gebhart/patrepeval huggingface dataset:
Chronic Heroin Self-Administration Desensitizes μ Opioid Receptor-Activated G-Proteins in Specific Regions of Rat Brain (2000)

In previous studies from our laboratory, chronic noncontingent morphine administration decreased mu opioid receptor-activated G-proteins in specific brainstem nuclei. In the present study, mu opioid receptor binding and receptor-activated G-proteins were examined after chronic heroin self-administration. Rats were trained to self-administer intravenous heroin for up to 39 d, achieving heroin intake up to 366 mg. kg(-1). d(-1). mu opioid-stimulated [(35)S]GTPgammaS and [(3)H]naloxone autoradiography were performed in adjacent brain sections. Agonist-stimulated [(35)S]GTPgammaS autoradiography also examined other G-protein-coupled receptors, including delta opioid, ORL-1, GABA(B), adenosine A(1), cannabinoid, and 5-HT(1A). In brains from heroin self-administering rats, decreased mu opioid-stimulated [(35)S]GTPgammaS binding was observed in periaqueductal gray, locus coeruleus, lateral parabrachial nucleus, and commissural nucleus tractus solitarius, as previously observed in chronic morphine-treated animals. In addition, decreased mu opioid-stimulated [(35)S]GTPgammaS binding was found in thalamus and amygdala after heroin self-administration. Despite this decrease in mu-activated G-proteins, [(3)H]naloxone binding demonstrated increased mu opioid receptor binding in several brain regions after heroin self-administration, and there was a significant decrease in mu receptor G-protein efficiency as expressed as a ratio between agonist-activated G-proteins and mu receptor binding. No effects on agonist-stimulated [(35)S]GTPgammaS binding were found for any other receptor examined. The effect of chronic heroin self-administration to decrease mu-stimulated [(35)S]GTPgammaS binding varied between regions and was highest in brainstem and lowest in the cortex and striatum. These results not only provide potential neuronal mechanisms that may contribute to opioid tolerance and dependence, but also may explain why various chronic effects of opioids develop to different degrees.
Baculovirus Infection Does not Alter N-Glycosylation inSpodoptera frugiperdaCells (1994)

Spodoptera frugiperda cells are the standard host system for baculovirus-vector-mediated expression of recombinant glycoproteins. In an attempt to explore their ability to produce complex N-glycans containing terminal neuraminic acid, we tested both mock- and AcMNPV-infected SF9 cells. To elucidate the structures of the carbohydrate chains of cellular glycoproteins, radiolabeled oligosaccharides were liberated by treatment with endo-H and glycopeptidase F. When the endo-H resistant material was subjected to sequential degradation with exoglycosidases, only truncated carbohydrates with the structures Man3GlcNAc2 and Man3[Fuc]GlcNAc2 were found. There was no evidence for the presence of neuraminic acid and complex N-glycans. The results indicate that SF9 cells have only a limited capacity to process N-glycans. Infection with AcMNPV has no significant effect on glycosylation in these cells.
Cyclic Nucleotide-Dependent Protein Kinases: Intracellular Receptors for cAMP and cGMP Action (1999)

Intracellular cAMP and cGMP levels are increased in response to a variety of hormonal and chemical stimuli; these nucleotides play key roles as second messenger signals in modulating myriad physiological processes. The cAMP-dependent protein kinase and cGMP-dependent protein kinase are major intracellular receptors for these nucleotides, and the actions of these enzymes account for much of the cellular responses to increased levels of cAMP or cGMP. This review summarizes many studies that have contributed significantly to an improved understanding of the catalytic, regulatory, and structural properties of these protein kinases. These accumulated findings provide insights into the mechanisms by which these enzymes produce their specific physiological effects and are helpful in considering the actions of other protein kinases as well.
Stochastic-algebraic wideband LSF quantization (2002)

This paper describes a fixed-rate quantizer using algebraic techniques as well as conventional stored codebooks to represent the wideband line spectral frequencies (LSF). It is based on two-stage split vector quantization with random and lattice codebooks in the first and second stage, respectively. We investigate the use of variable bit allocation in lattice quantization in order to capture outliers and reduce the overload distortion in spectral quantization, particularly for non-speech signals. Experimental results show that a variable bit allocation in split quantization yields performances slightly better than a fixed allocation at the same rate.
Diverse Effects of Nanosecond Pulsed Electric Fields on Cells and Tissues (2003)

The application of pulsed electric fields to cells is extended to include nonthermal pulses with shorter durations (10-300 ns), higher electric fields (< or =350 kV/cm), higher power (gigawatts), and distinct effects (nsPEF) compared to classical electroporation. Here we define effects and explore potential application for nsPEF in biology and medicine. As the pulse duration is decreased below the plasma membrane charging time constant, plasma membrane effects decrease and intracellular effects predominate. NsPEFs induced apoptosis and caspase activation that was calcium-dependent (Jurkat cells) and calcium-independent (HL-60 and Jurkat cells). In mouse B10-2 fibrosarcoma tumors, nsPEFs induced caspase activation and DNA fragmentation ex vivo, and reduced tumor size in vivo. With conditions below thresholds for classical electroporation and apoptosis, nsPEF induced calcium release from intracellular stores and subsequent calcium influx through store-operated channels in the plasma membrane that mimicked purinergic receptor-mediated calcium mobilization. When nsPEF were applied after classical electroporation pulses, GFP reporter gene expression was enhanced above that observed for classical electroporation. These findings indicate that nsPEF extend classical electroporation to include events that primarily affect intracellular structures and functions. Potential applications for nsPEF include inducing apoptosis in cells and tumors, probing signal transduction mechanisms that determine cell fate, and enhancing gene expression.
Architecture and IC implementation of a digital VRM controller (2002)

This paper develops the architecture of a digital PWM controller for application in multi-phase voltage regulation modules (VRMs) with passive current sharing. In this context, passive current sharing and VRM transient response are analyzed. A scheme for sensing a combination of the VRM output voltage and output current with a single low-resolution windowed analog-to-digital converter (ADC) is proposed. The architecture and IC implementation of a digital PWM (DPWM) generation module, using a ring-oscillator-MUX scheme, is discussed. Experimental results from a prototype VRM and a partial controller IC implementation are presented.
Flavobacterium heparinum 3‐O‐sulphatase for N‐substituted glucosamine 3‐O‐sulphate (1985)

A novel bacterial sulphatase has been discovered in an extract of Flavobacterium heparinum. The enzyme hydrolyses the 3-O-sulphate from 2-deoxy-2-sulphamido-3-O-sulpho-D-glucose and 2-acetamido-2-deoxy-3-O-sulpho-D-glucose. The activity was purified 10 800-fold by chromatography successively on CM-Sepharose CL-6B, hydroxyapatite, taurine-Sepharose CL-4B and CM-Sepharose CL-6B. Sodium dodecylsulphate/polyacrylamide gel electrophoresis showed the enzyme to be homogeneous and of relative molecular mass 56 000. Two novel assays were developed using 2-[14C]acetamido-2-deoxy-3-O-sulpho-D-glucose and 2-deoxy-2-sulphamido-3-O-sulpho-D-glucose as respective substrates. The purified 3-O-sulphatase was shown to be free of all other known heparin-degrading enzymes. Optimal activity was at pH 7.5 for the disulphated substrate and pH 8.0 for the N-acetylated substrate. Enzyme activity was virtually unaffected by Na+, K+ or Mg2+ ions. A 1.2-fold enhancement of activity was effected by 0.002 mol dm-3 Ca2+. Inorganic phosphate and sulphate inhibited 3-O-sulphatase activity. The Km value of the N-acetylated substrate was determined to be 42 mumol dm-3. No activity was detected with 2-amino-2-deoxy-3-O-sulpho-D-glucose.
The Pepper Transcription FactorCaPF1Confers Pathogen and Freezing Tolerance in Arabidopsis (2004)

An ERF/AP2-type transcription factor (CaPF1) was isolated by differential-display reverse transcription-PCR, following inoculation of the soybean pustule pathogen Xanthomonas axonopodis pv glycines 8ra, which induces hypersensitive response in pepper (Capsicum annuum) leaves. CaPF1 mRNA was induced under conditions of biotic and abiotic stress. Higher levels of CaPF1 transcripts were observed in disease-resistant tissue compared with susceptible tissue. CaPF1 expression was additionally induced using various treatment regimes, including ethephon, methyl jasmonate, and cold stress. To determine the role of CaPF1 in plants, transgenic Arabidopsis and tobacco (Nicotiana tabacum) plants expressing higher levels of CaPF1 were generated. Gene expression analyses of transgenic Arabidopsis and tobacco revealed that the CaPF1 level in transgenic plants affects expression of genes that contain either a GCC or a CRT/DRE box in their promoter regions. Furthermore, transgenic Arabidopsis plants expressing CaPF1 displayed tolerance against freezing temperatures and enhanced resistance to Pseudomonas syringae pv tomato DC3000. Disease tolerance was additionally observed in CaPF1 transgenic tobacco plants. The results collectively indicate that CaPF1 is an ERF/AP2 transcription factor in hot pepper plants that may play dual roles in response to biotic and abiotic stress in plants.
Docetaxel (Taxotere)-based chemotherapy for hormone-refractory and locally advanced prostate cancer. (1999)

Treatment of hormone-refractory prostate cancer (HRPC) historically has shown limited efficacy. However, taxane-based chemotherapy regimens recently have demonstrated more promising results. Several groups have reported significant efficacy and minimal toxicity in patients with hormone-refractory disease receiving estramustine plus docetaxel (Taxotere; Rhône-Poulenc Rorer, Collegeville, PA). Others have demonstrated single-agent activity of platinum compounds in HRPC. Therefore, the combination of estramustine, docetaxel, and carboplatin is currently being tested in two separate trials of HRPC. The first is a Dana-Farber/Partners Cancer Care phase I study of estramustine, carboplatin, and escalating doses of weekly docetaxel. The second study is a Cancer and Leukemia Group B multicenter phase II study evaluating the combination of estramustine, docetaxel, carboplatin, and granulocyte colony-stimulating factor. The promise of taxane-based regimens in the treatment of hormone-refractory disease has led to consideration of treating patients at high risk for developing metastatic disease earlier in their clinical course. At Dana-Farber/ Partners Cancer Care, we are evaluating neoadjuvant weekly docetaxel alone followed by surgery in patients with high-risk localized prostate cancer using pathologic response as the primary end point. Adding carboplatin to the active combination of estramustine and docetaxel may improve the response rate in HRPC. Furthermore, the use of promising chemotherapy agents earlier in high-risk localized disease may improve clinical outcomes in these patients by decreasing their risk for systemic relapse.
Rigid Molecular Tripod with an Adamantane Framework and Thiol Legs. Synthesis and Observation of an Ordered Monolayer on Au(111) (2006)

Tripod-shaped trithiols 1-3, containing CH2SH groups at the three bridgehead positions of the adamantane framework and a halogen-containing group [Br (1), p-BrC6H4 (2), or p-IC6H4 (3)] at the fourth bridgehead, were synthesized, and self-assembled monolayers (SAMs) were prepared on atomically flat Au111 surfaces. The three-point chemisorption of these tripods was confirmed by polarization modulation infrared reflection absorption spectroscopy, which showed the absence of a S-H stretching band. Scanning tunneling microscopy of the SAM of 1 exhibited a hexagonal arrangement of the adsorbed molecule with a lattice constant of 8.7 angstroms. A unidirectionally oriented, head-to-tail array of 1, which allows the close approach of neighboring molecules, is proposed as a reasonable model of the two-dimensional crystal, where the adsorbed sulfur atoms form a quasi-(radical3 x radical3)R30 degrees lattice. The charge of the electrochemical reductive desorption of the SAM of 1 was in good agreement with the expected surface coverage, while the SAMs of 2 and 3 showed somewhat less (ca. 70%) charge. The large negative reduction peak potentials, observed for the SAM of 1, are taken to indicate a tight anchoring of this tripod by three sulfur atoms.
Silicon Photonic Segmented Modulator-Based Electro-Optic DAC for 100 Gb/s PAM-4 Generation (2015)

We report on the design and characterization of a silicon-on-insulator traveling-wave multi-electrode Mach-Zehnder modulator (MZM). The 2-bit electro-optic (EO) digital-to-analog converter is formed by dividing a series push-pull MZM into two segments, one for each bit. The EO bandwidth of the longer segment of the MZM is measured to be 48 GHz at 0 V reverse bias. We operate the device at speeds up to 50 GBd to create a four-level pulse amplitude modulation signal, and thus generating 100 Gb/s on a single wavelength without signal processing at the transmitter or the receiver. The pre-forward error correction (FEC) bit error rate is estimated to be lower than the hard-decision FEC threshold of 3.8 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> over 1 km of standard single-mode fiber, and thus leading to error-free transmission at 100 Gb/s.
Association of Polymerase e–Mutated and Microsatellite-Instable Endometrial Cancers With Neoantigen Load, Number of Tumor-Infiltrating Lymphocytes, and Expression of PD-1 and PD-L1 (2015)

Polymerase e-mutated and MSI ECs are associated with high neoantigen loads and number of TILs, which is counterbalanced by overexpression of PD-1 and PD-L1. Polymerase e-mutated and MSI EC tumors may be excellent candidates for PD-1-targeted immunotherapies.
Immunocytochemical localization of APUD cells in the hypothalamus of the grass parakeet (Melopsittacus undulatus) and the lizard (Varanus exanthematicus) (1995)

We investigated the localization of APUD (amine content and amine precursor uptake and decarboxylation) cells and tyrosine hydroxylase (TH)-negative, aromatic L-amino acid decarboxylase (AADC)-positive neurons (D neurons) in the hypothalamus of the bird (Melopsittacus undulatus) and the lizard (Varanus exanthematicus), and compared the differences between the two species. L-DOPA was demonstrated in the paraventricular organ (PVO) which is a characteristic region in the hypothalamus of the bird and the lizard. In the PVO of the grass parakeet, there were a small number of dopamine neurons in addition to APUD cells. However, in the PVO of the lizard, there were APUD cells but no dopamine neurons. Furthermore, TH-negative, AADC-positive neurons (D neurons) were found in the medial part of nucleus arcuatus of the bird, but not of the lizard
Novel bacteriophage lambda cloning vector. (1980)

A simple method for generating phage collections representing eukaryotic genomes has been developed by using a novel bacteriophage lambda vector, lambda 1059. The phage is a BamHI substitution vector that accommodates DNA fragments 6-24 kilobases long. Production of recombinants in lambda 1059 requires deletion of the lambda red and gamma genes. The recombinants are therefore spi- and may be separated from the spi+ vector phages by plating on strains lysogenic for bacteriophage P2. Random fragments suitable for insertion into lambda 1059 are obtained by partial digestion of high molecular weight eukaryotic DNA with Sau3a. This restriction enzyme cleaves at the sequence G-A-T-C and leaves a 5'-tetranucleotide "sticky end." Because G-A-T-C extensions are also produced by BamHI cleavage, these fragments may be annealed directly to BamHI-cleaved lambda 1059. By using these methods, a set of clones covering the entire Caenorhabditis elegans genome was constructed. DNA segments which include the unc-54 myosin heavy chain gene have been isolated from this collection.
New developments in the diagnosis and management of cardiac allograft vasculopathy. (1995)

The major cause of late death in cardiac transplant recipients is cardiac allograft vasculopathy, also referred to as cardiac transplant atherosclerosis, which occurs in as many as 45% of transplant recipients who survive longer than 1 year. It differs from typical atherosclerosis in that intimal hyperplasia is concentric and diffuse, the internal elastic lamina remains intact, calcification is rare, and the disease tends to develop rapidly. Intravascular ultrasound and coronary angioscopy are more sensitive diagnostic measures of cardiac allograft vasculopathy than is coronary angiography. Although retransplantation at present seems to be the only definitive therapy for cardiac allograft vasculopathy, it has shown only fair results. Recent studies have suggested that calcium entry blockers and angiotensin-converting enzyme inhibitors may play a beneficial role in delaying the progression of cardiac allograft vasculopathy.
The Influence ofHLAGenotype on AIDS (2003)

Genetic resistance to infectious diseases is likely to involve a complex array of immune-response and other genes with variants that impose subtle but significant consequences on gene expression or protein function. We have gained considerable insight into the genetic determinants of HIV-1 disease, and the HLA class I genes appear to be highly influential in this regard. Numerous reports have identified a role for HLA genotype in AIDS outcomes, implicating many HLA alleles in various aspects of HIV disease. Here we review the HLA associations with progression to AIDS that have been consistently affirmed and discuss the underlying mechanisms behind some of these associations based on functional studies of immune cell recognition.
MUC1-C Oncoprotein Blocks Terminal Differentiation of Chronic Myelogenous Leukemia Cells by a ROS-Mediated Mechanism (2011)

Chronic myelogenous leukemia (CML) inevitably progresses to a blast phase by mechanisms that are not well understood. The MUC1-C oncoprotein is expressed in CML blasts but not chronic phase cells. The present studies demonstrate that treatment of KU812 and K562 CML cells with a cell-penetrating MUC1-C inhibitor, designated GO-203, is associated with increases in reactive oxygen species (ROS) and depletion of glutathione. GO-203 treatment resulted in the complete downregulation of Bcr-Abl expression and induced cell cycle arrest by a ROS-mediated mechanism that was blocked by the antioxidant N-acetylcysteine. Progression of CML to blast crisis has been linked to dysregulation of Wnt/β-catenin signaling and an arrest of differentiation. The present results show that inhibition of MUC1-C induces ROS-mediated suppression of β-catenin expression and induction of a differentiated myeloid phenotype. Our studies also show that GO-203 treatment is associated with ROS-induced decreases in ATP and loss of survival by late apoptosis/necrosis. These findings demonstrate that inhibition of the MUC1-C oncoprotein in CML cells disrupts redox balance and thereby 1) downregulates expression of both Bcr-Abl and β-catenin and 2) induces terminal myeloid differentiation by ROS-mediated mechanisms.
Predictors of morbidity and mortality in contemporary Fontan patients: results from a multicenter study including cardiopulmonary exercise testing in 321 patients (2010)

on short-term follow-up, most parameters of CPET are associated with increased risk of hospitalization but not death or transplantation in contemporary Fontan patients. Only decreased heart rate reserve and a history of clinically relevant arrhythmia, atriopulmonary/-ventricular Fontan, and/or heart failure requiring diuretic therapy are associated with poor prognosis, potentially identifying patients requiring medical and/or surgical attention.
Structural and Mechanistic Insights into NDM-1 Catalyzed Hydrolysis of Cephalosporins (2014)

Cephalosporins constitute a large class of β-lactam antibiotics clinically used as antimicrobial drugs. New Dehli metallo-β-lactamase (NDM-1) poses a global threat to human health as it confers on bacterial pathogen resistance to almost all β-lactams, including penicillins, cephalosporins, and carbapenems. Here we report the first crystal structures of NDM-1 in complex with cefuroxime and cephalexin, as well as NMR spectra monitoring cefuroxime and cefixime hydrolysis catalyzed by NDM-1. Surprisingly, cephalosporoate intermediates were captured in both crystal structures determined at 1.3 and 2.0 Å. These results provide detailed information concerning the mechanism and pathways of cephalosporin hydrolysis. We also present the crystal structure and enzyme assays of a D124N mutant, which reveals that D124 most likely plays a more structural than catalytic role.