gebhart/patrepeval huggingface dataset:
Expression of type I and type II bovine scavenger receptors in Chinese hamster ovary cells: lipid droplet accumulation and nonreciprocal cross competition by acetylated and oxidized low density lipoprotein. (1991)

Type I and type II scavenger receptors, which have been implicated in the development of atherosclerosis and other macrophage-associated functions, differ only by the presence in the type I receptor of an extracellular cysteine-rich C-terminal domain. Stable Chinese hamster ovary (CHO) cell transfectants expressing high levels of either the type I or type II bovine scavenger receptors have been generated. Type I and type II receptors in these cells mediated high-affinity saturable endocytosis of both 125I-labeled acetylated low density lipoprotein (LDL) and 125I-labeled oxidized LDL with the distinctive broad ligand specificity characteristic of scavenger receptors. After incubation for 2 days with acetylated LDL, the transfected cells accumulated oil red O-staining lipid droplets reminiscent of those in macrophage foam cells, whereas untransfected CHO cells did not. Thus, macrophage-specific gene products other than the scavenger receptor are not required for modified-LDL-induced intracellular lipid accumulation. In transfected cells, acetylated LDL efficiently competed for both its own endocytosis and that of oxidized LDL. In contrast, oxidized LDL competed effectively for its own endocytosis but only poorly for that of acetylated LDL. This nonreciprocal cross competition suggests that these ligands may bind to nonidentical but interacting sites on a single receptor. Results were similar for transfectants expressing either type I or type II scavenger receptors. Therefore, the nonreciprocal cross competition previously reported for cultured peritoneal macrophages may not be the result of differences between the type I and type II receptors. The nonreciprocal cross competition seen in the transfected CHO cells differs from that previously observed with cultured macrophages.
Color and luminance compensation for mobile panorama construction (2010)

This paper addresses the problem of color and luminance compensation for sequences of overlapping images where the source images have very different colors and luminance. We apply the method for panoramic image construction on mobile phones. A simple approach is proposed that minimizes both the color differences of neighboring images and the overall color correction over the whole sequence. We compare several combinations of gamma correction and linear adjustment over different color representations, and select the method with best results: use YCbCr and apply gamma correction for the luminance component and linear correction for the chrominance components
Rapid, noncontact, damage free shaping of optical and other surfaces with plasma assisted chemical etching (2003)

Experimental results are presented demonstrating that plasma-assisted chemical etching (PACE) can rapidly and controllably figure (shape) and smooth optical surfaces without mechanical contact. This process, for example, significantly reduces the constraints on the design of quartz optical elements imposed by mechanical processes, such as the requirement of substrate rigidity and the limitation of sphericity of the resulting surface. The pertinent chemistry and physics of this process is summarized to provide a basis for understanding its characteristics. A theory of surface evolution applicable to PACE is used to show the range of surface topographies predicted for PACE. It is shown, among other things, that both isotropic and anisotropic etch processes intrinsically microsmooth features smaller than 0.1 mm, and that removal smooths while deposition roughens.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Vaccines '87: Modern Approaches to New Vaccines : Prevention of AIDS And Other Viral, Bacterial, And Parasitic Diseases (1987)

This book contains five sections and a summary. Each section consists of several papers. The section titles are: Immunology, AIDS, Pathogenic Bacteria and Viral Glycoproteins, Pathogenesis and Attenuation, and Recombinant Vectors and Paraviruses.
Triple-Junction III–V Based Concentrator Solar Cells: Perspectives and Challenges (2006)

This paper gives a review of the work performed in the framework of the EC-funded project FULLSPECTRUM aiming for higher photovoltaic (PV) conversion efficiencies by investigating GaInP∕GaInAs∕Ge triple-junction concentrator solar cells. Lattice mismatched structures reached efficiencies beyond 35% at 600 sun concentration level. These cells are now ready to enter the terrestrial PV market. The perspectives and challenges associated with the market introduction of these cells are addressed. Specifically issues of reliability and on-wafer characterization are discussed. A new characterization tool MAPCON was developed and is presented.
Quantitative Tracking of Protein Trafficking to the Nucleus Using Cytosolic Protein Delivery by Nanoparticle-Stabilized Nanocapsules (2015)

We describe a method for quantitative monitoring of subcellular protein trafficking using nanoparticle-stabilized nanocapsules for protein delivery. This method provides rapid delivery of the protein into the cytosol, eliminating complications from protein homeostasis processes found with cellularly expressed proteins. After delivery, nuclear protein trafficking was followed by real time microscopic imaging. Quantitative analyses of the accumulation percentage and the import dynamics of the nuclear protein trafficking, demonstrate the utility of this method for studying intracellular trafficking systems.
Prolonged exposure of dendritic cells to maturation stimuli favors the induction of type‐2 cytotoxic T lymphocytes (2006)

Dendritic cell (DC) maturation influences the priming and polarization of T lymphocytes. We recently found that early activated DC (i.e. DC exposed to pro-maturation stimuli for 8 h) were more prone to prime in vivo a type-1 cytotoxic T cell (Tc1) response than DC exposed to pro-maturation stimuli for 48 h (48h-DC). We investigated whether 48h-DC, conversely, allowed the induction of Tc2 cells. Antigen-pulsed mouse bone-marrow-derived DC at any maturation stage, in the presence of exogenous IL-12, skewed in vitro naive CD8(+) T cells towards Tc1 cells, but 48h-DC most potently, in the presence of exogenous IL-4, favored the induction of Tc2 cells. In vivo, full maturation of DC promoted expansion of Tc2 and fall of Tc1 cells. Tc2 cells maintained a high cytolytic activity and produced significant amounts of IL-4, IL-5, IL-10 and TGF-beta. Our results indicate that polarization of naive CD8(+) T cells to Tc2 cells is dependent on the amount of time DC have been exposed to maturation stimuli, and might be favored in late and/or chronic phases of an immune response.
ChemInform Abstract: PHOSPHORUS PENTOXIDE IN ORGANIC SYNTHESIS. I. PHOSPHORUS PENTOXIDE‐AMINE HYDROCHLORIDE MIXTURES AS REAGENTS IN A NEW SYNTHESIS OF HYPOXANTHINES (1982)

Abstract Bei der Kondensation von Acylamino‐imidazolcarbonsäureestern, wie (I), mit primären Aminhydrochloriden entstehen Dihydropurinone, wie z.B. (II), während ein größerer Acylsubstituent am Imidazol, wie bei den Amidoestern (III), die Beteiligung des primären Amins am Ringschluß verhindert (Bildung der Imidazooxazinone (IV)).
Activation of type-2 chloride channels: a novel therapeutic target for the treatment of chronic constipation. (2007)

Chronic constipation affects up to 27% of the population and negatively impacts health-related quality-of-life. Prescription medications targeting chronic constipation currently include polyethylene glycol, lactulose and tegaserod, a serotonin type 4 receptor partial agonist. The most recent addition is lubiprostone (Amitiza), a type-2 chloride channel (ClC-2) activator which is a member of a new class of compounds known as prostones. Lubiprostone is a bicyclic fatty acid that acts locally on ClC-2 channels located in the apical membrane of intestinal epithelial cells. This stimulation of chloride secretion induces the passive movement of sodium and water into the intestinal lumen, yielding a net increase in isotonic fluid, which results in improved bowel function. In double-blind, placebo-controlled clinical trials, lubiprostone increased the number of spontaneous bowel movements compared with placebo and was generally well tolerated. The predominant adverse effects were nausea and diarrhea. Lubiprostone represents a new therapeutic class of compounds for the treatment of chronic constipation and will be the focus of this review.
Characterization of an acetylcholine receptor alpha 3 gene promoter and its activation by the POU domain factor SCIP/Tst-1. (1994)

Genes encoding neuronal nicotinic acetylcholine receptors exhibit restricted patterns of expression in the nervous system. We are interested in elucidating the molecular mechanisms responsible for establishing these patterns of expression. This paper presents the characterization of regulatory elements upstream of the neuronal nicotinic acetylcholine receptor alpha 3 gene. We have identified a GC-rich multistart site promoter adjacent to the alpha 3 coding region. Similar alpha 3 start sites were identified in PC12 cells and sympathetic ganglion neurons, suggesting similar control mechanisms in the clonal line and peripheral neurons. The start site region lacks TATA-like sequences but does contain initiator-like sequences. We show, in transient transfection assays, that the POU domain transcription factor, SCIP/Tst-1, specifically activates alpha 3 in a neural context. Other POU domain factors tested only weakly activated or repressed alpha 3. Unexpectedly, we found that alpha 3 basal activity and SCIP/Tst-1 activation of alpha 3 is not dependent on the SCIP/Tst-1 binding sites found upstream of the gene. In addition, mutations in the SCIP/Tst-1 coding region that prevent the factor from binding to DNA with high affinity do not obliterate alpha 3 activation. These results lead us to propose that alpha 3 activation by SCIP/Tst-1 is achieved via protein-protein interactions between SCIP/Tst-1 and a specific complement of transcription factors that act directly on the promoter.
Simple algorithm derived from a geno-/phenotypic database to predict HIV-1 protease inhibitor resistance (2000)

With an optimized algorithm, phenotypic PI resistance can be predicted by viral genotype with good sensitivity (89.1-93.0%) and specificity (82.6-93.3%). The reliability and relevance of this algorithm should be further evaluated in clinical practice.
IL-2-induced activation-induced cell death is inhibited in IL-15 transgenic mice (2000)

A transgenic (Tg) mouse expressing human IL-15 was generated to define the role of IL-15 in the normal immune response. Overexpression of IL-15 resulted in an increase of NK, CD44(hi)CD8 memory T cells, and gammadelta T cells. Additionally, we observed the emergence of a novel type of NK-T cells with CD8alphaalpha' expression. Due to the expansion and activation of NK cells, the IL-15Tg mouse showed enhanced innate immunity. In adaptive T cell immunity, the roles of IL-15 contrasted with those of IL-2. IL-15 inhibited IL-2-induced T cell death, which plays a role in the maintenance of peripheral self-tolerance. IL-15 thus seems to contribute to enhanced immune memory by selectively propagating memory T cells and by blocking T cell death mediated by IL-2.
The role of fibroblast growth factors and their receptors in prostate cancer (2004)

Prostate cancer is the most common malignancy in men in the USA and the second leading cause of cancer deaths. Fibroblast growth factors (FGFs), including FGF1 (acidic FGF), FGF2 (basic FGF), FGF6 and FGF8 are all expressed at increased levels in prostate cancer as paracrine and/or autocrine growth factors for the prostate cancer cells. In addition, increased mobilization of FGFs from the extracellular matrix in cancer tissues can increase the availability of FGFs to cancer cells. Prostate cancer epithelial cells express all four types of FGF receptors (FGFR-1 to -4) at variable frequencies. Expression of FGFR-1 and FGFR-4 is most closely linked to prostate cancer progression, while the role of FGFR-2 remains controversial. Activation of FGF receptors can activate multiple signal transduction pathways including the phospholipase Cgamma, phosphatidyl inositol 3-kinase, mitogen-activated protein kinase and signal transducers and activators of transcription (STAT) pathways, all of which play a role in prostate cancer progression. Sprouty proteins can negatively regulate FGF signal transduction, potentially limiting the impact of FGF signaling in prostate cancer, but in a significant fraction of prostate cancers there is decreased expression of Sprouty1 mRNA and protein. The effects of increased FGF receptor signaling are wide ranging and involve both the cancer cells and surrounding stroma, including the vasculature. The net result of increased FGF signaling includes enhanced proliferation, resistance to cell death, increased motility and invasiveness, increased angiogenesis, enhanced metastasis, resistance to chemotherapy and radiation and androgen independence, all of which can enhance tumor progression and clinical aggressiveness. For this reason, the FGF signaling system it is an attractive therapeutic target, particularly since therapies targeting FGF receptors and/or FGF signaling can affect both the tumor cells directly and tumor angiogenesis. A number of approaches that could target FGF receptors and/or FGF receptor signaling in prostate cancer are currently being developed.
Controlling PbS nanocrystal aggregation in conducting polymers (2005)

PbS nanocrystals were synthesized directly in the conducting polymer, poly(3-hexylthiophene-2,5-diyl). Transmission electron microscopy shows that the PbS nanocrystals are faceted and relatively uniform in size with a mean size of 10 nm. FFT analysis of the atomic lattice planes observed in TEM and selected area electron diffraction confirm that the nanocrystals have the PbS rock salt structure. The synthesis conditions are explored to show control over the aggregation of PbS nanocrystals in the thiophene conducting polymer.
A Compact and Modular Laparoscopic Grasper With Tridirectional Force Measurement Capability (2008)

The introduction of minimally invasive surgery (MIS) into the operating room has led to significant advantages over conventional open surgery. Furthermore, the migration toward robot-assisted MIS over the past decade has provided additional advantages. However, the lack of haptic feedback in these tele-operated robotic surgical systems has inhibited the surgeon’s ability to diagnose tissue as healthy or unhealthy, thereby creating a need for force feedback in these systems. This paper presents the design and development of a compact and modular laparoscopic grasper with tridirectional force measurement capability for applications in robot-assisted MIS. The instrumented laparoscopic grasper is capable of measuring the normal grasping force, as well as the manipulation forces (horizontal and vertical) during grasping tasks. The grasper also has a modular design that allows for easy conversion between different surgical modalities, such as grasping, cutting, and dissecting. Preliminary tele-operative experiments with force feedback capability through a haptic feedback device for artificial tissue characterization as well as knot tightening experiments indicate the capability of this grasper.
Vaccine adjuvants: The dream becomes real (2008)

After about 70 years two new adjuvants have been approved for human vaccines. The first is MF59 developed by the ex-Chiron now Novartis Vaccines and it consists in an oil-in-water emulsion, comprising a low content of biodegradable squalene oil (4.3%) as the dispersed phase, which is stabilized by two non-ionic surfactants (Tween 80 and Span 85), and a low ionic strength citrate buffer as the continuous phase. The second one, defined as AS04, has been developed by GSK Biologics and consists in 3-0-desacyl-4'-monophosphoryl lipid A (MPL) that comes from the cell wall LPS of Gram-negative Salmonella minnesota R595 and is detoxified by mild hydrolytic treatment and purification. It is absorbed on aluminum hydroxide or aluminum phosphate. Thus, new molecules are available to improve the immune response to vaccines also in humans: this is the beginning of a new era in vaccinology.
Activity of the Heat Shock Protein 90 Inhibitor Ganetespib in Melanoma (2013)

Heat shock protein 90 (HSP90) is involved in the regulation of diverse biological processes such as cell signaling, proliferation and survival, and has been recently recognized as a potential target for cancer therapy. Ganetespib is a potent ATP competitive inhibitor of HSP90. Ganetespib downregulated the expression of multiple signal transducing molecules including EGFR, IGF-1R, c-Met, Akt, B-RAF and C-RAF, resulting in pronounced decrease in phosphorylation of Akt and Erk1/2 in a panel of five cutaneous melanoma cell lines including those harboring B-RAF and N-RAS mutations. Ganetespib exhibited potent antiproliferative activity on all five of these cell lines, with IC50 values between 37.5 and 84 nM. Importantly, Ganetespib is active on B-RAF mutated melanoma cells that have acquired resistance to B-RAF inhibition. Ganetespib induced apoptosis and cell cycle arrest at G1 and/or G2/M phase. Ganetespib induced cell cycle arrest was accompanied by altered expression of cyclin-dependent kinase inhibitor (CDKI) p21(Cip1) and p27(Kip1), cyclins B1, D1 and E, and/or cyclin-dependent kinases 1, 2 and 4. HSP90 is functionally important for melanoma cells and HSP90 inhibitors such as ganetespib could potentially be effective therapeutics for melanoma with various genetic mutations and acquired resistance to B-RAF inhibition.
A REVIEW OF PRECLINICAL PROGRAM DEVELOPMENT FOR EVALUATING INJECTABLE CARRIERS FOR OSTEOGENIC FACTORS (2003)

Corresponding author: Howard Seeherman, PhD, VMDWyeth Research, 87 Cambridge Park Drive, Cambridge, MA 02140. E-mail address: [email protected]
Germ-line transmission and developmental regulation of a 150-kb yeast artificial chromosome containing the human beta-globin locus in transgenic mice. (1993)

Sequential expression of the genes of the human beta-globin locus requires the formation of an erythroid-specific chromatin domain spanning > 200 kb. Regulation of this gene family involves both local interactions with proximal cis-acting sequences and long-range interactions with control elements upstream of the locus. To make it possible to analyze the interactions of cis-acting sequences of the human beta-globin locus in their normal spatial and sequence context, we characterized two yeast artificial chromosomes (YACs) 150 and 230 kb in size, containing the entire beta-globin locus. We have now successfully integrated the 150-kb YAC into the germ line of transgenic mice as a single unrearranged fragment that includes the locus control region, structural genes, and 30 kb of 3' flanking sequences present in the native locus. Expression of the transgenic human beta-globin locus is tissue- and developmental stage-specific and closely follows the pattern of expression of the endogenous mouse beta-globin locus. By using homology-directed recombination in yeast and methods for the purification and transfer of YACs into transgenic mice, it will now be feasible to study the physiological role of cis-acting sequences in specifying an erythroid-specific chromatin domain and directing expression of beta-globin genes during ontogeny.
Synthesis and Antiviral Activity of 2-Substituted Analogs of Triciribine (2003)

Triciribine (TCN) and triciribine monophosphate (TCN-P) have antiviral and antineoplastic activity at low or submicromolar concentrations. In an effort to improve and better understand this activity, we have conducted a structure-activity relationship study to explore the effect of substitutions at the 2-position of triciribine. 2-Methyl- (2-Me-TCN), 2-ethyl- (2-Et-TCN), 2-phenyl- (2-Ph-TCN), 2-chloro- (2-Cl-TCN), and 2-aminotriciribine (2-NH2-TCN) were designed and synthesized to determine the effects of substitutions at the 2-position which change the steric, electronic, and hydrophobic properties of TCN, while maintaining the integrity of the tricyclic ring system. These compounds were evaluated for activity against human immunodeficiency virus (HIV-1), herpes simplex virus type 1 (HSV-1), and human cytomegalovirus (HCMV) and were found to be either less active than TCN and TCN-P or inactive at the highest concentrations tested, 100 microM. We conclude that substitutions at the 2-position of triciribine adversely affect the antiviral activity most likely because these analogs are not phosphorylated to active metabolites.
How are Java software developers using the Eclipse IDE? (2006)

The Eclipse integrated development environment continues to gain popularity among Java developers. Our usage monitoring approach allows tool builders to sample how developers are using their tools in the wild. The data gathered about tool use can be used to prevent feature bloat and to evolve the environments according to user needs. Information about how developers work in a development environment can also provide a baseline for assessing new software development tools. We hope this report provides a start in defining which in formation to collect and distribute on an on going basis to help improve Eclipse and other similar platforms and tools.
G protein diversity is increased by associations with a variety of gamma subunits. (1990)

Guanine nucleotide-binding regulatory proteins (G proteins) are heterotrimeric proteins that transduce extracellular signals into intracellular changes. Functionally different G proteins have been identified by their different alpha subunits. The beta and gamma subunits have been assumed to constitute a common pool shared among various G protein heterotrimers. Two gamma subunits (gamma 3 and gamma 4) have been identified through molecular cloning; these are in addition to two subunits (gamma 1 and gamma 2) that were previously characterized. G proteins purified from a variety of mammalian tissues were examined with antisera specific to three of the gamma subunits. The antisera react with different gamma subunits associated with some of the purified G proteins but not all. This demonstrates that different G protein heterotrimers from different tissues carry structurally distinct members of the gamma-subunit family. Diversity in the structure of the gamma as well as the alpha and beta subunits and preferential associations between members of subunit families increase structural and possibly functional diversity of G proteins.
Suppressors of the Arabidopsis lsd5 Cell Death Mutation Identify Genes Involved in Regulating Disease Resistance Responses (1999)

Cell death is associated with the development of the plant disease resistance hypersensitive reaction (HR). Arabidopsis lsd mutants that spontaneously exhibit cell death reminiscent of the HR were identified previously. To study further the regulatory context in which cell death acts during disease resistance, one of these mutants, lsd5, was used to isolate new mutations that suppress its cell death phenotype. Using a simple lethal screen, nine lsd5 cell death suppressors, designated phx (for the mythological bird Phoenix that rises from its ashes), were isolated. These mutants were characterized with respect to their response to a bacterial pathogen and oomycete parasite. The strongest suppressors-phx2, 3, 6, and 11-1-showed complex, differential patterns of disease resistance modifications. These suppressors attenuated disease resistance to avirulent isolates of the biotrophic Peronospora parasitica pathogen, but only phx2 and phx3 altered disease resistance to avirulent strains of Pseudomonas syringae pv tomato. Therefore, some of these phx mutants define common regulators of cell death and disease resistance. In addition, phx2 and phx3 exhibited enhanced disease susceptibility to different virulent pathogens, confirming probable links between the disease resistance and susceptibility pathways.