gebhart/patrepeval huggingface dataset:
Synthesis of Bovine Prolactin in <i>Escherichia coli</i> (1986)

Transformation of Escherichia coli cells with a recombinant plasmid (pESP4) containing a modified bovine prolactin cDNA clone in a pEMBL vector resulted in efficient expression of prolactin. The cDNA was modified by removal of a 5' nontranslated sequence as well as the sequence that specified the signal peptide of preprolactin. To achieve a high level of synthesis, a sequence of 30 nucleotides in the cDNA, which included the ATG initiation codon and the first 7 codons of mature bovine prolactin, was replaced by a chemically synthesized oligonucleotide duplex. The sequence of this duplex was chosen from the consensus sequence around the initiation codon of E. coli genes and by the amino acid sequence of the protein. Prolactin, a single-chain polypeptide of molecular weight 24,000, was identified by Coomassie Blue staining of NaDodSO4-polyacrylamide gels of total protein from transformed E. coli cells, and by reaction with specific antibody. Increased levels of expression of the hormone, corresponding to the form secreted from the pituitary, were observed in the presence of isopropyl-beta-D-thiogalactopyranoside (IPTG).
Inducible antisense RNA targeting amino acid transporter ATB<sup>0</sup>/ASCT2 elicits apoptosis in human hepatoma cells (2004)

Amino acid transporter B(0)/ASC transporter 2 (ATB(0)/ASCT2) is responsible for most glutamine uptake in human hepatoma cells. Because this transporter is not expressed in normal hepatocytes, we hypothesized that its expression is necessary for growth of human liver cancer cells. To test this hypothesis, Sloan Kettering hepatoma (SK-Hep) cells were stably transfected with an inducible 1.3-kb ATB(0)/ASCT2 antisense RNA expression plasmid under the transcriptional control of mifepristone, a synthetic steroid. Induced antisense RNA expression in monolayer cultures decreased ATB(0)/ASCT2 mRNA levels by 73% and glutamine transport rates by 65% compared with controls after 24 h, leading to a 98% decrease in cell number after 48 h. Cellular death was attributable to apoptosis based on cellular blebbing, caspase-3 activation, vital dye and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling staining, and poly-(ADP-ribose) polymerase (PARP) cleavage. Transporter knockdown also markedly increased activities of caspases-2 and -9, marginally enhanced caspase-8 activity, and dramatically increased ASCT1 mRNA levels, presumably as a futile compensatory response. Apoptosis elicited via transporter silencing was not attributable to the double-stranded RNA-dependent protein kinase R (PKR) pathway. For comparison, glutamine deprivation also caused apoptotic cell death but with slower temporal kinetics, stimulated caspases-2 and -3 but not caspases-8 or -9 activities, and led to considerable PARP cleavage. Thus ASCT2 suppression exerts proapoptotic effects transcending those of glutamine starvation alone. We conclude that ATB(0)/ASCT2 expression is necessary for SK-Hep cell growth and viability and suggest that it be further explored as a selective target for human hepatocellular carcinoma.
<i>Listeria</i> -Infected Myeloid Dendritic Cells Produce IFN-β, Priming T Cell Activation (2005)

The intracellular bacterium Listeria monocytogenes infects dendritic cells (DC) and other APCs and induces potent cell-mediated protective immunity. However, heat-killed bacteria fail to do so. This study explored whether DC differentially respond to live and killed Listeria and how this affects T cell activation. To control for bacterial number, a replication-deficient strain, Lmdd, defective in D-alanine biosynthesis, was used. We found that DC internalize both live and heat-killed Lmdd and similarly up-regulate the expression of costimulatory molecules, a necessary step for T cell activation. However, only live Lmdd-infected DC stimulate T cells to express the early activation marker CD69 and enhance T cell activation upon TCR engagement. Infection with live, but not heat-killed, Lmdd induces myeloid DC to secrete copious amounts of IFN-beta, which requires bacterial cytosolic invasion. Exposure to high concentrations of IFN-beta sensitizes naive T cells for Ag-dependent activation.
Glycogen Storage Disease in Adults (1994)

For GSD-Ia, hyperuricemia and pyelonephritis should be treated to prevent nephrocalcinosis and additional renal damage. For GSD-Ib, granulocyte-colony-stimulating factor may prevent bacterial infections. For GSD-III, more data are required to determine whether the myopathy and cardiomyopathy can be prevented. Most of the patients with GSD-I and GSD-III had 12 or more years of education and were either currently in school or employed.
Determination of the minimal clinically important difference in rheumatoid arthritis joint damage of the Sharp/van der Heijde and Larsen/Scott scoring methods by clinical experts and comparison with the smallest detectable difference (2002)

This study suggests that the SDD of the Sharp/van der Heijde method can be used as the MCID, i.e., as the threshold level for individual response criteria. The SDD of the Larsen/Scott method, however, turned out to be too insensitive to use as the threshold for individual clinically relevant change.
Multiscale estimation of regular image contours via a graph of local edgel hypotheses (1998)

The problem of estimating the regular and visible portions of the contours in an image is formulated in a probabilistic and multiscale framework. The objective is to compute a small set of polygonal lines which, with high probability, contains an approximation to every regular visible contour in the scene. These polygonal lines are represented by paths in a graph whose arcs represent local contour hypotheses. The main difficulty of this problem is that, in order to achieve high probability of accurate reconstruction according to a global metric, it is necessary to deal with a combinatorially large number of contour hypotheses. To control the complexity of the search, the notion of a compressible graph is introduced and an efficient contour estimation algorithm based on graph compression is proposed. Research supported by US Army grant DAAH04-95-1-0494, Center for Imaging Science, and MURI grant DAAH04-96-1-0445, Foundations of Performance Metrics for Object Recognition. fl 1 fl 2...
Improved correlation learning rule in continuously adapting floating-gate arrays using logarithmic pre-distortion of input and learning signals (2003)

Floating-gate pFETs can be used to implement analog signal multiplication with an adaptive analog gain, creating the possibility for compact, low-power analog adaptive filters and neural networks in VLSI. We have shown that the adaptation mechanism of this device yields a weight which is proportional to correlations between terminal voltage signals. However, the weight contains dependencies proportional to the variances of these terminal voltages as well. In addition, harmonic distortion of the input signals can mask thin correlation effect. In this paper we show how to eliminate or minimize these non-idealities through logarithmic pre-distortion of our input and learning signals as well as through the use of differential circuit structures. The result is a weight update mechanism which is closer to a pure correlation learning rule.
Flexible nanocrystalline‐titania/polyimide hybrids with high refractive index and excellent thermal dimensional stability (2010)

Abstract In this study, a novel synthetic route was developed to prepare polyimide–nanocrystalline–titania hybrid optical films with a relatively high titania content (up to 50 wt %) and thickness (20–30 μm) from soluble polyimides containing hydroxyl groups. Two series of newly soluble polyimides were synthesized from the hydroxy‐substituted diamines with various commercial tetracarboxylic dianhydrides. The hydroxyl groups on the backbone of the polyimides could provide the organic–inorganic bonding and resulted in homogeneous hybrid solutions by controlling the mole ratio of titanium butoxide/hydroxyl group. AFM, SEM, TEM, and XRD results indicated the formation of well‐dispersed nanocrystalline‐titania. The flexible hybrid films could be successfully obtained and revealed relatively good surface planarity, thermal dimensional stability, tunable refractive index, and high optical transparency. A three‐layer antireflection coating based on the hybrid films was prepared and showed a reflectance of less than 0.5% in the visible range indicated its potential optical applications. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 1433–1440, 2010
Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms (2016)

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements. Program title: RMG Catalogue identifier: AEZW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEZW_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: MIT/X11 License No. of lines in distributed program, including test data, etc.: 958681 No. of bytes in distributed program, including test data, etc.: 9495441 Distribution format: tar.gz Programming language: Python. Computer: Windows, Ubuntu, and Mac OS computers with relevant compilers. Operating system: Unix/Linux/Windows. RAM: 1 GB minimum, 16 GB or more for larger simulations Classification: 16.12. External routines: RDKit, Open Babel, DASSL, DASPK, DQED, NumPy, SciPy Nature of problem: Automatic generation of chemical kinetic mechanisms for molecules containing C, H, O, S, and N. Solution method: Rate-based algorithm adds most important species and reactions to a model, with rate constants derived from rate rules and other parameters estimated via group additivity methods. Additional comments: The RMG software package also includes CanTherm, a tool for computing the thermodynamic properties of chemical species and both high-pressure-limit and pressure-dependent rate coefficients for chemical reactions using results from quantum chemical calculations. CanTherm is compatible with a variety of ab initio quantum chemistry software programs, including but not limited to Gaussian, MOPAC, QChem, and MOLPRO. Running time: From 30 s for the simplest molecules, to up to several weeks, depending on the size of the molecule and the conditions of the reaction system chosen.
MicroRNA dysregulation in schizophrenia (2011)

Schizophrenia is a complex neuropsychiatric disorder that involves disturbances in neural circuitry and synaptic function. The exquisite network architecture and capacity for discreet post-synaptic remodeling of neurons requires coordination by an elaborate intracellular network of molecular signal transduction systems. The redundancy of these networks means that many combinations of gene variants have the potential to cause system dysfunction that manifest as related neurobehavioural syndromes. Recent investigation has revealed that posttranscriptional gene regulation and associated small non-coding microRNA (miRNA), are likely to be important factors shaping the topography of these networks. miRNA display complex temporospatial expression patterns in the mammalian brain and have the potential to regulate thousands of target genes by functioning as the specificity factor for intracellular gene-silencing machinery. They are emerging as key regulators of many neurodevelopmental and neurological processes as their dysregulation could lead to pervasive changes in the network structure during development and in the mature brain that are highly significant in the pathophysiology of schizophrenia. This review looks at mounting evidence that mature miRNA levels are altered in both the cerebral cortex and peripheral blood mononuclear cells (PBMCs) in schizophrenia. It also examines compelling evidence that the underlying miRNA biogenesis machinery and miRNA genes themselves are subject to disease-associated genetic mutation and epigenetic influence. Significantly, these changes in miRNA expression and associated machinery may represent new targets for pharmaceutical development, and the identification of miRNA signatures in PBMCs suggest that miRNA biomarkers of schizophrenia may also provide the basis for new clinical diagnostics. These developments have tremendous potential and highlight the significance of this avenue of research.
Online algorithm for identification of multiple narrowband burst-type interferers (2004)

We present an online algorithm to track multiple narrowband burst-type interferers in wideband communication systems. The arrivals/departures and the strengths of the interferers are identified with the use of HMM. This algorithm is targeted for wideband wireless systems which are overlaid on top of multiple narrowband services whose traffic can be bursty. This algorithm can be used to suppress or avoid interference for various kinds of communication systems including both single-carrier systems and multi-carrier systems such as OFDM. As an example, we apply the algorithm in a Direct-Sequence Spread-Spectrum system for interference suppression. Simulation results and analysis are presented. The simulation results show that our algorithm achieves very satisfactory performance in interference suppression compared to other NBI suppression methods in terms of both BER and robustness to the burst rate of the interferers.
Fractal properties of pulmonary blood flow: characterization of spatial heterogeneity (1990)

The heterogeneity of pulmonary blood flow was examined using a fractal analytic procedure, and the results were compared with the traditional gravitational model of flow distribution. 99mTc-labeled macroaggregate was injected intravenously at functional residual capacity in six supine anesthetized dogs. The lungs were fixed in situ and sliced in transverse sections. The slices were imaged on a planar gamma camera, and a three-dimensional array of blood flow measurements was reconstructed for each lung. Fractal analysis was used to examine the spatial heterogeneity or RDs (relative dispersion = SD/mean) as a function of the number of pieces into which the flow array was subdivided. RDs was fractal and could be characterized by a fractal dimension (Ds) of 1.09 +/- 0.02, where a Ds of 1.0 reflects homogeneous flow and 1.5 indicates a random flow distribution. The data fit the fractal model exceptionally well with an average r = 0.98. RDs was examined in gravitational and isogravitational planes and as expected was greatest in the gravitational direction. However, the difference was small, suggesting that gravitation plays a secondary role to an underlying process producing heterogeneity. Within the limits of resolution attained by this study (piece volumes greater than 0.25 cm3), the heterogeneity of pulmonary blood flow is well characterized by a fractal model.
Immobilization of Radioactive Wastes in Hydrothermal Synthetic Rock (1984)

KEYWORDS: hydrothermal hot-pressinghydrothermal synthetic rocklithificationimmobilizationradioactive wastessilica powdermechanical strength
Simulation, Animation and Visualization of Seaport Operations (1998)

PORTSIM is a seaport simulation model that computes throughput capability and determines resource utilization at a high level of detail. The ability to animate and to visualize these seaport processes will greatly enhance PORTSIM's capability and will allow planners to see operational constraints and bottlenecks, as opposed to inferring operational limitations through reviewing the existing PORTSIM statistical reports, graphs and charts. The animation and visualization will aid in the validation of the simulation processes and will provide a mechanism for planners to verify that the simulation executes in the desired manner. Playback and callback modes of animation and visualization will be described, and technical challenges to both modes of execution will be addressed.
On Maps of Period 2 on Prime and Semiprime Rings (2014)

A map f of the ring R into itself is of period 2 if<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:msup><mml:mrow><mml:mi>f</mml:mi></mml:mrow><mml:mrow><mml:mn fontstyle="italic">2</mml:mn></mml:mrow></mml:msup><mml:mfenced separators="|"><mml:mrow><mml:mi>x</mml:mi></mml:mrow></mml:mfenced><mml:mo>=</mml:mo><mml:mi>x</mml:mi></mml:math>for all<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mi>x</mml:mi><mml:mo>∈</mml:mo><mml:mi>R</mml:mi></mml:math>; involutions are much studied examples. We present some commutativity results for semiprime and prime rings with involution, and we study the existence of derivations and generalized derivations of period 2 on prime and semiprime rings.
Assembly of Arenavirus Envelope Glycoprotein GPC in Detergent-Soluble Membrane Microdomains (2009)

The family Arenaviridae includes a number of highly pathogenic viruses that are responsible for acute hemorrhagic fevers in humans. Genetic diversity among arenavirus species in their respective rodent hosts supports the continued emergence of new pathogens. In the absence of available vaccines or therapeutic agents, the hemorrhagic fever arenaviruses remain a serious public health and biodefense concern. Arenaviruses are enveloped virions that assemble and bud from the plasma membrane. In this study, we have characterized the microdomain organization of the virus envelope glycoprotein (GPC) on the cell surface by using immunogold electron microscopy. We find that Junín virus (JUNV) GPC clusters into discrete microdomains of 120 to 160 nm in diameter and that this property of GPC is independent of its myristoylation and of coexpression with the virus matrix protein Z. In cells infected with the Candid#1 strain of JUNV, and in purified Candid#1 virions, these GPC microdomains are soluble in cold Triton X-100 detergent and are thus distinct from conventional lipid rafts, which are utilized by numerous other viruses for assembly. Virion morphogenesis ultimately requires colocalization of viral components, yet our dual-label immunogold staining studies failed to reveal a spatial association of Z with GPC microdomains. This observation may reflect either rapid Z-dependent budding of virus-like particles upon coassociation or a requirement for additional viral components in the assembly process. Together, these results provide new insight into the molecular basis for arenavirus morphogenesis.
Effects of tunicamycin on B16 metastatic melanoma cell surface glycoproteins and blood-borne arrest and survival properties. (1981)

The role of cell surface glycoproteins in determining in vivo blood-borne arrest and survival characteristics of murine melanoma sublines of low (B16-F1) or high (B16-F10) potential to form experimental lung metastases after injection i.v. was assessed after inhibiting tumor cell protein glycosylation with tunicamycin. Incubation of B16-F1 or B16-F10 cells with 0.5 micrograms (or above) tunicamycin per ml for 12 to 36 hr inhibited significantly lung tumor colony formation. Examination of B16 cells in the presence of 0.5 micrograms drug per ml indicated that complex oligosaccharide synthesis was inhibited greater than 90%, while protein synthesis remained at about 50% of the control levels. Tunicamycin induced morphological changes in B16-F1 and B16-F10 cells such as cellular rounding. Cell growth was also inhibited by tunicamycin. These effects were reversible, and B16 cells recovered their normal morphologies and growth rates within 24 hr after removal of the drug. Exposed cell surface protein analyzed by lactoperoxidase-catalyzed 125I iodination-sodium dodecyl sulfate-polyacrylamide gel electrophoresis-autoradiography showed few changes after tunicamycin treatment; however, sialogalactoproteins (detected by the binding of 125I-labeled R. communis agglutinin I to polyacrylamide gels containing desialized B16 cell surface components) were reduced dramatically by the drug. The adhesive properties of untreated and tunicamycin-treated B16 cells were assessed by the binding of 51Cr-labeled B16 cells to endothelial cell monolayers. Tunicamycin-treated B16-F1 and B16-F10 cells adhered at lower rates to endothelial cells such that after 24 to 36 hr of drug (0.5 micrograms/ml) treatment adhesion was almost completely blocked, suggesting that tunicamycin-induced cell surface glycoprotein changes in B16 melanoma cells may interfere with tumor cell-host cell interactions that lead to arrest and survival of blood-borne malignant cells.
Level Anti‐Crossings are a Key Factor for Understanding <i>para</i>‐Hydrogen‐Induced Hyperpolarization in SABRE Experiments (2013)

Various hyperpolarization methods are able to enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) by several orders of magnitude. Among these methods are para-hydrogen-induced polarization (PHIP) and signal amplification by reversible exchange (SABRE), which exploit the strong nuclear alignment of para-hydrogen. Several SABRE experiments have been reported but, so far, it has not been possible to account for the experimentally observed sign and magnetic-field dependence of substrate polarization. Herein, we present an analysis based on level anti-crossings (LACs), which provides a complete understanding of the SABRE effect. The field-dependence of both net and anti-phase polarization is measured for several ligands, which can be reproduced by the theory. The similar SABRE field-dependence for different ligands is also explained. In general, the LAC concept allows complex spin dynamics to be unraveled, and is crucial for optimizing the performance of novel hyperpolarization methods in NMR and MRI techniques.