explanations.
ESTABLISHMENT AND CHARACTERIZATION OF HUMAN MYELOMONOCYTIC (TYS) AND HISTIOCYTIC (TYH) CELL LINES (1985)

Two human hematopoietic cell lines (TYS and TYH) with monocytic characteristics were derived from the peripheral blood of a patient with acute myelomonocytic leukemia and of another with a follicular large-cell type of malignant lymphoma. The TYS cells, derived from the leukemia patient, revealed a monocytic appearance with microvilli at one side and had many granules and vacuoles. They showed strongly positive reactions with alpha-NBE, NASDAE, and AcP, and were reactive with monoclonal antibodies such as OKlal, 12 and Bl. The TYS cells, which phagocytized carbon particles and antibody-coated SRBC but not latex particles, released lysosomal enzymes and tumoricidal factor into the supernatant. The TYH cells, derived from the malignant lymphoma patient, had abundant cytoplasm and pseudopods detectable by electron microscopy with a monocytoid appearance and virus-like particles in the cytoplasm. They showed strongly positive reactions with alpha-NBE, NASDAE and beta-Gase, but no reactivity with monoclonal antibodies or with surface markers except Fc gamma-R. TYH cells phagocytized latex particles very well. Two different human monocyte-histiocyte lineages were thus established. During culture, the TYS and TYH cells maintained their characteristics over 28 and 16 months of passage, respectively.
A novel cancer therapy based on oxygen radicals. (1995)

The antitumor effect of oxygen radicals produced by hypoxanthine and xanthine oxidase reaction was studied in an experimental rabbit model. VX2 carcinomas were transplanted into rabbit hind legs. Hypoxanthine was administered continuously through the ear vein, while xanthine oxidase was administered simultaneously through the femoral artery. As a result, hypoxanthine and xanthine oxidase reacted only in the hind leg, and superoxide was produced in that area. The volume of the VX2 carcinoma was measured immediately prior to treatment and 7 days later. As an index of lipid peroxidation, thiobarbituric acid-reactive substances in the tumor tissue were measured 60 min following infusion of hypoxanthine and xanthine oxidase. Tumor growth was suppressed significantly by the hypoxanthine-xanthine oxidase reaction, and thiobarbituric acid-reactive substances in the tumor tissue infused with hypoxanthine and xanthine oxidase were significantly increased. In addition, the antitumor effect of the hypoxanthine and xanthine oxidase reaction was significantly inhibited by the administration of superoxide dismutase and catalase. Pathological examination showed that oxygen radicals produced by hypoxanthine and xanthine oxidase reaction were selectively more destructive for VX2 carcinoma tissue than muscle tissue surrounding the tumor region. These results suggest that oxygen radicals produced by hypoxanthine and xanthine oxidase reaction produce an anticancer effect and that the VX2 carcinoma used in this study was more sensitive to oxygen radicals than normal muscle tissue.
Isolation of Endohyphal Bacteria from Foliar Ascomycota and In Vitro Establishment of Their Symbiotic Associations (2016)

Endohyphal bacteria (EHB) can influence fungal phenotypes and shape the outcomes of plant-fungal interactions. Previous work has suggested that EHB form facultative associations with many foliar fungi in the Ascomycota. These bacteria can be isolated in culture, and fungi can be cured of EHB using antibiotics. Here, we present methods for successfully introducing EHB into axenic mycelia of strains representing two classes of Ascomycota. We first establish in vitro conditions favoring reintroduction of two strains of EHB (Luteibacter sp.) into axenic cultures of their original fungal hosts, focusing on fungi isolated from healthy plant tissue as endophytes: Microdiplodia sp. (Dothideomycetes) and Pestalotiopsis sp. (Sordariomycetes). We then demonstrate that these EHB can be introduced into a novel fungal host under the same conditions, successfully transferring EHB between fungi representing different classes. Finally, we manipulate conditions to optimize reintroduction in a focal EHB-fungal association. We show that EHB infections were initiated and maintained more often under low-nutrient culture conditions and when EHB and fungal hyphae were washed with MgCl2 prior to reassociation. Our study provides new methods for experimental assessment of the effects of EHB on fungal phenotypes and shows how the identity of the fungal host and growth conditions can define the establishment of these widespread and important symbioses.
Single Nanotube Raman Spectroscopy (2002)

A review is presented on the observation of the resonant Raman spectra from one isolated single wall carbon nanotube, focusing on the important structural information that is provided by single nanotube spectroscopy including the (n, m) determination of the individual tubes. The special sensitivity of the radial breathing mode to the (n, m) determination is emphasized, and the corroboration of this (n, m) assignment by diameter- and chirality-dependent phenomena in other Raman modes, such as the G-band, D-band, and G'-band features is also discussed. The significance of single nanotube spectroscopy for future nanotube research in general is briefly reviewed.
Metric constraints for maintaining appointments: dates and repeated activities (1991)

Reasoning about one&amp;apos;s personal schedule of appointments is a common but surprisingly complex activity. Motivated by the novel application of planning and temporal reasoning techniques to this problem, we have extended the formalization of the temporal distance model of Dechter, Meiri, and Pearl. We have developed methods for using dates as reference intervals and for meeting the challenge of repeated activities, such as weekly recurring appointments. Introduction Intelligently managing a busy personal schedule is not an easy task, but it is a ubiquitous one. The benefit to be derived from an automated facility for maintaining an appointment calendar---with all of the complex constraint management that that entails 1 ---is potentially enormous. In the context of CLASM, 2 an intelligent appointment manager, we have begun to explore the utility of AI methods for maintaining a library of complex activity descriptions, verifying whether an activity is possible, and checking the cons...
Design of virotherapy for effective tumor treatment. (2010)

The use of viruses as therapeutic agents against cancer is an old concept that has had a significant revival in the past two decades, in parallel with advances in methods to modify viral genomes genetically. From the initial stage of proof of concept, the field of virotherapy quickly progressed to the clinical setting, where serious limitations, yet promising opportunities, were identified. After demonstrating good safety profiles in humans, the objective in virotherapy has become to improve the efficacy of oncolytic viruses. Virotherapy approaches include incorporating therapeutic genes, evaluating alternative viruses with stronger oncolytic potential, employing new methods to improve biodistribution, and establishing greater insight into the influence of the immune system on both the success and failure of therapies. This review summarizes the most significant advances in recent years in the design of virotherapy for effective tumor treatment.
First line combination chemotherapy with docetaxel and vinorelbine in advanced breast cancer. A phase II study. (2002)

This combination of docetaxel and vinorelbine, a non-anthracycline-containing regimen, is a moderately effective regimen for the treatment of chemotherapy-naive breast cancer patients with metastases, causing only mild to moderate toxicity.
Analysis of the Borrelia burgdorferi GeHo fla gene and antigenic characterization of its gene product (1991)

The fla gene of Borrelia burgdorferi GeHo was analyzed and expressed in Escherichia coli. The structural gene encodes a flagellar protein of 336 amino acids. Comparative sequence analysis of the amino acid sequence revealed a high degree of sequence conservation with flagellins from both phylogenetically related and unrelated bacteria. The antigenic properties of the B. burgdorferi Fla protein were studied by synthesizing overlapping octapeptides, which were screened by using a battery of different monoclonal and polyclonal antibodies from various species directed against native and denatured flagellar proteins. No single species-independent immunodominant epitope could be located. However, immunoreactive oligopeptides clustered within the variable middle region (N-180 to I-260). This region could constitute a candidate antigen for more specific and sensitive serodiagnosis of Lyme borreliosis.
The T-box transcription factor Brachyury promotes renal interstitial fibrosis by repressing E-cadherin expression (2014)

Epithelial-to-mesenchymal transition (EMT) induced by TGF-β1 is one of well-recognized factors contributing to renal fibrosis. However, the underlying molecular mechanisms of EMT are not fully understood. Brachyury, an evolutionarily conserved transcription factor, was recently identified as an important factor promoting EMT in human carcinoma cell lines. There is no evidence that Brachyury is involved in renal tubular EMT. Our results demonstrated that Brachyury was prominently induced in TGF-β1-treated human proximal tubular epithelial (HK-2) cells and that this induction was accompanied by changes characteristic of EMT. Blockage of Brachyury expression by short interfering RNA (siRNA) in HK-2 cells effectively reversed the TGF-β1-induced EMT phenotype. Brachyury induction repressed E-cadherin transcription; the E-cadherin promoter contains a Brachyury binding site, and decreased expression of E-cadherin occurred in Brachyury-overexpressing cells when they were transfected with reporter constructs using the promoter. This effect was partially mediated by Slug and Snail, as knockdown of Snail and Slug by siRNA effectively reversed Brachyury-mediated EMT and partially restored E–cadherin expression. The expression of Brachyury also presented in a rat model of obstructive nephropathy and in tubulointerstitial fibrosis tissues of IgA nephropathy, suggesting that it may have a role in EMT and renal fibrosis in vivo. Our results demonstrate for the first time that Brachyury plays an important role in regulating TGF-β1–mediated renal EMT and could be an attractive target for progression of renal disease therapies.
Sonochemical process for the preparation of α-CuSe nanocrystals and flakes (2002)

α-CuSe crystals of different sizes and shapes have been synthesized by a sonochemical method using the less hazardous elemental Se and Cu(Ac)2 as precursors under an atmosphere of H2/Ar (5 ∶ 95 v/v). X-ray diffraction (XRD), energy-dispersive analytical X-ray (EDAX) and inductively coupled plasma (ICP) have been applied to characterize the products. Transmission electron microscopy (TEM) and selected area electron diffraction (SAED) results show that they are crystallized nanoparticles of tens of nanometers or flakes of 1 µm, depending on the irradiation time. Thermogravimetric analysis (TGA) indicates that the products are stable up to about 480 °C. Diffusion reflection spectra (DRS) reveal that both of them show an indirect band gap with a similar value of about 1.31 eV. Photoacoustic spectra results show that the nanoparticles and the flakes have direct band gaps of about 2.39 eV and 2.21 eV, respectively. This is the first report of the optical properties of α-CuSe. We propose an in situ reduction/reaction mechanism to explain the formation of CuSe. The influence of ultrasound on the shape and the size of the product is discussed. The chelating role of the DMSO solvent in the reaction has also been studied.
Diminishing catalyst concentration in atom transfer radical polymerization with reducing agents (2006)

The concept of initiators for continuous activator regeneration (ICAR) in atom transfer radical polymerization (ATRP) is introduced, whereby a constant source of organic free radicals works to regenerate the Cu(I) activator, which is otherwise consumed in termination reactions when used at very low concentrations. With this technique, controlled synthesis of polystyrene and poly(methyl methacrylate) (Mw/Mn < 1.2) can be implemented with catalyst concentrations between 10 and 50 ppm, where its removal or recycling would be unwarranted for many applications. Additionally, various organic reducing agents (derivatives of hydrazine and phenol) are used to continuously regenerate the Cu(I) activator in activators regenerated by electron transfer (ARGET) ATRP. Controlled polymer synthesis of acrylates (Mw/Mn < 1.2) is realized with catalyst concentrations as low as 50 ppm. The rational selection of suitable Cu complexing ligands {tris[2-(dimethylamino)ethyl]amine (Me6TREN) and tris[(2-pyridyl)methyl]amine (TPMA)} is discussed in regards to specific side reactions in each technique (i.e., complex dissociation, acid evolution, and reducing agent complexation). Additionally, mechanistic studies and kinetic modeling are used to optimize each system. The performance of the selected catalysts/reducing agents in homo and block (co)polymerizations is evaluated.
Aerobic deammonification: a new experience in the treatment of wastewaters (1997)

The leachate treatment plant of the landfill in Mechernich including biological pretreatment, reverse osmosis and evaporation and drying of the concentrate has been in operation since the beginning of 1994. Balancing the nitrogen transformations in the biological contactor plant as the nitrification step in the biological pretreatment, a large amount of the ammonium can be eliminated under aerobic conditions by deammonification. It succeeded obviously under the special conditions to establish a non-negligible amount of denitrifying ammonia oxidants. Experiences concerning this effect were described several times in the past.
Visualization of O-2A progenitor cells in developing and adult rat optic nerve by quisqualate-stimulated cobalt uptake (1992)

Some macroglial cells of the O-2A lineage express glutamate receptor channels of the quisqualate/kainate type and take up extracellular cobalt when activated by glutamate agonists. These cells can be identified both in vitro and in situ following precipitation and intensification of the intracellular cobalt. We have used this technique to characterize these cells in the developing and adult rat optic nerve. In purified cultures of optic nerve cells, O-2A progenitor cells and type 2 astrocytes took up cobalt in the presence of quisqualate, while oligodendrocytes, type 1 astrocytes, and microglial cells did not. When whole optic nerves of various postnatal ages were exposed to quisqualate and cobalt, a subpopulation of glial cells took up cobalt. Cobalt uptake in vitro and in situ was blocked by 6-cyano-7-nitroquinoxaline-2,3-dione. The number, morphology, and spatial distribution of cobalt-filled cells in situ varied with age. In perinatal nerves, 9% of glial cells took up cobalt. These cells had a simple unipolar or bipolar morphology and were two to three times more concentrated at the chiasm end than at the eye end of the nerve. During subsequent development, this gradient disappeared and the cobalt-filled cells became progressively more complex in morphology and increased in number and density, reaching a peak toward the end of the second postnatal week. The number subsequently declined to about 16,000 (7%) in the adult nerve. The processes of some cobalt-filled cells appeared to contact nodes of Ranvier. All cobalt-filled cells in 2 1/2-week-old optic nerves had a similar ultrastructural appearance and did not resemble either mature oligodendrocytes or astrocytes. Our results suggest that the cells stimulated by quisqualate to take up cobalt in the optic nerve are the in vivo counterpart of O-2A progenitor cells. We found no evidence that any of these cells are type 2 astrocytes.
Regulation of phospholipid metabolism in differentiating cells from rat brain cerebral hemispheres in culture. I. Uptake and phosphorylation of [U-14C]ethanoloamine and the effect of various inhibitors. (1975)

Cultured dissociated cells from rat embryo cerebral hemispheres were incubated with [U-14C]ethanolamine and the resulting cellular labeled products were identified. A highly efficient uptake for ethanolamine with a Km of approximately 8.3 muM was calculated. A rapid labeling of phosphorylethanolamine was observed prior to the appearance of label in lipids. A lag period of 2.5 min for the phosphorylation reaction was observed, followed by an almost linear rate for up to 40 min. After a 1-min incubation, a plateau for free ethanolamine taken up by the cells was established. Respiratory inhibitiors such as cyanide, 2,4-dinitrophenol, and N-ethylmaleimide decreased by the formation of phosphorylethanolamine. However, the amount offree ethanolamine present in the cells increased 1.6-fold after 10 min of incubation with N-ethylmaleimide. 2-Chloroethylamine, a structural analog of ethanolamine, and choline were both competitive inhibitiors with an apparent Ki of 0.1 mM and 0.36 mM, respectively. Incubations of short duration suggest that both compounds affect ethanolamine transport into the cells. Based on these studies it is suggested that ethanolamine transport and the phosphorylation reaction are independent events. Evidence based on studies with hemicholinium-3 and chloroethylamine suggest that ethanolamine uptake may proceed by a pathway independent of either choline or serine uptake.
Analytical model for viscous damping and the spring force for perforated planar microstructures acting at both audible and ultrasonic frequencies (2008)

The paper presents a model for the squeezed film damping, the resistance of the holes, and the corresponding spring forces for a periodic perforated microstructure including the effects of compressibility, inertia, and rarefied gas. The viscous damping and spring forces are obtained by using the continuity equation. The analytical formula for the squeezed film damping is applied to analyze the response of an ultrasonic transducer. The inclusion of these effects in a model significantly improves the agreement with measured results. Finally, it is shown that the frequency dependence of the total damping and total spring force for a cell are very similar to those corresponding to a rectangular open microstructure without holes. A separate analysis reveals the importance of each particular correction. The most important is the compressibility correction; the inertia has to be considered only for determining the spring force and the damping force for sufficiently high frequencies.