gebhart/patrepeval huggingface dataset:
Phosphoproteomics identified Endofin, DCBLD2, and KIAA0582 as novel tyrosine phosphorylation targets of EGF signaling and Iressa in human cancer cells (2007)

With the completion of the human genome project, analysis of enriched phosphotyrosyl proteins from epidermal growth factor (EGF)-induced phosphotyrosine proteome permits the identification of novel downstream substrates of the EGF receptor (EGFR). Using cICAT-based LC-MS/MS method, we identified and relatively quantified the tyrosine phosphorylation levels of 21 proteins between control and EGF-treated A431 human cervical cancer cells. Of these, Endofin, DCBLD2, and KIAA0582 were validated to be novel tyrosine-phosphorylation targets of EGF signaling and Iressa, a highly selective inhibitor of EGFR. In addition, EGFR activity was shown to be necessary for EGF-induced localization of Endofin, an FYVE domain-containing protein regulated by phosphoinositol lipid and engaged in endosome-mediated receptor modulation. Although several groups have conducted phosphoproteomics of EGF signaling in recent years, our study is the first to identify and validate Endofin, DCBLD2, and KIAA0582 as part of a complex EGF phosphotyrosine signaling network. These novel data will provide new insights into the complex EGF signaling and may have implications on target-directed cancer therapeutics.
New directions in research: report from the 10th International Conference on AIDS. (1995)

Research findings presented at the 10th International Conference on AIDS, held in Yokohama, Japan, in August 1994, indicate that few advances have been made in standard antiretroviral therapy for HIV infection. The perinatal administration of AZT (zidovudine) was reported to reduce transmission of HIV from mother to child, and its use in combination with acyclovir appears to improve survival among patients with advanced disease. Other research has focused on asymptomatic patients with long-standing HIV infection. Their survival may be related to the activity of cell antiviral factor, a cytokine produced by CD8+ cells. In gene therapy research, one approach involved the genetic alteration of target cells to enable them to render the virus harmless. A second approach consisted of enhancing the function of CD8+ cells to allow them to compensate for dysfunctional CD4+ cells. The author believes that gene therapy may offer the greatest hope of an effective treatment for HIV infection.
Cutting Edge: Bacterial Flagellin Activates Basolaterally Expressed TLR5 to Induce Epithelial Proinflammatory Gene Expression (2001)

Flagellin, the structural component of bacterial flagella, is secreted by pathogenic and commensal bacteria. Flagellin activates proinflammatory gene expression in intestinal epithelia. However, only flagellin that contacts basolateral epithelial surfaces is proinflammatory; apical flagellin has no effect. Pathogenic Salmonella, but not commensal Escherichia coli, translocate flagellin across epithelia, thus activating epithelial proinflammatory gene expression. Investigating how epithelia detect flagellin revealed that cell surface expression of Toll-like receptor 5 (TLR5) conferred NF-kappaB gene expression in response to flagellin. The response depended on both extracellular leucine-rich repeats and intracellular Toll/IL-1R homology region of TLR5 as well as the adaptor protein MyD88. Furthermore, immunolocalization and cell surface-selective biotinylation revealed that TLR5 is expressed exclusively on the basolateral surface of intestinal epithelia, thus providing a molecular basis for the polarity of this innate immune response. Thus, detection of flagellin by basolateral TLR5 mediates epithelial-driven inflammatory responses to Salmonella.
Fine needle aspiration cytology of paraganglioma of the retroperitoneum. (1992)

A case of paraganglioma of the retroperitoneum diagnosed by fine needle aspiration cytology is described. A 60-year-old man presented with abdominal discomfort for 4 months. The smear revealed cellular sheets with partly rosettoid appearance. Many piexiform capillaries were distributed between the cellular sheets or encircled the cellular nests forming zell-ballen pattern. The tumor cells were monotonous and oval to round. The cytoplasm was amphophillc, finely granular and poorly defined. The nuclei were round and had evenly dispersed chromatin and small nucleoli. Cells having large or spindle nuclei were some-times observed. The tissue sections showed typical findings of paragnglima. The cytological differential diagnoses included islet cell tumor of the pancreas and carcinold tumor. The clinical and histoloigic findings as well as cytologic findings were helpful to confirm the diagnosis.
Combustion Modeling in Advanced Gas Turbine Systems (1995)

Goal of DOE`s Advanced Turbine Systems program is to develop and commercialize ultra-high efficiency, environmentally superior, cost competitive gas turbine systems for base-load applications in utility, independent power producer, and industrial markets. Primary objective of the program here is to develop a comprehensive combustion model for advanced gas turbine combustion systems using natural gas (coal gasification or biomass fuels). The efforts included code evaluation (PCGC-3), coherent anti-Stokes Raman spectroscopy, laser Doppler anemometry, and laser-induced fluorescence.
The effectiveness of styrene-maleic acid (SMA) copolymers for solubilisation of integral membrane proteins from SMA-accessible and SMA-resistant membranes (2017)

Solubilisation of biological lipid bilayer membranes for analysis of their protein complement has traditionally been carried out using detergents, but there is increasing interest in the use of amphiphilic copolymers such as styrene maleic acid (SMA) for the solubilisation, purification and characterisation of integral membrane proteins in the form of protein/lipid nanodiscs. Here we survey the effectiveness of various commercially-available formulations of the SMA copolymer in solubilising Rhodobacter sphaeroides reaction centres (RCs) from photosynthetic membranes. We find that formulations of SMA with a 2:1 or 3:1 ratio of styrene to maleic acid are almost as effective as detergent in solubilising RCs, with the best solubilisation by short chain variants (<30kDa weight average molecular weight). The effectiveness of 10kDa 2:1 and 3:1 formulations of SMA to solubilise RCs gradually declined when genetically-encoded coiled-coil bundles were used to artificially tether normally monomeric RCs into dimeric, trimeric and tetrameric multimers. The ability of SMA to solubilise reaction centre-light harvesting 1 (RC-LH1) complexes from densely packed and highly ordered photosynthetic membranes was uniformly low, but could be increased through a variety of treatments to increase the lipid:protein ratio. However, proteins isolated from such membranes comprised clusters of complexes in small membrane patches rather than individual proteins. We conclude that short-chain 2:1 and 3:1 formulations of SMA are the most effective in solubilising integral membrane proteins, but that solubilisation efficiencies are strongly influenced by the size of the target protein and the density of packing of proteins in the membrane.
Human Cofilin Forms Oligomers Exhibiting Actin Bundling Activity (2001)

Human cofilin possesses the tendency for self-association, as indicated by the rapid formation of dimers and oligomers when reacted with water-soluble carbodiimide, Ellman's reagent, or glutathione disulfide. Intermolecular disulfide bonds involve Cys(39) and probably Cys(147) of two adjacent cofilin units. The disulfide-linked dimers and oligomers exhibit a biological activity distinct from the monomer. While monomeric cofilin decreased viscosity and light-scattering of F-actin solutions, dimers and oligomers caused an increase in viscosity and light scattering. Electron microscopy revealed that cofilin oligomers induce the formation of highly ordered actin bundles with occasionally blunt ends similar to actin-cofilin rods observed in cells under oxidative stress. Bundling activity of the disulfide-linked oligomers could be completely reversed into severing activity by dithiothreitol. Formation of cofilin oligomers occurred also in the presence of actin at pH 8, but not at pH 6.6, and was significantly enhanced in the presence of phosphatidylinositol 4,5-bisphosphate. Our data are consistent with the idea that cofilin exists in two forms in vivo also: as monomers exhibiting the known severing activity and as oligomers exhibiting actin bundling activity. However, stabilization of cofilin oligomers in cytoplasm is probably achieved not by disulfide bonds but by a local increase in cofilin concentration and/or binding of regulatory proteins.
E5 Murine Monoclonal Antiendotoxin Antibody in Gram-Negative Sepsis<SUBTITLE>A Randomized Controlled Trial</SUBTITLE> (2000)

Despite adequate sample size and high enrollment of patients with confirmed gram-negative sepsis, E5 did not improve short-term survival. Current study rationale and designs should be carefully reviewed before further large-scale studies of patients with sepsis are conducted.
73.1 Invited Paper : Performance of High Power Light Emitting Diodes in Projection Applications (2006)

Abstract High Power LEDs are potentially attractive light sources for projection because of color, lifetime, speed, and environmental benefits. An update and outlook of luminance performance of LEDs will be given, showing performance is getting to an entry level required for commercial projection applications.
GnRH agonist versus GnRH antagonist in in vitro fertilization and embryo transfer (IVF/ET) (2012)

Several protocols are actually available for in Vitro Fertilization and Embryo Transfer. The review summarizes the main differences and the clinic characteristics of the protocols in use with GnRH agonists and GnRH antagonists by emphasizing the major outcomes and hormonal changes associated with each protocol. The majority of randomized clinical trials clearly shows that in "in Vitro" Fertilization and Embryo Transfer, the combination of exogenous Gonadotropin plus a Gonadotropin Releasing Hormone (GnRH) agonist, which is able to suppress pituitary FSH and LH secretion, is associated with increased pregnancy rate as compared with the use of gonadotropins without a GnRH agonist. Protocols with GnRH antagonists are effective in preventing a premature rise of LH and induce a shorter and more cost-effective ovarian stimulation compared to the long agonist protocol. However, a different synchronization of follicular recruitment and growth occurs with GnRH agonists than with GnRH antagonists. Future developments have to be focused on timing of the administration of GnRH antagonists, by giving a great attention to new strategies of stimulation in patients in which radio-chemotherapy cycles are needed.
Headache and Sex Hormone Therapy (1978)

SYNOPSIS A review of the literature suggested that falling levels of estrogen may trigger headaches for many women. A double blind controlled cross‐over study was carried out on 49 women, all of whom had undergone a surgical menopause. During the study each woman was randomly allocated each of the following drugs daily for three months: ethinyl estradiol 50 μg; d norgestrel 250 μg; combination of ethinyl estradiol 50 μg and d norgestrel 250 μg; and placebo. Women who reported they were headache free sufferers in the past had higher neuroticism and lower extraversion scores than others. Women who suffered headaches during a hormone free time interval had significantly higher plasma testosterone levels. An increase in the frequency of headaches occurred in association with a fall in estrogen content of the medication.
An Iterative Ensemble Kalman Filter for Multiphase Fluid Flow Data Assimilation (2007)

Summary The dynamical equations for multiphase flow in porous media are highly non-linear and the number of variables required to characterize the medium is usually large, often two or more variables per simulator gridblock. Neither the extended Kalman filter nor the ensemble Kalman filter is suitable for assimilating data or for characterizing uncertainty for this type of problem. Although the ensemble Kalman filter handles the nonlinear dynamics correctly during the forecast step, it sometimes fails badly in the analysis (or updating) of saturations. This paper focuses on the use of an iterative ensemble Kalman filter for data assimilation in nonlinear problems, especially of the type related to multiphase flow in porous media. Two issues are key: (1) iteration to enforce constraints and (2) ensuring that the resulting ensemble is representative of the conditional pdf (i.e. that the uncertainty quantification is correct). The new algorithm is compared to the ensemble Kalman filter on several highly nonlinear example problems, and shown to be superior in the prediction of uncertainty.
Structural Determinants for Affinity Enhancement of a Dual Antagonist Peptide Entry Inhibitor of Human Immunodeficiency Virus Type-1 (2008)

Structure-activity correlations were investigated for substituted peptide conjugates that function as dual receptor site antagonists of HIV-1 gp120. A series of peptide conjugates were constructed via click reaction of both aryl and alkyl acetylenes with an internally incorporated azidoproline 6 derived from the parent peptide 1 (12p1, RINNIPWSEAMM). Compared to 1, many of these conjugates were found to exhibit several orders of magnitude increase in both affinity for HIV-1 gp120 and inhibition potencies at both the CD4 and coreceptor binding sites of gp120. We sought to determine structural factors in the added triazole grouping responsible for the increased binding affinity and antiviral activity of the dual inhibitor conjugates. We measured peptide conjugate potencies in both kinetic and cell infection assays. High affinity was sterically specific, being exhibited by the cis- but not the trans-triazole. The results demonstrate that aromatic, hydrophobic, and steric features in the residue 6 side-chain are important for increased affinity and inhibition. Optimizing these features provides a basis for developing gp120 dual inhibitors into peptidomimetic and increasingly smaller molecular weight entry antagonist leads.
Fast motion deblurring (2009)

This paper presents a fast deblurring method that produces a deblurring result from a single image of moderate size in a few seconds. We accelerate both latent image estimation and kernel estimation in an iterative deblurring process by introducing a novel prediction step and working with image derivatives rather than pixel values. In the prediction step, we use simple image processing techniques to predict strong edges from an estimated latent image, which will be solely used for kernel estimation. With this approach, a computationally efficient Gaussian prior becomes sufficient for deconvolution to estimate the latent image, as small deconvolution artifacts can be suppressed in the prediction. For kernel estimation, we formulate the optimization function using image derivatives, and accelerate the numerical process by reducing the number of Fourier transforms needed for a conjugate gradient method. We also show that the formulation results in a smaller condition number of the numerical system than the use of pixel values, which gives faster convergence. Experimental results demonstrate that our method runs an order of magnitude faster than previous work, while the deblurring quality is comparable. GPU implementation facilitates further speed-up, making our method fast enough for practical use.
PARACEST Agents:  Modulating MRI Contrast via Water Proton Exchange (2003)

Scientific interest in optimizing the properties of gadolinium (III) complexes as MRI contrast agents has led to many new insights into lanthanide ion coordination chemistry in the last two decades. Among these was the surprising observation that water exchange in lanthanide (III) derivatives of DOTA can be modulated dramatically by judicious choice of ligand side chain and Ln(3+) ionic radii. This resulted in the discovery of paramagnetic CEST agents for altering MRI image contrast based upon the chemical exchange saturation transfer mechanism. The goal of this article is to review the factors that govern water molecule and water proton exchange in these complexes and to compare the potential sensitivity of PARACEST agents versus Gd(3+)-based T(1) relaxation agents for altering tissue contrast.
Evaluation of Ipilimumab in Combination With Allogeneic Pancreatic Tumor Cells Transfected With a GM-CSF Gene in Previously Treated Pancreatic Cancer (2013)

Preclinical reports support the concept of synergy between cancer vaccines and immune checkpoint blockade in nonimmunogenic tumors. In particular, cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) antibodies have been successfully combined with GM-CSF cell-based vaccines (GVAX). Ipilimumab (anti-CTLA-4) has been tested as a single agent in patients with pancreatic ductal adenocarcinoma (PDA) resulting in a delayed response at a dose of 3 mg/kg. Our study evaluated ipilimumab 10 mg/kg (arm 1) and ipilimumab 10 mg/kg + GVAX (arm 2). A total of 30 patients with previously treated advanced PDA were randomized (1:1). Induction doses were administered every 3 weeks for a total of 4 doses followed by maintenance dosing every 12 weeks. Two patients in arm 1 showed evidence of stable disease (7 and 22 wk) but none demonstrated CA19-9 biochemical responses. In contrast, 3 patients in arm 2 had evidence of prolonged disease stabilization (31, 71, and 81 wk) and 7 patients experienced CA19-9 declines. In 2 of these patients, disease stabilization occurred after an initial period of progression. The median overall survival (OS) (3.6 vs. 5.7 mo, hazards ratio: 0.51, P = 0.072) and 1 year OS (7 vs. 27%) favored arm 2. Similar to prior ipilimumab studies, 20% of patients in each arm had grade 3/4 immune-related adverse events. Among patients with OS > 4.3 months, there was an increase in the peak mesothelin-specific T cells (P = 0.014) and enhancement of the T-cell repertoire (P = 0.031). In conclusion, checkpoint blockade in combination with GVAX has the potential for clinical benefit and should be evaluated in a larger study.
Intrauterine Endotoxin Administration Leads to White Matter Diffusivity Changes in Newborn Rabbits (2009)

Maternal intrauterine inflammation has been implicated in the development of periventricular leukomalacia and white matter injury in the neonate. We hypothesized that intrauterine endotoxin administration would lead to microstructural changes in the neonatal rabbit white matter in vivo that could be detected at birth using diffusion tensor magnetic resonance imaging (MRI). Term newborn rabbit kits (gestational age 31 days) born to dams exposed to saline or endotoxin in utero on gestational day 28 underwent diffusion tensor imaging, and brain sections were stained for microglia. Comparison between normal and endotoxin groups showed significant decreases in both fractional anisotropy and eigenvalue (e(1)) in all periventricular white matter regions that showed an increase in the number of activated microglial cells, indicating that after maternal inflammation, microglial infiltration may predominantly explain this change in diffusivity in the immediate neonatal period. Diffusion tensor imaging may be a clinically useful tool for detecting neuroinflammation induced by maternal infection in neonatal white matter.
Molecular Role for the Rab Binding Platform of Guanine Nucleotide Dissociation Inhibitor in Endoplasmic Reticulum to Golgi Transport (1998)

Guanine nucleotide dissociation inhibitor (GDI) regulates the recycling of Rab GTPases involved in vesicle targeting and fusion. We have analyzed the requirement for conserved amino acid residues in the binding of Rab1A and the function of GDI in transport of cargo between the endoplasmic reticulum (ER) and the Golgi apparatus. Using a new approach to monitor GDI-Rab interactions based on the change in fluorescence associated with the release of methylanthraniloyl guanosine di(tri)phosphate-GDP (mGDP) from Rab, we show that residues previously implicated in the binding of the synapse-specific Rab3A, including Gln-236, Arg-240, and Thr-248, are essential for the binding of Rab1A. Mutation of each of these residues has potent effects on the ability of GDI to remove Rab1A from membranes and inhibit ER to Golgi transport in vitro. Given the sequence divergence between Rab1A and 3A (35% identity), these residues are proposed to play a general role in GDI function in the cell. In contrast, several other residues found within or flanking the Rab-binding region were found to have differential effects in the recognition and recycling of Rab1A and 3A, and therefore direct selective interaction of GDI with individual Rab proteins. Intriguingly, mutation of one residue, Arg-70, led to a reduction of Rab1A binding, failed to extract Rab1A from membranes in vitro, yet bound membranes tightly and potently inhibited ER to Golgi transport. These results provide evidence that novel membrane-associated factor(s) mediate Rab-independent GDI interaction with membranes.
Muse: A Multimedia Filing System (1987)

New technology is changing the way we store documents. This experimental system features flexible document retrieval, a distributed architecture, and the capacity to store many very large documents.
Transposon-induced non-motile mutants of Vibrio cholerae (1990)

Non-motile mutants of Vibrio cholerae were isolated after transposon insertion mutagenesis with either Tn5 on a plasmid or Tn10ptac mini-kan in bacteriophage lambda. The physical location and number of transposon insertions was determined. Eighteen Tn5 insertion mutants and 11 Tn10ptac mini-kan insertion mutants had single unique insertion sites. The 18 Tn5 insertions were contained within six different EcoRI fragments and the 11 Tn10ptac mini-kan insertions were contained within eight different fragments of V. cholerae chromosomal DNA. These data suggest that multiple genes are involved in motility. Immunoblot analysis of non-motile mutants with antibody to wild-type flagellar core protein indicated that two of the non-motile mutants made flagellar core protein. Three additional mutants reacted weakly with the antibodies. However, these mutants with immunopositive reactions did not produce any structures which resembled flagella by transmission electron microscopy. In addition, none of the other non-motile mutants produced wild-type flagella. However, five mutants which did not react in the immunoblot produced a structure which resembled a flagellar sheath without the internal flagellar core. In addition to having no filamentous core, the sheaths often extended from the sides of the bacteria, rather than from the poles where the flagellum is normally located. The data suggest that sheath formation is independent of flagellar filament formation, but that proper positioning of the sheath may require the flagellar filament.
Dietary Intake and Cell Membrane Levels of Long-Chain n-3 Polyunsaturated Fatty Acids and the Risk of Primary Cardiac Arrest (1995)

Dietary intake of n-3 polyunsaturated fatty acids from seafood is associated with a reduced risk of primary cardiac arrest.
Focal Hyperhidrosis (1998)

Intracutaneous botulinum toxin seems preferable to any hitherto used conservative or surgical procedures and may become the therapy of choice in pathological focal hyperhidrosis.