gebhart/patrepeval huggingface dataset:
A generic multicast-key determination protocol (2002)

This paper examines a generic deadlock-free protocol for the automated maintenance of a commonly-shared multicast-key within a group in communication with each other. The protocol's use under conditions of both centralized and distributed controls is described. Distributed schemes are inherently more robust and more readily available compared with the centralized scheme of establishing the common multicast-key. Three schemes of use of the protocol are proposed. Simulation results are provided.
Molecular Diversity of the Calcium Channel α2δ Subunit (1999)

Sequence database searches with the alpha2delta subunit as probe led to the identification of two new genes encoding proteins with the essential properties of this calcium channel subunit. Primary structure comparisons revealed that the novel alpha2delta-2 and alpha2delta-3 subunits share 55.6 and 30.3% identity with the alpha2delta-1 subunit, respectively. The number of putative glycosylation sites and cysteine residues, hydropathicity profiles, and electrophysiological character of the alpha2delta-3 subunit indicates that these proteins are functional calcium channel subunits. Coexpression of alpha2delta-3 with alpha1C and cardiac beta2a or alpha1E and beta3 subunits shifted the voltage dependence of channel activation and inactivation in a hyperpolarizing direction and accelerated the kinetics of current inactivation. The kinetics of current activation were altered only when alpha2delta-1 or alpha2delta-3 was expressed with alpha1C. The effects of alpha2delta-3 on alpha1C but not alpha1E are indistinguishable from the effects of alpha2delta-1. Using Northern blot analysis, it was shown that alpha2delta-3 is expressed exclusively in brain, whereas alpha2delta-2 is found in several tissues. In situ hybridization of mouse brain sections showed mRNA expression of alpha2delta-1 and alpha2delta-3 in the hippocampus, cerebellum, and cortex, with alpha2delta-1 strongly detected in the olfactory bulb and alpha2delta-3 in the caudate putamen.
A Novel MATE Family Efflux Pump Contributes to the Reduced Susceptibility of Laboratory-Derived Staphylococcus aureus Mutants to Tigecycline (2005)

ABSTRACT Tigecycline, an expanded-broad-spectrum glycylcycline antibiotic is not affected by the classical tetracycline resistance determinants found in Staphylococcus aureus . The in vitro selection of mutants with reduced susceptibility to tigecycline was evaluated for two methicillin-resistant S. aureus strains by serial passage in increasing concentrations of tigecycline. Both strains showed a stepwise elevation in tigecycline MIC over a period of 16 days, resulting in an increase in tigecycline MIC of 16- and 32-fold for N315 and Mu3, respectively. Transcriptional profiling revealed that both mutants exhibited over 100-fold increased expression of a gene cluster, mepRAB (multidrug export protein), encoding a MarR-like transcriptional regulator ( mepR ), a novel MATE family efflux pump ( mepA ), and a hypothetical protein of unknown function ( mepB ). Sequencing of the mepR gene in the mutant strains identified changes that presumably inactivated the MepR protein, which suggested that MepR functions as a repressor of mepA . Overexpression of mepA in a wild-type background caused a decrease in susceptibility to tigecycline and other substrates for MATE-type efflux pumps, although it was not sufficient to confer high-level resistance to tigecycline. Complementation of the mepR defect by overexpressing a wild-type mepR gene reduced mepA transcription and lowered the tigecycline MIC in the mutants. Transcription of tet (M) also increased by over 40-fold in the Mu3 mutant. This was attributed to a deletion in the promoter region of the gene that removed a stem-loop responsible for transcriptional attenuation. However, overexpression of the tet (M) transcript in a tigecycline-susceptible strain was not enough to significantly increase the MIC of tigecycline. These results suggest that the overexpression of mepA but not tet (M) may contribute to decreased susceptibility of tigecycline in S. aureus .
Neurobiological consequences of traumatic brain injury (2011)

Traumatic brain injury (TBI) is a worldwide public health problem typically caused by contact and inertial forces acting on the brain. Recent attention has also focused on the mechanisms of injury associated with exposure to blast events or explosions. Advances in the understanding of the neuropathophysiology of TBI suggest that these forces initiate an elaborate and complex array of cellular and subcellular events related to alterations in Ca++ homeostasis and signaling. Furthermore, there is a fairly predictable profile of brain regions that are impacted by neurotrauma and the related events. This profile of brain damage accurately predicts the acute and chronic sequelae that TBI survivors suffer from, although there is enough variation to suggest that individual differences such as genetic polymorphisms and factors governing resiliency play a role in modulating outcome. This paper reviews our current understanding of the neuropathophysiology of TBI and how this relates to the common clinical presentation of neurobehavioral difficulties seen after an injury.
A Triple Mutant of Escherichia coli Lacking Secondary Acyl Chains on Lipid A (2002)

All possible combinations of insertion mutations in the three genes encoding the acyl carrier protein-dependent late acyltransferases of lipid A biosynthesis, designated lpxL(htrB), lpxM(msbB), and lpxP, were generated in Escherichia coli K12 W3110. Mutants defective in lpxM synthesize penta-acylated lipid A molecules and grow normally. Strains lacking lpxP fail to incorporate palmitoleate into their lipid A at 12 degrees C but make normal amounts of hexa-acylated lipid A and are viable. Although lpxL mutants and lpxL lpxM double mutants grow slowly on minimal medium at all temperatures, they do not grow on nutrient broth above 32 degrees C. Such mutants retain the ability to synthesize some penta- and hexa-acylated lipid A molecules because of limited induction of lpxP at 30 degrees C but not above 32 degrees C. MKV15, an E. coli lpxL lpxM lpxP triple mutant, likewise grows slowly on minimal medium at all temperatures but not on nutrient broth at any temperature. MKV15 synthesizes a lipid A molecule containing only the four primary (R)-3-hydroxymyristoyl chains. The outer membrane localization and content of lipid A are nearly normal in MKV15, as is the glycerophospholipid and membrane protein composition. However, the rate at which the tetra-acylated lipid A of MKV15 is exported to the outer membrane is reduced compared with wild type. The integrity of the outer membrane of MKV15 is compromised, as judged by antibiotic hypersensitivity, and MKV15 undergoes lysis following centrifugation. MKV15 may prove useful as a host strain for expressing late acyltransferase genes from other Gram-negative bacteria, facilitating the re-engineering of lipid A structure in living cells and the design of novel vaccines.
Color Tuning Based on a Six-membered Chelated Iridium(III) Complex with Aza-aromatic Ligand (2005)

Abstract A six-membered chelated iridium complex containing aza-aromatic ligand is prepared. Emission color tuning from yellow to deep red is observed for electroluminescent devices with different doping concentrations.
Synthesis of Electro-Optic Shutters having a Prescribed Transmission vs Voltage Characteristic* (1966)

A procedure is described for the synthesis of electro-optic shutters having arbitrarily prescribed characteristics of transmittance vs voltage. The procedure is an adaptation of the birefringent-network-synthesis procedure of Harris et al. The synthesized shutter consists of n identical cascaded cells between an input and output polarizer. The synthesis procedure prescribes the angles to which the cells should be rotated and the angle of the output polarizer. Although it is assumed in this paper that each cell contains a Kerr-effect material, the synthesis procedure is equally applicable if each cell utilizes the Pockels effect. The technique of this paper is of possible use in many situations where standard Kerr-cell (or Pockels-cell) shutters are now employed. By controlling the shutter’s transmission vs voltage characteristic, we are able to control the shape and duration of the transmitted optical pulse independently of the form of the applied voltage pulse. Thus by this procedure the duration of the optical pulse resulting from a given applied voltage pulse can be reduced. Possible applications are briefly discussed in the areas of high-speed photography and Q switching of lasers.
A single dose of citalopram increases fear recognition in healthy subjects (2007)

We have previously shown that a single dose of intravenous citalopram in healthy volunteers enhances the detection of fearful facial expressions, suggesting an effect of acute selective serotonin re-uptake inhibitor (SSRI) treatment on the processing of anxiety-related stimuli. The aim of the present study was to confirm and extend this finding by studying the effects of a single dose of oral citalopram on a range of tasks designed to assess different aspects of emotional processing. A total of 32 healthy volunteers were randomly allocated to double-blind treatment with either citalopram 20 mg orally or placebo. Participants then completed a series of tasks assessing emotional aspects of attention (visual-probe task), perception (categorization of facial affect), memory (emotional memory task) and reactivity to threat (emotion potentiated startle). Relative to placebo-treated subjects, participants treated with citalopram demonstrated improved recognition of fearful faces and increased baseline startle response. However, the citalopram group also showed an attentional bias towards positive words. Our data suggest that acute oral citalopram increases the processing of anxiety-related stimuli in healthy volunteers. This mechanism could underlie the known tendency of SSRIs to increase anxiety in patients early in treatment. Our data also suggests that some of the positive biases in emotional processing produced by SSRI treatment might be detectable at the beginning of treatment.
Tumor-Associated Macrophages: The Double-Edged Sword in Cancer Progression (2004)

The interaction of lung cancer cells and macrophages can promote the invasiveness and matrix-degrading activity of cancer cells. Our results also suggest that a great diversity of gene expression occurs in this interaction, which may assist us in understanding the process of cancer metastasis.
Transactional memory implementation overview (2006)

This article consists of a collection of slides from the author's conference presentation on transactional memory (TM). Some of the specific topics discussed include: TM implementation that provide atomicity and isolation; basic TM implementation requirements; and implementation options that incorporate hardware TM, software TM and hybrid TM.
Antibody-Drug Conjugates in Cancer Therapy (2012)

An antibody-drug conjugate (ADC) provides the possibility of selectively ablating cancer cells by combining the specificity of a monoclonal antibody (mAb) for a target antigen with the delivery of a highly potent cytotoxic agent. ADC target antigens are typically highly expressed on the surface of cancer cells compared to normal cells. The tumor target, the cytotoxic agent, and the manner in which the agent is attached to the antibody are key determinants of clinical activity and tolerability. Recently, several clinical trials have demonstrated that ADCs achieve higher clinical response rates than unconjugated mAbs targeting the same cell surface antigen. Brentuximab vedotin represents one such ADC that has recently been approved for the treatment of relapsed Hodgkin and systemic anaplastic large cell lymphomas--both characterized by high expression of the target antigen, CD30, on the surface of malignant cells. This review summarizes key characteristics of current, clinically active ADCs and highlights recent clinical data illustrating the benefit of antibody-targeted delivery of cytotoxic agents to cancer cells.
Nuclear Receptors Have Distinct Affinities for Coactivators: Characterization by Fluorescence Resonance Energy Transfer (1998)

1) FRET-based coactivator association is a novel approach for characterizing nuclear receptor agonists or antagonists; individual ligands display potencies that are predictive of in vivo effects and distinct profiles of maximal activity that are suggestive of alternative receptor conformations. 2) PPARgamma interacts with both CBP and SRC-1; transcriptional activation and coactivator association are AF2 dependent. 3) Nuclear receptor LBDs have distinct affinities for individual coactivators; thus, PPARgamma has a greater apparent affinity for CBP than for SRC-1, whereas ERalpha interacts preferentially with SRC-1 but very weakly with CBP.
Microfluidic Paper-Based Analytical Device for Particulate Metals (2012)

A microfluidic paper-based analytical device (μPAD) fabricated by wax printing was designed to assess occupational exposure to metal-containing aerosols. This method employs rapid digestion of particulate metals using microliters of acid added directly to a punch taken from an air sampling filter. Punches were then placed on a μPAD, and digested metals were transported to detection reservoirs upon addition of water. These reservoirs contained reagents for colorimetric detection of Fe, Cu, and Ni. Dried buffer components were used to set the optimal pH in each detection reservoir, while precomplexation agents were deposited in the channels between the sample and detection zones to minimize interferences from competing metals. Metal concentrations were quantified from color intensity images using a scanner in conjunction with image processing software. Reproducible, log-linear calibration curves were generated for each metal, with method detection limits ranging from 1.0 to 1.5 μg for each metal (i.e., total mass present on the μPAD). Finally, a standard incineration ash sample was aerosolized, collected on filters, and analyzed for the three metals of interest. Analysis of this collected aerosol sample using a μPAD showed good correlation with known amounts of the metals present in the sample. This technology can provide rapid assessment of particulate metal concentrations at or below current regulatory limits and at dramatically reduced cost.
Dewetting Instability during the Formation of Polymersomes from Block-Copolymer-Stabilized Double Emulsions (2006)

We investigate the formation of polymer vesicles, or polymersomes, of polystyrene-block-poly(ethylene oxide) diblock copolymers using double emulsion droplets of controlled architecture as templates. To engineer the structure of the polymersomes, it is important to consider the concentration of diblock copolymer in the middle phase of the double emulsion. We describe how the presence of excess polymer can induce a transition from complete wetting to partial wetting of the middle phase, resulting in polymer shells with inhomogeneous thicknesses.
Comparison of four laser types for experimental pain stimulation on oral mucosa and hairy skin (1991)

The use of different lasers for stimulation in human experimental pain research has provided a sensitive method for evaluation of thin nerve fiber functions. In this study, sensory and pain thresholds were compared to argon-, copper vapour-, Nd:YAG-, and CO2 laser stimulation on hairy skin and on oral mucosa. The influence on thresholds with respect to laser type, stimulation site, surface colour, and stimulus parameters (laser beam diameter and pulse duration) was investigated. Significant differences in thresholds between the four lasers were found on both surfaces; however, no significant differences existed between thresholds on the skin and on the tongue when the same laser was used. The observations imply that wavelength-dependent optical properties of the stimulated tissue influence on threshold determinations. Furthermore, the results indicate that temporal and spatial summation mechanisms may exist for laser induced warmth and pain perceptions. Laser stimulation may be a new tool for the investigation of origin and genesis of various orofacial pain syndromes.
A molecular approach to leukemogenesis: mouse lymphomas contain an activated c-ras oncogene. (1984)

By inducing mouse thymomas with carcinogens and gamma-radiation, we have studied the potential of tumor DNA to induce foci in rodent fibroblasts. A high percentage of the tumors used transformed the cultured cells, and the oncogenic phenotype segregated with extra copies of the c-ras gene family. There appears to be selectivity in the activated gene because so far all analyzed tumors induced by carcinogen have activated the N-ras gene, and those induced by radiation have activated the K-ras gene. The K-ras gene is the cellular counterpart of the viral ras oncogene in Kirsten murine sarcoma virus, but the N-ras has not yet been found in a retrovirus. The transformed cells have a marked increase in expression of the oncogene at the RNA and protein level. This model system might be a powerful tool in the study of leukemogenesis.
Combined oxygen and glucose deprivation in cortical cell culture: calcium-dependent and calcium-independent mechanisms of neuronal injury (1993)

Murine neocortical cell cultures were transiently deprived of both oxygen and glucose, producing widespread neuronal swelling in less than 60 min, followed by neuronal degeneration over the ensuing several hours, despite return to normal medium. Cultured glia (> 95% astrocytes) were irreversibly injured only by oxygen-glucose deprivation exposures exceeding 4-6 hr. Replacing either Na+ or Cl- with impermeant ions blocked acute neuronal swelling but did not prevent delayed neuronal degeneration. While neuronal swelling and death were increased by removing Ca2+ from the exposure medium, combined removal of extracellular Ca2+ together with Na+ or Cl- substitution blocked both acute and delayed injury. If acute swelling was limited by a hyperosmolar medium, then neuronal loss depended on extracellular [Ca2+]. Oxygen-glucose deprivation was associated with a large increase in extracellular glutamate concentration. Both early swelling and later neuronal degeneration were blocked by addition of NMDA receptor antagonists to the exposure medium but not by the AMPA/kainate receptor antagonist 6-cyano-7-dinitroquinoxaline-2,3-dione (CNQX), dihydropyridines nifedipine or nimodipine, or TTX. Oxygen-glucose deprivation induced substantial neuronal uptake of tracer 45Ca2+ from the exposure medium that was reduced by NMDA receptor antagonists and closely paralleled the degree of subsequent neuronal loss. These observations suggest the presence of two distinct components of hypoxic injury, each involving NMDA receptor activation and each capable of leading to neuronal death. Acute swelling is mediated by influx of Na+, Cl-, and water, and is enhanced by removal of extracellular Ca2+. Delayed neuronal degeneration depends on the presence of extracellular Ca2+ and correlates closely with cellular uptake of 45Ca2+.
The T4 DNA polymerase accessory proteins form an ATP-dependent complex on a primer-template junction. (1991)

The DNA polymerase holoenzyme of bacteriophage T4 contains, besides the DNA polymerase itself (the gene 43 protein), a complex of the protein products of T4 genes 44 and 62 (a DNA-dependent ATPase) and of gene 45. Together, the 44/62 and 45 proteins form an ATP-dependent "sliding clamp" that holds a moving DNA polymerase molecule at the 3' terminus of a growing DNA chain. We have used a unique DNA fragment that forms a short hairpin helix with a single-stranded 5' tail (a "primer-template junction") to map the binding sites for these polymerase accessory proteins by DNA footprinting techniques. In the absence of the DNA polymerase, the accessory proteins protect from DNase I cleavage 19-20 nucleotides just behind the 3' end of the primer strand and 27-28 nucleotides on the complementary portion of the template strand. Detection of this DNA-protein complex requires the 44/62 and 45 proteins plus the nonhydrolyzable ATP analogue adenosine 5'-O-(thiotriphosphate). The complex is not detected in the presence of ATP. We suggest that ATP hydrolysis by the 44/62 protein normally activates the accessory proteins at a primer-template junction, permitting the DNA polymerase to bind and thus form the complete holoenzyme. However, when the polymerase is missing, as in these experiments, ATP hydrolysis is instead followed by a release (or loosening) of the accessory protein complex.
A Portable Surface-Enhanced Raman Spectrometer (1994)

Abstract We describe the development of a simple and compact spectrometer for use in Raman and Surface-enhanced Raman Scattering (SERS) analysis. The instrument using an avalanche photodiode is designed to use under field conditions with simple optical samples. Examples of measurement of a variety of chemicals are used to illustrate the performance of the instrument.
Scarless and site-directed mutagenesis in Salmonella enteritidischromosome (2007)

We have successfully used this method to produce multiple mutants with no antibiotic gene on the genome or extra sequence except those nucleotides required for expression of epitope regions. This method is advantageous over other protocols in that it does not require cloning or creating extra duplicate regions to facilitate homologous recombination, contains a universal construct in which an epitope of choice can be placed to check for cell surface expression, and shows high efficiency when screening for positive mutants. Other opportunities of this mutational strategy include creating attenuated mutants and site-specific, chromosomal deletion mutations. Furthermore, this method should be applicable in other gram-negative bacterial species where Red recombinase enzymes can be functionally expressed.
Synthesis and structure-activity study of protease inhibitors. III. Amidinophenols and their benzoil esters. (1984)

Various amidinophenol derivatives (27-47) and their benzoates (4-26) were synthesized and evaluated for inhibitory activities against trypsin, plasmin, kallikrein, thrombin, Clr and Cls as well as in vitro complement-mediated hemolysis. 4-(β-Amidinoethenyl) phenyl 4-guanidinobenzoate (15) and 4-amidino-2-benzoylphenyl 4-guanidinobenzoate (26) were found to have potent inhibitory activities with IC50s of 9×10-8M (trypsin) and 2×10-7M (Cls) for the former and 3×10-8M (trypsin) and 2×10-7M (Cls) for the latter.
Mechanism of Anti-Inflammatory Action of Glycyrrhizin: Effect on Neutrophil Functions Including Reactive Oxygen Species Generation (1991)

The effect of glycyrrhizin on inflammatory mediators such as neutrophil functions including reactive oxygen species (ROS) generation was examined. Glycyrrhizin significantly decreased neutrophil-generated O2-, H2O2 and OH in a dose-dependent manner. However, the drug did not reduce any of the ROS generated in a cell-free, xanthine-xanthine oxidase system. The drug did not affect neutrophil chemotaxis or phagocytosis, either. The present study indicates that glycyrrhizin is not an ROS scavenger but exerts an anti-inflammatory action by inhibiting the generation of ROS by neutrophils, the most potent inflammatory mediator at the site of inflammation.