gebhart/patrepeval huggingface dataset:
Analysis of Capsid Formation of Human Polyomavirus JC (Tokyo-1 Strain) by a Eukaryotic Expression System: Splicing of Late RNAs, Translation and Nuclear Transport of Major Capsid Protein VP1, and Capsid Assembly (2000)

Human polyomavirus JC (JCV) can encode the three capsid proteins VP1, VP2, and VP3, downstream of the agnoprotein in the late region. JCV virions are identified in the nucleus of infected cells. In this study, we have elucidated unique features of JCV capsid formation by using a eukaryotic expression system. Structures of JCV polycistronic late RNAs (M1 to M4 and possibly M5 and M6) generated by alternative splicing were determined. VP1 would be synthesized from M2 RNA, and VP2 and VP3 would be synthesized from M1 RNA. The presence of the open reading frame of the agnoprotein or the leader sequence (nucleotides 275 to 409) can decrease the expression level of VP1. VP1 was efficiently transported to the nucleus in the presence of VP2 and VP3 but distributed both in the cytoplasm and in the nucleus in their absence. Mutation analysis indicated that inefficiency in nuclear transport of VP1 is due to the unique structure in the N-terminal sequence, KRKGERK. Within the nucleus, VP1 was localized discretely and identified as speckles in the presence of VP2 and VP3 but distributed diffusely in their absence. These results suggest that VP1 was efficiently transported to the nucleus and localized in the discrete subnuclear regions, possibly with VP2 and VP3. By electron microscopy, recombinant virus particles were identified in the nucleus, and their intranuclear distribution was consistent with distribution of speckles. This system provides a useful model with which to understand JCV capsid formation and the structures and functions of the JCV capsid proteins.
The Dopamine D<sub>3</sub>Receptor Is Part of a Homeostatic Pathway Regulating Ethanol Consumption (2006)

We recently identified a homeostatic pathway that inhibits ethanol intake. This protective pathway consists of the scaffolding protein RACK1 and brain-derived neurotrophic factor (BDNF). RACK1 translocates to the nucleus after exposure of neurons to ethanol and increases expression of BDNF (McGough et al., 2004). We also found that increasing the levels of BDNF via systemic administration of RACK1 expressed as a Tat-fusion protein (Tat-RACK1) reduces ethanol consumption, whereas reduction of BDNF levels augments this behavior (McGough et al., 2004). Based on these results, we hypothesized that activation of the BDNF receptor TrkB is necessary for the effects of BDNF on ethanol intake and that gene products downstream of BDNF negatively regulate ethanol consumption. Here, we show that inhibition of the BDNF receptor TrkB increases voluntary ethanol consumption in wild-type mice but not in mice lacking one copy of the BDNF gene (BDNF(+/-)). We also find that increases in the levels of BDNF, mediated by ethanol or RACK1, lead to increased dorsal striatal levels of the dopamine D3 receptor (D3R), a gene downstream of BDNF, via activation of the TrkB receptor. Finally, we show that the Tat-RACK1-mediated reduction of ethanol consumption is attenuated by coinjection with either the Trk inhibitor K252a or the dopamine D3R-prefering antagonist U-99194A [5, 6-dimethoxy-2-(di-n-propylamino)indan], suggesting that activation of the BDNF pathway via RACK1 leads to increased expression of the dopamine D3R, which in turn mediates the attenuation of ethanol consumption.
Powers of tensors and fast matrix multiplication (2014)

This paper presents a method to analyze the powers of a given trilinear form (a special kind of algebraic construction also called a tensor) and obtain upper bounds on the asymptotic complexity of matrix multiplication. Compared with existing approaches, this method is based on convex optimization, and thus has polynomial-time complexity. As an application, we use this method to study powers of the construction given by Coppersmith and Winograd [Journal of Symbolic Computation, 1990] and obtain the upper bound ω < 2.3728639 on the exponent of square matrix multiplication, which slightly improves the best known upper bound.
Cytochrome P450 enzymes in drug metabolism: Regulation of gene expression, enzyme activities, and impact of genetic variation (2013)

Cytochromes P450 (CYP) are a major source of variability in drug pharmacokinetics and response. Of 57 putatively functional human CYPs only about a dozen enzymes, belonging to the CYP1, 2, and 3 families, are responsible for the biotransformation of most foreign substances including 70-80% of all drugs in clinical use. The highest expressed forms in liver are CYPs 3A4, 2C9, 2C8, 2E1, and 1A2, while 2A6, 2D6, 2B6, 2C19 and 3A5 are less abundant and CYPs 2J2, 1A1, and 1B1 are mainly expressed extrahepatically. Expression of each CYP is influenced by a unique combination of mechanisms and factors including genetic polymorphisms, induction by xenobiotics, regulation by cytokines, hormones and during disease states, as well as sex, age, and others. Multiallelic genetic polymorphisms, which strongly depend on ethnicity, play a major role for the function of CYPs 2D6, 2C19, 2C9, 2B6, 3A5 and 2A6, and lead to distinct pharmacogenetic phenotypes termed as poor, intermediate, extensive, and ultrarapid metabolizers. For these CYPs, the evidence for clinical significance regarding adverse drug reactions (ADRs), drug efficacy and dose requirement is rapidly growing. Polymorphisms in CYPs 1A1, 1A2, 2C8, 2E1, 2J2, and 3A4 are generally less predictive, but new data on CYP3A4 show that predictive variants exist and that additional variants in regulatory genes or in NADPH:cytochrome P450 oxidoreductase (POR) can have an influence. Here we review the recent progress on drug metabolism activity profiles, interindividual variability and regulation of expression, and the functional and clinical impact of genetic variation in drug metabolizing P450s.
Solubility of <i>n</i>-Butane in Athabasca Bitumen and Saturated Densities and Viscosities at Temperatures Up to 200°C (2016)

Summary The steam- and/or solvent-based recovery processes are efficient methods for recovery of heavy and extraheavy oils. The performance of these techniques depends on the amount of solvent dissolved in the oil and the variation of oil viscosity with temperature. Thus, full understanding of the quantitative effects of the solvent on heavy-oil viscosity and phase behavior is crucial for feasibility studies, design, and prediction of field-scale processes. Phase-behavior study of bitumen diluted with heavy hydrocarbon solvents, such as butane and pentane, has gained less attention in recent years. These solvents, as good candidates for recently developed recovery methods such as expanding solvent steam-assisted gravity drainage (ES-SAGD), could provide promising oil-production rates. Thus, the aim of this research is the development of an understanding of the phase behavior of n-butane/Athabasca-bitumen mixtures. It includes both experimental and modeling studies of solubilities and saturated liquid densities and viscosities over wide ranges of temperatures (up to 200 °C) and pressures (up to 8 MPa). Experimental results indicate that the dissolved n-butane in bitumen leads to a significant oil-viscosity reduction, and the effect is more pronounced at lower temperatures and/or higher pressures. The modeling results show that the measured solubilities are adequately represented by the Peng-Robinson equation of state (EOS) with an average absolute relative deviation (AARD) of 9.7%. The saturated liquid densities are also correlated with both the EOS and the effective liquid-density approach with 0.86 and 0.55% AARDs, respectively. The viscosity data are reasonably matched with Pedersen corresponding state.
Acquisition of Pseudonoise Signals by Sequential Estimation (1965)

A new method of acquisition of pseudonoise signals is described. This method is based on sequential estimation of the present state of an incoming pseudonoise signal by examining a small number of input bits. Performance of the sequential estimation system is compared with the stepping correlation system, and significant improvement of acquisition time is shown for signal-to-noise ratios down to approximately -15 dB. The system also automatically gives shorter acquisition times for improved signal-to-noise ratios. Experimental results are included which verify the analytical results. In particular an average acquisition time of 74 ms is demonstrated for a -10 dB signal-to-noise ratio using a pseudonoise signal suitable for high accuracy range measurement to 3300 km unambiguous range.
Use of Phosphorus Pentoxide. Preparation of Half-esters through Selective Esterification (1987)

Chemistry Department, Jadavpur University, Calcutta-700 032 <em>Manuscript received 31 January 1986, revised 13 August 1986, accepted 26 November 1986</em> Methyl 2-, 3-, 4-carboxyphenylacetate and methyl 2-, 3-, 4-carboxyphenoxyacetate have been prepared through selective esterification of the aliphatic carboxylic acid function of the corresponding dicarbuxy lie acids using a mixture of phosphorus pen­toxide (1 part), anhydrous cooper sulphate (5 parts) and anhydrous sodium sulphate (3 parts). All the isomeric half-esters have been prepared through partial hydrolysis of the corresponding dimethylesters.
Towards an Ontology-based Security Management (2006)

The paramount complexity of enterprise in formation leads to hard-to-deal security management issues and system configurations. We present a security management framework of an arbitrary information system (IS) which builds upon knowledge-based resources, such as security ontology (SO) providing reusable security knowledge interoperability, aggregation and reasoning exploiting security knowledge from diverse sources; in addition, the separation of security requirements from their technical implementations facilitates the security management. We provide a feasible framework which links the high-level policy statements and deployable security controls and facilitates the security expert's work
A Spatial–Temporal model for grid impact analysis of plug-in electric vehicles (2013)

A Spatial–Temporal model (STM) was developed to evaluate the impact of large scale deployment of plug-in electric vehicles (EVs) on urban distribution networks. The STM runs based on the integration of power system analysis and transportation analysis. Origin–Destination (OD) analysis from intelligent transportation research was used to model the EV mobility. Based on the EV technical and market information provided by the EU MERGE project and the output of OD analysis, a Monte Carlo simulation method was developed within the STM to obtain the EV charging load of each load busbar over time. The STM aims to facilitate power system evaluation and planning, and is able to provide both average values and probabilities of nodal bus voltages and branch loadings. The STM is able to identify the critical network components that will require to be upgraded. A high customer density urban network from the United Kingdom Generic Distribution System combined with geographic information was used as a test system. Two EV charging strategies, “dumb” charging and “smart” charging, were simulated and compared under different EV penetration levels (0%, 25% and 50%) to verify the effectiveness of STM.
Bidentate Ligands by Self‐Assembly through Hydrogen Bonding: A General Room Temperature/Ambient Pressure Regioselective Hydroformylation of Terminal Alkenes (2005)

Abstract The 6‐DPPon ( 1 )/rhodium catalyst allows for the first time a room temperature/ambient pressure regioselective hydroformylation of terminal alkenes with low catalyst loadings in good activity. The generality of this catalyst under these conditions was demonstrated for a wide range of structurally diverse alkenes equipped with many important functional groups. Thus, this practical and highly selective hydroformylation protocol, which omits the need for special pressure equipment, should find wide application in organic synthesis.
Address tracing for parallel machines (1991)

Recently implemented parallel system address-tracing methods based on several metrics are surveyed. The issues specific to collection of traces for both shared and distributed memory parallel computers are highlighted. Five general categories of address-trace collection methods are examined: hardware-captured, interrupt-based, simulation-based, altered microcode-based, and instrumented program-based traces. The problems unique to shared memory and distributed memory multiprocessors are examined separately.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
QOS-Enabled Networks: Tools and Foundations (2011)

This book discusses the theory of Quality of Service (QoS) mechanisms in packet networks and shows how to apply them in practice. QOS-Enabled Networks: Tools and Foundations provides an understanding of the theory of QOS mechanisms in packet networks and how to apply them in practice. It explains QOS management features found in modern routers used by Internet Service Providers (ISP) and large companies. The goal of this book is to provide the background and tools to help network managers and engineers configure production networks for providing services with quality of service (QOS) guarante
Functionalizations of Conducting Polymers Toward Molecular Devices (1992)

Abstract There are many molecules and they have their own specific functions. For their exploitation through materialization, conducting polymers are considered as a suitable matrix, for its electron conductive property is to be used to prove the electronic structure and state which relate directly functions of these molecules. To construct molecular device, materialization of those functional molecules and the ultra-fine fabrication of the conducting polymer are essential problems. The concept of the functional molecular material in which molecular device is to be included is illustrated in the following scheme.
High speed pattern matching for deep packet inspection (2009)

In communication equipments, pattern matching techniques are used to handle various requirements, such as network security, QoS and so on. This paper presents a pattern matching technique to process multiple characters at a single clock cycle. And this paper presents the way to find a particular pattern from communication packets using TCAMs.
A flexible parallel architecture adapted to block-matching motion-estimation algorithms (1996)

This paper describes a novel architecture that offers the flexibility of implementing widely varying motion-estimation algorithms. To achieve real-time performance, we employ multiple processing elements (PE's) which communicate with multiple memory banks via a multistage interconnection network. Three different block-matching algorithms-full search, three-step search, and conjugate-direction search-have been mapped onto this architecture to illustrate its programmability. We schedule the desired operations and design the required data-flow in such a way that processor utilization is high and memory bandwidth is at a feasible level. The details regarding the flow of the pixel data and the scheduling and allocation of the desired ALU operations (which pixels are processed on which processors in which clock cycles) are described in the paper. We analyze the performance of the proposed architecture for several different interconnection networks and data-memory organizations.
Optical fiber up-tapers modeling and performance analysis (1989)

An extensive CRAY-computer-based simulator using the propagating beam method for the accurate evaluation of the performance of optical fiber up-tapers is discussed. Up-tapers with and without straight tips and with arbitrary index profiles and tapering functions can be evaluated. Results of the evaluation of various 1.5-cm-long optical up-tapers followed by a straight tip and drawn from special preforms with various index profiles are quite encouraging. They show that beam expansion ratios in the range of 5-10 are feasible with a corresponding insertion loss per taper of less than 0.01-0.025 dB. Tapers shorter than 1.5 cm with insertion loss in the same range are also feasible but have slightly smaller beam expansion ratios.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A gallium arsenide ballistic transistor? (1986)

The authors review the work done in 1985 at the IBM Thomas J. Watson Research Center on measuring the ballistic transport of electrons in a gallium arsenide heterostructure hot-electron transistor. The device is referred to as the tunneling hot-electron transfer amplifier (Theta). The way in which the transistor functions as its own spectrometer is explained. The experimental results obtained with Theta are summarized. It was found that when no voltage is applied across the base-collector heterojunction, essentially only ballistic electrons are collected. These account for about 40% of the total number of electrons injected from the emitter at low temperatures. As the voltage across the collector is increased positively, up to 75% of them are collected.
Binding of Glycyrrhetinic Acid to Kidney Mineralocorticoid and Glucocorticoid Receptors<sup>1</sup> (1975)

Whether the mineralocorticoid effect of glycyrrhetinic acid is mediated by the adrenal glands or is due to a direct action on the renal tubule remains controversial. The affinity of glycyrrhetinic acid for mineralocorticoid receptors has been studied by several types of competition experiments. When rat kidney slices were incubated with 2 times 10- minus 9 M [3H]aldosterone, glycyrrhetinic acid (2 times 10- minus 5 M) was able to compete with aldosterone for the cytosolic receptor and to decrease the formation of a chromatin-[3Hi1 aldosterone-receptor complex. In cytosol, in vitro, 6 times 10- minus 4 M glycyrrhetinic acid was able to inhibit aldosterone binding by 70 percent, whereas the same dose produced only a 20 percent inhibition of dexamethasone binding. The apparent KDiss of glycyrrhetinic acid for the mineralocorticoid receptor was 2 times 10- minus 6 M. That glycyrrhetinic acid appeared to compete mainly with mineralocorticoid receptors was confirmed by sedimentation in the sucrose gradients: [3H]Aldosterone specifically bound to an 8 S peak was displaced by 5 times 10- minus 5 M glycyrrhetinic acid, whereas the [3H]dexamethasone peak was not affected by this compound. Glycyrrhizic acid showed no significant affinity for mineralocorticoid or glucocorticoid kidney receptor sites. Glycyrrhetinic acid and glycyrrhizic acid had no affinity for rat cortisol binding globulin. Glycyrrhetinic acid has a low but definite affinity for mineralocorticoid receptors and thus appears to have a direct mineralocorticoid action. The low affinity of this compound for mineralocorticoid receptors is in good agreement with the very high doses required to exhibit its biological activity.
Orally Active Osteoanabolic Agent GTDF Binds to Adiponectin Receptors, With a Preference for AdipoR1, Induces Adiponectin-Associated Signaling, and Improves Metabolic Health in a Rodent Model of Diabetes (2014)

Adiponectin is an adipocytokine that signals through plasma membrane-bound adiponectin receptors 1 and 2 (AdipoR1 and -2). Plasma adiponectin depletion is associated with type 2 diabetes, obesity, and cardiovascular diseases. Adiponectin therapy, however, is yet unavailable owing to its large size, complex multimerization, and functional differences of the multimers. We report discovery and characterization of 6-C-β-D-glucopyranosyl-(2S,3S)-(+)-5,7,3',4'-tetrahydroxydihydroflavonol (GTDF) as an orally active adiponectin mimetic. GTDF interacted with both AdipoRs, with a preference for AdipoR1. It induced adiponectin-associated signaling and enhanced glucose uptake and fatty acid oxidation in vitro, which were augmented or abolished by AdipoR1 overexpression or silencing, respectively. GTDF improved metabolic health, characterized by elevated glucose clearance, β-cell survival, reduced steatohepatitis, browning of white adipose tissue, and improved lipid profile in an AdipoR1-expressing but not an AdipoR1-depleted strain of diabetic mice. The discovery of GTDF as an adiponectin mimetic provides a promising therapeutic tool for the treatment of metabolic diseases.
The Net: progress and opportunity (1992)

article Free AccessThe Net: progress and opportunity Author: Larry Press View Profile Authors Info & Claims Communications of the ACMVolume 35Issue 12Dec. 1992 pp 21–25https://doi.org/10.1145/138859.138871Published:01 December 1992Publication History 10citation325DownloadsMetricsTotal Citations10Total Downloads325Last 12 Months26Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Potential of Anti-MUC1 Antibodies as a Targeted Therapy for Gastrointestinal Cancers (2020)

Gastrointestinal cancers (GI) account for 26% of cancer incidences globally and 35% of all cancer-related deaths. The main challenge is to target cancer specific antigens. Mucins are heavily O-glycosylated proteins overexpressed in different cancers. The transmembrane glycoprotein MUC1 is the most likeable target for antibodies, owing to its specific overexpression and aberrant glycosylation in many types of cancers. For the past 30 years, MUC1 has remained a possible diagnostic marker and therapeutic target. Despite initiation of numerous clinical trials, a comprehensively effective therapy with clinical benefit is yet to be achieved. However, the interest in MUC1 as a therapeutic target remains unaltered. For all translational studies, it is important to incorporate updated relevant research findings into therapeutic strategies. In this review we present an overview of the antibodies targeting MUC1 in GI cancers, their potential role in immunotherapy (i.e., antibody-drug and radioimmunoconjugates, CAR-T cells), and other novel therapeutic strategies. We also present our perspectives on how the mechanisms of action of different anti-MUC1 antibodies can target specific hallmarks of cancer and therefore be utilized as a combination therapy for better clinical outcomes.
The PML gene is not involved in the regulation of MHC class I expression in human cell lines (2003)

The promyelocytic leukemia gene, PML, is a growth and transformation suppressor. An additional role for PML as a regulator of major histocompatibility complex (MHC) class I antigen presentation has been proposed in a murine model, which would account for evasion from host immunity of tumors bearing malfunctioning PML, such as acute promyelocytic leukemia. Here we investigated a possible role of PML for the control MHC class I expression in human cells. PML function was perturbed in human cell lines either by PML/RAR alpha transfection or by PML- specific RNA interference. Impairment of wild-type PML function was proved by a microspeckled disassembly of nuclear bodies (NBs), where the protein is normally localized, or by their complete disappearance. However, no MHC class I down-regulation was observed in both instances. We next constructed a PML mutant, PML mut ex3, that is a human homolog of the murine PML mutant, truncated in exon 3, that was shown to down-regulate murine MHC class I. PML mut ex3 transfected in human cell lines exerted a dominant-negative effect since no PML molecules were detected in NBs but, instead, in perinuclear and cytoplasmic larger dot-like structures. Nevertheless, no down-regulation of MHC class I expression was evident. Moreover, neither transfection with PML mut ex3 nor PML-specific RNA interference affected the ability of gamma-interferon to up-regulate MHC class I expression. We conclude that, in human cell lines, PML is not involved directly in the regulation of MHC class I expression.