Fabrication of SiGe rings and holes on Si(001) by flash annealing

We show that SiGe islands are transformed into nanoholes and rings by annealing treatments only and without Si capping. Rings are produced by a rapid flash heating at temperatures higher than the melting point of Ge, whereas nanoholes are produced by several minute annealing. The rings are markedly rich in Si with respect to the pristine islands, suggesting that the evolution path from islands to rings is driven by the selective dissolution of Ge occurring at high temperature.

Vibrational spectroscopic study of the minerals nekoite Ca3Si6O15•7H2O and okenite Ca10Si18O46•18H2O : implications for the molecular structure

Nekoite Ca3Si6O15•7H2O and okenite Ca10Si18O46•18H2O are both hydrated calcium silicates found respectively in contact metamorphosed limestone and in association with zeolites from the alteration of basalts. The minerals form two-Dimensional infinite sheets with other than six-membered rings with 3-, 4-, or 5-membered rings and 8-membered rings. The two minerals have been characterised by Raman, near-infrared and infrared spectroscopy. The Raman spectrum of nekoite is characterised by two sharp peaks at 1061 and 1092 cm-1 with bands of lesser intensity at 974, 994, 1023 and 1132 cm-1. The Raman spectrum of okenite shows an intense single Raman band at 1090 cm-1 with a shoulder band at 1075 cm-1.These bands are assigned to the SiO stretching vibrations of Si2O5 units. Raman water stretching bands of nekoite are observed at 3071, 3380, 3502 and 3567 cm-1. Raman spectrum of okenite shows water stretching bands at 3029, 3284, 3417, 3531 and 3607 cm-1. NIR spectra of the two minerals are subtly different inferring water with different hydrogen bond strengths. By using a Libowitzky empirical formula, hydrogen bond distances based upon these OH stretching vibrations. Two types of hydrogen bonds are distinguished: strong hydrogen bonds associated with structural water and weaker hydrogen bonds assigned to space filling water molecules.

Conserved and variable features of gag structure and arrangement in immature retrovirus particles

The assembly of retroviruses is driven by oligomerization of the Gag polyprotein. We have used cryo-electron tomography together with subtomogram averaging to describe the three-dimensional structure of in vitro-assembled Gag particles from human immunodeficiency virus, Mason-Pfizer monkey virus, and Rous sarcoma virus. These represent three different retroviral genera: the lentiviruses, betaretroviruses and alpharetroviruses. Comparison of the three structures reveals the features of the supramolecular organization of Gag that are conserved between genera and therefore reflect general principles of Gag-Gag interactions and the features that are specific to certain genera. All three Gag proteins assemble to form approximately spherical hexameric lattices with irregular defects. In all three genera, the N-terminal domain of CA is arranged in hexameric rings around large holes. Where the rings meet, 2-fold densities, assigned to the C-terminal domain of CA, extend between adjacent rings, and link together at the 6-fold symmetry axis with a density, which extends toward the center of the particle into the nucleic acid layer. Although this general arrangement is conserved, differences can be seen throughout the CA and spacer peptide regions. These differences can be related to sequence differences among the genera. We conclude that the arrangement of the structural domains of CA is well conserved across genera, whereas the relationship between CA, the spacer peptide region, and the nucleic acid is more specific to each genus.

Taxonomy and redescription of the Yellow-footed Antechinus, Antechinus flavipes (Waterhouse) (Marsupialia: Dasyuridae)

We provide a taxonomic redescription of the ubiquitous and variable dasyurid marsupial Yellow-footed Antechinus, Antechinus flavipes (Waterhouse), which comprises three currently recognized subspecies whose combined geographic distribution spans almost the length and breadth of Australia. A. flavipes leucogaster Gray is confined to south-west Western Australia; A. flavipes flavipes is distributed in south-eastern Australia across four states—South Australia, Victoria, New South Wales and Queensland; A. flavipes rubeculus Van Dyck is confined to the wet tropics of Queensland. A. flavipes is readily distinguished from all extant congeners based on external morphology by the following combination of features: a grey head; orange-yellow toned flanks/rump, feet and tail base; pale eye-rings and a darkened tail tip. A. flavipes skulls are stout, being broad at the level of the rear upper molars, have small palatal vacuities and small entoconid cusps on the lower molars. However, notable differences among subspecies of A. flavipesprevent any obvious collection of skull characters being diagnostic for species-level discrimination among congeners. A. flavipes rubeculus is the largest of the three subspecies of Yellow-footed Antechinus and most similar in skull morphology to A. leo, A. bellus and A. godmani—all four species are geographically limited to tropical Australia. A. f. rubeculus is notably larger in many characters than its conspecifics: A. f. flavipes, the next largest, and A. f. leucogaster, the smallest of the group. A. f. flavipes and A. f. leucogaster diverge significantly at only a few skull characters, and both subspecies have cranial morphological affinities with the recently discovered A. mysticus, most notably A. f. leucogaster. Phylogenies generated from mt- and nDNA data strongly support Antechinus flavipes as monophyletic with respect to other members of the genus; within A. flavipes, each of the three recognized subspecies form distinctive monophyletic clades.

Diporphyrins linked by two-atom bridges synthestic, structural and theoretical studies

The syntheses, properties and electronic structures of a series of porphyrin dimers connected by two-atom bridges were compared. The study found that an azo linker results in the most efficient electronic communication between the two porphyrin rings, and is the superior connector for dimers, trimers and oligomers in the design of nonlinear optical materials. This has implications for the design of molecular probes and sensors, photodynamic therapy, microfabrication, and three-dimensional optical data storage. The research led to the synthesis of a number of new porphyrin monomers and dimers, which were characterised using structural, spectroscopic and spectrometric techniques.

A longitudinal assessment of chronic wound fluid to detect biochemical indicators of healing

Chronic venous leg ulcers are a detrimental health issue plaguing our society, resulting in long term pain, immobility and decreased quality of life for a large proportion of sufferers. The frequency of these chronic wounds has led current research to focus on the wound environment to provide important information regarding the prolonged, fluctuated or static healing patterns of these wounds. Disruption to the normal wound healing process results in release of multiple factors in the wound environment that could correlate to wound chronicity. These biochemical factors can often be detected through non-invasively sampling chronic wound fluid (CWF) from the site of injury. Of note, whilst there are numerous studies comparing acute and chronic wound fluids, there have not been any reports in the literature employing a longitudinal study in order to track biochemical changes in wound fluid as patients transition from a non-healing to healed state. Initially the objective of this study was to identify biochemical changes in CWF associated with wound healing using a proteomic approach. The proteomic approach incorporated a multi-dimensional liquid chromatography fractionation technique coupled with mass spectrometry (MS) to enable identification of proteins present in lower concentrations in CWF. Not surprisingly, many of the proteins identified in wound fluid were acute phase proteins normally expressed during the inflammatory phase of healing. However, the number of proteins positively identified by MS was quite low. This was attributed to the diverse range in concentration of protein species in CWF making it challenging to detect the diagnostically relevant low molecular weight proteins. In view of this, SELDI-TOF MS was also explored as a means to target low molecular weight proteins in sequential patient CWF samples during the course of healing. Unfortunately, the results generated did not yield any peaks of interest that were altered as wounds transitioned to a healed state. During the course of proteomic assessment of CWF, it became evident that a fraction of non-proteinaceous compounds strongly absorbed at 280 nm. Subsequent analyses confirmed that most of these compounds were in fact part of the purine catabolic pathway, possessing distinctive aromatic rings and which results in high absorbance at 254 nm. The accumulation of these purinogenic compounds in CWF suggests that the wound bed is poorly oxygenated resulting in a switch to anaerobic metabolism and consequently ATP breakdown. In addition, the presence of the terminal purine catabolite, uric acid (UA), indicates that the enzyme xanthine oxidoreductase (XOR) catalyses the reaction of hypoxanthine to xanthine and finally to UA. More importantly, the studies provide evidence for the first time of the exogenous presence of XOR in CWF. XOR is the only enzyme in humans capable of catalysing the production of UA in conjunction with a burst of the highly reactive superoxide radical and other oxidants like H2O2. Excessive release of these free radicals in the wound environment can cause cellular damage disrupting the normal wound healing process. In view of this, a sensitive and specific assay was established for monitoring low concentrations of these catabolites in CWF. This procedure involved combining high performance liquid chromatography (HPLC) with tandem mass spectrometry and multiple reaction monitoring (MRM). This application was selective, using specific MRM transitions and HPLC separations for each analyte, making it ideal for the detection and quantitation of purine catabolites in CWF. The results demonstrated that elevated levels of UA were detected in wound fluid obtained from patients with clinically worse ulcers. This suggests that XOR is active in the wound site generating significant amounts of reactive oxygen species (ROS). In addition, analysis of the amount of purine precursors in wound fluid revealed elevated levels of purine precursors in wound fluid from patients with less severe ulcers. Taken together, the results generated in this thesis suggest that monitoring changes of purine catabolites in CWF is likely to provide valuable information regarding the healing patterns of chronic venous leg ulcers. XOR catalysis of purine precursors not only provides a method for monitoring the onset, prognosis and progress of chronic venous leg ulcers, but also provides a potential therapeutic target by inhibiting XOR, thus blocking UA and ROS production. Targeting a combination of these purinogenic compounds and XOR could lead to the development of novel point of care diagnostic tests. Therefore, further investigation of these processes during wound healing will be worthwhile and may assist in elucidating the pathogenesis of this disease state, which in turn may lead to the development of new diagnostics and therapies that target these processes.

4-(4-Aminophenylsulfonyl)aniline-1,3-5-trinitrobenzene (1/2)

The asymmetric unit of the title co-crystalline 1:2 adduct C12H12N2O2 . 2(C6H3N3O6) contains two independent molecules of bis(4-aminophenyl)sulfone (the drug Dapsone) and four molecules of 1,3,5-trinitrobenzene and is extended into a two-dimensional hydrogen-bonded network structure through amino N-H...O hydrogen-bonding associations with nitro O- atom acceptors. In the two independent Dapsone molecules the inter-ring dihedral angles are 69.0(2) and 63.59(11)deg. Aromatic pi-pi interactions are also found between one of the Dapsone aromatic rings and a trinitrobenzene ring [minimum ring centroid separation 3.576(5)Ang.]. A 4-aminophenyl ring moiety of one of the Dapsone molecules and two nitro groups of a trinitrobenzene are disordered in a 50:50 ratio.

4-(4-Aminophenylsulfonyl)aniline-3,5-dinitrobenzoic acid (1/1)

In the title co-crystalline adduct of the drug Dapsone with 3,5-dinitrobenzoic acid, C~12~H~12~N~2~O~2~S . C~7~H~4~N~4~O~6~, the dihedral angle between the two aromatic rings of the Dapsone molecule is 75.4(2)deg. and those between these rings and that of the 3,5-dinitrobenzoic acid are 64.5(2) and 68.4(2)deg. A strong inter-species carboxylic acid O-H---N(amine) hydrogen-bond is found, which together with intermolecular amine N-H...O hydrogen-bonding associations with carboxyl, nitro and sulfone O-atom acceptors as well as weak pi-pi interactions between one of the Dapsone phenyl rings and the 3,5-dinitrobenzoic acid ring [minimum ring centroid separation 3.774(2)Ang.], give a two-dimensional network structure.

4-Amino-N-(4,6-dimethylpyrimidin-2-yl)benzenesulfonamide-4-nitrobenzoic acid

In the asymmetric unit of the title co-crystal, C12H14N4O2S . C7H5NO4 there are two independent but conformationally similar heterodimers, which are formed through intermolecular N-H...O(carboxy) and carboxyl O-H...N hydrogen-bond pairs, giving a cyclic motif [graph set R2/2(8)]. The dihedral angles between the rings in the sulfonamide molecules are 78.77(8) and 82.33(9)deg. while the dihedral angles between the ring and the CO2H group in the acids are 2.19(9) and 7.02(10)deg. A two-dimensional structure parallel to the ab plane is generated from the heterodimer units through hydrogen-bonding associations between NH2 and sulfone groups. Between neighbouring two-dimensional arrays there are two types of aromatic pi-pi stacking interactions involving either one of the pyrimidine rings and a 4-nitrobenzoic acid molecule [minimum ring centroid separation = 3.5886(9)A] or two acid molecules [minimum ring centroid separation = 3.7236(10)A].

Non-covalent surface modification of boron nitride nanotubes for enhanced catalysis

Boron nitride nanotubes were functionalized by microperoxidase-11 in aqueous media, showing improved catalytic performance due to a strong electron coupling 10 between the active centre of microperoxidase-11 and boron nitride nanotubes. One main application challenge of enzymes as biocatalysts is molecular aggregation in the aqueous solution. This issue is addressed by immobilization of enzymes on solid supports which 15 can enhance enzyme stability and facilitate separation, and recovery for reuse while maintaining catalytic activity and selectivity. The protein-nanoparticle interactions play a key role in bio-nanotechnology and emerge with the development of nanoparticle-protein “corona”. Bio-molecular coronas provide a 20 unique biological identity of nanosized materials.1, 2 As a structural analogue to carbon nanotubes (CNTs), Boron nitride nanotubes have boron and nitrogen atoms distributed equally in hexagonal rings and exhibit excellent mechanical strength, unique physical properties, and chemical stability at high-temperatures. 25 The chemical inertness of BN materials suits to work in hazardous environments, making them an optimal candidate in practical applications in biological and medical field.3, 4

4-(4-Aminophenylsulfonyl)anilinium toluene-4-sulfonate

In the title p-toluenesulfonate salt of the drug dapsone, C12H13N2O2S+ C7H7O3S-, the dihedral angle between the two aromatic rings of the dapsone monocation is 70.19(17)deg. and those between these rings and that of the p-toluenesulfonate anion are 72.34(17) and 46.43(17)deg. All amine and aminium H-atoms are involved in intermolecular N-H...O hydrogen-bonding associations with sulfonyl O-atom acceptors as well as one of the sulfone O-atoms, giving a three-dimensional structure.

Carbon nanotube-based super nanotubes: Tunable thermal conductivity in three dimensions

Advances in nanomaterials/nanostructures offer the possibility of fabricating multifunctional materials for use in engineering applications. Carbon nanotube (CNT)-based nanostructures are a representative building block for these multifunctional materials. Based on a series of in silico studies, we investigated the possibility of tuning the thermal conductivity of a three-dimensional CNT-based nanostructure: a single-walled CNT-based super-nanotube. The thermal conductivity of the super-nanotubes was shown to vary with different connecting carbon rings and super-nanotubes with longer constituent single-walled CNTs and larger diameters had a smaller thermal conductivity. The inverse of the thermal conductivity of the super-nanotubes showed a good linear relationship with the inverse of the length. The thermal conductivity was approximately proportional to the inverse of the temperature, but was insensitive to the axial strain as a result of the Poisson ratio. These results provide a fundamental understanding of the thermal conductivity of the super-nanotubes and will guide their future design/fabrication and engineering applications.

Multifocal electroretinogram responses in Nepalese diabetic patients without retinopathy

Purpose To determine neuroretinal function with multifocal electroretinogram (mfERG) in diabetic subjects without retinopathy. Methods Multifocal electroretinogram (mfERG) was performed in 18 eyes of 18 diabetic subjects without retinopathy and 17 eyes of 17 age and gender-matched healthy control participants. Among 18 diabetic subjects, two had type 1 and 16 had type 2 diabetes. MfERG responses were averaged by the retinal areas of six concentric rings and four quadrants, and 103 retinal locations; N1–P1 amplitude and P1-implicit time were analysed. Results Average mfERG N1–P1 amplitude (in nv/deg2) of 103 retinal locations was 56.3 ± 17.2 (mean ± SD) in type 1 diabetic subjects, 47.2 ± 9.3 in type 2 diabetic subjects and 71.5 ± 12.7 in controls. Average P1-implicit time (in ms) was 43.0 ± 1.3 in type 1 diabetic subjects, 43.9 ± 2.3 in type 2 diabetic subjects and 41.9 ± 2.1 in controls. There was significant reduction in average N1–P1 amplitude and delay in P1-implicit time in type 2 diabetic subjects in comparison to controls. mfERG amplitude did not show any significant correlation with diabetes duration and blood sugar level. However, implicit time showed a positive correlation with diabetes duration in type 2 diabetic subjects with diabetes duration ≥5 years. Conclusions This is the first study in a Nepalese population with diabetes using multifocal electroretinography. We present novel findings that mfERG N1–P1 amplitude is markedly reduced along with delay in P1-implicit time in type 2 diabetic subjects without retinopathy. These findings indicate that there might be significant dysfunction of inner retina before the development of diabetic retinopathy in the study population, which have higher prevalence of diabetes than the global estimate and uncontrolled blood sugar level.