gebhart/patrepeval huggingface dataset:
Applications of retrovirus-mediated expression cloning. (1996)

We have recently established a novel expression cloning system using retroviral vectors. The system is based on a high-efficiency packaging cell line, BOSC23, and a simplified retroviral vector, pBabeX, carrying no selection marker. cDNA libraries, constructed in the pBabeX vector, are transiently transfected into BOSC23 cells. The supernatant contains more than 3X10(6)/mL, which would cover large complexities of cDNA libraries. The retrovirus stock gave 100% infection efficiency in NIH3T3 cells and 5-40% infection efficiency in various hematopoietic cell lines. In contrast to the conventional expression cloning system, in which it is necessary to transfect cDNA libraries transiently into particular cell types such as COS cells, retrovirus-mediated expression cloning allows us to transduce cDNAs into a wide variety of cell types. This method therefore makes it possible to select cells expressing a cDNA of interest by various functional assays. When combined with polymerase chain reaction (PCR)-driven random mutagenesis, this system is also useful in searching for mutations of various molecules that will result in alterations of their functions.
Rational Design of a Sugar-Appended Porphyrin Gelator That Is Forced To Assemble into a One-Dimensional Aggregate (2001)

[structure--see text] As an attempt to rationally design organogelators, an amphiphilic porphyrin bearing four beta-D-galactopyranoside groups at its periphery was synthesized. This compound tends to aggregate in a one-dimensional direction, resulting in very robust gels in DMF/alcohol mixed solvents. Spectroscopic studies and electron-micrographic observations support the view that the pi-pi stacking interaction among porphyrin moieties and the hydrogen-bonding interaction among sugar moieties operate synergistically to give rise to a stable one-dimensional aggregate structure indispensable for gel formation.
Capillary electrophoresis of rat liver microsomes in polymer solutions (1995)

Rat liver microsome components were separated by capillary zone electrophoresis in buffers containing substituted agarose, agarose crosslinked polyacrylamide, polyacrylamide, polyethylene glycol and dextran of various molecular weights. The best resolution of the components was obtained with polymers of 10-21 nm geometric mean radius. Both the crude and the purified preparations of microsomes exhibit a single major peak. In a Tris-borate-EDTA (TBE) buffer, containing polyacrylamide of 5 x 10(6) molecular weight, it has a retardation coefficient, KR, of 0.77 +/- 0.02. Translation of the KR value to geometric mean radii, R, on the basis of the standard curve applicable to polymer solutions, KR vs. R, with polystyrene carboxylate size standards in both dextran and polyacrylamide solution allows one to estimate a value of R as 13-16 nm for the major microsome component. The value is smaller than expected from electron microscopic measurements (100-250 nm), possibly due to the chemical and geometric differences between microsomes and the polystyrene particles used as size standards. The crude preparation also contains a minor component which is smaller and less charged than the major component. Another component, apparently very much larger than the major one, is seen in TBE buffer but not in a potassium-N-(2-hydroxyethyl)piperazine-2'-(2-ethanesulfonic acid) buffer and is therefore thought to be an artifact of interaction with borate. After a short incubation under conditions promoting delayed microsome fusion, i.e. in presence of GTP and Mg++ and in the absence of polyethylene glycol, the electrophoretic pattern changes dramatically: it now exhibits five unretarded, highly mobile and, therefore, presumably large components in addition to the two original retarded components of the microsome and a less highly charged species similar in KR to the smaller of the original two components.
Cellular basis for the negative inotropic effects of tumor necrosis factor-alpha in the adult mammalian heart. (1993)

To define the mechanism(s) responsible for the negative inotropic effects of tumor necrosis factor-alpha (TNF alpha) in the adult heart, we examined the functional effects of TNF alpha in the intact left ventricle and the isolated adult cardiac myocyte. Studies in both the ventricle and the isolated adult cardiac myocyte showed that TNF alpha exerted a concentration- and time-dependent negative inotropic effect that was fully reversible upon removal of this cytokine. Further, treatment with a neutralizing anti-TNF alpha antibody prevented the negative inotropic effects of TNF alpha in isolated myocytes. A cellular basis for the above findings was provided by studies which showed that treatment with TNF alpha resulted in decreased levels of peak intracellular calcium during the systolic contraction sequence; moreover, these findings did not appear to be secondary to alterations in the electrophysiological properties of the cardiac myocyte. Further studies showed that increased levels of nitric oxide, de novo protein synthesis, and metabolites of the arachidonic acid pathway were unlikely to be responsible for the TNF alpha-induced abnormalities in contractile function. Thus, these studies constitute the initial demonstration that the negative inotropic effects of TNF alpha are the direct result of alterations in intracellular calcium homeostasis in the adult cardiac myocyte.
The Minnesota Scanner: a prototype sensor for three-dimensional tracking of moving body segments (1989)

An advanced method for tracking the three-dimensional motion of bodies is presented. This system, which is presently being used for human motion tracking, has the potential for dynamically characterizing robot motion and also provides a means for facilitating robot endpoint control. Three rotating planes of laser light, fixed and moving photovoltaic diode targets, and a pipelined architecture composed of analog and digital electronics are used to locate multiple targets whose number is only limited by available computer memory. Data collection rates are a function of the laser scan rotation speed and are selectable up to 480 Hz. The tested performance on a preliminary prototype designed for 0.1-in. accuracy at a 480-Hz data rate includes a resolution of 0.8 mm, a repeatability of +or-0.636 mm, and an absolute accuracy of +or-2.0 mm within an eight cubic meter volume with all results applicable at the 95% level of confidence along each coordinate direction. The system can be used to reduce XYZ target position data to body angular orientation which, for this first prototype, ranges in accuracy from +or-0.5 degrees to +or-1 degrees . Moving targets can be tracked at speeds exceeding 1 m/s with signal integrity tested but not limited to 25-Hz motions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Accumulation of methotrexate and methotrexate polyglutamates in lymphoblasts at diagnosis of childhood acute lymphoblastic leukemia: a pilot prognostic factor analysis (1990)

Lymphoblasts in bone marrow samples, obtained from 43 children with acute lymphoblastic leukemia at diagnosis, were incubated with 1.0 mumols/L [3H] methotrexate for 24 hours in vitro. Nonexchangeable methotrexate and methotrexate polyglutamates were separated and quantitated. Event-free survival at 5 years was 38% +/- 9% for all 43 patients (27 failures), and 44% +/- 10% for the 35 with non-T, non-B- cell acute lymphoblastic leukemia (20 failures). Of these 35 children, those whose lymphoblasts accumulated more than 100 pmol methotrexate and 500 pmol methotrexate polyglutamates per billion cells experienced better 5-year event-free survival than those whose lymphoblasts did not (65% +/- 12% v 22% +/- 9%, P = .010). This difference characterized “good-risk” patients who were female (P = .014), less than age 7 at diagnosis (P = .005), or had low initial white blood cell counts (less than 20 X 10(9)/L, P = .018). Findings were similar for the 43 children with acute lymphoblastic leukemia and for the “good-risk” children in this total group. Thus, the ability of lymphoblasts to accumulate methotrexate and form methotrexate polyglutamates may be important to the curative properties of current therapy of acute lymphoblastic leukemia in children, particularly for “good-risk” patients. In such patients, inherent rather than acquired drug resistance may be the initial event leading to treatment failure.
Heterogeneous Catalytic Chemistry by Example of Industrial Applications (2012)

Worldwide, more than 85% of all chemical products are manufactured with the help of catalysts. Virtually all transition metals of the periodic table are active as catalysts or catalyst promoters. Catalysts are divided into homogeneous catalysts, which are soluble in the reaction medium, and heterogeneous catalysts, which remain in the solid state. A heterogeneous metal catalyst typically consists of the active metal component, promoters, and a support material. In some cases, the metallic state itself forms the active ingredient. However, this situation is largely restricted to precious metal catalysts and to some base metals used under reducing conditions. In most cases and especially in homogeneous catalysis, it is a metal compound or a complex that forms the active catalyst. Catalysis can be rather puzzling as a given metal can catalyze a variety of different chemical transformations, while the same substrate, passed over different catalysts, can give different products. It is therefore helpful to be familiar with the fundamentals of catalytic science before being exposed to the uncountable applications, which form the backbone of industrial chemistry. Examples of practical importance are used in this paper to highlight important principles of catalysis.
Monoclonal antibody against non-histone chromosomal protein high mobility group 1 Co-migrates with high mobility group 1 into the nucleus. (1986)

Non-histone chromosomal protein high mobility group 1 (HMG-1) rapidly migrates into the nucleus when injected into the cytoplasm of bovine fibroblasts and HeLa cells by red cell-mediated microinjection (Rechsteiner, M., and Kuehl, L. (1979) Cell 16, 901-908). We isolated hybridomas secreting monoclonal antibodies against HMG-1. One of these monoclonal antibodies, FR-1, inhibited in vitro binding of 125I-HMG-1 to chromatin isolated from FL cells. When 125I-HMG-1 was co-introduced with antibody FR-1 by red cell-mediated microinjection, antibody FR-1 did not prevent the accumulation of 125I-HMG-1 in the nucleus. When 125I-antibody FR-1 or fluorescein isothiocyanate antibody FR-1 was introduced into the cytoplasm of FL cells, most of the antibody did not accumulate in the nucleus. But when 125I- or fluorescein isothiocyanate antibody FR-1 was co-introduced with HMG-1 into the cytoplasm of FL cells, it did migrate into the nucleus.
Lipoxygenase inhibitors induce arrest of tumor cells in S-phase of the cell cycle. (2002)

Inhibitors of the lipoxygenase pathway of arachidonic acid metabolism represent a potential anti-tumor drugs. These compounds have been found to inhibit the growth and induce the apoptosis of various tumor cells both in vitro and in vivo. In this study, the effects of the lipoxygenase inhibitors esculetin and nordihydroguaiaretic acid (NDGA) on the progression of the cell cycle were investigated in eight mammalian cell lines of different origin. Flow cytometric analyses of cell cycle distribution after staining of DNA with propidium iodide or 7-aminoactinomycin D and DNA synthesis using incorporation of 5-bromo-2'-deoxy-uridine showed that both esculetin and NDGA suppress cell growth by interrupting the progression of cells through S-phase that results in their accumulation in this phase of the cell cycle. The possible mechanisms of these effects and the significance of the findings for the improvement of anticancer therapy targeted on cell cycle is discussed.
Selective delivery of liposome-associated cis-dichlorodiammineplatinum(II) by heat and its influence on tumor drug uptake and growth. (1981)

In an attempt to optimize the chemotherapeutic treatment of mouse tumor Sarcoma 180, liposomes containing cis-dichlorodiammineplatinum(II) (PDD), having transition temperatures of few degrees higher than the rectal temperature of mice, were used in combination with local hyperthermia. The uptake of radioactive PDD by tumors heated for 1 hr at 42 degrees was almost four-fold greater when the drug was associated in liposomes than if administered as free drug. Uptake of liposome-administered radioactive platinum by liver was twice that obtained with free PDD, whereas its incorporation by the kidney was the same by either method of drug administration. The effect of various combinations of hyperthermia, drug-containing liposomes, and free PDD on tumor growth was also studied. Treatment with liposome-associated PDD plus local heating resulted in a dose-modifying factor of 7 when compared with free drug and no hyperthermia. The dose-modifying factor was 2.5 when PDD liposomes and heat were compared within free drug and heat. Thus, PDD could be specifically released from liposomes by heat and resulted in both a greater drug uptake and a delayed tumor growth following treatment. Potential normal tissue toxicity problems, however, still need to be resolved before clinical application of this combined modality will be possible.
Adeno-Associated Virus Type 2-Mediated Transduction of Human Monocyte-Derived Dendritic Cells: Implications for Ex Vivo Immunotherapy (2001)

Dendritic cells (DCs) are pivotal antigen-presenting cells for regulating immune responses. A major focus of contemporary vaccine research is the genetic modification of DCs to express antigens or immunomodulatory molecules, utilizing a variety of viral and nonviral vectors, to induce antigen-specific immune responses that ameliorate disease states as diverse as malignancy, infection, autoimmunity, and allergy. The present study has evaluated adeno-associated virus (AAV) type 2 as a vector for ex vivo gene transfer to human peripheral blood monocyte (MO)-derived DCs. AAV is a nonpathogenic parvovirus that infects a wide variety of human cell lineages in vivo and in vitro, for long-term transgene expression without requirements for cell proliferation. The presented data demonstrate that recombinant AAV (rAAV) can efficiently transduce MOs as well as DCs generated by MO culture with granulocyte-macrophage colony-stimulating factor plus interleukin in vitro. rAAV transgene expression in MO-derived DCs could be enhanced by etoposide, previously reported to enhance AAV gene expression. rAAV transduction of freshly purified MO followed by 7 days of culture with cytokines to generate DCs, and subsequent sorting for coexpression of DC markers CD1a and CD40, showed robust transgene expression as well as evidence of nuclear localization of the rAAV genome in the DC population. Phenotypic analyses using multiple markers and functional assays of one-way allogeneic mixed leukocyte reactions indicated that rAAV-transduced MO-derived DCs were as equivalent to nontransduced DCs. These results support the utility of rAAV vectors for future human DC vaccine studies.
The Saccharomyces cerevisiae RAD6 Group Is Composed of an Error-Prone and Two Error-Free Postreplication Repair Pathways (2000)

The RAD6 postreplication repair and mutagenesis pathway is the only major radiation repair pathway yet to be extensively characterized. It has been previously speculated that the RAD6 pathway consists of two parallel subpathways, one error free and another error prone (mutagenic). Here we show that the RAD6 group genes can be exclusively divided into three rather than two independent subpathways represented by the RAD5, POL30, and REV3 genes; the REV3 pathway is largely mutagenic, whereas the RAD5 and the POL30 pathways are deemed error free. Mutants carrying characteristic mutations in each of the three subpathways are phenotypically indistinguishable from a single mutant such as rad18, which is defective in the entire RAD6 postreplication repair/tolerance pathway. Furthermore, the rad18 mutation is epistatic to all single or combined mutations in any of the above three subpathways. Our data also suggest that MMS2 and UBC13 play a key role in coordinating the response of the error-free subpathways; Mms2 and Ubc13 form a complex required for a novel polyubiquitin chain assembly, which probably serves as a signal transducer to promote both RAD5 and POL30 error-free postreplication repair pathways. The model established by this study will facilitate further research into the molecular mechanisms of postreplication repair and translesion DNA synthesis. In view of the high degree of sequence conservation of the RAD6 pathway genes among all eukaryotes, the model presented in this study may also apply to mammalian cells and predicts links to human diseases.
Biochemical and serological characteristics of natural 9-O-acetyl GD3 from human melanoma and bovine buttermilk and chemically O-acetylated GD3. (1990)

Because its expression appears to be largely restricted to human melanomas, 9-O-acetyl-GD3 is a candidate antigen for vaccine construction. Searching for potential sources, we compared chemically O-acetylated calf brain GD3 and 9-O-acetyl-GD3 extracted from bovine buttermilk with 9-O-acetyl-GD3 from human melanoma. Three fractions (F1-F3) of chemically O-acetylated GD3 differed in the number and position of O-acetyl groups. O-Acetylation sites were the lactose portion in F1 and lactose as well as sialic acid in F2 and F3. Natural (melanoma- or buttermilk-derived) 9-O-acetyl-GD3 was O-acetylated solely on the sialic acid moiety. While F1 was not reactive with monoclonal antibodies against 9-O-acetyl-GD3, F2 and F3 were as reactive as the natural products. Immunization with the natural products induced high-titer antibodies against natural 9-O-acetyl-GD3 as well as F2 and F3. In contrast, mice immunized with the synthetic fractions produced antibodies only against the immunogen but not against natural 9-O-acetyl-GD3. Only immunization with the natural products induced production of antibodies reactive with surface antigens of melanoma cells expressing 9-O-acetyl-GD3. The findings suggest (a) that C-9 of the subterminal sialic acid is the site of chemical O-acetylation in F2 and F3, as opposed to C-9 of the terminal sialic acid in the natural products; (b) that O-acetylation of both the terminal and subterminal sialic acid moieties of GD3 results in recognition by three murine monoclonal antibodies (D1.1, ME 311, and Jones) reactive with human melanoma cells; (c) that O-acetylation of the terminal sialic acid is critical, on the other hand, for inducing an immune response against melanoma 9-O-acetyl-GD3; and (d) that O-acetyl GD3 from bovine buttermilk can substitute as immunogen for inducing an immune response against human melanoma cell surface antigens in the mouse.
Repeated implantation of skeletal myoblast in a swine model of chronic myocardial infarction (2009)

Repeated injection of SkM in a model of chronic MI is feasible and safe and induces a significant improvement in cardiac function.
Blind Image Quality Assessment: From Natural Scene Statistics to Perceptual Quality (2011)

Our approach to blind image quality assessment (IQA) is based on the hypothesis that natural scenes possess certain statistical properties which are altered in the presence of distortion, rendering them un-natural; and that by characterizing this un-naturalness using scene statistics, one can identify the distortion afflicting the image and perform no-reference (NR) IQA. Based on this theory, we propose an (NR)/blind algorithm-the Distortion Identification-based Image Verity and INtegrity Evaluation (DIIVINE) index-that assesses the quality of a distorted image without need for a reference image. DIIVINE is based on a 2-stage framework involving distortion identification followed by distortion-specific quality assessment. DIIVINE is capable of assessing the quality of a distorted image across multiple distortion categories, as against most NR IQA algorithms that are distortion-specific in nature. DIIVINE is based on natural scene statistics which govern the behavior of natural images. In this paper, we detail the principles underlying DIIVINE, the statistical features extracted and their relevance to perception and thoroughly evaluate the algorithm on the popular LIVE IQA database. Further, we compare the performance of DIIVINE against leading full-reference (FR) IQA algorithms and demonstrate that DIIVINE is statistically superior to the often used measure of peak signal-to-noise ratio (PSNR) and statistically equivalent to the popular structural similarity index (SSIM). A software release of DIIVINE has been made available online: "http://live.ece.utexas.edu/research/quality/DIIVINE_release.zip" xmlns:xlink="http://www.w3.org/1999/xlink">http://live.ece.utexas.edu/research/quality/DIIVINE_release.zip for public use and evaluation.
A retrospective analysis of therapy for acute graft-versus-host disease: initial treatment (1990)

Abstract We have reviewed results of therapy in 740 patients with grades II-IV acute graft-versus-host disease (GVHD) after allogeneic marrow transplantation. At the beginning of therapy, 597 patients (81%) had rash, 369 (50%) had liver dysfunction and 396 (54%) had gut dysfunction. Initial treatment was with glucocorticoids (n = 531), cyclosporine (n = 170), antithymocyte globulin (ATG) (n = 156) or monoclonal antibody (n = 3) either singly (n = 633) or in combination (n = 107). Parameters of GVHD severity in each organ were recorded weekly, and evaluation of response was made using values at the initiation of secondary treatment or, for patients without such treatment, using values on day 29 of primary treatment or the last recorded value before death, whichever occurred first. Minimal criteria for improvement or progression were defined for each organ, but no attempt was made to define liver or gut outcome if another complication such as venocclusive disease or infectious enteritis was present. Improvement rates were 43% for skin disease, 35% for evaluable liver disease and 50% for evaluable gut disease. Overall complete or partial responses were seen in 44% of patients. Multivariate analyses were carried out to identify patient, disease or treatment factors associated with likelihood of overall improvement and likelihood of response in at least one organ. A similar analysis was also carried out to identify covariates associated with time to treatment failure (defined as initiation of secondary therapy or death not due to relapse of malignancy). In all three models, GVHD prophylaxis using cyclosporine combined with methotrexate was associated with favorable GVHD treatment outcome compared to prophylaxis with either agent alone, and treatment with glucocorticoids or cyclosporine was more successful than treatment with ATG. Other factors associated with unfavorable outcome in the model of time to treatment failure and also entered in one of the response models were recipient HLA disparity with the donor, presence of a liver complication other than GVHD, and early onset of GVHD. Results of this analysis indicate that glucocorticoids represent the best initial therapy available for treatment of acute GVHD, although much room for improvement remains.
A Review of CE Detection Methodologies (2000)

Click to increase image sizeClick to decrease image sizeKeywords: capillary electrophoresisabsorbance detection(laser-induced) fluorescenceelectrochemical detectionrefractive indexphotothermal refraction
Oral Fingolimod or Intramuscular Interferon for Relapsing Multiple Sclerosis (2010)

This trial showed the superior efficacy of oral fingolimod with respect to relapse rates and MRI outcomes in patients with multiple sclerosis, as compared with intramuscular interferon beta-1a. Longer studies are needed to assess the safety and efficacy of treatment beyond 1 year. (ClinicalTrials.gov number, NCT00340834.)