Molecular response properties in equation of motion coupled cluster theory: A time-dependent perspective

Molecular response properties for ground and excited states and for transitions between these states are defined by solving the time-dependent Schr\uf6dinger equation for a molecular system in a field of a time-periodic perturbation. In equation of motion coupled cluster (EOM-CC) theory, molecular response properties are commonly obtained by replacing, in configuration interaction (CI) molecular response property expressions, the energies and eigenstates of the CI eigenvalue equation with the energies and eigenstates of the EOM-CC eigenvalue equation. We show here that EOM-CC molecular response properties are identical to the molecular response properties that are obtained in the coupled cluster\u2013configuration interaction (CC-CI) model, where the time-dependent Schr\uf6dinger equation is solved using an exponential (coupled cluster) parametrization to describe the unperturbed system and a linear (configuration interaction) parametrization to describe the time evolution of the unperturbed system. The equivalence between EOM-CC and CC-CI molecular response properties only holds when the CI molecular response property expressions\u2014from which the EOM-CC expressions are derived\u2014are determined using projection and not using the variational principle. In a previous article [F. Paw\u142owski, J. Olsen, and P. J\uf8rgensen, J. Chem. Phys. 142, 114109 (2015)], it was stated that the equivalence between EOM-CC and CC-CI molecular response properties only held for a linear response function, whereas quadratic and higher order response functions were mistakenly said to differ in the two approaches. Proving the general equivalence between EOM-CC and CC-CI molecular response properties is a challenging task, that is undertaken in this article. Proving this equivalence not only corrects the previous incorrect statement but also first and foremost leads to a new, time-dependent, perspective for understanding the basic assumptions on which the EOM-CC molecular response property expressions are founded. Further, the equivalence between EOM-CC and CC-CI molecular response properties highlights how static molecular response properties can be obtained from finite-field EOM-CC energy calculations

Iohexol Clearance for Determination of Glomerular Filtration Rate in Rats Induced to Acute Renal Failure

IntroductionThe glomerular filtration rate (GFR) is considered an especially important tool for the measurement of renal function. Inulin clearance (InCl) is the classic reference method for this purpose, although it is associated with a number of disadvantages; thus, other markers have been proposed, including iohexol. Determination of iohexol clearance (IoCl) has been established for clinical use; however, its application as a GFR marker in experimental rat models has not been reported.ObjectivesThis study aims to standardize a methodology for the measurement of iohexol clearance and to evaluate its applicability as a marker of GFR in rats with induced toxic acute renal failure (ARF), using InCl as the gold standard.Materials and MethodsTwenty-six Wistar male rats (200-300 g) were divided into the following two groups: a control group (n=7) and an ARF group (n=19). ARF was induced by the subcutaneous administration of cisplatin (5 mg/kg); IoCl and InCl were determined simultaneously, and plasma creatinine (pCreat) dosage was measured colorimetrically.ResultsThe pCreat, InCl and IoCl levels were consistent with the expected values for the renal function ranges of the evaluated animals, and the IoCl and InCl levels were significantly correlated (r=0.792). An inverse moderate linear correlation between the IoCl and pCreat measurements (r=-0.587) and between the InCl and pCreat measurements (r=-0.722) were observed.ConclusionThese results confirm a correlation between IoCl and the gold standard of GFR, InCl measurement. IoCl offers a relevant advantage over InCl because determination of the former allows the animal to live after the procedure.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Universidade Federal de São Paulo, Dept Med, Div Nephrol, São Paulo, SP, BrazilUniv São Paulo, Inst Biomed Sci, Dept Immunol, São Paulo, SP, BrazilUniv São Paulo, Sch Med, Dept Nephrol, São Paulo, SP, BrazilUniversidade Federal de São Paulo, Dept Med, Div Nephrol, São Paulo, SP, BrazilWeb of Scienc

New Optical Reddening Maps of the Large and Small Magellanic Clouds

We present new reddening maps of the SMC and LMC based on the data of the third phase of the Optical Gravitational Lensing Experiment (OGLE III). We have used two different methods to derive optical reddening maps. We adopt a theoretical mean unreddened colour for the red clump in the SMC and LMC, respectively. We subdivide the photometric data for both Clouds into subfields and calculate the difference between the observed red clump position and the theoretical value for each field, which provides us with the reddening value in (V-I). Furthermore reddening values are obtained for 13490 LMC RR Lyrae ab and 1529 SMC RR Lyrae ab stars covering the whole OGLE III region of the MCs. The observed colours (V-I) of the RR Lyrae stars are compared with the colour from the absolute magnitudes. The absolute magnitude of each RR Lyrae star is computed using its period and metallicity derived from Fourier decomposition of its lightcurve. In general we find a low and uniform reddening distribution in both Magellanic Clouds. The red clump method indicates a mean reddening of the LMC of E(V-I) = 0.09 +/- 0.07 mag, while for the SMC E(V-I) = 0.04 +/- 0.06 mag is obtained. With RR Lyrae stars a median value of E(V-I) = 0.11 +/- 0.06 mag for the LMC and E(V-I) = 0.07 +/- 0.06 mag for the SMC is found. The LMC shows very low reddening in the bar region, whereas the reddening in the star-forming leading edge and 30 Doradus is considerably higher. In the SMC three pronounced regions with higher reddening are visible. Two are located along the bar, while the highest reddening is found in the star-forming wing of the SMC. In general the regions with higher reddening are in good spatial agreement with infrared reddening maps as well as with reddening estimations of other studies. The position-dependent reddening values from the red clump method are available via the Virtual Observatory interface.Comment: 15 pages, 22 Figures, AJ publishe

An RxLR effector from phytophthora infestans prevents re-localisation of two plant NAC transcription factors from the endoplasmic reticulum to the nucleus

The plant immune system is activated following the perception of exposed, essential and invariant microbial molecules that are recognised as non-self. A major component of plant immunity is the transcriptional induction of genes involved in a wide array of defence responses. In turn, adapted pathogens deliver effector proteins that act either inside or outside plant cells to manipulate host processes, often through their direct action on plant protein targets. To date, few effectors have been shown to directly manipulate transcriptional regulators of plant defence. Moreover, little is known generally about the modes of action of effectors from filamentous (fungal and oomycete) plant pathogens. We describe an effector, called Pi03192, from the late blight pathogen Phytophthora infestans, which interacts with a pair of host transcription factors at the endoplasmic reticulum (ER) inside plant cells. We show that these transcription factors are released from the ER to enter the nucleus, following pathogen perception, and are important in restricting disease. Pi03192 prevents the plant transcription factors from accumulating in the host nucleus, revealing a novel means of enhancing host susceptibility

The early intestinal immune response in experimental neonatal ovine cryptosporidiosis is characterized by an increased frequency of perforin expressing NCR1(+) NK cells and by NCR1(-) CD8(+) cell recruitment

Cryptosporidium parvum, a zoonotic protozoan parasite, causes important losses in neonatal ruminants. Innate immunity plays a key role in controlling the acute phase of this infection. The participation of NCR1+ Natural Killer (NK) cells in the early intestinal innate immune response to the parasite was investigated in neonatal lambs inoculated at birth. The observed increase in the lymphocyte infiltration was further studied by immunohistology and flow cytometry with focus on distribution, density, cellular phenotype related to cytotoxic function and activation status. The frequency of NCR1+ cells did not change with infection, while their absolute number slightly increased in the jejunum and the CD8+/NCR1- T cell density increased markedly. The frequency of perforin+ cells increased significantly with infection in the NCR1+ population (in both NCR1+/CD16+ and NCR1+/CD16- populations) but not in the NCR1-/CD8+ population. The proportion of NCR1+ cells co-expressing CD16+ also increased. The fraction of cells expressing IL2 receptor (CD25), higher in the NCR1+/CD8+ population than among the CD8+/NCR1- cells in jejunal Peyer's patches, remained unchanged during infection. However, contrary to CD8+/NCR1- lymphocytes, the intensity of CD25 expressed by NCR1+ lymphocytes increased in infected lambs. Altogether, the data demonstrating that NK cells are highly activated and possess a high cytotoxic potential very early during infection, concomitant with an up-regulation of the interferon gamma gene in the gut segments, support the hypothesis that they are involved in the innate immune response against C. parvum. The early significant recruitment of CD8+/NCR1- T cells in the small intestine suggests that they could rapidly drive the establishment of the acquired immune response

Chemical abundances of metal-poor RR Lyrae stars in the Magellanic Clouds

We present for the first time a detailed spectroscopic study of chemical element abundances of metal-poor RR Lyrae stars in the Large and Small Magellanic Cloud (LMC and SMC). Using the MagE echelle spectrograph at the 6.5m Magellan telescopes, we obtain medium resolution (R ~ 2000 - 6000) spectra of six RR Lyrae stars in the LMC and three RR Lyrae stars in the SMC. These stars were chosen because their previously determined photometric metallicities were among the lowest metallicities found for stars belonging to the old populations in the Magellanic Clouds. We find the spectroscopic metallicities of these stars to be as low as [Fe/H]_{spec} = -2.7dex, the lowest metallicity yet measured for any star in the Magellanic Clouds. We confirm that for metal-poor stars, the photometric metallicities from the Fourier decomposition of the lightcurves are systematically too high compared to their spectroscopic counterparts. However, for even more metal-poor stars below [Fe/H]_{phot} < -2.8dex this trend is reversed and the spectroscopic metallicities are systematically higher than the photometric estimates. We are able to determine abundance ratios for ten chemical elements, which extend the abundance measurements of chemical elements for RR Lyrae stars in the Clouds beyond [Fe/H] for the first time. For the overall [alpha/Fe] ratio, we obtain an overabundance of 0.36dex, which is in very good agreement with results from metal-poor stars in the Milky Way halo as well as from the metal-poor tail in dwarf spheroidal galaxies. Comparing the abundances with those of the stars in the Milky Way halo we find that the abundance ratios of stars of both populations are consistent with another. Therefore we conclude that from a chemical point of view early contributions from Magellanic-type galaxies to the formation of the Galactic halo as claimed in cosmological models are plausible.Comment: accepted for publication in AJ, 19 pages, 12 figure

Harmonization of Food-Frequency Questionnaires and Dietary Pattern Analysis in 4 Ethnically Diverse Birth Cohorts

Background: Canada is an ethnically diverse nation, which introduces challenges for health care providers tasked with providing evidence-based dietary advice. Objectives: We aimed to harmonize food-frequency questionnaires (FFQs) across 4 birth cohorts of ethnically diverse pregnant women to derive robust dietary patterns to investigate maternal and newborn outcomes. Methods: The NutriGen Alliance comprises 4 prospective birth cohorts and includes 4880 Canadian mother-infant pairs of predominantly white European [CHILD (Canadian Healthy Infant Longitudinal Development) and FAMILY (Family Atherosclerosis Monitoring In earLY life)], South Asian [START (SouTh Asian birth cohoRT)-Canada], or Aboriginal [ABC (Aboriginal Birth Cohort)] origins. CHILD used a multiethnic FFQ based on a previously validated instrument designed by the Fred Hutchinson Cancer Research Center, whereas FAMILY, START, and ABC used questionnaires specifically designed for use in white European, South Asian, and Aboriginal people, respectively. The serving sizes and consumption frequencies of individual food items within the 4 FFQs were harmonized and aggregated into 36 common food groups. Principal components analysis was used to identify dietary patterns that were internally validated against self-reported vegetarian status and externally validated against a modified Alternative Healthy Eating Index (mAHEI). Results: Three maternal dietary patterns were identified—“plant-based,” “Western,” and “health-conscious”—which collectively explained 29% of the total variability in eating habits observed in the NutriGen Alliance. These patterns were strongly associated with self-reported vegetarian status (OR: 3.85; 95% CI: 3.47, 4.29; r2 = 0.30, P < 0.001; for a plant-based diet), and average adherence to the plant-based diet was higher in participants in the fourth quartile of the mAHEI than in the first quartile (mean difference: 46.1%; r2 = 0.81, P < 0.001). Conclusion: Dietary data collected by using FFQs from ethnically diverse pregnant women can be harmonized to identify common dietary patterns to investigate associations between maternal dietary intake and health outcomes

Genomics and proteomics approaches to the study of cancer-stroma interactions

<p>Abstract</p> <p>Background</p> <p>The development and progression of cancer depend on its genetic characteristics as well as on the interactions with its microenvironment. Understanding these interactions may contribute to diagnostic and prognostic evaluations and to the development of new cancer therapies. Aiming to investigate potential mechanisms by which the tumor microenvironment might contribute to a cancer phenotype, we evaluated soluble paracrine factors produced by stromal and neoplastic cells which may influence proliferation and gene and protein expression.</p> <p>Methods</p> <p>The study was carried out on the epithelial cancer cell line (Hep-2) and fibroblasts isolated from a primary oral cancer. We combined a conditioned-medium technique with subtraction hybridization approach, quantitative PCR and proteomics, in order to evaluate gene and protein expression influenced by soluble paracrine factors produced by stromal and neoplastic cells.</p> <p>Results</p> <p>We observed that conditioned medium from fibroblast cultures (FCM) inhibited proliferation and induced apoptosis in Hep-2 cells. In neoplastic cells, 41 genes and 5 proteins exhibited changes in expression levels in response to FCM and, in fibroblasts, 17 genes and 2 proteins showed down-regulation in response to conditioned medium from Hep-2 cells (HCM). Nine genes were selected and the expression results of 6 down-regulated genes (<it>ARID4A</it>, <it>CALR</it>, <it>GNB2L1</it>, <it>RNF10</it>, <it>SQSTM1</it>, <it>USP9X</it>) were validated by real time PCR.</p> <p>Conclusions</p> <p>A significant and common denominator in the results was the potential induction of signaling changes associated with immune or inflammatory response in the absence of a specific protein.</p