gebhart/patrepeval huggingface dataset:
A 40-Amino Acid Segment of the Growth Hormone Receptor Cytoplasmic Domain Is Essential for GH-induced Tyrosine-phosphorylated Cytosolic Proteins (1995)

It has become evident that intracellular protein phosphorylation plays an important role in mediating signal transduction of hormones and growth factors, including growth hormone (GH). We have previously demonstrated that GH can stimulate tyrosine phosphorylation of cellular proteins with approximate molecular masses of 95,000 daltons (pp95) in GH-treated 3T3-F442A preadipocytes and in mouse L cells that express recombinant porcine or bovine GH receptors. In the present study, a series of GH receptor (GHR) truncation analogs were constructed and examined for their abilities to induce pp95. The results revealed that a region of approximately 40 amino acids in the porcine GHR cytoplasmic domain is essential for induction of pp95. The results also established that the 115 amino acids (517-638) near the C terminus of porcine GHR are not required for pp95 induction. Moreover, the basal levels of GH-induced pp95 in parental mouse L cells was suppressed by expression of these GHR truncation analogs. This suggests that pp95 induced by GH may be mediated by GHR dimerization and can be inhibited by overexpression of truncated porcine GHRs.
Metopimazine is primarily metabolized by a liver amidase in humans (2021)

Metopimazine (MPZ) is a peripherally restricted, dopamine D2 receptor antagonist used for four decades to treat acute nausea and vomiting. MPZ is currently under clinical investigation for the treatment of gastroparesis (GP). MPZ undergoes high first-pass metabolism that produces metopimazine acid (MPZA), the major circulating metabolite in humans. Despite a long history of use, the enzymes involved in the metabolism of MPZ have not been identified. Here we report a series of studies designed to identify potential MPZ metabolites in vitro, determine their clinical relevance in humans, and elucidate the enzymes responsible for their formation. The findings demonstrated that the formation of MPZA was primarily catalyzed by human liver microsomal amidase. Additionally, human liver cytosolic aldehyde oxidase (AO) catalyzes the formation of MPZA, in vitro, although to a much lesser extent. Neither cytochrome P450 enzymes nor flavin-monooxygenases (FMO) were involved in the formation MPZA, although two minor oxidative pathways were catalyzed by CYP3A4 and CYP2D6 in vitro. Analysis of plasma samples from subjects dosed 60 mg of MPZ verified that these oxidative pathways are very minor and that CYP enzyme involvement was negligible compared to microsomal amidase/hydrolase in overall MPZ metabolism in humans. The metabolism by liver amidase, an enzyme family not well defined in small molecule drug metabolism, with minimal metabolism by CYPs, differentiates this drug from current D2 antagonists used or in development for the treatment of GP.
Synthesis of Methyl Halides from Biomass Using Engineered Microbes (2009)

Methyl halides are used as agricultural fumigants and are precursor molecules that can be catalytically converted to chemicals and fuels. Plants and microorganisms naturally produce methyl halides, but these organisms produce very low yields or are not amenable to industrial production. A single methyl halide transferase (MHT) enzyme transfers the methyl group from the ubiquitous metabolite S-adenoyl methionine (SAM) to a halide ion. Using a synthetic metagenomic approach, we chemically synthesized all 89 putative MHT genes from plants, fungi, bacteria, and unidentified organisms present in the NCBI sequence database. The set was screened in Escherichia coli to identify the rates of CH(3)Cl, CH(3)Br, and CH(3)I production, with 56% of the library active on chloride, 85% on bromide, and 69% on iodide. Expression of the highest activity MHT and subsequent engineering in Saccharomyces cerevisiae results in productivity of 190 mg/L-h from glucose and sucrose. Using a symbiotic co-culture of the engineered yeast and the cellulolytic bacterium Actinotalea fermentans, we are able to achieve methyl halide production from unprocessed switchgrass (Panicum virgatum), corn stover, sugar cane bagasse, and poplar (Populus sp.). These results demonstrate the potential of producing methyl halides from non-food agricultural resources.
Functional Mapping of Protective Domains and Epitopes in the Rotavirus VP6 Protein (2000)

The purpose of this study was to determine which regions of the VP6 protein of the murine rotavirus strain EDIM are able to elicit protection against rotavirus shedding in the adult mouse model following intranasal (i.n.) immunization with fragments of VP6 and a subsequent oral EDIM challenge. In the initial experiment, the first (fragment AB), middle (BC), or last (CD) part of VP6 that was genetically fused to maltose-binding protein (MBP) and expressed in Escherichia coli was examined. Mice (BALB/c) immunized with two 9-microg doses of each of the chimeras and 10 microg of the mucosal adjuvant LT(R192G) were found to be protected against EDIM shedding (80, 92, and nearly 100% reduction, respectively; P </= 0.01) following challenge. Because CD produced almost complete protection, we prepared four E. coli-expressed, MBP-fused chimeras containing overlapping fragments of the CD region (i.e., CD1, CD2, CD3, and CD4) whose lengths ranged from 61 to 67 amino acid residues. Following i.n. immunization, CD1, CD2, and CD4 induced significant (P </= 0.004) protection (88, 84, and 92% reduction, respectively). In addition, 11 peptides (18 to 30 residues) of the CD region with between 0 and 13 overlapping amino acids were synthesized. Two 50-microg doses of each peptide with LT(R192G) were administered i.n. to BALB/c mice. Five peptides were found to elicit significant (P </= 0.02) protection. Moreover, a 14-amino-acid region within peptide 6 containing a putative CD4(+) T-cell epitope was found to confer nearly complete protection, suggesting a protective role for CD4(+) T cells. Mice that were protected by fragments BC and CD1 and four of the five protective synthetic peptides did not develop measurable rotavirus antibodies in serum or stool, implying that protection induced by these domains was not dependent on antibody. Together, these observations suggest that multiple regions of VP6 can stimulate protection, a region of VP6 as small as 14 amino acids containing a CD4(+) T-cell epitope can stimulate nearly complete protection, and protection mediated by a subset of epitopes in the VP6 protein does not require antibodies in BALB/c mice.
Advanced techniques for glancing angle deposition (1998)

When a thin film is deposited by physical vapor deposition, with the vapor flux arriving at an oblique angle from the substrate normal, and under conditions of sufficiently limited adatom mobility to create a columnar microstructure, the resulting structure is somewhat porous and grows at an angle inclined toward the vapor source. For a given material and set of deposition conditions, there is a fixed relationship between the angle of vapor flux incident on the substrate and the inclination angle at which the columnar thin film grows. As the porosity of the film is also dependent on the incident flux angle, column growth angle and porosity cannot be chosen independently. If a large columnar angle (more parallel to the substrate) is desired, the flux must be deposited at a large oblique angle resulting in a very porous film. Conversely, if a near vertical columnar film is desired, the flux must arrive more perpendicular to the substrate and the resulting film has a tightly packed, dense microstructure. We present a technique, based on glancing angle deposition, employing substrate motion during deposition, which allows the columnar growth inclination angle and film density to be controlled independently. With this method, microstructurally controlled materials can be fabricated with three dimensional control on a 10 nm scale for use in optical, chemical, biological, mechanical, magnetic, and electrical applications.
Video segmentation for content-based coding (1999)

To provide multimedia applications with new functionalities, the new video coding standard MPEG-4 relies on a content-based representation. This requires a prior decomposition of sequences into semantically meaningful, physical objects. We formulate this problem as one of separating foreground objects from the background based on motion information. For the object of interest, a 2D binary model is derived and tracked throughout the sequence. The model points consist of edge pixels detected by the Canny operator. To accommodate rotation and changes in shape of the tracked object, the model is updated every frame. These binary models then guide the actual video object plane (VOP) extraction. Thanks to our new boundary postprocessor and the excellent edge localization properties of the Canny operator, the resulting VOP contours are very accurate. Both the model initialization and update stages exploit motion information. The main assumption underlying our approach is the existence of a dominant global motion that can be assigned to the background. Areas that do not follow this background motion indicate the presence of independently moving physical objects. Two alternative methods to identify such objects are presented. The first one employs a morphological motion filter with a new filter criterion, which measures the deviation of the locally estimated optical flow from the corresponding global motion. The second method computes a change detection mask by taking the difference between consecutive frames. The first version is more suitable for sequences with little motion, whereas the second version is better at dealing with faster moving or changing objects. Experimental results demonstrate the performance of our algorithm.
Halide-Free Dehydrative Allylation Using Allylic Alcohols Promoted by a Palladium−Triphenyl Phosphite Catalyst (2004)

The triphenyl phosphite-palladium complex was found to effect catalytic substitution reactions of allylic alcohols via a direct C-O bond cleavage. The dehydrative etherification proceeded efficiently without any cocatalysts and bases to give allylic ethers in good to excellent yields.
A Principal Component Regression Approach for Estimation of Ventricular Repolarization Characteristics (2010)

The time interval between Q-wave onset and T-wave offset, i.e., QT interval, in an ECG corresponds to the total ventricular activity, including both depolarization and repolarization times. It has been suggested that abnormal QT variability could be a marker of cardiac diseases such as ventricular arrhythmias, and QT-interval has also been observed to lengthen during hypoglycemia. In this paper, we propose a robust method for estimating ventricular repolarization characteristics such as QT interval and T-wave amplitude. The method is based on principal component regression. In the method, QT epochs are first extracted from ECG in respect of R-waves. Then, correlation matrix of the extracted epochs is formed and its eigenvectors computed. The most significant eigenvectors are then fitted to the data to obtain noise-free estimates of QT epochs. Nonstationarities in QT-epoch characteristics can also be modeled by updating the eigenvectors dynamically. The main benefit of the proposed method is robustness to noise, i.e., it works also when using ECGs that have low SNR, for example, signals measured during normal-life environments. One application of the proposed method could be the detection of the hypoglycemia.
Specific degenerate codons enhanced selective expression of human parathyroid hormone in Escherichia coli. (1991)

Specific degenerate codons in the amino-terminal region of a synthetic human parathyroid hormone (PTH) gene exerted dramatic effects on both products and yield of expression of this 84-amino acid polypeptide in Escherichia coli. With adenine-rich degenerate codons constituting the PTH-(1-5) region, intact PTH has been expressed as the only PTH product at 6.5 mg/liter. In contrast, with guanine-rich degenerate codons, the predominent product was analogue PTH-(8-84). Use of cytosine- or thymine-rich degenerate codons generated only a small amount of immunoreactive product (0.2 mg/l). With the amino terminal region reconstituted with adenine-rich degenerate codons, the mid and carboxyl regions of the synthetic gene were also reconstructed to imitate the E. coli-favored codon degeneracy. Expression yielded the intact PTH at 20 mg/liter. Gel electrophoresis and Western blots, with antibodies specific to the amino or carboxyl terminus of PTH, indicated only a single PTH-related polypeptide, with the same mobility as a synthetic intact PTH sample. Amino acid sequencing, composition analysis, mass spectrometry, and the adenylate cyclase bioassays confirmed the purified product as the processed intact PTH.
Peptide hormones and lung cancer. (2006)

Several peptide hormones have been identified which alter the proliferation of lung cancer. Small cell lung cancer (SCLC), which is a neuroendocrine cancer, produces and secretes gastrin releasing peptide (GRP), neurotensin (NT) and adrenomedullin (AM) as autocrine growth factors. GRP, NT and AM bind to G-protein coupled receptors causing phosphatidylinositol turnover or elevated cAMP in SCLC cells. Addition of GRP, NT or AM to SCLC cells causes altered expression of nuclear oncogenes, such as c-fos, and stimulation of growth. Antagonists have been developed for GRP, NT and AM receptors which function as cytostatic agents and inhibit SCLC growth. Growth factor antagonists, such as the NT1 receptor antagonist SR48692, facilitate the ability of chemotherapeutic drugs to kill lung cancer cells. It remains to be determined if GRP, NT and AM receptors will served as molecular targets, for development of new therapies for the treatment of SCLC patients. Non-small cell lung cancer (NSCLC) cells also have a high density of GRP, NT, AM and epidermal growth factor (EGF) receptors. Several NSCLC patients with EGF receptor mutations respond to gefitinib, a tyrosine kinase inhibitor. Gefitinib relieves NSCLC symptoms, maintaining stable disease in patients who are not eligible for systemic chemotherapy. It is important to develop new therapeutic approaches using translational research techniques for the treatment of lung cancer patients.
Constitutive Expression of Human Immunodeficiency Virus Type 1 tat Gene Inhibits Interleukin 2 and Interleukin 2 Receptor Expression in a Human CD4 + T Lymphoid (H9) Cell Line (1995)

Human immunodeficiency virus (HIV-1) tat, a trans-activator of the HIV long terminal repeat, is essential for HIV replication and causes inhibition of antigen-mediated T cell proliferation. To understand the mechanism of inhibition of T cell proliferation, we have investigated the regulation of IL-2 production and its receptor expression on a human CD4+ T lymphoid cell line (H9) transfected with HIV-1 tat gene. When cells were activated by mitogens, as compared to control cells, a significant decrease in both IL-2 mRNA and protein was observed in tat-transfected cells. Similarly, mitogen-induced IL-2R alpha and IL-2R beta mRNA and surface expression of IL-2R alpha and IL-2R beta chains were also significantly decreased in tat-transfected cells compared to control cells. Only IL-2 receptor density was decreased; the affinity of the ligand for the receptor appeared to be unchanged. In contrast to our previous studies with B-lymphoblastoid cell line (Puri RK and Aggarwal BB: Cancer Res 1992; 52:3787-3790), IL-4R expression was unaltered by HIV tat transfection in the H9 T cell line, indicating a cell type-specific phenomenon. Owing to the central role of IL-2 immunoregulation, our data suggest that immunosuppressive effects of HIV-1 tat may be mediated at least in part through the inhibition of both IL-2 production and IL-2 receptor expression.
Highly Recurrent TERT Promoter Mutations in Human Melanoma (2013)

Systematic sequencing of human cancer genomes has identified many recurrent mutations in the protein-coding regions of genes but rarely in gene regulatory regions. Here, we describe two independent mutations within the core promoter of telomerase reverse transcriptase (TERT), the gene coding for the catalytic subunit of telomerase, which collectively occur in 50 of 70 (71%) melanomas examined. These mutations generate de novo consensus binding motifs for E-twenty-six (ETS) transcription factors, and in reporter assays, the mutations increased transcriptional activity from the TERT promoter by two- to fourfold. Examination of 150 cancer cell lines derived from diverse tumor types revealed the same mutations in 24 cases (16%), with preliminary evidence of elevated frequency in bladder and hepatocellular cancer cells. Thus, somatic mutations in regulatory regions of the genome may represent an important tumorigenic mechanism.
The MPEG-DASH Standard for Multimedia Streaming Over the Internet (2011)

MPEG has recently finalized a new standard to enable dynamic and adaptive streaming of media over HTTP. This standard aims to address the interoperability needs between devices and servers of various vendors. There is broad industry support for this new standard, which offers the promise of transforming the media-streaming landscape.
Patterned Arrays of Au Rings for Localized Surface Plasmon Resonance (2006)

In this paper, we examined the characteristic behavior of localized surface plasmon resonances (LSPR) of Au dot and ring arrays in response to the selective binding of biomolecules. To do this, patterned arrays of Au rings and dots with various feature scales were fabricated over large areas by an imprint lithography technique. Our results showed that the LSPR spectra of the Au nanorings exhibited a blue shift with increase in the ring widths and asymptotically converged to those for Au nanodots. This clearly implies that the LSPR spectra can be tuned over an extended wavelength range by varying the ring width. For an illustrative purpose, the patterned Au structures were used to detect the binding of streptavidin to biotin. In doing this, the Au patterns were chemically modified with G4 dendrimers of amine terminated poly(amidoamine), which facilitated the tethering of biotin onto the Au pattern. Exposure of the biotinylated Au nanorings to aqueous streptavidin solution induced both red-shifts of the LSPR spectra and changes in the peak intensities. The sensitivity of the LSPR spectra to the binding of the biomolecules was enhanced as the ring width of Au rings was decreased.
Knobs-into-holes antibody production in mammalian cell lines reveals that asymmetric afucosylation is sufficient for full antibody-dependent cellular cytotoxicity (2013)

Knobs-into-holes is a well-validated heterodimerization technology for the third constant domain of an antibody. This technology has been used to produce a monovalent IgG for clinical development (onartuzumab) and multiple bispecific antibodies. The most advanced uses of this approach, however, have been limited to E. coli as an expression host to produce non-glycosylated antibodies. Here, we applied the technology to mammalian host expression systems to produce glycosylated, effector-function competent heterodimeric antibodies. In our mammalian host system, each arm is secreted as a heavy chain-light chain (H-L) fragment with either the knob or hole mutations to allow for preferential heterodimer formation in vitro with low levels of homodimer contaminants. Like full antibodies, the secreted H-L fragments undergo Fc glycosylation in the endoplasmic reticulum. Using a monospecific anti-CD20 antibody, we show that full antibody-dependent cell-mediated cytotoxicity (ADCC) activity can be retained in the context of a knobs-into-holes heterodimer. Because the knobs-into-holes mutations convert the Fc into an asymmetric heterodimer, this technology was further used to systematically explore asymmetric recognition of the Fc. Our results indicate that afucosylation of half the heterodimer is sufficient to produce ADCC-enhancement similar to that observed for a fully afucosylated antibody with wild-type Fc. However, the most dramatic effect on ADCC activity is observed when two carbohydrate chains are present rather than one, regardless of afucosylation state.
Low-Dose Danazol in the Treatment of Livedoid Vasculitis (1997)

We concluded that low-dose danazol was effective in the treatment of livedoid vasculitis, without unacceptable side effects.
Induction of the hepatic mixed-function oxidase system by synthetic glucocorticoids. Transcriptional and post-transcriptional regulation. (1987)

Quantitative evaluation of transcriptional rates in isolated nuclei and intranuclear and cytoplasmic mRNA levels demonstrates that the catatoxic steroids pregnenolone-16 alpha-carbonitrile (PCN) and dexamethasone modulate microsomal drug metabolizing enzymes both positively and negatively at the transcriptional level. Additionally, a strong post-transcriptional influence, believed to be message stabilization, was found to be exerted by dexamethasone. Both NADPH-cytochrome P-450b-homologous mRNA are induced 7- and 12-fold, respectively, presumably through message stabilization. Under these conditions, however, the oxidoreductase content of the cell is only marginally increased while the cytochrome P-450b level is actually decreased by 40% within three days after a single injection of dexamethasone. In contrast, genes coding for cytochromes P-450PCN show a definite increase in transcription following administration of either pre gnenolone-16 alpha-carbonitrile or dexamethasone, whereas transcription of the epoxide hydrolase gene is markedly reduced by administration of these compounds.
Active Compliance And Damping In Telemanipulator Control (1991)

Experimental telemanipulator system of force-reflecting-hand-controller type provides for active compliance and damping in remote, robotic manipulator hand. Distributed-computing and -control system for research in various combinations of force-reflecting and active-compliance control regimes. Shared compliance control implemented by low-pass-filtered force/torque feedback. Variable simulated springs and shock absorbers soften collisions and increase dexterity.
Biphasic Kinetics of Activation and Signaling for PAR1 and PAR4 Thrombin Receptors in Platelets (2000)

Thrombin activates platelets in an ordered sequence of events that includes shape change, increase in cytoplasmic Ca(2+), activation of the alphaIIbbeta3 integrin, granule secretion, aggregation, and formation of a stable hemostatic plug. Activation of this process has also been implicated in the pathogenesis of atherosclerosis, stroke, and thrombosis. There are two identified thrombin-activated receptors on the surface of human platelets. PAR1 is a high-affinity thrombin receptor, and PAR4 is a low apparent affinity thrombin receptor of uncertain function. The goal of these studies is to determine the kinetics of thrombin activation of PAR1 and PAR4 and to relate the individual inputs from each receptor to platelet Ca(2+) signaling, secondary autocrine stimulation, and aggregation. Using a combination of PAR-specific peptide ligands and anti-PAR1 reagents, we separated the biphasic thrombin Ca(2+) response of platelets into two discrete components-a rapid spike response caused by PAR1, followed by a slower prolonged response from PAR4. Despite having a 20-70-fold slower rate of activation, PAR4 produces the majority of the integrated Ca(2+) signal that is sustained by the continuous presence of catalytically active thrombin. Surprisingly, PAR4 activation is much more effective than PAR1 activation in mounting secondary autocrine Ca(2+) signals from secreted ADP. The strong ADP response due to activated PAR4, however, requires prior activation of PAR1 as would normally occur during treatment of platelets with thrombin. Thus, the late signal generated by activated PAR4 is not redundant with the early signal from PAR1 and instead serves to greatly extend the high intracellular Ca(2+) levels that support the late phase of the platelet aggregation process.