gebhart/patrepeval huggingface dataset:
Synthetic Control of Excited-State Properties in Cyclometalated Ir(III) Complexes Using Ancillary Ligands (2005)

The synthesis and photophysical characterization of a series of (N,C(2')-(2-para-tolylpyridyl))2 Ir(LL') [(tpy)2 Ir(LL')] (LL' = 2,4-pentanedionato (acac), bis(pyrazolyl)borate ligands and their analogues, diphosphine chelates and tert-butylisocyanide (CN-t-Bu)) are reported. A smaller series of [(dfppy)2 Ir(LL')] (dfppy = N,C(2')-2-(4',6'-difluorophenyl)pyridyl) complexes were also examined along with two previously reported compounds, (ppy)2 Ir(CN)2- and (ppy)2 Ir(NCS)2- (ppy = N,C(2')-2-phenylpyridyl). The (tpy)2 Ir(PPh2CH2)2 BPh2 and [(tpy)2 Ir(CN-t-Bu)2](CF3SO3) complexes have been structurally characterized by X-ray crystallography. The Ir-C(aryl) bond lengths in (tpy)2 Ir(CN-t-Bu)2+ (2.047(5) and 2.072(5) A) and (tpy)2 Ir(PPh2CH2)2 BPh2 (2.047(9) and 2.057(9) A) are longer than their counterparts in (tpy)2 Ir(acac) (1.982(6) and 1.985(7) A). Density functional theory calculations carried out on (ppy)2 Ir(CN-Me)2+ show that the highest occupied molecular orbital (HOMO) consists of a mixture of phenyl-pi and Ir-d orbitals, while the lowest unoccupied molecular orbital is localized primarily on the pyridyl-pi orbitals. Electrochemical analysis of the (tpy)2 Ir(LL') complexes shows that the reduction potentials are largely unaffected by variation in the ancillary ligand, whereas the oxidation potentials vary over a much wider range (as much as 400 mV between two different LL' ligands). Spectroscopic analysis of the cyclometalated Ir complexes reveals that the lowest energy excited state (T1) is a triplet ligand-centered state (3LC) on the cyclometalating ligand admixed with 1MLCT (MLCT = metal-to-ligand charge-transfer) character. The different ancillary ligands alter the 1MLCT state energy mainly by changing the HOMO energy. Destabilization of the 1MLCT state results in less 1MLCT character mixed into the T1 state, which in turn leads to an increase in the emission energy. The increase in emission energy leads to a linear decrease in ln(k(nr)) (k(nr) = nonradiative decay rate). Decreased 1MLCT character in the T1 state also increases the Huang-Rhys factors in the emission spectra, decreases the extinction coefficient of the T1 transition, and consequently decreases the radiative decay rates (k(r)). Overall, the luminescence quantum yields decline with increasing emission energies. A linear dependence of the radiative decay rate (k(r)) or extinction coefficient (epsilon) on (1/deltaE)2 has been demonstrated, where deltaE is the energy difference between the 1MLCT and 3LC transitions. A value of 200 cm(-1) for the spin-orbital coupling matrix element 3LC absolute value(H(SO)) 1MLCT of the (tpy)2 Ir(LL') complexes can be deduced from this linear relationship. The (fppy)2 Ir(LL') complexes with corresponding ancillary ligands display similar trends in excited-state properties.
Fusion of phosphatidylethanolamine-containing liposomes and mechanism of L.alpha.-HII phase transition (1986)

The initial kinetics of fusion and leakage of liposomes composed of N-methylated dioleoylphosphatidylethanolamine (DOPE-Me) have been correlated with the phase behavior of this lipid. Gagné et al. [Gagné, J., Stamatatos, L., Diacovo, T., Hui, S. W., Yeagle, P., & Silvius, J. (1985) Biochemistry 24, 4400-4408] have shown that this lipid is lamellar (L alpha) below 20 degrees C, is hexagonal (HII) above 70 degrees C, and shows isotropic 31P NMR resonances at intermediate temperatures. This isotropic state is also characterized by complex morphological structures. We have prepared DOPE-Me liposomes at pH 9.5 and monitored the temperature dependence of the mixing of aqueous contents, leakage, and changes in light scattering upon reduction of the pH to 4.5. At and below 20 degrees C, where the lipid is in the L alpha phase, there is very little aggregation or destabilization of the liposomes. Between 30 and 60 degrees C, i.e., where the lipid is in the isotropic state, the initial rates of liposome fusion (mixing of aqueous contents) and leakage increase. At temperatures approaching that where the hexagonal HII phase transition occurs, the initial rates and extents of fusion decrease, whereas leakage is enhanced. Similar results were found for dioleoylphosphatidylethanolamine/dioleoylphosphatidylcholine (2:1) liposomes. These results clearly establish a common mechanism between the appearance of the isotropic state (between the L alpha and HII phases) and the promotion of liposome fusion. We propose a simple model to explain both the observed behavior of phosphatidylethanolamine-containing membranes with respect to liposome fusion and/or lysis and the beginning of the L alpha-HII phase transition.
Growth ofCampylobacter jejuniSupported by Respiration of Fumarate, Nitrate, Nitrite, Trimethylamine-N-Oxide, or Dimethyl Sulfoxide Requires Oxygen (2002)

ABSTRACT The human gastrointestinal pathogen Campylobacter jejuni is a microaerophilic bacterium with a respiratory metabolism. The genome sequence of C. jejuni strain 11168 reveals the presence of genes that encode terminal reductases that are predicted to allow the use of a wide range of alternative electron acceptors to oxygen, including fumarate, nitrate, nitrite, and N - or S -oxides. All of these reductase activities were present in cells of strain 11168, and the molybdoenzyme encoded by Cj0264c was shown by mutagenesis to be responsible for both trimethylamine- N -oxide (TMAO) and dimethyl sulfoxide (DMSO) reduction. Nevertheless, growth of C. jejuni under strictly anaerobic conditions (with hydrogen or formate as electron donor) in the presence of any of the electron acceptors tested was insignificant. However, when fumarate, nitrate, nitrite, TMAO, or DMSO was added to microaerobic cultures in which the rate of oxygen transfer was severely restricted, clear increases in both the growth rate and final cell density compared to what was seen with the control were obtained, indicative of electron acceptor-dependent energy conservation. The C. jejuni genome encodes a single class I-type ribonucleotide reductase (RNR) which requires oxygen to generate a tyrosyl radical for catalysis. Electron microscopy of cells that had been incubated under strictly anaerobic conditions with an electron acceptor showed filamentation due to an inhibition of cell division similar to that induced by the RNR inhibitor hydroxyurea. An oxygen requirement for DNA synthesis can thus explain the lack of anaerobic growth of C. jejuni . The results indicate that strict anaerobiosis is a stress condition for C. jejuni but that alternative respiratory pathways can contribute significantly to energy conservation under oxygen-limited conditions, as might be found in vivo.
Regulatory role of peritoneal NK1.1+ alpha beta T cells in IL-12 production during Salmonella infection. (1999)

NK1.1+ alpha beta T cells emerge in the peritoneal cavity after an i.p. infection with Salmonella choleraesuis in mice. To elucidate the role of the NK1.1+ alpha beta T cells during murine salmonellosis, mice lacking NK1.1+ alpha beta T cells by disruption of TCR beta (TCR beta-/-), beta 2m (beta 2m-/-), or J alpha 281 (J alpha 281-/-) gene were i.p. inoculated with S. choleraesuis. The peritoneal exudate T cells in wild type (wt) mice on day 3 after infection produced IL-4 upon TCR alpha beta stimulation, whereas those in TCR beta-/-, beta 2m-/-, or J alpha 281-/- mice showed no IL-4 production upon the stimulation, indicating that NK1.1+ alpha beta T cells are the main source of IL-4 production at the early phase of Salmonella infection. Neutralization of endogenous IL-4 by administration of anti-IL-4 mAb to wt mice reduced the number of Salmonella accompanied by increased IL-12 production by macrophages after Salmonella infection. The IL-12 production by the peritoneal macrophages was significantly augmented in mice lacking NK1.1+ alpha beta T cells after Salmonella infection accompanied by increased serum IFN-gamma level. The aberrantly increased IL-12 production in infected TCR beta-/- or J alpha 281-/- mice was suppressed by adoptive transfer of T cells containing NK1.1+ alpha beta T cells but not by the transfer of T cells depleted of NK1.1+ alpha beta T cells or T cells from J alpha 281-/- mice. Taken together, it is suggested that NK1. 1+ alpha beta T cells eliciting IL-4 have a regulatory function in the IL-12 production by macrophages at the early phase of Salmonella infection.
Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling (2011)

Successful development of fruit flies depends on a gut bacterium that interacts with its host’s insulin-signaling pathway.
Automatic delineation of lateral facies changes in clastic environments (1989)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1989Automatic delineation of lateral facies changes in clastic environmentsAuthors: Donald A. VosslerDonald A. VosslerLandmark Graphics Corp.https://doi.org/10.1190/1.1889778 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1889778FiguresReferencesRelatedDetailsCited bySand fraction prediction from seismic attributes using optimized support vector regression in an oil reservoir6 February 2020 | Earth Science Informatics, Vol. 13, No. 2 SEG Technical Program Expanded Abstracts 1989ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1989 Pages: 1375 publication data© 1989 Copyright © 1989 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 10 Feb 2005 CITATION INFORMATION Donald A. Vossler, (1989), "Automatic delineation of lateral facies changes in clastic environments," SEG Technical Program Expanded Abstracts : 803-804. https://doi.org/10.1190/1.1889778 Plain-Language Summary PDF DownloadLoading ...
Down-Regulation of Human Complement Factor H Sensitizes Non-Small Cell Lung Cancer Cells to Complement Attack and Reduces In Vivo Tumor Growth (2007)

Malignant cells are often resistant to complement activation through the enhanced expression of complement inhibitors. In this work, we examined the protective role of factor H, CD46, CD55, and CD59 in two non-small cell lung cancer cell lines, H1264 and A549, upon activation of the classical pathway of complement. Complement was activated with polyclonal Abs raised against each cell line. After blocking factor H activity with a neutralizing Ab, C3 deposition and C5a release were more efficient. Besides, a combined inhibition of factor H and CD59 significantly increased complement-mediated lysis. CD46 and CD55 did not show any effect in the control of complement activation. Factor H expression was knockdown on A549 cells using small interfering RNA. In vivo growth of factor H-deficient cells in athymic mice was significantly reduced. C3 immunocytochemistry on explanted xenografts showed an enhanced activation of complement in these cells. Besides, when mice were depleted of complement with cobra venom factor, growth was recovered, providing further evidence that complement was important in the reduction of in vivo growth. In conclusion, we show that expression of the complement inhibitor factor H by lung cancer cells can prevent complement activation and improve tumor development in vivo. This may have important consequences in the efficiency of complement-mediated immunotherapies.
Inhibition of 5-lipoxygenase blocks IL-1 beta-induced vascular adhesion molecule-1 gene expression in human endothelial cells (1997)

Inflammation is characterized by the recruitment of leukocytes and their subsequent migration from the vasculature into the tissue, where they often cause severe damage. Endothelial cells play a major role in this cascade by expressing cell surface adhesion molecules, such as VCAM-1 and ICAM-1, and chemokines, in response to cytokines. Many of these genes are under the control of inflammatory response transcription factors such as nuclear factor (NF)-kappa B. In this study, we examined the effects of 5-lipoxygenase inhibitors (nordihydroguaiaretic acid and AA861) on IL-1 beta-induced VCAM-1 gene expression in HUVECs. We demonstrated that 5-lipoxygenase inhibitors, but not cyclooxygenase inhibitors, block IL-1 beta-induced VCAM-1 cell surface expression and promoter activity. In transiently transfected HUVECs, NF-kappa B-dependent gene expression was inhibited by 5-lipoxygenase inhibitors. These inhibitors did not block IL-1 beta-induced nuclear translocation of NF-kappa B, inhibitor of kappa B-alpha proteolytic degradation, or significantly reduce phosphorylation of p65. These studies indicate that inhibition of 5-lipoxygenase blocks cytokine-induced VCAM-1 gene expression by reducing the functional activity of NF-kappa B/Rel proteins in HUVECs.
Improving NAND Flash Based Disk Caches (2008)

Flash is a widely used storage device that provides high density and low power, appealing properties for general purpose computing. Today, its usual application is in portable special purpose devices such as MP3 players. In this paper we examine its use in the server domain—a more general purpose environment. Aggressive process scaling and the use of multi-level cells continues to improve density ahead of Moore’s Law predictions, making Flash even more attractive as a general purpose memory solution. Unfortunately, reliability limits the use of Flash. To seriously consider Flash in the server domain, architectural support must exist to address this concern. This paper first shows how Flash can be used in today’s server platforms as a disk cache. It then proposes two improvements. The first improves performance and reliability by splitting Flash based disk caches into separate read and write regions. The second improves reliability by employing a programmable Flash memory controller. It can change the error code strength (number of correctable bits) and the number of bits that a memory cell can store (cell density) according to the demands of the application. Our studies show that Flash reduces overall power consumed by the system memory and hard disk drive up to 3 times while maintaining performance. We also show that Flash lifetime can be improved by a factor of 20 when using a programmable Flash memory controller, if some performance degradation (below 5%) is acceptable.
The Severity of Chorioamnionitis in Pregnant Sheep Is Associated with In Vivo Variation of the Surface-Exposed Multiple-Banded Antigen/Gene of Ureaplasma parvum (2010)

Ureaplasma species are the bacteria most frequently isolated from human amniotic fluid in asymptomatic pregnancies and placental infections. Ureaplasma parvum serovars 3 and 6 are the most prevalent serovars isolated from men and women. We hypothesized that the effects on the fetus and chorioamnion of chronic ureaplasma infection in amniotic fluid are dependent on the serovar, dose, and variation of the ureaplasma multiple-banded antigen (MBA) and mba gene. We injected high- or low-dose U. parvum serovar 3, serovar 6, or vehicle intra-amniotically into pregnant ewes at 55 days of gestation (term = 150 days) and examined the chorioamnion, amniotic fluid, and fetal lung tissue of animals delivered by cesarean section at 125 days of gestation. Variation of the multiple banded antigen/mba generated by serovar 3 and serovar 6 ureaplasmas in vivo were compared by PCR assay and Western blot. Ureaplasma inoculums demonstrated only one (serovar 3) or two (serovar 6) MBA variants in vitro, but numerous antigenic variants were generated in vivo: serovar 6 passage 1 amniotic fluid cultures contained more MBA size variants than serovar 3 (P = 0.005), and ureaplasma titers were inversely related to the number of variants (P = 0.025). The severity of chorioamnionitis varied between animals. Low numbers of mba size variants (five or fewer) within amniotic fluid were associated with severe inflammation, whereas the chorioamnion from animals with nine or more mba variants showed little or no inflammation. These differences in chorioamnion inflammation may explain why not all women with in utero Ureaplasma spp. experience adverse pregnancy outcomes.
Isolation and Analysis of a T Cell Clone Variant Exhibiting Constitutively Phosphorylated Ser133 cAMP Response Element-Binding Protein (1998)

In driving T cell proliferation, IL-2 stimulates a new program of gene expression that includes proliferating cell nuclear antigen (PCNA), a requisite processivity factor for DNA polymerase delta. PCNA transcription is regulated in part through tandem CRE sequences in the promoter and CRE binding proteins; IL-2 stimulates CREB phosphorylation in the resting cloned T lymphocyte, L2. After culturing L2 cells for greater than 91 days, we consistently isolate a stable variant that exhibits constitutive CREB phosphorylation. L2 and L2 variant cells were tested for IL-2 responsiveness and rapamycin sensitivity with respect to specific kinase activity, PCNA expression and proliferation. In L2 cells, IL-2 stimulated and rapamycin inhibited the following: cAMP-independent CREB kinase activity, PCNA expression and proliferation. In L2 variant cells, CREB kinase activity was constitutively high; IL-2 stimulated and rapamycin blocked PCNA expression and proliferation. These results indicate that IL-2 induces a rapamycin-sensitive, cAMP-independent CREB kinase activity in L2 cells. However, phosphorylation of CREB alone is not sufficient to drive PCNA expression and L2 cell proliferation in the absence of IL-2.
Effect of zinc(II) and other divalent cations on binding of 3,5,3′-triiodo-L-thyronine to nuclear receptors from cultured GC cells (1989)

The effect of Zn(II) in 3,5,3'-triiodo-L-thyronine (T3) binding to nuclear receptors was studied in dialyzed 0.4 M NaCl extracts of nuclei from cultured GC cells. Addition of ZnCl2 to nuclear extracts resulted in a time- and concentration-dependent dissociation of T3 from nuclear receptors. Half-maximal dissociation occurred at 6 microM ZnCl2. Addition of ZnCl2 also resulted in a concentration-dependent inhibition of binding of T3 to nuclear receptors. Half-maximal inhibition of binding occurred at 1-3 microM ZnCl2. Scatchard analysis indicated that Zn(II) addition decreased kA and did not alter receptor concentration. These effects of Zn(II) were prevented when ZnCl2 was added to nuclear extracts in the presence of 5 mM EDTA or 5 mM dithiothreitol. Moreover, Zn(II)-induced inhibition of T3 binding was reversed by the addition of 5 mM EDTA. The inhibitory effect of Zn(II) on T3 binding seemed specific for nuclear receptors; no effect of Zn(II) on the binding of T3 to proteins in rat serum or GC cell cytosol or to rabbit anti-T3 serum was observed. Cd(II) had a similar concentration-dependent inhibition of T3 binding to nuclear receptors which was reversible. Our findings suggest that Zn(II) may play a role in T3 binding to nuclear receptors as well as its putative role in the binding of receptor to DNA.
Non-Poissonian Quantum Jumps of a Fluxonium Qubit due to Quasiparticle Excitations (2014)

As the energy relaxation time of superconducting qubits steadily improves, nonequilibrium quasiparticle excitations above the superconducting gap emerge as an increasingly relevant limit for qubit coherence. We measure fluctuations in the number of quasiparticle excitations by continuously monitoring the spontaneous quantum jumps between the states of a fluxonium qubit, in conditions where relaxation is dominated by quasiparticle loss. Resolution on the scale of a single quasiparticle is obtained by performing quantum nondemolition projective measurements within a time interval much shorter than T₁, using a quantum-limited amplifier (Josephson parametric converter). The quantum jump statistics switches between the expected Poisson distribution and a non-Poissonian one, indicating large relative fluctuations in the quasiparticle population, on time scales varying from seconds to hours. This dynamics can be modified controllably by injecting quasiparticles or by seeding quasiparticle-trapping vortices by cooling down in a magnetic field.
Phosphatidylinositol-3-Kinase/Akt Signaling Pathway and Kidney Cancer, and the Therapeutic Potential of Phosphatidylinositol-3-Kinase/Akt Inhibitors (2009)

The PI3K/Akt pathway has a pivotal role in renal cell carcinoma pathogenesis and, thus, represents an ideal target for therapeutic intervention. Of the several compounds in early phases of development only perifosine has already proved to be clinically active. Thus, it should be considered an extremely interesting drug to be used alone or in combination.
Safety and efficacy of neratinib (HKI-272) in combination with paclitaxel in patients with solid tumors (2009)

3557 Background: Neratinib (HKI-272) is a potent irreversible pan-ErbB inhibitor of the tyrosine kinase receptors, erbB-1,-2 and -4. In this phase 1 study, a combination dose of neratinib plus paclitaxel that is tolerable was determined in patients (pts) with solid tumors, and safety and preliminary efficacy were assessed in pts with erbB-2+ metastatic breast cancer. Methods: In this open label, 2-part study, ascending multiple daily oral doses of neratinib (160 mg, 240 mg) were administered in combination with IV paclitaxel 80 mg/m 2 , if tolerable, or 70 mg/m 2 on days 1, 8 and 15. Pts with solid tumors and pts with only metastatic erbB-2+ breast cancer are enrolled in part 1 and 2, respectively. Tumor measurements were made at screening and at every 8 weeks (2 cycles) by modified RECIST criteria. Timed blood samples were collected for neratinib and paclitaxel plasma concentration determination, and PK analyses were performed using a noncompartmental method. Results: Data for 54 pts as of 30 Oct 2008 are presented (median age [range] of 51.5 [20–74] yrs; 91% female; 26 % with prior trastuzumab treatment of median duration [range] 32.5 [10–52] wks; 15% with prior lapatinib treatment). Tumor types in part 1 included breast, endometrial, cervical, colorectal and esophageal cancer. There were no dose-limiting toxicities (DLTs) at the 240 mg neratinib-80 mg/m 2 paclitaxel dose, and as standard doses of neratinib and paclitaxel were reached, there was no reason for further escalation. Neratinib-related AEs, any grade in ≥10% of pts included diarrhea (50%), neutropenia (17%), rash (13%), nausea (11%) and vomiting (11%). Neratinib- related AEs, grade ≥3 in ≥2% of pts were diarrhea (20%), neutropenia (9%) and dehydration (4%). Only 2 pts (at the 240 mg neratinib-80 mg/m 2 paclitaxel dose) had dose reductions due to diarrhea. In 35 efficacy evaluable pts, 5 had confirmed partial response (PR). Confirmed clinical benefit (PR and prolonged disease stabilization) was seen in 2 pts in part 1, 1 pt with endometrial cancer and 1 pt with cervical cancer. Conclusions: This combination of 240 mg neratinib and 80 mg/m 2 paclitaxel was tolerable with a toxicity profile similar to that observed for neratinib, and had promising antitumor activity in pts with solid tumors and erbB-2 + breast cancer. [Table: see text]
Classification of transversal gates in qubit stabilizer codes (2016)

This work classifies the set of diagonal gates that can implement a single or two-qubit transversal logical gate for qubit stabilizer codes. We show that individual physical diagonal gates on the underlying qubits that compose the code are restricted to have entries of the form e iπc/2 k along their diagonal, resulting in a similarly restricted class of logical gates that can be implemented in this manner. As such, we show that all diagonal logical gates that can be implemented transversally by individual physical diagonal gates must belong to the Clifford hierarchy. Moreover, we show that for a given stabilizer code, the two-qubit diagonal transversal gates must belong to the same level of Clifford hierarchy as the single-qubit diagonal transversal gates available for the given code. We use this result to prove a conjecture about arbitrary transversal gates made by Zeng et al. in 2007.