The seasonal distribution of airborne fungi in two hospitals in Istanbul

Changes in fungal concentrations depend on seasonal and environmental conditions. The aim of this study was to determine the seasonal distributions of the fungal flora in Dr. Siyami Ersek Chest, Heart and Vascular Center Education and Research Hospital (SEH) and Kartal Yavuz Selim State Hospital (KYSH) in İstanbul. Samples were collected seasonally from different stations (microbiology laboratory, toilet, patient waiting saloons, hospital garden and library) in these hospitals. Distributional patterns of the isolated micro fungi were evaluated for each season. In SEH, the highest number of the fungi was isolated in summer, followed by autumn, spring and winter, respectively. Among the 257 micro fungi isolated from this hospital, the most common species were Alternaria alternata (25.8%), Cladosporium cladosporioides (21.9%), Penicillium glabrum (12.9%), Penicillium brevicompactum (7.4%) and Cladosporium herbarum (3.9%). In KYSH, the highest number of fungi was isolated in summer followed by autumn, spring and winter, respectively. Among the 221 micro fungi isolated from this hospital, the most common species were Cladosporium cladosporioides (19.5%), Alternaria alternata (15.8%), Cladosporium herbarum (11.3%) and Penicillium brevicompactum (9.0%).Keywords: Istanbul, airborne fungi, hospital flora, seasonal flor

Correcting Density Functional Methods For Dispersion Interactions Using Pseudopotentials

The development of practical density functional theory (DFT) methods has provided the science community with a very important tool for modeling variety of systems such as materials, molecular and bio–molecular systems. Nonetheless, most practitioners of the method did not give enough attention to the deficiencies in modeling the dispersion interactions with the commonly used density functionals until a few years ago. Since then there have been many methods proposed to solve this problem and it is still a very active research area. I have tested a number of these dispersion–corrected DFT schemes for various systems that are of interest to our research group such as a water molecule interacting with a series of acenes and isomers of the water hexamer to see which of these methods give accurate results. Based on the tests, DFT–D3 of Grimme et al. and dispersion–corrected atom–centered pseudopotentials (DCACPs) attracted on our attention. DCACP procedure provided accurate interaction energies for the test cases, but the interaction energies fall too quickly as the distance between the molecules increases. I further investigated the effects of DCACPs on the employed density functionals with a detailed study of the interaction energies of isomers of the water hexamers and determined that with the original implementation it corrects for limitations of the BLYP functional in describing exchange-repulsion interaction as well as for dispersion interactions. We propose two different methods, namely DCACP+D and DCACP2, for improving the problems associated with the DCACP approach. These methods both provide improvements in the accuracy of the original DCACPs and also correct the quick fall-off problem of the interaction energies at long–range

A metal dicyanamide cluster with high CO2/N2 selectivity

A new microporous metal dicyanamide cluster, Co(hmt)(dca)2 (hmt: hexamethylenetetramine, dca: dicyanamide), with accessible N-donor sites exhibits high CO2/N2 selectivity, 83 at 295 K and 1 bar, for a mixture with a 15:85 CO2 to N2 ratio. Adsorption studies show that the use of hmt and dca moieties as building blocks for solid adsorbents can enhance the CO2:surface interactions due to N atoms available inside the pores, which is confirmed by X-ray single crystal studies. © 2016 Elsevier Inc. All rights reserved

Does the donor-acceptor concept work for designing synthetic metals? III. Theoretical investigation of copolymers between quinoid acceptors and aromatic donors

Homopolymers of quinoxaline (QX), benzothiadiazole (BT), benzobisthiadiazole (BBT), thienopyrazine (TP), thienothiadiazole (TT), and thienopyrazinothiadiazole (TTP) and copolymers of these acceptors with thiophene (TH) and pyrrole (PY) were investigated with density functional theory. Theoretical band-gap predictions reproduce experimental data well. For all but six copolymers, band-gap reductions with respect to either homopolymer are obtained. Four of the acceptors, BBT, TP, TT, and TTP, give rise to copolymers with band gaps that are smaller than that of polyacetylene. BBT and TTP copolymers with PY in 1:2 stoichiometry are predicted to be synthetic metals. Band-gap reductions result from upshifts of HOMO energies and much smaller upshifts of LUMO values. The smallest band gaps are predicted with TTP, since changes in LUMO energies upon copolymerization are particularly small. The consequence of the small interactions between LUMO levels of donor and acceptor are vanishingly small conduction bandwidths. © Springer-Verlag 2006

Noncovalent Interactions by QMC: Speedup by One-Particle Basis-Set Size Reduction

While it is empirically accepted that the fixed-node diffusion Monte-Carlo (FN-DMC) depends only weakly on the size of the one-particle basis sets used to expand its guiding functions, limits of this observation are not settled yet. Our recent work indicates that under the FN error cancellation conditions, augmented triple zeta basis sets are sufficient to achieve a benchmark level of 0.1 kcal/mol in a number of small noncovalent complexes. Here we report on a possibility of truncation of the one-particle basis sets used in FN-DMC guiding functions that has no visible effect on the accuracy of the production FN-DMC energy differences. The proposed scheme leads to no significant increase in the local energy variance, indicating that the total CPU cost of large-scale benchmark noncovalent interaction energy FN-DMC calculations may be reduced.Comment: ACS book chapter, accepte

Fusarium : more than a node or a foot-shaped basal cell

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).http://www.studiesinmycology.org/BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyPlant Production and Soil Scienc

Fusarium: more than a node or a foot-shaped basal cell

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org)

Benchmark calculations of water-acene interaction energies: Extrapolation to the water-graphene limit and assessment of dispersion-corrected DFT methods

In a previous study (J. Phys. Chem. C, 2009, 113, 10242-10248) we used density functional theory based symmetry-adapted perturbation theory (DFT-SAPT) calculations of water interacting with benzene (C6H6), coronene (C24H12), and circumcoronene (C54H18) to estimate the interaction energy between a water molecule and a graphene sheet. The present study extends this earlier work by use of a more realistic geometry with the water molecule oriented perpendicular to the acene with both hydrogen atoms pointing down. We also include results for an intermediate C48H18 acene. Extrapolation of the water-acene results gives a value of -3.0 ± 0.15 kcal mol-1 for the binding of a water molecule to graphene. Several popular dispersion-corrected DFT methods are applied to the water-acene systems and the resulting interacting energies are compared to results of the DFT-SAPT calculations in order to assess their performance. © the Owner Societies

Adsorption of a water molecule on the MgO(100) surface as described by cluster and slab models

The interaction of a water molecule with the (100) surface of MgO as described by cluster models is studied using MP2, coupled MP2 (MP2C) and symmetry-adapted perturbation theory (SAPT) methods. In addition, diffusion Monte Carlo (DMC) results are presented for several slab models as well as for the smallest, 2X2 cluster model. For the 2X2 model it is found that the MP2C, DMC, and CCSD(T) methods give nearly the same potential energy curve for the water-cluster interaction, whereas the potential energy curve from the SAPT calculations differs slightly from those of the other methods. The interaction of the water molecule with the cluster models of the MgO(100) surface is weakened upon expanding the number of layers from one to two and also upon expanding the description of the layers from 2X2 to 4X4 to 6X6. The SAPT calculations reveal that both these expansions of the cluster model are accompanied by reductions in the magnitudes of the induction and dispersion constributions. The best estimate of the energy for binding an isolated water molecule to the surface obtained from the cluster model calculations is in good agreement with that obtained from the DMC calculations using a 2-layer slab model with periodic boundary conditions