Towards a comprehensive understanding of the Si(100)-2×1 surface termination through hydrogen passivation using methylamine and methanol: a theoretical approach

Using density functional theory, we explored the termination process of Si (100)-2?×?1 reconstructed surface mechanistically through the dehydrogenation of small molecules, considering methyl amine and methanol as terminating reagents. At first, both the terminating reagents form two types of adduct through adsorption on the Si (100)-2?×?1 surface, one in chemisorption mode and the other via physisorption, from which the dehydrogenation process is initiated. By analyzing the activation barriers, it was observed that termination of the Si-surface through the dehydrogenation is kinetically almost equally feasible using either reagent. We further examined in detail the mechanism for each termination process by analyzing geometrical parameters and natural population analysis charges. From bonding evaluation, it is evident that hydrogen abstraction from adsorbates on the Si-surface is asymmetric in nature, where one hydrogen is abstracted as hydride by the electrophilic surface Si and the other hydrogen is abstracted as proton by the neucleophilic surface Si. Moreover, it was also observed that hydride transfer from adsorbate to the Si-surface occurs first followed by proton transfer. Overall, our theoretical interpretation provides a mechanistic understanding of the Si (100)-2?×?1 reconstructed surface termination by amine and alcohol that will further motivate researchers to design different types of decorated semiconductor devices.

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Graphical Abstract Surface termination process of Si(100)-2×1 through formation of non-polar Si–H bonds via dehydrogenation of methylamine and methanol as terminating reagents

     

Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record

Foraminifera have one of the best known fossil records among the unicellular eukaryotes. However, the origin and phylogenetic relationships of the extant foraminiferal lineages are poorly understood. To test the current paleontological hypotheses on evolution of foraminifera, we sequenced about 1,000 base pairs from the 3' end of the small subunit rRNA gene (SSU rDNA) in 22 species representing all major taxonomic groups. Phylogenies were derived using neighbor- joining, maximum-parsimony, and maximum-likelihood methods. All analyses confirm the monophyletic origin of foraminifera. Evolutionary relationships within foraminifera inferred from rDNA sequences, however, depend on the method of tree building and on the choice of analyzed sites. In particular, the position of planktonic foraminifera shows important variations. We have shown that these changes result from the extremely high rate of rDNA evolution in this group. By comparing the number of substitutions with the divergence times inferred from the fossil record, we have estimated that the rate of rDNA evolution in planktonic foraminifera is 50 to 100 times faster than in some benthic foraminifera. The use of the maximum-likelihood method and limitation of analyzed sites to the most conserved parts of the SSU rRNA molecule render molecular and paleontological data generally congruent.      

Fire and succession in the ultramafic maquis of New Caledonia

Aim This study investigates the role of fire and post fire succession in determining the structure and composition of vegetation on ultramafic iron crust soils. Location The study was conducted in the Plaines des Lacs region of southern New Caledonia. Methods A survey was made of eighty-eight sites, recording floristic composition, trunk size-class distributions, regeneration after fire, growth ring counts of Dacrydium araucarioides (Podocarpaceae) and historical information on past fires. Floristic data was ordinated using multidimensional scaling and an index of succession based on structural and historical information. A transition matrix model was developed to predict the effect of fire frequency on vegetation composition. Results The vegetation is undergoing postfire succession from maquis to forest, after about 75 years, and eventually to rainforest. Gymnostoma deplancheanum has a key role as an early colonist that produces shade, the bulk of the litter, and forms nitrogen fixing nodules with Frankia sp. However, the open canopy of Gymnostoma and slow litter decay creates flammable conditions. Though many species resprout from rootstocks, only thirty-nine persist through fires while 114 others colonize at later successional stages, as the litter layer and shade increase. Some early successional species are later excluded but these can persist locally in swamps and on rocky hill tops. Forest and rainforest are less flammable and the matrix model suggests that ignition frequency has a critical role in determining the abundance of maquis or forest. Main conclusions The vegetation mosaic represents a post fire succession from open maquis to forest. Palynological and charcoal records from late Pleistocene sediments suggest that fire has been a major factor determining the development of maquis vegetation since before the arrival of humans. Recently, frequent fires have converted much of the vegetation to maquis, posing a threat to some forest species and largely eliminating rainforest from iron crust soils.     

Identification and characterization of intramolecular γ-halo interaction in d<Superscript>0</Superscript> complexes: a theoretical approach

A mechanistic investigation to detect intramolecular M?X–C type interactions in d⁰ neutral and cationic complexes was carried out through a benchmark study employing different density functional methods. As γ-halogen is involved in M?X–C type interactions, it is denoted as a γ-halo interaction and the respective conformers are designated as halo-conformers. By analyzing the geometrical parameters of halo-conformers, it was observed that, irrespective of the nature of the metal and the halogen, the C_γ–X bond distance increases compared to the usual C–X bond, which brings the M and X centers close enough to generate a weak interaction. Generation of the M?X–C interaction was confirmed by performing NBO, AIM and Wiberg bond index analyses, from which the persistence of γ-halo interaction was seen to be prominent. Moreover, for each neutral and cationic complex, the values of Wiberg bond order are in good agreement with the AIM results. The effect of the metal center, as well as γ-halogen substitution, on γ-halo interaction was also studied in the present work. To justify the practical subsistence of the halo-conformers, we checked the stability of the conformers with respect to their β-conformers by comparing the zero-point-corrected electronic energies. Therefore, the entire study was designed in such a way that it can provide evidence in support of intramolecular M?X–C interactions, where, instead of the C–H bond, the C_γ–X bond will interact with the central transition metal.     

Apoptosis as a mechanism of T-regulatory cell homeostasis and suppression

Activation-induced cell death is a general mechanism of immune homeostasis through negative regulation of clonal expansion of activated immune cells. This mechanism is involved in the maintenance of self- and transplant tolerance through polarization of the immune responses. The Fas/Fas-ligand interaction is a major common executioner of apoptosis in lymphocytes, with a dual role in regulatory T cell (Treg) function: Treg cell homeostasis and Treg cell-mediated suppression. Sensitivity to apoptosis and the patterns of Treg-cell death are of outmost importance in immune homeostasis that affects the equilibrium between cytolytic and suppressor forces in activation and termination of immune activity. Naive innate (naturally occurring) Treg cells present variable sensitivities to apoptosis, related to their turnover rates in tissue under steady state conditions. Following activation, Treg cells are less sensitive to apoptosis than cytotoxic effector subsets. Their susceptibility to apoptosis is influenced by cytokines within the inflammatory environment (primarily interleukin-2), the mode of antigenic stimulation and the proliferation rates. Here, we attempt to resolve some controversies surrounding the sensitivity of Treg cells to apoptosis under various experimental conditions, to delineate the function of cell death in regulation of immunity.     

Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus

Background  

Pseudorabies virus (PRV) is an alphaherpesviruses whose native host is pig. PRV infection mainly causes signs of central nervous system disorder in young pigs, and respiratory system diseases in the adult.     

Defining the healthy "core microbiome" of oral microbial communities

Background  

Most studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing).     

Mitochondrial heteroplasmy and DNA barcoding in Hawaiian <Emphasis Type="Italic">Hylaeus</Emphasis> (<Emphasis Type="Italic">Nesoprosopis</Emphasis>) bees (Hymenoptera: Colletidae)

Background  

The past several years have seen a flurry of papers seeking to clarify the utility and limits of DNA barcoding, particularly in areas such as species discovery and paralogy due to nuclear pseudogenes. Heteroplasmy, the coexistence of multiple mitochondrial haplotypes in a single organism, has been cited as a potentially serious problem for DNA barcoding but its effect on identification accuracy has not been tested. In addition, few studies of barcoding have tested a large group of closely-related species with a well-established morphological taxonomy. In this study we examine both of these issues, by densely sampling the Hawaiian Hylaeus bee radiation.     

Cestodes (Caryophyllidea) of the stinging catfish Heteropneustes fossilis (Siluriformes: Heteropneustidae) from Asia

The stinging catfish Heteropneustes fossilis (Bloch) (Siluriformes: Heteropneustidae) has been reported to harbor as many as 19 species of caryophyllidean tapeworms (Cestoda) of 11 genera in tropical Asia (Indomalayan zoogeographical region). However, a critical review of the species composition has shown that only 1 species, Lucknowia fossilisi Gupta, 1961 (Lytocestidae), is a specific parasite of H. fossilis. Three other species, Djombangia penetrans Bovien, 1926 (syn., Djombangia caballeroi Sahay and Sahay, 1977 ), Pseudocaryophyllaeus ritai Gupta and Singh, 1983 (syn. Pseudocaryophyllaeus lucknowensis Gupta and Sinha, 1984 ), and Pseudocaryophyllaeus tenuicollis (Bovien, 1926) Ash, Scholz, Oros and Kar, 2011 (syn. P. mackiewiczi Gupta and Parmar, 1982 ), were found only once. Lucknowia fossilisi is redescribed on the basis of new material collected in West Bengal and voucher specimens from Maharashtra, India. A total of 9 species of Capingentoides, Lucknowia, Lytocestus, Pseudoadenoscolex, Pseudocaryophyllaeus, Pseudoheteroinverta, and Sukhapatae are newly synonymized with L. fossilisi and previous synonymies of 9 other species, proposed by Hafeezulah (1993), are confirmed. Generic diagnosis of Lucknowia Gupta, 1961 is amended. In addition, 1 species of Pseudobatrachus and 2 species of the monotypic genera Pseudoneckinverta and Sudhaena are invalidated as nomina nuda.