Nanoplasmonics simulations at the basis set limit through completeness-optimized, local numerical basis sets

We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers. We obtain basis sets of improving accuracy up to the complete basis set limit and demonstrate that the performance of the basis sets transfers to simulations of larger nanoparticles and nanoalloys as well as to calculations with various exchange-correlation functionals. This work promotes the use of the local basis set approach of controllable accuracy in first-principles nanoplasmonics simulations and beyond.Comment: 11 pages, 6 figure

Reexamining the Lyman-Birge-Hopfield band of N2

Motivated by fundamental molecular physics and by atmospheric and planetary sciences, the valence excitations of N2 gas have seen several decades of intensive study, especially by electron-energy-loss spectroscopy (EELS). It was consequently surprising when a comparison of nonresonant inelastic x-ray scattering (NIXS) and nonresonant EELS found strong evidence for violations of the first Born approximation for EELS when leaving the dipole scattering limit. Here we reassess the relative strengths of the constituent resonances of the lowest-energy excitations of N2, encompassed by the so-called Lyman-Birge-Hopfield (LBH) band, expanding on the prior, qualitative interpretation of the NIXS results for N2 by both quantifying the generalized oscillator strength of the lowest-energy excitations and also presenting a time-dependent density functional theory (TDDFT) calculation of the q dependence of the entire low-energy electronic excitation spectrum. At high q, we find that the LBH band has an unexpectedly large contribution from the octupolar w 1Δu resonance exactly in the regime where theory and EELS experiment for the presumed-dominant a 1Πg resonance have previously had substantial disagreement, and also where the EELS results must now be expected to show violations of the Born approximation. After correcting for this contamination, the a 1Πg generalized oscillator strength from the NIXS results is in good agreement with prior theory. The NIXS spectra, over their entire q range, also find satisfactory agreement with the TDDFT calculations for both bound and continuum excitations.This work was supported by the US Department of Energy, the Natural Sciences and Engineering Research Council (NSERC) of Canada, the Australian Research Council, the Research Funds of the University of Helsinki, and the Academy of Finland (Contract No. 1127462, Centers of Excellence Program 2006-2011, and National Graduate School in Materials Physics). A.R. acknowledges support by MICINN (FIS2010-21282-C02-01),ACI-promociona (ACI2009-1036), Grupos Consolidados UPV/EHU del Gobierno Vasco (IT-319- 07), and the European Community through e-I3 ETSF project (Contract No. 211956).Peer Reviewe

Inversed linear dichroism in F <em>K</em>-edge NEXAFS spectra of fluorinated planar aromatic molecules

et al.The symmetry and energy distribution of unoccupied molecular orbitals is addressed in this work by means of NEXAFS and density functional theory calculations for planar, fluorinated organic semiconductors (perfluorinated copper phthalocyanines and perfluoropentacene). We demonstrate how molecular orbitals with significant density of states on the fluorine atoms show different symmetry from those mainly located on C and N atoms. As a result, the angle-dependent linear dichroism in NEXAFS F K-edge spectra is inversed with respect to that in the C and N K-edges. In addition, the significant overlap in energy of π * and σ * orbitals throughout the F K-edge spectrum hampers its use for analysis of molecular orientations from angle-dependent NEXAFS measurements. © 2012 American Physical Society.J.E.O. and A.R. acknowledge funding from the Spanish MEC through Grants No. FIS2011-65702-C02-01, No. MAT2010-21156-C03-01, and No. PIB2010US-00652, and from the Basque Government through Grants No. IT-257-07 and No. IT-319-07. A.R. additionally acknowledges that financial support was provided by ACI-Promociona Grant No. ACI2009-1036 and the European Research Council Advanced Grant DYNamo (ERC-2010-AdG, Proposal No. 267374). A.S. acknowledges the support of the Research Funds of the University of Helsinki and the Academy of Finland through Contract No. 1127462, Centers of Excellence Program, and the National Graduate School in Materials Physics. J.M.G.L. acknowledges support from The Lundbeck Foundation’s Center for Atomic-Scale Materials Design and the Danish Center for Scientific Computing.Peer Reviewe

The Magnitude of Androgen Receptor Positivity in Breast Cancer Is Critical for Reliable Prediction of Disease Outcome

Purpose: Consensus is lacking regarding the androgen receptor (AR) as a prognostic marker in breast cancer. The objectives of this study were to comprehensively review the literature on AR prognostication and determine optimal criteria for AR as an independent predictor of breast cancer survival. Experimental Design: AR positivity was assessed by immunostaining in two clinically validated primary breast cancer cohorts [training cohort, n = 219; validation cohort, n = 418; 77% and 79% estrogen receptor alpha (ERα) positive, respectively]. The optimal AR cut-point was determined by ROC analysis in the training cohort and applied to both cohorts. Results: AR was an independent prognostic marker of breast cancer outcome in 22 of 46 (48%) previous studies that performed multivariate analyses. Most studies used cut-points of 1% or 10% nuclear positivity. Herein, neither 1% nor 10% cut-points were robustly prognostic. ROC analysis revealed that a higher AR cut-point (78% positivity) provided optimal sensitivity and specificity to predict breast cancer survival in the training (HR, 0.41; P = 0.015) and validation (HR, 0.50; P = 0.014) cohorts. Tenfold cross-validation confirmed the robustness of this AR cut-point. Patients with ERα-positive tumors and AR positivity ≥78% had the best survival in both cohorts (P 0.87) had the best outcomes (P < 0.0001). Conclusions: This study defines an optimal AR cut-point to reliably predict breast cancer survival. Testing this cut-point in prospective cohorts is warranted for implementation of AR as a prognostic factor in the clinical management of breast cancer

Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy

addresses: School of Biosciences, University of Exeter, Exeter EX4 5DE, UK. [email protected]: PMCID: PMC2777180types: Journal Article; Research Support, Non-U.S. Gov't© 2009 Yang; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Tyrosine sulfation is one of the most important posttranslational modifications. Due to its relevance to various disease developments, tyrosine sulfation has become the target for drug design. In order to facilitate efficient drug design, accurate prediction of sulfotyrosine sites is desirable. A predictor published seven years ago has been very successful with claimed prediction accuracy of 98%. However, it has a particularly low sensitivity when predicting sulfotyrosine sites in some newly sequenced proteins

Versican but not decorin accumulation is related to malignancy in mammographically detected high density and malignant-appearing microcalcifications in non-palpable breast carcinomas

<p>Abstract</p> <p>Background</p> <p>Mammographic density (MD) and malignant-appearing microcalcifications (MAMCs) represent the earliest mammographic findings of non-palpable breast carcinomas. Matrix proteoglycans versican and decorin are frequently over-expressed in various malignancies and are differently involved in the progression of cancer. In the present study, we have evaluated the expression of versican and decorin in non-palpable breast carcinomas and their association with high risk mammographic findings and tumor characteristics.</p> <p>Methods</p> <p>Three hundred and ten patients with non-palpable suspicious breast lesions, detected during screening mammography, were studied. Histological examination was carried out and the expression of decorin, versican, estrogen receptor α (ERα), progesterone receptor (PR) and c-erbB2 (HER-2/neu) was assessed by immunohistochemistry.</p> <p>Results</p> <p>Histological examination showed 83 out of 310 (26.8%) carcinomas of various subtypes. Immunohistochemistry was carried out in 62/83 carcinomas. Decorin was accumulated in breast tissues with MD and MAMCs independently of the presence of malignancy. In contrast, versican was significantly increased only in carcinomas with MAMCs (median ± SE: 42.0 ± 9.1) and MD (22.5 ± 10.1) as compared to normal breast tissue with MAMCs (14.0 ± 5.8), MD (11.0 ± 4.4) and normal breast tissue without mammographic findings (10.0 ± 2.0). Elevated levels of versican were correlated with higher tumor grade and invasiveness in carcinomas with MD and MAMCs, whereas increased amounts of decorin were associated with <it>in situ </it>carcinomas in MAMCs. Stromal deposition of both proteoglycans was related to higher expression of ERα and PR in tumor cells only in MAMCs.</p> <p>Conclusions</p> <p>The specific accumulation of versican in breast tissue with high MD and MAMCs only in the presence of malignant transformation and its association with the aggressiveness of the tumor suggests its possible use as molecular marker in non-palpable breast carcinomas.</p

Antimicrobial activity and suitability of 2-hydroxyisocaproic acid for the treatment of root canal infections

Abstract Microbial infection in dental root canal induces an inflammatory reaction called apical periodontitis. In post-treament disease, Enterococcus faecalis is the most commonly found organism, which may survive well in root canal despite calcium hydroxide paste medication. In these cases, effective irrigation or repeated chlorhexidine medication are recommended. New medications with long-lasting antimicrobial activity are needed for the treatment of persistent root canal infections. 2-hydroxyisocaproic acid (HICA) is a protein fermentation product of lactobacilli and few other bacterial or fungal species express enzymes required for its metabolism. However, mammalian cells can metabolise it and use it for protein production. It is known to be well-tolerated by humans and have anti-inflammatory properties as well. Therefore, the hypothesis was that it affects microbe-specific metabolic pathways and have potential as a novel antimicrobial agent. The aim of this study was to evaluate the antibacterial and antifungal spectrum of HICA using in vitro microdilution methods for susceptibility testing and an ex vivo extracted tooth root canal infection-model. The impact of dentine on the antimicrobial activity of HICA was also evaluated. The results showed that HICA has broad-spectrum bactericidal activity for gram-positive and gram-negative organisms. It is also fungicidal for several fungal species and it is only marginally inactivated by clinically-relevant concentrations of dentine. It is at least as active against E. faecalis as presently-used interappointment medications in infected root canals after a seven-day incubation ex vivo. Since HICA has a broad-spectrum and long-term antimicrobial activity as well as an anti-inflammatory effect, it may be a useful new agent for clinical endodontology. However, controlled clinical studies are needed for evaluation of the efficacy of HICA in clinical conditions.Tiivistelmä Hampaan juurikanavan mikrobi-infektio aiheuttaa apikaalisen parodontiitin eli tulehdusreaktion juuren kärjen läheisyydessä oleviin kudoksiin. Silloin, kun infektio ei parane hoidon jälkeen, Enterococcus faecalis on yleisin löydös. Jos kalsiumhydroksidilääkitys ei ole tehokas, hoitoon suositellaan huolellista desinfektiohuuhtelua ja uusittavaa lyhytkestoista klooriheksidiinilääkitystä. Juurikanavainfektioiden hoitoon tarvitaan uusia antimikrobiaineita, joilla on pitkäaikainen vaikutus. Lactobacillus-bakteerit tuottavat proteiiniaineenvaihdunnassa 2-hydroksi-isokapronihappoa eli HICAa, jonka metaboloimiseen tarvittavia entsyymejä tunnetaan vain muutamilla muilla bakteereilla. Ihmissolut metaboloivat ja käyttävät sitä proteiinituotantoon. Se on hyvin siedetty aine ja se lieventää tulehdusreaktiota. Tutkimuksen hypoteesina oli, että HICA vaikuttaa mikrobien aineenvaihduntaan ja se voisi olla mahdollinen uusi antimikrobiaine. Tässä tutkimuksessa HICAn antimikrobitehoa tutkittiin bakteereita ja sienilajeja vastaan pienerälaimennusmenetelmällä tehdyissä herkkyystesteissä. Sen soveltuvuutta hampaiden juurikanavainfektioiden hoitoon arvioitiin dentiinin läsnäollessa sekä potilailta poistetuissa ja kokeellisesti infektoiduissa hampaissa. Tulokset osoittavat, että HICA tappaa laajakirjoisesti gram-positiivisia ja gram-negatiivisia bakteereita sekä hiivoja ja muita sienilajeja. Dentiinin vaikutus HICAn antimikrobitehoon on vähäinen. Sen vaikutus E. faecalista vastaan poistettujen hampaiden juurikanavissa on viikon jälkeen yhtä hyvä tai parempi kuin nykyisten lääkeaineiden vaikutus. Laajakirjoisen, pitkäkestoisen antimikrobitehon ja anti-inflammatorisuuden vuoksi HICA voisi olla uusi vaihtoehto juurikanavainfektioiden hoitoon. HICAn kliinisen tehokkuuden arviointiin tarvitaan kontrolloituja kliinisiä tutkimuksia

Whole rock Pb—Pb isochron age for the Pääkkö iron formation in Väyrylänkylä, South Puolanka area, Finland

This paper is a short comment on the first whole rock Pb—Pb isochron age determination for the Marine Jatulian rocks of the Karelides (Middle Precambrian) in Finland. According to this method the age of the Pääkkö iron formation is 2 080 ± 45 Ma

The proteoglycan versican: an important regulator of cell locomotion in development and disease

One of the major keys to understanding tissue reorganization during embryological development and pathophysiology will be to decipher the mechanisms that regulate cell locomotion. This review focuses on what is known about versican, a large extracellular proteoglycan intimately involved in cellular relocation and tissue reorganization during normal processes and pathological states, including cancer metastasis. A member of the lectican family, versican plays diverse roles in cell adhesion, proliferation, migration and angiogenesis. These wide ranging functions have been attributed to the N-(G1) and C-(G3) terminal globular domains and the central glycosaminoglycan-binding region of versican, which collectively interact with a large number of extracellular matrix and cell surface structural components. Consequently, the diverse roles of versican may depend on the level of specific isoforms and/or levels of G1 and G3 domains which can be generated as a result of processing by specific proteases. Little is known about versican catabolism and whether its proteolytic fragments have altered biological activity compared to the intact molecule in physiological and disease processes. Studies over the last ten years have confirmed a significant role for versican in regulating cell locomotion in normal development and disease.Carmela Ricciardelli, Andrew Sakko, Miranda Ween, Darryl Russell and David Horsfal