gebhart/patrepeval huggingface dataset:
Why Triple Bonds Protect Acenes from Oxidation and Decomposition (2012)

An experimental and computational study on the impact of functional groups on the oxidation stability of higher acenes is presented. We synthesized anthracenes, tetracenes, and pentacenes with various substituents at the periphery, identified their photooxygenation products, and measured the kinetics. Furthermore, the products obtained from thermolysis and the kinetics of the thermolysis are investigated. Density functional theory is applied in order to predict reaction energies, frontier molecular orbital interactions, and radical stabilization energies. The combined results allow us to describe the mechanisms of the oxidations and the subsequent thermolysis. We found that the alkynyl group not only enhances the oxidation stability of acenes but also protects the resulting endoperoxides from thermal decomposition. Additionally, such substituents increase the regioselectivity of the photooxygenation of tetracenes and pentacenes. For the first time, we oxidized alkynylpentacenes by using chemically generated singlet oxygen ((1)O(2)) without irradiation and identified a 6,13-endoperoxide as the sole regioisomer. The bimolecular rate constant of this oxidation amounts to only 1 × 10(5) s(-1) M(-1). This unexpectedly slow reaction is a result of a physical deactivation of (1)O(2). In contrast to unsubstituted or aryl-substituted acenes, photooxygenation of alkynyl-substituted acenes proceeds most likely by a concerted mechanism, while the thermolysis is well explained by the formation of radical intermediates. Our results should be important for the future design of oxidation stable acene-based semiconductors.
Control of rpoS transcription in Escherichia coli and Pseudomonas: why so different? (2003)

In Escherichia coli, the stationary phase alternative sigma factor sigmas controls the expression of genes involved cell survival in response to cessation of growth (stationary phase) and provides cross-protection to various stresses. Levels of sigmas increase dramatically at the onset of stationary phase and are regulated at the transcriptional, post-transcriptional and post-translational level, making this one of the most complex regulatory systems in bacteria. The basic mechanisms for the control of translation and sigmas proteolysis have been understood. However, studies on the transcriptional control in E. coli lag behind and are controversial. The cAMP-CRP complex and the two component BarA/UvrY system have been implicated and, ppGpp and polyphosphate appear to have a signalling role. sigmas has also been reported to be a general stress regulator in the fluorescent pseudomonads (Pseudomonas aeruginosa, P. fluorescens and P. putida) and recent studies on sigmas regulation highlight that transcriptional regulation in these bacteria apparently plays a major role. Global regulatory systems, the GacA/GacS two component system and quorum sensing all affect rpoS expression, as does the TetR family PsrA regulator that directly binds to- and activates the rpoS promoter in stationary phase. This striking difference in regulation between E. coli and Pseudomonas can be partly attributed to the differences in the functional role of sigmas in the two bacterial species. This report will review mainly recent studies on rpoS transcriptional regulation and will try to rationalize the current knowledge into a working model.
Ultrahigh-vacuum scanning tunneling microscopy and spectroscopy of single-walled carbon nanotubes on hydrogen-passivated Si(100) surfaces (2003)

Single-walled carbon nanotubes (SWNTs) have been studied on a Si(100)-2×1:H surface using an ultrahigh-vacuum (UHV) scanning tunneling microscope (STM). Dry deposition of SWNTs in situ establishes the pristine interface necessary to elucidate fundamental physical and electronic interactions between SWNTs and silicon. We have achieved simultaneous atomic resolution STM images of isolated SWNTs and the local H-passivated Si(100) substrate. Scanning tunneling spectroscopy served to characterize both semiconducting and metallic SWNTs. In each case, electronic features unique to the nanotube can be identified within the substrate band gap. In contrast to previous UHV STM studies of SWNTs on Au(111), our investigation is motivated by the technological relevance of the Si(100) substrate and the potential for nanofabrication of hybrid SWNT-Si electronic devices on the Si(100)-2×1:H platform.
Cell-mediated immunological responses in cervical and vaginal cancer patients immunized with a lipidated epitope of human papillomavirus type 16 E7. (1998)

Human papillomavirus (HPV) infection has been causally associated with cervical cancer. We tested the effectiveness of an HLA-A*0201-restricted, HPV-16 E7 lipopeptide vaccine in eliciting cellular immune responses in vivo in women with refractory cervical cancer. In a nonrandomized Phase I clinical trial, 12 women expressing the HLA-A2 allele with refractory cervical or vaginal cancer were vaccinated with four E786-93 lipopeptide inoculations at 3-week intervals. HLA-A2 subtyping was also performed, and HPV typing was assessed on tumor specimens. Induction of epitope-specific CD8+ T-lymphocyte (CTL) responses was analyzed using peripheral blood leukapheresis specimens obtained before and after vaccination. CTL specificity was measured by IFN-gamma release assay using HLA-A*0201 matched target cells. Clinical responses were assessed by physical examination and radiographic images. All HLA-A*0201 patients were able to mount a cellular immune response to a control peptide. E786-93-specific CTLs were elicited in 4 of 10 evaluable HLA-A*0201 subjects before vaccination, 5 of 7 evaluable HLA-A*0201 patients after two vaccinations, and 2 of 3 evaluable HLA-A*0201 cultures after all four inoculations. Two of three evaluable patients' CTLs converted from unreactive to reactive after administration of all four inoculations. There were no clinical responses or treatment toxicities. The ability to generate specific cellular immune responses is retained in patients with advanced cervical cancer. Vaccination with a lipidated HPV peptide epitope appears capable of safely augmenting CTL reactivity. Although enhancements of cellular immune responses are needed to achieve therapeutic utility in advanced cervical cancer, this approach might prove useful in treating preinvasive disease.
Differentiation-induced gene expression in 3T3-L1 preadipocytes: CCAAT/enhancer binding protein interacts with and activates the promoters of two adipocyte-specific genes. (1989)

Previous studies have shown that differentiation of 3T3-L1 preadipocytes leads to the transcriptional activation of a group of adipose-specific genes. As an approach to defining the mechanism responsible for activating the expression of these genes, we investigated the binding of nuclear factors to the promoters of two differentiation-induced genes, the 422(aP2) and stearoyl-CoA desaturase 1 (SCD1) genes. DNase I footprinting and gel retardation analysis identified two binding regions within the promoters of each gene that interact with nuclear factors present in differentiated 3T3-L1 adipocytes. One differentiation-induced nuclear factor interacts specifically with a single binding site in the promoter of each gene. Competition experiments showed that the interaction of this nuclear factor with the SCD1 promoter was prevented specifically by a synthetic oligonucleotide corresponding to the site footprinted in the 422(aP2) promoter. Several lines of evidence indicate that the differentiation-induced nuclear factor is CCAAT/enhancer binding protein (C/EBP), a DNA-binding protein first isolated from rat liver. Bacterially expressed recombinant C/EBP binds to the same site at which the differentiation-specific nuclear factor interacts within the promoter of each gene. Northern analysis with RNA from 3T3-L1 cells shows that C/EBP mRNA abundance increases markedly during differentiation. Transient cotransfection studies using a C/EBP expression vector demonstrate that C/EBP can function as a trans-activator of both the 422(aP2) and SCD1 gene promoters.
Two conjugation systems associated with Streptococcus faecalis plasmid pCF10: identification of a conjugative transposon that transfers between S. faecalis and Bacillus subtilis (1987)

The tetracycline resistance plasmid pCF10 (58 kilobases [kb]) of Streptococcus faecalis possesses two separate conjugation systems. A 25-kb region of the plasmid (designated TRA) was shown previously to determine pheromone response and conjugation functions required for transfer of pCF10 between S. faecalis cells (P. J. Christie and G. M. Dunny, Plasmid 15:230-241, 1986). When S. faecalis cells were mixed with Bacillus subtilis in broth, tetracycline resistance was transferred from S. faecalis. The tetracycline-resistant B. subtilis cells contained a 16-kb region of pCF10 (distinct from TRA) that carried the tetracycline resistance determinant (Tetr). This Tetr element was found to transfer between S. faecalis and B. subtilis strains in the absence of plasmids. Genetic and molecular techniques were used to establish locations of the element at several different sites on the B. subtilis chromosome. The Tetr element could be transferred in filter matings from B. subtilis to S. faecalis strains and between recombination-proficient and -deficient S. faecalis strains in the absence of any plasmid DNA. The transfer required direct cell-to-cell contact and was not inhibited by DNase. The Tetr element was shown to transpose from the S. faecalis chromosome to various locations within the hemolysin plasmid pAD1. Together, the data indicate that the Tetr element, termed transposon Tn925, is very similar to the conjugative transposon Tn916 in both structure and function. A derivative of Tn925, containing transposon Tn917 inserted into a site approximately 3 kb from one end, exhibited elevated transfer frequencies and may provide a useful means for delivering Tn917 by conjugation into various gram-positive species.
Glycomic Analysis of Human Respiratory Tract Tissues and Correlation with Influenza Virus Infection (2013)

The first step in influenza infection of the human respiratory tract is binding of the virus to sialic (Sia) acid terminated receptors. The binding of different strains of virus for the receptor is determined by the α linkage of the sialic acid to galactose and the adjacent glycan structure. In this study the N- and O-glycan composition of the human lung, bronchus and nasopharynx was characterized by mass spectrometry. Analysis showed that there was a wide spectrum of both Sia α2-3 and α2-6 glycans in the lung and bronchus. This glycan structural data was then utilized in combination with binding data from 4 of the published glycan arrays to assess whether these current glycan arrays were able to predict replication of human, avian and swine viruses in human ex vivo respiratory tract tissues. The most comprehensive array from the Consortium for Functional Glycomics contained the greatest diversity of sialylated glycans, but was not predictive of productive replication in the bronchus and lung. Our findings indicate that more comprehensive but focused arrays need to be developed to investigate influenza virus binding in an assessment of newly emerging influenza viruses.
Identification of Three NFAT Binding Motifs in the 5′-Upstream Region of the Human CD3γ Gene That Differentially Bind NFATc1, NFATc2, and NF-κB p50 (2002)

Human immunodeficiency virus, type 1 (HIV-1) infection of CD4(+) T cells progressively abrogates T cell receptor (TCR).CD3 function and surface expression by specifically interfering with CD3gamma gene transcription. Our data show that the loss of CD3gamma transcripts begins very early after infection and accumulates to a >90% deficiency before a significant effect on surface receptor density is apparent. Blocking TCR.CD3-directed NFAT activation with cyclosporin A provokes a partial re-expression of CD3gamma gene transcripts and surface complexes in a time- and dose-dependent manner. We have identified three NFAT consensus sequences (5'-GGAAA-3') in the 5'-upstream region of the human CD3gamma gene at: -124 to -120 (NFAT(gamma1)), -384 to -380 (NFAT(gamma2)), and +450 to +454 (NFAT(gamma3)) from the first transcription initiation site. Using electrophoretic mobility shift and supershift assays, we show that NFATc2 alone binds to the NFAT(gamma2) motif; however, complexes containing either NFATc2 or NFATc1 plus NF-kappaB p50 bind to the NFAT(gamma1) and NFAT(gamma3) sites. We further demonstrate that NFATc1 and NF-kappaB p50 bind in the same protein.DNA complex and that a fourth Ala added to the core sequence (5'-GGAAAA-3') in NFAT(gamma1), and NFAT(gamma3) is critical for their binding. Finally, we have shown that an increase in the binding of nuclear NFATc2, NFATc1, and NF-kappaB p50 to these three motifs is correlated with a progressive loss of CD3gamma transcripts after HIV-1 infection.
Moore's Law: The First Ending and a New Beginning (2013)

Moore's law has accurately predicted roughly biennial doubling of component capacity at minimal cost for almost 50 years. Recent flash memory scaling exhibits increased density, but reduced write and read lifetimes effectively constitute an ending of Moore's law. However, new resilience techniques, including adaptive management algorithms, and storage technologies based on information theory could maintain progress for a decade or more.
An analysis of open information extraction based on semantic role labeling (2011)

Open Information Extraction extracts relations from text without requiring a pre-specified domain or vocabulary. While existing techniques have used only shallow syntactic features, we investigate the use of semantic role labeling techniques for the task of Open IE. Semantic role labeling (SRL) and Open IE, although developed mostly in isolation, are quite related. We compare SRL-based open extractors, which perform computationally expensive, deep syntactic analysis, with TextRunner, an open extractor, which uses shallow syntactic analysis but is able to analyze many more sentences in a fixed amount of time and thus exploit corpus-level statistics. Our evaluation answers questions regarding these systems, including, can SRL extractors, which are trained on PropBank, cope with heterogeneous text found on the Web? Which extractor attains better precision, recall, f-measure, or running time? How does extractor performance vary for binary, n-ary and nested relations? How much do we gain by running multiple extractors? How do we select the optimal extractor given amount of data, available time, types of extractions desired?
Effects of Nitrogen Plasma Treatment on Tantalum Diffusion Barriers in Copper Metallization (2003)

In this study, the barrier properties of ultrathin Ta, TaN, and nitrogen plasma-treated Ta films were investigated by Cu/Ta(N)/Si structure. The barrier properties were evaluated by sheet resistance, film stress, X-ray diffraction, transmission electron microscopy, scanning electron microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. Nitrogen plasma-treated Ta films possess better barrier performance than sputtered Ta and TaN films. The sheet resistance of Cu/Ta/Si and Cu/TaN/Si increases, apparently, after annealing at 600 and 625°C, respectively. The Cu/30 min plasma-treated Ta/Si is fairly stable up to annealing at 700°C for 1 h. Diffusion resistance of the plasma-treated Ta barrier is more effective. It is believed that a new amorphous layer forms on the surface of Ta film after plasma treatment. The new amorphous layer possesses some nanocrystalline phases with lattice constant 0.305 nm. It is believed that the amorphous layer containing some nanocrystals can alleviate Cu diffusion into the Si substrate and, hence, improve barrier performance. © 2002 The Electrochemical Society. All rights reserved.
Induction of DARPP-32 by Brain-Derived Neurotrophic Factor in Striatal Neurons In Vitro Is Modified by Histone Deacetylase Inhibitors and Nab2 (2013)

Neurotrophins and modifiers of chromatin acetylation and deacetylation participate in regulation of transcription during neuronal maturation and maintenance. The striatal medium spiny neuron is supported by cortically-derived brain derived neurotrophic factor and is the most vulnerable neuron in Huntington's disease, in which growth factor and histone deacetylase activity are both disrupted. We examined the ability of three histone deacetylase inhibitors, trichostatin A, valproic acid and Compound 4 b, alone and combined with brain derived neurotrophic factor (BDNF), to promote phenotypic maturation of striatal medium spiny neurons in vitro. Exposure of these neurons to each of the three compounds led to an increase in overall histone H3 and H4 acetylation, dopamine and cyclic AMP-regulated phosphoprotein, 32 kDa (DARPP-32) mRNA and protein, and mRNA levels of other markers of medium spiny neuron maturation. We were, however, unable to prove that HDAC inhibitors directly lead to remodeling of Ppp1r1b chromatin. In addition, induction of DARPP-32 by brain-derived neurotrophic factor was inhibited by histone deacetylase inhibitors. Although BDNF-induced increases in pTrkB, pAkt, pERK and Egr-1 were unchanged by combined application with VPA, the increase in DARPP-32 was relatively diminished. Strikingly, the NGF1A-binding protein, Nab2, was induced by BDNF, but not in the presence of VPA or TSA. Gel shift analysis showed that α-Nab2 super-shifted a band that is more prominent with extract derived from BDNF-treated neurons than with extracts from cultures treated with VPA alone or VPA plus BDNF. In addition, overexpression of Nab2 induced DARPP-32. We conclude that histone deacetylase inhibitors inhibit the induction of Nab2 by BDNF, and thereby the relative induction of DARPP-32.
Epidermal Growth Factor Receptors during Postnatal Development of the Mouse Colon* (1987)

The present study was undertaken to establish the postnatal profile of specific epidermal growth factor (EGF) binding in the maturing mouse colon, with particular emphasis on possible regional differences between both proximal and distal colonic binding patterns vs. those of the small intestine. Binding studies using [125I]EGF were performed on isolated epithelial cells obtained from 2-, 5-, 9-, 16-, and 22-day-old mice as well as adults. At 2 days, cells isolated from the entire colon bound 4 times more [125I]EGF than did corresponding intestinal cells, whereas between the ages of 5 days to adult, colonic cells bound between 1.7-2.5 times more labeled EGF than their intestinal counterparts. The immature colon already exhibited maximal binding after birth as opposed to the small intestine where binding only reached maximal values by the third week of life. Comparison between the proximal and distal colon in 9-, 16-, and 22-day-old mice revealed a further 2-fold increase in EGF binding in the distal colon compared to that in the proximal colon. Scatchard plots of [125I]EGF displacement by native EGF in both proximal and distal colonic segments also revealed the presence of two classes of binding sites, with high affinity constants (K1) significantly greater in the distal colon. These results demonstrate for the first time not only the continued presence of EGF receptors in mouse colonic epithelium, but also significant regional differences in EGF-binding capacity within the digestive tract throughout the postnatal period.
Pig skin as test substrate for evaluating topical antimicrobial activity (1986)

The feasibility of using pathogen-contaminated pig skin as a model substrate for evaluating skin disinfectants was demonstrated. A test methodology is described that is safe, convenient to use, and adaptable to a variety of hand-washing conditions. The treatment protocol, pathogen contamination conditions, and application technique variables can all be carefully controlled to simulate clinical use conditions. The number of organisms transferred by contact was compared with the total organism count on the pig skin. The quantity of organisms transferred ranged from 10 to 60% of the total organisms, depending on the nature of the contamination conditions. The cumulative results of multiple imprint and stripping measurements were consistent with the concentration of inoculated organisms. Tests with alcohol solutions validated the methodology and clearly showed the dependence of topical antimicrobial activity on both the concentration and structure of the alcohol. Activity increased with increasing alcohol concentration and in the following order: ethanol, isopropanol, and n-propanol. All of the alcohols became less active as the severity of the test conditions was increased, i.e., higher inoculum levels for a longer incubation time before treatment. The contact imprint and stripping methods used to evaluate bacterial growth on the skin clearly showed that the alcohol treatments reduced but did not eliminate the inoculated pathogens. It was found that long lifetimes (several hours) for pathogens on the skin are possible under some environmental conditions. This observation strongly suggests that frequent hand washing is a necessary infection control practice even when opportunities for repeated pathogen contamination have not occurred.
l-Type amino acids stimulate gastric acid secretion by activation of the calcium-sensing receptor in parietal cells (2005)

Parietal cells are the primary acid secretory cells of the stomach. We have previously shown that activation of the calcium-sensing receptor (CaSR) by divalent (Ca(2+)) or trivalent (Gd(3+)) ions stimulates acid production in the absence of secretagogues by increasing H(+),K(+)-ATPase activity. When overexpressed in HEK-293 cells, the CaSR can be allosterically activated by L-amino acids in the presence of physiological concentrations of extracellular Ca(2+) (Ca(o)(2+); 1.5-2.5 mM). To determine whether the endogenously expressed parietal cell CaSR is allosterically activated by L-amino acids, we examined the effect of the amino acids L-phenylalanine (L-Phe), L-tryptophan, and L-leucine on acid secretion. In ex vivo whole stomach preparations, exposure to L-Phe resulted in gastric luminal pH significantly lower than controls. Studies using D-Phe (inactive isomer) failed to elicit a response on gastric pH. H(+)-K(+)-ATPase activity was monitored by measuring the intracellular pH (pH(i)) of individual parietal cells in isolated rat gastric glands and calculating the rate of H(+) extrusion. We demonstrated that increasing Ca(o)(2+) in the absence of secretagogues caused a dose-dependent increase in H(+) extrusion. These effects were amplified by the addition of amino acids at various Ca(o)(2+) concentrations. Blocking the histamine-2 receptor with cimetidine or inhibiting system L-amino acid transport with 2-amino-2-norbornane-carboxylic acid did not affect the rate of H(+) extrusion in the presence of L-Phe. These data support the conclusion that amino acids, in conjunction with a physiological Ca(o)(2+) concentration, can induce acid secretion independent of hormonal stimulation via allosteric activation of the stomach CaSR.
Water Intoxication and Syntocinon Infusion (1979)

A case of severe water intoxication with convulsion and prolonged coma, following the use of a high dose Syntocinon infusion is described. The pathogenesis and treatment of the condition are discussed.