gebhart/patrepeval huggingface dataset:
Human immunodeficiency virus type 1 envelope protein does not stimulate either prostaglandin formation or the expression of prostaglandin H synthase in THP-1 human monocytes/macrophages (1995)

Prostaglandin E2 is observed at elevated levels during human immunodeficiency virus (HIV) infection and thus may contribute to the HIV-dependent immunosuppression. The mechanisms responsible for this increase are not understood. Evidence indicates that the viral envelope proteins perturb membrane signaling mediated by the CD4 receptor, suggesting that the free envelope protein and/or the intact virus may be responsible for the increase in prostaglandin E2 levels. In this study, we have used THP-1 human monocytes and THP-1 cells differentiated by 12-O-tetradecanoylphorbol-13-acetate treatment into macrophages to determine if the HIV envelope protein, gp120, or an anti-CD4 receptor antibody stimulates prostaglandin formation by interacting with the CD4 receptor. Incubation of THP-1 cells with OKT4A antibody greatly stimulated the CD4-p56lck receptor complex as estimated by enhanced p56lck autophosphorylation, while the gp120 gave small but significant responses. Monocytic THP-1 cells poorly metabolized arachidonic acid to prostaglandin E2 and thromboxane B2 as measured by high-pressure liquid chromatography analysis. Western blot (immunoblot) and Northern (RNA) blot analyses revealed that unstimulated monocytes expressed little prostaglandin H synthase 1 and 2 (PGHS-1 and -2). Incubation of the monocytes with lipopolysaccharide, OKT4A, or gp120 did not increase the formation of prostaglandins. The expression of PGHS-1 or PGHS-2 was also not increased. Differentiation of the monocytes to macrophages by 12-O-tetradecanoylphorbol-13-acetate treatment resulted in increased expression of PGHS-1 and increased formation of prostaglandins compared with that for the monocytes. Lipopolysaccharide stimulation of the macrophages increased the formation of prostaglandins and increased the expression of PGHS-2 in the macrophages. However, OKT4A or gp120 preparation, at concentrations that stimulated p56lck autophosphorylation, did not enhance the formation of prostaglandins or the expression of PGHS-1 or PGHS-2. OKT4A and gp120 also did not stimulate the release of arachidonic acid, indicating that phospholipase A2 was not activated by the CD4 receptor in either the THP-1 monocytes or macrophages. These results indicate that activation of the CD4-p56lck receptor signal transduction pathway by the HIV envelope protein does not increase prostaglandin formation.
Neural 1D Barcode Detection Using the Hough Transform (2014)

Barcode reading mobile applications to identify products from pictures acquired by mobile devices are widely used by customers from all over the world to perform online price comparisons or to access reviews written by other customers. Most of the currently available 1D barcode reading applications focus on effectively decoding barcodes and treat the underlying detection task as a side problem that needs to be solved using general purpose object detection methods. However, the majority of mobile devices do not meet the minimum working requirements of those complex general purpose object detection algorithms and most of the efficient specifically designed 1D barcode detection algorithms require user interaction to work properly. In this work, we present a novel method for 1D barcode detection in camera captured images, based on a supervised machine learning algorithm that identifies the characteristic visual patterns of 1D barcodes' parallel bars in the two-dimensional Hough Transform space of the processed images. The method we propose is angle invariant, requires no user interaction and can be effectively executed on a mobile device; it achieves excellent results for two standard 1D barcode datasets: WWU Muenster Barcode Database and ArTe-Lab 1D Medium Barcode Dataset. Moreover, we prove that it is possible to enhance the performance of a state-of-the-art 1D barcode reading library by coupling it with our detection method.
Human Embryonic Stem Cell Differentiation Toward Regional Specific Neural Precursors (2008)

Human embryonic stem cells (hESCs) are self-renewing pluripotent cells that have the capacity to differentiate into a wide variety of cell types. This potentiality represents a promising source to overcome many human diseases by providing an unlimited supply of all cell types, including cells with neural characteristics. Therefore, this review summarizes early neural development and the potential of hESCs to differentiate under in vitro conditions, examining at the same time the potential use of differentiated hESCs for therapeutic applications for neural tissue and cell regeneration.
Phenotypic analysis of mouse hematopoietic stem cells shows a Thy-1- negative subset (1992)

Mouse hematopoietic stem cells can be identified and enriched from populations of normal bone marrow cells by immunofluorescent labeling of cell surface molecules followed by flow cytometric separation. We show here that the majority of hematopoietic stem cell activity, as defined by long-term competitive repopulation of irradiated animals and by a secondary transplant assay for spleen colony-forming units (CFU- S), could be localized in Ly-6b haplotype mice to a fraction of bone marrow cells that expresses the Ly-6A/E (Sca-1) molecule. Further, an analysis of hematopoietic stem cell activity in bone marrow of mouse strains expressing the Thy-1.1 allele indicated that the vast majority of activity was included in the Thy-1low population. In contrast, hematopoietic stem cell activity found in the bone marrow of Thy-1.2 genotype mouse strains was recovered in both the Thy-1neg and the Thy- 1low populations. However, similar to Thy-1.1 strains, most activity was localized to the Ly-6A/E+ population of cells. The difference in Thy-1 phenotype of hematopoietic stem cell activity apparent between Thy-1.1- and Thy-1.2-expressing mouse strains was not caused by differences in the staining intensity of monoclonal antibodies (MoAbs) specific for the Thy-1 alleles. Furthermore, an antiframework MoAb that stains both alleles of Thy-1 separated hematopoietic stem cell activity from mice expressing the two alleles in the same manner as did allele- specific MoAb. The results of this study show that Thy-1 expression is not an invariant characteristic of mouse hematopoietic stem cells, and that mice expressing the Thy-1.1 allele are unique in that hematopoietic stem cell activity is found exclusively in the Thy-1low population.
The Synthetic Triterpenoid CDDO-Im Inhibits Fatty Acid Synthase Expression and Has Antiproliferative and Proapoptotic Effects in Human Liposarcoma Cells (2008)

Liposarcomas constitute a rare group of tumors of mesenchymal origin that are often poorly responsive to therapy. This study characterizes a novel human liposarcoma cell line (LiSa-2) and defines the mechanism of its response to a synthetic triterpenoid. Fatty acid synthase (FAS) is a key enzyme of de-novo fatty acid synthesis and is highly expressed in both human liposarcoma tissue specimens and LiSa-2 cells. Treatment of the LiSa-2 cell line with the synthetic triterpenoid 2-cyano-3,12-dioxooleana-1,9-dien-28-oic imidazolide (CDDO-Im) markedly inhibited FAS mRNA expression, FAS protein production and FAS gene promoter activity. As expected, fatty acid synthesis was down regulated, but there was no effect on cellular fatty acid uptake or glycerol-3-phosphate synthesis suggesting a selective inhibition of endogenous fatty acid synthesis. Importantly, CDDO-Im produced a dose-dependent apoptotic effect in the LiSa-2 cell line, and simultaneous treatment with CDDO-Im and the fatty acid synthase inhibitor Cerulenin produced a synergistic cytotoxic effect. Thus, CDDO-Im and Cerulenin act at different loci to inhibit long chain fatty acid synthesis in liposarcoma cells. This study's demonstration of CDDO-Im inhibition of FAS and Spot 14 (S14) expression is the first report of triterpenoid compounds affecting the fatty acid synthesis pathway. The observed dependence of liposarcomas on lipogenesis to support their growth and survival provides a novel approach to the treatment of liposarcomas with agents that target fatty acid production.
Metal–ligand induced supramolecular polymerization: A route to responsive materials (2004)

The use of metal-ligand binding as the driving force for the self-assembly polymerizations of a ditopic ligand offers a facile route to the preparation of organic/inorganic hybrid materials. Such metallo-supramolecular polymers potentially offer the functionality of the metal ion along with the processibility of a polymer. We report, herein, the preparation of gel-like metallo-supramolecular polymers prepared from a monomer unit, which consists of a 2,6-bis-(benzimidazolyl)-4-hydroxypyridine unit attached to either end of a polyether chain, mixed with a lanthanoid metal (e.g. La(III), Eu(III)) and a transition metal ion (e.g. Co(II) or Zn(II)). Such materials show dramatic reversible responses to a variety of stimuli, including thermal, mechanical, chemical and light. The nature of the response can be controlled by the nature of the combination of transition metal ion and lanthanoid metal ion used.
Antimutagenic Properties of 3,5-Disubstituted 2-Thiohydantoins (1998)

3,5-Disubstituted 2-thiohydantoins, which were prepared by the reaction of allyl isothiocyanate (AITC) or 4-(methylthio)-3-butenyl isothiocyanate (MTBI) with various amino acids, were assayed for their inhibitory effects on the mutagenicity of 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) on Salmonella typhimurium TA 98. When the 3,5-disubstituted 2-thiohydantoins (125−500 μg/mL) were simultaneously preincubated with the bacterial strain, IQ (0.5 μg/mL), and rat microsomal fraction (S9 mix) for 20 min, a dose-dependent inhibition of IQ mutagenicity was observed in the tested compounds except one prepared from MTBI and l-methionine. This inhibition ranged from 23% to 86%. The inhibitory effect either disappeared or was largely reduced to 5−19%, when the 3,5-disubstituted 2-thiohydantoins were added after metabolic activation of IQ with S9 mix. These results suggest that the 3,5-disubstituted 2-thiohydantoins probably acted as an inhibitor of the S9 mix-mediated metabolic activation of the mutagen. Keywords: 2-Thiohydantoins; allyl isothiocyanate; 4-(methylthio)-3-butenyl isothiocyanate; blocking agent; Salmonella typhimurium TA 98
Prognostic value of cell cycle regulators p27 and cyclin E: Tissue microarray analysis of 1753 women enrolled in SWOG breast cancer trial 9313 (2005)

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Crystal Structures of Two Potent Nonamidine Inhibitors Bound to Factor Xa, (2002)

There has been intense interest in the development of factor Xa inhibitors for the treatment of thrombotic diseases. Our laboratory has developed a series of novel non-amidine inhibitors of factor Xa. This paper presents two crystal structures of compounds from this series bound to factor Xa. The first structure is derived from the complex formed between factor Xa and compound 1. Compound 1 was the first non-amidine factor Xa inhibitor from our lab that had measurable potency in an in vitro assay of anticoagulant activity. The second compound, 2, has a molar affinity for factor Xa (K(iapp)) of 7 pM and good bioavailability. The two inhibitors bind in an L-shaped conformation with a chloroaromatic ring buried deeply in the S1 pocket. The opposite end of these compounds contains a basic substituent that extends into the S4 binding site. A chlorinated phenyl ring bridges the substituents in the S1 and S4 pockets via amide linkers. The overall conformation is similar to the previously published structures for amidine-based inhibitors complexed with factor Xa. However, there are significant differences in the interactions between the inhibitor and the protein at the atomic level. Most notably, there is no group that forms a salt bridge with the carboxylic acid at the base of the S1 pocket (Asp189). Each inhibitor forms only one well-defined hydrogen bond to the protein. There are no direct charge-charge interactions. The results indicate that electrostatic interactions play a secondary role in the binding of these potent inhibitors.
Carrier tunneling and device characteristics in polymer light-emitting diodes (1994)

In this paper it is demonstrated that the characteristics of light-emitting diodes based upon MEH-PPV [more fully known as poly(2-methoxy,5-(2′-ethyl-hexoxy)-1,4-phenylene- vinylene)] are determined by tunneling of both the holes and the electrons through interface barriers caused by the band offset between the polymer and the electrodes. It is shown that manipulating these offsets can control the useful operating voltage of the device as well as its efficiency. A model is developed that clearly explains the device characteristics of a wide range of diodes based upon MEH-PPV. The turn-on voltage for an ideal device is shown to be equal to the band gap, i.e., 2.1 eV for MEH-PPV, and is slightly lower at 1.8 eV for an indium-tin oxide/MEH-PPV/Ca device. If there is a significant difference in the barrier height, the smaller of the two barriers controls the I–V characteristics, while the larger barrier determines the device efficiency. In indium-tin-oxide/MEH-PPV/Ca devices, the barrier to hole injection is 0.2 eV and the barrier to electron injection is only 0.1 eV. This combination of electrodes is close to optimal for MEH-PPV, but lowering the hole barrier can still lead to a doubling of the device efficiency.
An Inquiry into the Constructivist Approach to Science Education Classes for Pre-Service Early Childhood Teachers (2012)

This study investigated the contents and methods of science education classes based on the largely constructivist approach of pre-service early childhood teachers. The subjects of this study consisted of 8 junior students from the Early Childhood department and for reference data, reflective journals, interviews, activity planning sheets, recordings of trial lessons, and lesson analysis were used. The results of this study were as follows. First, changes in key points and contents for children science education were found, and reflective journals, interviews, activity planning sheets, recording of trial lessons, and lesson analysis clearly supported these results. Second, the actual changes in the constructivist approach to children`s science education had a great impact upon the individual characters of the pre-service early childhood teachers. However, with the study period being limited to only one semester, it was found that the potential of this study to lead to any practical changes was simlilarly limited.
5-Azacytidine stimulates fetal hemoglobin synthesis in anemic baboons. (1982)

In an attempt to stimulate Hb F synthesis in baboons by means other than erythropoietic stress, we considered the possibility that an agent that inhibits methylation of CpG sequences in DNA may be effective. 5-Azacytidine, a cytosine analogue that cannot be methylated, is such an agent. Animals whose packed red cell volume was maintained at approximately 20% by bleeding were given 10 daily intravenous injections of the drug (6 mg/kg) in 12 days. Hb F levels in these animals started to increase on day 5 of this regimen and peak levels, which were 6-30 times higher than those produced by bleeding alone, occurred 5-7 days after the last dose of the drug. In animals previously identified as genetically "high" or "low" Hb F responders, the maximal Hb F levels were 70-85% and 35-40% respectively. In dose-response studies 5-azacytidine given daily at 3-4 mg/kg produced maximal Hb F increases. The drug did not correlate the percentage (number) of Hb F-containing cells (F cells) beyond the maximal number achieved by bleeding alone and thus its main effect was to increase Hb F per F cell. The finding that Hb F synthesis can be modulated to such a high degree by a drug may have therapeutic implications--e.g., in sickle cell anemia, in which stimulation of Hb F synthesis may prevent sickling.
Creating stable stem regions for loop elongation in Fcabs — Insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations (2014)

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules.
MRI R2 and R2* mapping accurately estimates hepatic iron concentration in transfusion-dependent thalassemia and sickle cell disease patients (2005)

Measurements of hepatic iron concentration (HIC) are important predictors of transfusional iron burden and long-term outcome in patients with transfusion-dependent anemias. The goal of this work was to develop a readily available, noninvasive method for clinical HIC measurement. The relaxation rates R2 (1/T2) and R2* (1/T2*) measured by magnetic resonance imaging (MRI) have different advantages for HIC estimation. This article compares noninvasive iron estimates using both optimized R2 and R2* methods in 102 patients with iron overload and 13 controls. In the iron-overloaded group, 22 patients had concurrent liver biopsy. R2 and R2* correlated closely with HIC (r2 > or = .95) for HICs between 1.33 and 32.9 mg/g, but R2 had a curvilinear relationship to HIC. Of importance, the R2 calibration curve was similar to the curve generated by other researchers, despite significant differences in technique and instrumentation. Combined R2 and R2* measurements did not yield more accurate results than either alone. Both R2 and R2* can accurately measure hepatic iron concentration throughout the clinically relevant range of HIC with appropriate MRI acquisition techniques.
Apoptosis: Key to the Attenuated Malaria Vaccine? (2005)

Malaria starts with infection of the host liver by Plasmodium sporozoites. Inoculation with radiation-attenuated Plasmodium sporozoites induces complete protection against malaria. Protection is mediated by dendritic cells (DCs) and CD8 + T cells, but the source of parasite antigens mediating this response remains unclear. Here, we show that hepatocytes infected with irradiated Plasmodium sporozoites undergo apoptosis shortly after infection. Infection with irradiated sporozoites induces the recruitment of DCs to the liver, where they phagocytose apoptotic infected hepatocytes containing parasite antigens. We propose that apoptotic Plasmodium-infected hepatocytes provide a source of parasite antigens for the initiation of the protective immune response.
A MRI-guided concentric tube continuum robot with piezoelectric actuation: A feasibility study (2012)

This paper presents a versatile magnetic resonance imaging (MRI) compatible concentric tube continuum robotic system. The system enables MR image-guided placement of a curved, steerable active cannula. It is suitable for a variety of clinical applications including image-guided neurosurgery and percutaneous interventions, along with procedures that involve accessing a desired image target, through a curved trajectory. This 6 degree-of-freedom (DOF) robotic device is piezoelectrically actuated to provide precision motion with joint-level precision of better than 0.03mm, and is fully MRI-compatible allowing simultaneous robotic motion and imaging with no image quality degradation. The MRI compatibility of the robot has been evaluated under 3 Tesla MRI using standard prostate imaging sequences, with an average signal to noise ratio loss of less than 2% during actuator motion. The accuracy of active cannula control was evaluated in benchtop trials using an external optical tracking system with RMS error in tip placement of 1.00mm. Preliminary phantom trials of three active cannula placements in the MRI scanner showed cannula trajectories that agree with our kinematic model, with a RMS tip placement error of 0.61 - 2.24 mm.
Hidden Markov modeling and fuzzy controllers in FPGAs (2002)

This paper compares software and FPGA-based hardware implementations of two applications. The first application uses hidden Markov models, and the second application is a fuzzy controller. Hidden Markov modeling is used for temporal pattern recognition and speech recognition in particular. Both applications are accelerated when implemented in FPGA-based hardware, but this acceleration is obtained by using different algorithms than those used in software implementations. These different algorithms produce slightly different outputs; therefore both solution quality and performance must be evaluated to compare hardware and software implementations. The experience of designing these applications has implications for hardware/software codesign tools and for the migration of existing software applications to FPGA-based hardware.
T cell gamma gene rearrangements in hematologic neoplasms (1987)

Rearrangements of the T cell gamma (T gamma) gene were studied in primary neoplastic cells from 75 patients with leukemia or lymphoma. T gamma gene rearrangements were observed in 19 of 21 T cell neoplasms; 14 of 21 immature B cell leukemias, including 4 out of 5 patients with rearrangements of both immunoglobulin heavy-chain (JH) and T cell receptor beta chain (T beta) genes; none out of 16 nonlymphoid leukemias. Thus, T gamma gene rearrangement is frequently found in immature B cells and is not always found in T cells showing T beta gene rearrangement, but it is not detected in nonlymphoid cells. Furthermore, T gamma gene rearrangement in cells with the germline configuration of the JH and T beta genes was observed. These results indicate that the detection of T gamma gene rearrangement does not allow a clear assignment to a particular lineage. However, an analysis of T gamma gene rearrangement provides a further potential tool to establish the lymphoid cellular origin and clonality of hematologic neoplasms and identify the normal stages of lymphocyte differentiation.