gebhart/patrepeval huggingface dataset:
Serodiagnostic Potential of Culture Filtrate Antigens of <i>Mycobacterium tuberculosis</i> (2000)

Our studies of the humoral responses of tuberculosis (TB) patients have defined the repertoire of culture filtrate antigens of Mycobacterium tuberculosis that are recognized by antibodies from cavitary and noncavitary TB patients and demonstrated that the profile of antigens recognized changes with disease progression (K. Samanich et al., J. Infect. Dis. 178:1534-1538, 1998). We have identified several antigens with strong serodiagnostic potential. In the present study we have evaluated the reactivity of cohorts of human immunodeficiency virus (HIV)-negative, smear-positive; HIV-negative, smear-negative; and HIV-infected TB patients, with three of the candidate antigens, an 88-kDa protein, antigen (Ag) 85C, and MPT32, and compared the reactivity of the same patient cohort with the 38-kDa antigen and Ag 85A. We have also compared the reactivity of native Ag 85C and MPT32 with their recombinant counterparts. The evaluation of the reactivity was done by a modified enzyme-linked immunosorbent assay described earlier (S. Laal et al., Clin. Diag. Lab. Immunol. 4:49-56, 1997), in which all sera are preadsorbed against Escherichia coli lysates to reduce the levels of cross-reactive antibodies. Our results demonstrate that (i) antigens identified on the basis of their reactivity with TB patients' sera provide high sensitivities for serodiagnosis, (ii) recombinant Ag 85C and MPT32, expressed in E. coli, show reduced reactivity with human TB sera, and (iii) of the panel of antigens tested, the 88-kDa protein is the most promising candidate for serodiagnosis of TB in HIV-infected individuals. Moreover, these results reaffirm that both the extent of the disease and the bacterial load may play a role in determining the antigen profile recognized by antibodies.
ChemInform Abstract: Synthesis of Functionalized Olefins by Cross and Ring‐Closing Metatheses. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Coupled Carbon Dioxide Sequestration and Energy Production From Geopressured/Geothermal Aquifers (2013)

Summary The current approach to carbon capture and sequestration (CCS) from pulverized-coal-fired power plants is not economically viable without either large subsidies or a very high price on carbon. Current schemes require roughly one-third of a power-plant's energy for carbon dioxide (CO2) capture and pressurization. The production of energy from geopressured aquifers has evolved as a separate, independent technology from the sequestration of CO2 in deep, saline aquifers. A game-changing new idea is described here that combines the two technologies and adds another—the dissolution of CO2 into extracted brine that is then reinjected. A systematic investigation covering a range of conditions was performed to explore the best strategy for the coupled process of CO2 sequestration and energy production. Geological models of geopressured/geothermal aquifers were developed with available data from studies of Gulf Coast aquifers. These geological models were used to perform compositional reservoir simulations of realistic processes with coupled aquifer and wellbore models.
Irreversible and noncompetitive mu opioid receptor agonists (2022)

The ability of a ligand to preferentially promote engagement of one signaling pathway over another downstream of GPCR activation has been referred to as signaling bias, functional selectivity or biased agonism. The presentation of ligand bias reflects selectivity between active states of the receptor which may result in the display of preferential engagement with one signaling pathway over another. In this study, we provide evidence that the G protein‐biased MOR agonists, SR‐17018 and SR‐14968 stabilize the mu opioid receptor in a wash‐resistant, yet antagonist‐reversible, G protein signaling state. Furthermore, we demonstrate that these structurally related biased agonists, are noncompetitive for radiolabeled MOR antagonist binding and while they stimulate G protein signaling in mouse brain, partial agonists of this class do not compete with full agonist activation. Importantly, opioid antagonists can readily reverse their effects in vivo. Given that chronic treatment with SR‐17018 does not lead to tolerance in several mouse pain models, this feature may be desirable for the development of long lasting opioid analgesics that remain sensitive to antagonist reversal of respiratory suppression.
Identification of a potent and highly efficacious, yet slowly desensitizing CB1 cannabinoid receptor agonist (2004)

1 The relationship of agonist efficacy to the rate of G protein-coupled receptor signaling desensitization is controversial. 2 Expressing inwardly rectifying potassium channels (GIRKs) in Xenopus oocytes, we have devised a signaling assay that clearly identifies CB1 cannabinoid receptor agonists with low intrinsic efficacy. 3 In this assay, the synthetic CB1 agonists, AM411, AM782, AM1902, AM2233 and WIN55,212-2 and the endogenous cannabinoid, 2-arachidonoyl ester, were full agonists. 4 The synthetic CB1 agonist AM356 (methanandamide), the endogenous cannabinoids, anandamide and 2-arachidonoyl ether, and the phytocannabinoid, Delta9THC, were partial agonists. 5 The rate of desensitization of CB1 was independent of agonist efficacy. WIN55,212-2, AM782, AM1902, AM2233, and 2-arachidonoyl glycerol ester all desensitized quickly, with desensitization rates varying from 14% min(-1) to 10% min(-1). AM356, AM411, anandamide, and Delta9THC all desensitized considerably slower, at a rate of 5% min(-1). 6 Despite high potency and efficacy, AM411 desensitized as slowly as anandamide and Delta9THC. 7 CB1 agonist efficacy and rate of desensitization are not necessarily related.
ChemInform Abstract: Engaging Isatins in Solvent‐Free, Sterically Congested Passerini Reaction. (2013)

Abstract The Passerini reaction of isatins (I) with isocyanides and carboxylic acids affords desired oxindole derivatives such as (IV) and (VI).
ChemInform Abstract: High‐Value Alcohols and Higher‐Oxidation‐State Compounds by Catalytic Z‐Selective Cross‐Metathesis. (2015)

Abstract An electronically modified ruthenium—disulfide catalyst that is effective in cross‐metathesis is presented.
Gyroscope based on a crystalline optical WGM microresonator (Conference Presentation) (2017)

We report on a study of performance of both active and passive optical gyroscopes based on high finesse crystalline whispering gallery mode (WGM) resonators. We show that the sensitivity of the devices is ultimately limited due to the nonlinearity of the resonator host material. A gyroscope characterized with 0.02 deg/hr^<sup>1/2</sup> angle random walk and 2 deg/hr bias drift is demonstrated.
Multi-octave linear-to-circular polarizers (2017)

Linear-to-circular polarizers operating at mm-wave frequencies with multiple octaves of bandwidth are reported. First, a polarizer constructed from cascaded anisotropic dielectrics is discussed. This polarizer scales the design of achromatic waveplates from optical frequencies down to mm-wave frequencies. In addition, the polarizer is constructed from artificial dielectrics (metamaterials) rather than naturally occurring crystals, which would be too bulky at these lower frequencies. Next, a broadband polarizer utilizing a meanderline/metamaterial combination is reported. The polarizer significantly extends the bandwidth over previous microwave designs by optimizing the orientation of each metallic layer, as well as combining meanderline and metallic patch geometries into the design. Both polarizers operate at incident angles up to 60° from normal.
An order of magnitude improvement in optical fiber bandwidth using spatial domain multiplexing/space division multiplexing (SDM) in conjunction with orbital angular momentum (OAM) (2014)

Spatial Domain Multiplexing/Space Division Multiplexing (SDM) can increase the bandwidth of existing and futuristic optical fibers by an order of magnitude or more. In the SDM technique, we launch multiple single mode pigtail laser sources of same wavelength into a carrier fiber at different angles. The launching angles decide the output of the carrier fiber by allocating separate spatial locations for each channel. Each channel follows a helical trajectory while traversing the length of the carrier fiber, thereby allowing spatial reuse of optical frequencies. In this endeavor we launch light from five different single mode pigtail laser sources at different angles (with respect to the axis of the carrier fiber) into the carrier fiber. Owing to helical propagation we get five distinct concentric donut shaped rings with negligible crosstalk at the output end of the fiber. These SDM channels also exhibit Orbital Angular Momentum (OAM), thereby adding an extra degree of photon freedom. We present the experimental data of five spatially multiplexed channels and compare them with simulated results to show that this technique can potentially improve the data capacity of optical fibers by an order of magnitude: A factor of five using SDM and another factor of two using OAM.
Evolution of the capsular gene locus of Streptococcus pneumoniae serogroup 6 (2010)

Streptococcus pneumoniae expressing serogroup 6 capsules frequently causes pneumococcal infections and the evolutionary origins of the serogroup 6 strains have been extensively studied. However, these studies were performed when serogroup 6 had only two known members (serotypes 6A and 6B) and before the two new members (serotypes 6C and 6D) expressing wciN(β) were found. We have therefore reinvestigated the evolutionary origins of serogroup 6 by examining the profiles of the capsule gene loci and the multilocus sequence types (MLSTs) of many serogroup 6 isolates from several continents. We confirmed that there are two classes of cps locus sequences for serogroup 6 isolates. In our study, class 2 cps sequences were limited to a few serotype 6B isolates. Neighbour-joining analysis of cps sequence profiles showed a distinct clade for 6C and moderately distinct clades for class 1 6A and 6B sequences. The serotype 6D cps profile was found within the class 1 6B clade, suggesting that it was created by recombination between 6C and 6B cps loci. Interestingly, all 6C isolates also had a unique wzy allele with a 6 bp deletion. This suggests that serotype switching to 6C involves the transfer of a large (>4 kb) gene segment that includes both the wciN(β) allele and the 'short' wzy allele. The MLST studies of serotype 6C isolates suggest that the 6C cps locus is incorporated into many different pneumococcal genomic backgrounds but that, interestingly, 6C cps may have preferentially entered strains of the same genomic backgrounds as those of serotype 6A.
Cytotoxic T lymphocyte response to hepatitis C virus-derived peptides containing the HLA A2.1 binding motif. (1995)

The HLA class I-restricted cytotoxic T lymphocyte (CTL) response is a major defense mechanism in viral infections. It has been suggested that the CTL response may contribute to viral clearance and liver cell injury during hepatitis C virus (HCV) infection. To test this hypothesis requires an understanding of the characteristics of HCV-specific cytotoxic effector cells and identification of the target antigens to which they respond. To begin this process we stimulated peripheral blood mononuclear cells (PBMC) from a group of HLA-A2 positive patients with chronic hepatitis C with a panel of 130 HCV-derived peptides containing the HLA-A2 binding motif. Effector cells were tested for their capacity to lyse HLA-A2-matched target cells that were either sensitized with peptide or infected with a vaccinia virus construct containing HCV sequences. Using this approach we have identified nine immunogenic peptides in HCV, three of which are derived from the putative core protein, three from the nonstructural (NS) 3 domain, two from NS4 and one from NS5. Selected responses were shown to be HLA-A2 restricted, mediated by CD8+ T cells and to recognize endogenously synthesized viral antigen. Unexpectedly, peptide-specific CTL responses could also be induced in sero-negative individuals, suggesting in vitro activation of naive CTL precursors. The precursor frequency of peptide-specific CTL was 10 to 100-fold higher in infected patients compared to uninfected controls, and the responses were greatly diminished by removal of CD45 RO+ (memory) T cells. Further quantitative studies are clearly required to establish whether a correlation exists between the HCV-specific CTL response and the clinical course of this disease. Definition of the molecular targets of the human CTL response to HCV creates this opportunity, and may also contribute to the development of a T cell-based HCV vaccine.
Melanoma Morphology Change &#x00026; Apoptosis Induced by Multiple Nanosecond Pulsed Electric Fields (2007)

Our initial in vitro (HL-60 cells) and in vivo (B16-F10 murine) studies showed nanosecond pulsed electric fields (nsPEFs) caused intracellular changes and melanoma involution, respectively. We wanted to describe the morphologic changes in cell ultrastructure and investigate the mechanism for change due to nsPEFs in B16-F10 melanoma tumors in SKH-1 mice. We injected B16-F10 cells into 120 female SKH-1 mice to derive melanoma tumors. After multiple nsPEF treatments (40 kV/cm field strength; 5 ns rise time; 300 ns duration), morphologic changes of melanoma size, shape, tumor nesting pattern, blood vessel structure and cell ultrastructure were observed. Nuclear changes were recorded with light-and transmission electron-microscopy (TEM). Apoptosis in situ was detected by several immunohistochemistry (IHC) methods: (1) terminal deoxynucleotidyl transferase biotin-dUTP nick end labeling (TUNEL); (2) caspase 3, 6 and 7; and (3) histone H2AX. After multiple nsPEF treatments the melanoma blood supply was disrupted and melanomas shrank an average of 90% within two weeks. TEM showed increased rough endoplasmic reticulum and condensed dark-staining nucleoli; TUNEL presented fluorescent increase. Together these suggest post-treatment apoptotic activity, which was concurrently allied with increased caspase 3, 6 and 7, and histone H2AX fluorescence (DNA damage) after pulsing. Our study shows that blood flow and apoptotic changes play a central role in the biological effects caused by nsPEFs. Therefore nsPEFs may have application potential in cancer therapy, gene regulation and biophysical research by non-invasively disrupting intracellular components and inducing apoptosis in malignant tumors.
Identification of Thermolabile Pectin Methylesterases from Sweet Orange Fruit by Peptide Mass Fingerprinting (2010)

The multiple forms of the enzyme pectin methylesterase (PME) present in citrus fruit tissues vary in activity toward juice cloud-associated pectin substrates and, thus, in their impact on juice cloud stability and product quality. Because the proteins responsible for individual PME activities are rarely identified by structural properties or correlated to specific PME genes, matrix-assisted laser desorption-ionization with tandem time-of-flight mass spectrometry (MALDI-TOF/TOF MS) was investigated as a direct means to unequivocally identify the thermolabile (TL-) PME isoforms isolated from sweet orange [ Citrus sinensis (L.) Osbeck] fruit tissue. Affinity-purified TL-PME preparations were separated by SDS-PAGE prior to trypsin digestion and analyzed by MS for peptide mass fingerprinting. The two major PME isoforms accumulated in citrus fruit matched existing accessions in the SwissProt database. Although similar in size by SDS-PAGE, isoform-specific peptide ion signatures easily distinguished the two PMEs.
A 7‐phenyl substituted triazolopyridazine has inverse agonist activity at the benzodiazepine receptor site (1987)

To investigate further the structural requirements for benzodiazepine (BZD) receptor ligands, we synthesized SR 95195, [7-phenyl-3-methyl-1,2,4-triazolo-(4,3-b) pyridazine], a positional isomer of the 6-phenyl-triazolo-pyridazines, which were the first non-BZD derivatives to exhibit high affinity for the BZD receptor and BZD-like activity in vivo. In vitro, SR 95195 displaced specifically bound [3H]-flunitrazepam from rat cerebellar and hippocampal membranes with respective IC50 values of 4 and 8 microM. In vivo, SR 95195 lacked BZD-like activity. At high doses SR 95195 induced clonic seizures in mice (threshold convulsant dose: 150 mg kg-1; CD50: 160 mg kg-1 i.p.) which were antagonized by Ro 15-1788. At non-convulsant doses (25 mg kg-1 i.p. and 100 mg kg-1 i.p.) SR 95195 significantly decreased punished responding in an operant conflict procedure in the rat, suggesting SR 95195 has intrinsic anxiogenic activity. SR 95195, in mice, reversed the anticonvulsant and myorelaxant actions of diazepam 3 mg kg-1, orally (respective ED50 values: 45 mg kg-1 i.p. and 44 mg kg-1 i.p.). In an operant-conflict test in rats, SR 95195 at non-anxiogenic doses, antagonized the disinhibitory action of diazepam 4 mg kg-1, i.p. (ED50: 8.6 mg kg-1, i.p.), but not that of pentobarbitone 15 mg kg-1, i.p. It is concluded that SR 95195 has the pharmacological profile of an inverse BZD agonist and that displacing the phenyl from the 6- to the 7-position in the triazolopyridazine series causes a shift from agonist to inverse agonist type activity at the BZD receptor site.
A Review of Testing of Hollow Cathodes for the International Space Station Plasma Contactor (2001)

Since October 2000, two plasma contactors have been providing charge control on the International Space Station (ISS). At the heart of each of the two plasma contactors is a hollow cathode assembly (HCA) that produces the contacting xenon plasma. The HCA is the result of 9 years of design and testing at the NASA Glenn Research Center. This paper summarizes HCA testing that has been performed to date. As of this time, one cathode has demonstrated approximately 28,000 hr of lifetime during constant, high current use. Another cathode, HCA.014. has demonstrated 42,000 ignitions before cathode heater failure. In addition to these cathodes, four cathodes. HCA.006, HCA.003, HCA.010, and HCA.013 have undergone cyclic testing to simulate the variable current demand expected on the ISS. HCA.006 accumulated 8,000 hr of life test operation prior to being voluntarily stopped for analysis before the flight units were fabricated. HCA.010 has accumulated 15,876 hr of life testing, and 4,424 ignitions during ignition testing. HCA.003 and HCA.0 13 have accumulated 12,415 and 18,823 hr of life testing respectively.
Adapting ranking functions to user preference (2008)

Learning to rank has become a popular method for web search ranking. Traditionally, expert-judged examples are the major training resource for machine learned web ranking, which is expensive to get for training a satisfactory ranking function. The demands for generating specific web search ranking functions tailored for different domains, such as ranking functions for different regions, have aggravated this problem. Recently, a few methods have been proposed to extract training examples from user click through log. Due to the low cost of getting user preference data, it is attractive to combine these examples in training ranking functions. However, because of the different natures of the two types of data, they may have different influences on ranking function. Therefore, it is challenging to develop methods for effectively combining them in training ranking functions. In this paper, we address the problem of adapting an existing ranking function to user preference data, and develop a framework for conveniently tuning the contribution of the user preference data in the tuned ranking function. Experimental results show that with our framework it is convenient to generate a batch of adapted ranking functions and to select functions with different tradeoffs between the base function and the user preference data.
Fluorescence-Labeled Peptide p<i>I</i> Markers for Capillary Isoelectric Focusing (2002)

Nineteen fluorescent pH standards or pI markers ranging pH 3.64-10.12 were developed for use in capillary isoelectric focusing using laser-induced fluorescence detection. Tetra- to tridecapeptides containing one cysteine residue were designed to focus sharply at their respective isoelectric points by including amino acids that contain charged side chains, the pKa values of which are close to the corresponding pI values. An iodoacetylated derivative of tetramethylrhodamine was coupled to the thiol group of cysteine to yield fluorescent pI markers. The pI values of the labeled peptides were precisely determined after isoelectric focusing on polyacrylamide gel slabs by direct measurement of the pH of the focused bands. The markers were subjected to capillary isoelectric focusing for 10-15 min in coated capillaries under conditions of low electroosmosis and were detected by means of a scanning laser-induced fluorescence detector down to a level of subpicomolar range. The markers permitted the calibration of a wide-range pH gradient formed in a capillary by fluorescence detection for the first time and should facilitate the development of highly sensitive analytical methods based on a combination of capillary isoelectric focusing and laser-induced fluorescence detection.
C-Axis-Oriented Superconducting Oxide Film by the Sol-Gel Method (1988)

In R-Ba-Cu-O systems (R=Y, Nd, Y-Nd), c -axis-oriented superconducting oxide films with T c (zero)=90 K have been fabricated on yttrium-stabilized zirconia substrates. Oxide pastes for printing on the substrates are made by the sol-gel method using liquid alkoxides. Starting paste compositions that are Cu-rich and R-poor are found to be suitable for forming the c -axis-oriented superconducting oxide film.
Enhancement of the enzymatic hydrolysis of fines from recycled paper mill waste rejects (2015)

A significant fraction of short fibers commonly called “reject fines” is produced while recycling wastepaper at paper mills producing linerboard. These fines are usually rejected into the solid waste stream that further requires land filling and poses environmental problems. The major component of these rejects is cellulose that can be a potential source of fermentable sugars for biofuels, bioplastics or other products. Therefore, a feasible process for converting these reject fines into sugars can profit the paper mills by producing value for their waste products while simultaneously mitigating their adverse environmental impact by avoided solid waste. Additionally, the sugar feedstocks can be used to reduce fossil carbon contributing to the sustainability of the industry. Enzymatic conversion of rejects fines from paper mills was achieved using commercial cellulases from Trichoderma reesei. The presence of mineral particles along with the cellulosic fines was found to have potent inhibitory effects on enzyme hydrolysis. The mineral particles are kaolin and calcium carbonate and originate from the fillers used in the wastepaper. The adsorption of the cellulase onto these mineral components was measured and quantified by the slope of the adsorption isotherm. The application of a nonionic surfactant Tween-80, decreased the adsorption of cellulase and this improved the hydrolysis yield of sugars. Enzymatic hydrolysis of rejects from recycled paper mills is feasible and provides a source of sugars for biofuels and bioplastics. However, the presence of mineral particles can be detrimental to this bioconversion. Calcium carbonate which occurs as a filler in waste paper shows high adsorption affinity to the cellulase enzymes and thus reduces the available enzyme for cellulolysis. This can be remedied by the application of surfactants which preferentially occlude to the mineral surfaces and thus increase enzyme availability in solution. The non-ionic surfactant, Tween-80, shows the best hydrolysis enhancement at a dosage of 3 % based on the dry weight of the biomass.