gebhart/patrepeval huggingface dataset:
A potent broad-spectrum protective human monoclonal antibody crosslinking two haemagglutinin monomers of influenza A virus (2015)

Effective annual influenza vaccination requires frequent changes in vaccine composition due to both antigenic shift for different subtype hemagglutinins (HAs) and antigenic drift in a particular HA. Here we present a broadly neutralizing human monoclonal antibody with an unusual binding modality. The antibody, designated CT149, was isolated from convalescent patients infected with pandemic H1N1 in 2009. CT149 is found to neutralize all tested group 2 and some group 1 influenza A viruses by inhibiting low pH-induced, HA-mediated membrane fusion. It promotes killing of infected cells by Fc-mediated antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity. X-ray crystallographic data reveal that CT149 binds primarily to the fusion domain in HA2, and the light chain is also largely involved in binding. The epitope recognized by this antibody comprises amino-acid residues from two adjacent protomers of HA. This binding characteristic of CT149 will provide more information to support the design of more potent influenza vaccines.
A human purine nucleoside phosphorylase deficiency caused by a single base change. (1987)

Purine nucleoside phosphorylase (PNP) deficiency in humans is associated with a severe defect in T-lymphocyte function. The mutant gene was cloned from one PNP-deficient patient who was the offspring of a consanguineous mating. The exons and intron/exon boundaries of the mutant PNP gene were sequenced and compared with the wild-type cDNA sequence. A single base difference was found in the coding region of the mutant gene, a G to A transition in the third exon. This single base mutation alters the codon at position 89 from Glu to Lys, a result which is consistent with previously published peptide mapping data. The patient was demonstrated to be autozygous for the single base mutation on the basis of hybridization of synthetic oligomers to genomic DNA digests. A mammalian expression vector was constructed containing the entire mutant gene under the transcriptional regulation of its own promoter. In another construction, the single base mutation was reverted to the wild-type sequence by in vitro mutagenesis. An isoelectric focusing gel containing extracts of the cells transfected with the mutant and reverted PNP gene was stained histochemically for PNP activity. The proteins from a similar gel were blotted on a nitrocellulose membrane, and immunoreactive human PNP protein was visualized. Cells transfected with the mutant gene contained no human PNP activity, but expressed immunoreactive PNP which focused at an abnormally alkaline pI. Cells transfected with the reverted gene expressed human PNP activity which co-focused with human PNP from a HeLa cell control, proving that the observed single base change was responsible for the loss of catalytic function.
Sequence Information from 42−108-mer DNAs (Complete for a 50-mer) by Tandem Mass Spectrometry (1996)

Complete sequence information for an “unknown” 50-mer DNA and extensive sequence verification for another 50-mer and 42-, 51-, 55-, 60-, 72-, 100-, and 108-mer DNAs is obtained by electrospray ionization/Fourier transform mass spectrometry that supplies 10−100× higher accuracy and resolving-power data using nozzle-skimmer (NS), collisionally activated, and infrared multiphoton dissociation (IRMPD). In addition to the previously recognized 3‘- and 5‘-terminal (w and a) ions, internal ions (i) and MS/MS/MS of fragment ions provide unique structural information across the DNA. NS dissociation can also yield other new backbone cleavages (forming b, c, d, and r ions) that provide extensive 5‘-end information. These spectra indicate that loss of the base T rarely triggers formation of w, a, or i fragment ions, a correlation of further sequencing utility. Point mutation screening is demonstrated using a modified 50-mer unknown; a 9.04 (theory 9.01) decrease in the molecular weight (Mr) value indicates A → T, while three IRMPD fragment ions pinpoint this mutation at base 27. Introduction (measurement time <1 min) of 8 × 10-16 mol of the 50-mer gave an Mr value with only a 0.2 error.
Estimation of maximum interference-free power level for opportunistic spectrum access (2009)

We consider a scenario in which frequency agile radios opportunistically share a fixed spectrum resource with a set of primary nodes. We develop a collaborative scheme for a group of frequency agile radios to estimate the maximum power at which they can transmit on a given frequency channel, without causing harmful interference to the primary receivers. The proposed scheme relies on signal strength measurements taken by a group of frequency agile radios, which are then used by a target node to characterize the spatial size of its perceived spectrum hole in terms of the maximum permissible transmit power. We derive an approximation to the maximum interference-free transmit power using the Cramer-Rao bound on localization accuracy. We present numerical results to demonstrate the effectiveness of the proposed scheme under a variety of scenarios.
Reduced-complexity equalization techniques for broadband wireless channels (1997)

This paper presents reduced-complexity equalization techniques for broadband wireless communications, both outdoors (fixed or mobile wireless asynchronous transfer mode (ATM) networks) and indoors [high-speed local-area networks (LANs)]. The two basic equalization techniques investigated are decision-feedback equalization (FE) and delayed decision-feedback sequence estimation (DDFSE). We consider the use of these techniques in highly dispersive channels, where the impulse response can last up to 100 symbol periods. The challenge is in minimizing the complexity as well as providing fast equalizer start-up for transmissions of short packets. We propose two techniques which, taken together, provide an answer to this challenge. One is an open-loop timing recovery approach (for both DFE and DDFSE) which can be executed prior to equalization; the other is a modified DFE structure for precanceling postcursors without requiring training of the feedback filter. Simulation results are presented to demonstrate the feasibility of the proposed techniques for both indoor and outdoor multipath channel models. The proposed open-loop timing recovery technique plays a crucial role in maximizing the performance of DFE and DDFSE with short feedforward spans (the feedforward section of DDFSE is a Viterbi sequence estimator). A feedforward span of only five is quite sufficient for channels with symbol rate-delay spread products approaching 100. The modified DFE structure speeds up the training process for these channels by 10-20 times, compared to the conventional structure without postcursor precancellation. The proposed techniques offer the possibility of practical equalization for broadband wireless systems.
Understanding Ionic Liquids at the Molecular Level: Facts, Problems, and Controversies (2007)

Ionic liquids (ILs) are organic salts with melting points near room temperature (or by convention below 100 degrees C). Recently, their unique materials and solvent properties and the growing interest in a sustainable, "green" chemistry has led to an amazing increase in interest in such salts. A huge number of potential cation and anion families and their many substitution patterns allows the desired properties for specific applications to be selected. Because it is impossible to experimentally investigate even a small fraction of the potential cation-anion combinations, a molecular-based understanding of their properties is crucial. However, the unusual complexity of their intermolecular interactions renders molecular-based interpretations difficult, and gives rise to many controversies, speculations, and even myths about the properties that ILs allegedly possess. Herein the current knowledge about the molecular foundations of IL behavior is discussed.
In vitro reversion of activated primary human hepatic stellate cells (2015)

We provide evidence for the ability of human primary aHSCs to revert in vitro to a transitional state through synergistic action of EGF, FGF2, dietary fatty acids and retinol, and provide a first phenotypic and genomic characterization of human in vitro rHSCs.
Heterologous Expression of the Desulfovibrio gigas [NiFe] Hydrogenase in Desulfovibrio fructosovorans MR400 (1998)

The ability of Desulfovibrio fructosovorans MR400 DeltahynABC to express the heterologous cloned [NiFe] hydrogenase of Desulfovibrio gigas was investigated. The [NiFe] hydrogenase operon from D. gigas, hynABCD, was cloned, sequenced, and introduced into D. fructosovorans MR400. A portion of the recombinant heterologous [NiFe] hydrogenase was totally matured, exhibiting catalytic and spectroscopic properties identical to those of the native D. gigas protein. A chimeric operon containing hynAB from D. gigas and hynC from D. fructosovorans placed under the control of the D. fructosovorans hynAp promoter was constructed and expressed in D. fructosovorans MR400. Under these conditions, the same level of activity was obtained as with the D. gigas hydrogenase operon.
Triplet exciton confinement in phosphorescent polymer light-emitting diodes (2003)

A series of iridium complexes, with triplet energy levels above or below the triplet level of host polymer, were used to study the flow of excitons between the host and the dopants. The performance of phosphorescent polymer light-emitting diodes has been shown to be sensitive to the triplet energy of the dopant. When the dopant exciton level was higher than that of the host polymer, a “backward excitation energy transfer” occurred; hence, the photoluminescence is quenched and the device performance is poor. When the triplet energy level of the dopant was lower than that of the host polymer, the exciton is confined to the dopant site, and the device shows better performance due to this confinement.
Toxicity of human monocytic THP-1 cells and microglia toward SH-SY5Y neuroblastoma cells is reduced by inhibitors of 5-lipoxygenase and its activating protein FLAP (2003)

To explore whether the proinflammatory products of the 5-lipoxygenase (5-LOX) pathway are involved in microglia-mediated toxicity toward neuronal cells, we evaluated the effects of 5-LOX inhibitors using an in vitro assay system where human neuronal SH-SY5Y cells are exposed to toxic secretions from THP-1 monocytic cells or human microglia. The specific 5-LOX inhibitors, REV 5901, zileuton, and 5-hydroxyeicosatetraenoic acid lactone; the nonselective LOX inhibitors, phenidone and dapsone; the dual 5-LOX/cyclooxygenase inhibitor, tepoxalin; and the selective inhibitor of the 5-LOX-activating protein (FLAP), MK-886, inhibited such toxicity. The toxicity was enhanced by the 5-LOX product leukotriene (LT)D(4) and reduced by the selective cysteinyl LT receptor (CysLT(1)) antagonist MK-571. The mRNAs for 5-LOX and FLAP were detected in THP-1 cells and human microglia but not in SH-SY5Y cells. The data suggest that inhibition of proinflammatory LT production by 5-LOX inhibition could selectively reduce toxicity of microglial cells and thus be beneficial in neuroinflammatory diseases.
Protein-tyrosine phosphatases: Structure, mechanism, and inhibitor discovery (1998)

Protein-tyrosine kinases (PTKs) and their associated signaling pathways are crucial for the regulation of numerous cell functions including growth, mitogenesis, motility, cell-cell interactions, metabolism, gene transcription, and the immune response. Since tyrosine phosphorylation is reversible and dynamic in vivo, the phosphorylation states of proteins are governed by the opposing actions of PTKs and protein-tyrosine phosphatases (PTPs). In this light, both PTKs and PTPs play equally important roles in signal transduction in eukaryotic cells, and comprehension of mechanisms behind the reversible pTyr-dependent modulation of protein function and cell physiology must necessarily encompass the characterization of PTPs as well as PTKs. In spite of the large number of PTPs identified to date and the emerging role played by PTPs in disease, a detailed understanding of the role played by PTPs in signaling pathways has been hampered by the absence of PTP-specific agents. Such PTP-specific inhibitors could potentially serve as useful tools in determining the physiological significance of protein tyrosine phosphorylation in complex cellular signal transduction pathways and may constitute valuable therapeutics in the treatment of several human diseases. The goal of this review is therefore to summarize current understandings of PTP structure and mechanism of catalysis and the relationship of these to PTP inhibitor development. The review is organized such that enzyme structure is covered first, followed by mechanisms of catalysis then PTP inhibitor development. In discussing PTP inhibitor development, nonspecific inhibitors and those obtained by screening methods are initially presented with the focus then shifting to inhibitors that utilize a more structure-based rationale.
The entropia virtual machine for desktop grids (2005)

Desktop distributed computing allows companies to exploit the idle cycles on pervasive desktop PC systems to increase the available computing power by orders of magnitude (10x - 1000x). Applications are submitted, distributed, and run on a grid of desktop PCs. Since the applications may be malformed, or malicious, the key challenges for a desktop grid are how to 1) prevent the distributed computing application from unwarranted access or modification of data and files on the desktop PC, 2) control the distributed computing application's resource usage and behavior as it runs on the desktop PC, and 3) provide protection for the distributed application's program and its data. In this paper we describe the Entropia Virtual Machine, and the solutions it embodies for each of these challenges.
The BaeSR Two-Component Regulatory System Activates Transcription of the yegMNOB ( mdtABCD ) Transporter Gene Cluster in Escherichia coli and Increases Its Resistance to Novobiocin and Deoxycholate (2002)

Screening of random fragments of Escherichia coli genomic DNA for their ability to increase the novobiocin resistance of a hypersusceptible (Delta)acrAB mutant resulted in the isolation of a plasmid containing baeR, which codes for the response regulator of the two-component regulatory system BaeSR. When induced for expression, baeR cloned in multicopy plasmid pTrc99A significantly increased the resistance of the (Delta)acrAB host strain to novobiocin (16-fold) and to deoxycholate (8-fold). Incubation of cells with novobiocin followed by a chromatographic assay for intracellular drug showed that overproduced BaeR decreased drastically the drug accumulation, presumably via increased active efflux. The genes baeSR are part of a putative operon, yegMNOB baeSR. Direct binding of BaeR to the yegM promoter was demonstrated in vitro by gel retardation assay. The gene yegB, which codes for a major facilitator superfamily transporter, was not necessary for increased resistance, but deletion of yegO or an in-frame deletion of yegN, both of which code for resistance-nodulation-cell division-type multidrug transporters, abolished the BaeR-induced increase in resistance. It is likely that both YegN and YegO produce a complex(es) with the membrane fusion protein family member YegM and pump out novobiocin and deoxycholate. We accordingly propose to rename yegMNOB as mdtABCD (mdt for multidrug transporter). Finally, the expression of two other genes, yicO and ygcL, was shown to be regulated by BaeR, but it is not known if they play any roles in resistance.
Nonsteroidal anti-inflammatory drug hydroxamic acids. Dual inhibitors of both cyclooxygenase and 5-lipoxygenase (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNonsteroidal anti-inflammatory drug hydroxamic acids. Dual inhibitors of both cyclooxygenase and 5-lipoxygenaseDaniel L. Flynn, Thomas Capiris, W. J. Cetenko, David T. Connor, Richard D. Dyer, Catherine R. Kostlan, Donald E. Nies, Denis J. Schrier, and Jagadish C. SircarCite this: J. Med. Chem. 1990, 33, 8, 2070–2072Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/jm00170a004https://doi.org/10.1021/jm00170a004research-articleACS PublicationsRequest reuse permissionsArticle Views272Altmetric-Citations40LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A Research Trail Over Half A Century (1995)

Since the spread of tobacco from the Americas hundreds of years ago, tobacco cigarettes and, more recently, alternative tobacco products have become global products of nicotine addiction. Within the evolving alternative tobacco product space, electronic ...Read More
Effects of Protein Kinase Inhibitor, HA1077, on Intraocular Pressure and Outflow Facility in Rabbit Eyes (2001)

Use of HA1077 caused a reduction in IOP and an increase in the outflow facility. The results of in vitro experiments suggest that the IOP-lowering effects of HA1077 may be related to the altered cellular behavior of TM cells and relaxation of CM contraction. The results of these studies suggested that protein kinase inhibitors have the potential to be developed into a treatment modality for glaucoma.
Two Aromatic Residues in the PB2 Subunit of Influenza A RNA Polymerase Are Crucial for Cap Binding (2003)

mRNAs are capped at their 5'-end by a unique cap structure containing N7-methyl guanine. Recognition of the cap structure is of paramount importance in some of the most central processes of gene expression as well as in some viral processes, such as priming of influenza virus transcription. The recent resolution of the structure of three evolutionary unrelated cap binding proteins, the vaccinia viral protein VP39, the eukaryotic translation factor eIF4E, and the nuclear cap-binding protein CBP20 showed that the recognition of the cap structure is achieved by the same general mechanism, i.e. by "sandwiching" of the N7-methyl guanine of the cap structure between two aromatic amino acid residues. The purpose of the present study was to test whether a similar cap recognition mechanism had independently evolved for the RNA polymerase of influenza virus. Combining in vivo and in vitro methods, we characterized two crucial aromatic amino acids, Phe363 and Phe404, in the PB2 subunit of the viral RNA polymerase that are essential for cap binding. The aromaticity of these two residues is conserved in influenza A, B, and C and even in the divergent Thogoto virus PB2 subunits. Thus, our results favor a similar mechanism of cap binding by the influenza RNA polymerase as in the evolutionary unrelated VP39, eIF4E, and CBP20.
Effect of time delay on telesurgical performance (2009)

In the area of surgical robotics no standard means of performance evaluation has been established. Thousands of surgeons have gone through the SAGES FLS Program, and the psychomotor skill portion of the program is considered the gold standard in laparoscopic skills evaluation. This research describes the use of the FLS block transfer task to evaluate the performance of both surgeons and non-surgeons teleoperating under different time delay conditions on the University of Washington RAVEN Surgical Robot. Time delays of 0 ms, 250 ms, and 500 ms were used and a statistically significant difference in mean block transfer time as well as mean tool tip path length were shown. For this task no significant difference was shown between the surgeon and non-surgeon groups. Clearly surgeon input and feedback is key to surgical robotic system development, but this result implies that non-surgeon subjects can be tested for simple usability evaluations.
UTILIZAÇÃO DE GEOTECNOLOGIAS DE GEOPROCESSAMENTO NO LEVANTAMENTO DE CLASSES DE SOLOS (2011)

A análise da qualidade de obtenção de mapa de classes de solos a partir do cruzamento de mapas de geologia e declividade utilizando sistema de informação geográfica – SIG é o objetivo principal desse trabalho. No ambiente do SIG foram elaborados os planos de informação (layers) de hipsometria, altimetria, declividade, geologia e solos. A partir da vetorização das curvas de nível constantes na carta topográfica Ilha do Funil, delimitada pelas coordenadas geográficas 48º 7’ 30’’/18º 52’ 30’’ e 48º 00’ 00’’/19º 00’00’’, Folha SE. 22-Z-B-VI-4-SE MI-2451/4-SE com eqüidistância de 10 metros foi elaborada camada altimetria. A camada de altimetria foi utilizada como base para a modelagem dos layers de modelo numérico de terreno – MNT, declividade e relevo, respectivamente. Os resultados permitiram a conclusão da inviabilidade da geração de mapa de evolução de solos considerando-se apenas a declividade, portanto, é necessario que se considere além da declividade do terreno, as demais variáveis do ambiente. Sendo neste caso, o diversos tipo de rocha e os diferentes processos intempéricos a que sua mineralogia estará exposta, traduz em diferentes processos pedogênicos.
Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC) (1989)

The crystal structure of a complex of spermine with the DNA octamer d(GTGTACAC) has been determined at 2.0-A resolution. The alternating sequence adopts an A-DNA conformation with a novel purine-purine extra-Watson-Crick hydrogen bond involving the central guanine G3 (G11) and adenine A13 (A5) in the deep groove. The oligocation spermine binds in the floor of the deep groove by interacting with the bases and assumes an S-shape. Its dyad is coincident with that of the DNA, reminiscent of repressor binding to B-DNA. The terminal and central ammonium groups of the top half of spermine form hydrogen-bonding interactions to the 5'-bases, GTG, of one strand; then the spermine winds across the groove to interact with the corresponding set of bases on the other strand. The methylene groups of spermine form a hydrophobic cluster with the methyl groups of the thymines and the O6 atoms of the guanines of the TGT sequences on either side of the dyad. The observed mode of binding of spermine to A-DNA can serve as a model for deep groove binding in RNA and DNA-RNA hybrids that show a propensity also for the A-conformation. It will be of interest to see if base binding of spermine to DNA is involved in the regulation of gene expression, since spermine and other oligocations are ubiquitous in cells and their concentration is coupled to stages in cell cycle.