Enhancing the effectiveness of clustering with spectra analysis

For many clustering algorithms, such as K-Means, EM, and CLOPE, there is usually a requirement to set some parameters. Often, these parameters directly or indirectly control the number of clusters, that is, k, to return. In the presence of different data characteristics and analysis contexts, it is often difficult for the user to estimate the number of clusters in the data set. This is especially true in text collections such as Web documents, images, or biological data. In an effort to improve the effectiveness of clustering, we seek the answer to a fundamental question: How can we effectively estimate the number of clusters in a given data set? We propose an efficient method based on spectra analysis of eigenvalues (not eigenvectors) of the data set as the solution to the above. We first present the relationship between a data set and its underlying spectra with theoretical and experimental results. We then show how our method is capable of suggesting a range of k that is well suited to different analysis contexts. Finally, we conclude with further  empirical results to show how the answer to this fundamental question enhances the clustering process for large text collections.

FTIR and thermal analysis of cashmere and other animal fibres

In this paper, sereval varieties of animal fibres including cashmere and Australian fine Merino wool have been analysed by Fourier transform infrared microscope and differential scanning calorimeter. The results showed that both Chinese and Australian cashmere fibres started absorbing heat at a relatively higher temperature but were thermally degraded quicker than other animal fibres tested. However, the mass changes (within the temperature range of 200oC to 350oC) and associated onset temperatures varied among fibre varieties. From the attenuated total reflectance spectra, the Chinese cashmere was clearly different from Australian cashmere and wool in a peak near 1040 cm-1 wavelength for S-O stretching of cysteic acid residues. The Chinese cashmere presented a stronger absorption at 1019 cm-1 wavelength, while Australian cashmere and wool peaked at 1079 cm-1 wavelength and had a weaker absorption. Combined with thermal analysis, the normalised R-SO3 - content of cysteic acid residues to the amide II peak of the protein backbone may have potential use in identifying Australian fine Merino wool from Chinese cashmere.

Generalised 2D-correlation NMR analysis of a wine fermentation

A wine fermentation has been monitored on a daily basis by 1H NMR spectroscopy. Following data pre-processing that includes synthesis of the spectra to ensure all peaks are of constant half-width, the series of spectra were examined using generalised two-dimensional correlation techniques. Synchronous and asynchronous data maps have been generated and employed to interpret the changes in the fermentation process as a function of time. The results illustrate the potential of high resolution NMR with multivariate data analysis as a tool for process monitoring and the manner in which two-dimensional correlation mapping can aid in data interpretation.

TOF-SIMS analysis using C60. Effect of impact energy on yield and damage

C₆₀ has been shown to give increased sputter yields and, hence, secondary ions when used as a primary particle in SIMS analysis. In addition, for many samples, there is also a reduction in damage accumulation following continued bombardment with the ion beam. In this paper, we report a study of the impact energy (up to 120 keV) of C₆₀ on the secondary ion yield from a number of samples with consideration of any variation in yield response over mass ranges up to m/z 2000. Although increased impact energy is expected to produce a corresponding increase in sputter yield/rate, it is important to investigate any increase in sample damage with increasing energy and, hence, efficiency of the ion beams. On our test samples including a metal, along with organic samples, there is a general increase in secondary ion yield of high-mass species with increasing impact energy. A corresponding reduction in the formation of low-mass fragments is also observed. Depth profiling of organic samples demonstrates that when using C₆₀, there does not appear to be any increase in damage evident in the mass spectra as the impact energy is increased.

Finding and filling the gaps in the Australian governments' innovation and entrepreneurship support spectra

A national innovation system is concerned with the full process of converting new knowledge into commercially viable results. Governments are policy-active in trying to create productive national innovation systems. This paper reviews ways of thinking about entrepreneurship as the commercialisation component of Australia’s innovation system. The paper explores the impact and relevance of selected existing Australian Commonwealth, and to a lesser extent State government, programs for the commercialisation channels so identified, using four frameworks for the analysis: financial, management/start-up, innovation and entrepreneurial. The analysis indicates program initiatives covering the later development and commercialization phases, but serious gaps in the support available for the entrepreneurship phase involving the act of new entry. This gap is covered by research provider business development people and to a limited extent by incubator and State government initiatives. A critical issue has been and is access to smaller amounts of seed finance. The critical human component is the education of public servants and politicians about the nature and operation of entrepreneurship.

Comparative analysis of surface-enhanced Raman spectroscopy of daidzein and formononetin

Phytoestrogens daidzein (4′,7-dihydroxy-isoflavone) and formononetin (4′-methoxy-7-hydroxy-isoflavone) have been studied by surface-enhanced Raman (SER) spectroscopy. Spectra were acquired in the presence of citratereduced silver colloids, over a range of pH and concentrations. Density functional theory calculations were used to assist assignment of the normal Raman spectra and help determine the mode of interaction of isoflavones with the silver nanoparticles. Formononetin does not show SER activity unless the 7-OH group is deprotonated, and accordingly, the interaction with the silver surface occurs via the deprotonated site. Daidzein, on the other hand, appears to contain multiple species at the surface, interacting via both the hydroxyl groups at 7-OH and 4′-OH, after deprotonation. This is an important result that points to potential future SERS applications in phytoestrogen analysis and provides a foundation for understanding the SER spectra of isoflavones.

Analysis of 5-hydroxyisoflavones by surface-enhanced Raman spectroscopy : genistein and methoxy derivatives

A series of 5-hydroxy-isoflavones—genistein, biochanin A, prunetin, and 4′,7-dimethoxygenistein—have been studied by surface-enhanced Raman spectroscopy (SERS). Citrate reduced silver colloids were employed as a standard technique to measure SER spectra over a range of pH and concentrations. Density functional theory calculations were used to assist in determining the mode of interaction of isoflavones with the silver nanoparticles. It is revealed that biochanin A and prunetin interact with the silver nanoparticles upon deprotonation of the 7- and the 4′-OH groups, respectively, to show SERS activity. Correlations of their spectra with SERS of genistein strongly support the presence of multiple interaction modes involving both of the OH groups in genistein, in a similar manner to daidzein. Surprisingly, however, under these conditions, the 5-OH group was found to be noninteractive as revealed by attempts to measure SERS of 4′,7-dimethoxygenistein. This was attributed partly to the low solubility and, more importantly, to the influence of steric hindrance, caused by the position of the pendant phenyl ring, which prevented interaction with the Ag colloid surface. These results complement recent work on daidzein and formononetin and provide further insight into understanding the SER spectra of isoflavones.

Two-dimensional correlation localized surface plasmon resonance spectroscopy for analysis of the interaction between metal nanoparticles and bovine serum albumin

Time-resolved extinction spectra assisted with two-dimensional correlation spectroscopy (2DCOS) analysis and principal component analysis (PCA) were employed to investigate the interaction between bovine serum albumin (BSA) and metal nanoparticles (NPs). A series of localized surface plasmon resonance (LSPR) spectra of metal NPs were measured just after a small amount of BSA was added into metal colloids. Through 2DCOS analysis, remarkable changes in the intensities of the LSPR were observed. The interaction process was totally divided into three periods according to the PCA. Transmission electron microscopy, dynamic light scattering, and ζ-potential measurements were also employed to characterize the interaction between BSA and metal NPs. The addition of BSA brings silver NPs to aggregate through the electrostatic interaction between them, but it has less effect on gold NPs. In a gold and silver mixed system, gold NPs can affect the interaction of silver NPs and BSA, leading it to weaken. The combination of 2DCOS analysis and LSPR spectroscopy is powerful for exploring the LSPR spectra of the metal NP involved systems. This combined technique holds great potential in LSPR sensing through analysis of slight, slim spectral changes of metal colloids

Rapid determination of protein contents in microencapsulated fish oil supplements by ATR-FTIR spectroscopy and partial least square regression (PLSR) analysis

Following the recent success in quantitative analysis of essential fatty acid compositions in a commercial microencapsulated fish oil (?EFO) supplement, we extended the application of portable attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopic technique and partial least square regression (PLSR) analysis for rapid determination of total protein contents-the other major component in most commercial ?EFO powders. In contrast to the traditional chromatographic methodology used in a routine amino acid analysis (AAA), the ATR-FTIR spectra of the ?EFO powder can be acquired directly from its original powder form with no requirement of any sample preparation, making the technique exceptionally fast, noninvasive, and environmentally friendly as well as being cost effective and hence eminently suitable for routine use by industry. By optimizing the spectral region of interest and number of latent factors through the developed PLSR strategy, a good linear calibration model was produced as indicated by an excellent value of coefficient of determination R2 = 0.9975, using standard ?EFO powders with total protein contents in the range of 140-450 mg/g. The prediction of the protein contents acquired from an independent validation set through the optimized PLSR model was highly accurate as evidenced through (1) a good linear fitting (R2 = 0.9759) in the plot of predicted versus reference values, which were obtained from a standard AAA method, (2) lowest root mean square error of prediction (11.64 mg/g), and (3) high residual predictive deviation (6.83) ranked in very good level of predictive quality indicating high robustness and good predictive performance of the achieved PLSR calibration model. The study therefore demonstrated the potential application of the portable ATR-FTIR technique when used together with PLSR analysis for rapid online monitoring of the two major components (i.e., oil and protein contents) in finished ?EFO powders in the actual manufacturing setting.

Synchrotron-FTIR microspectroscopy enables the distinction of lipid accumulation in thraustochytrid strains through analysis of individual live cells

The superior characteristics of high photon flux and diffraction-limited spatial resolution achieved by synchrotron-FTIR microspectroscopy allowed molecular characterization of individual live thraustochytrids. Principal component analysis revealed distinct separation of the single live cell spectra into their corresponding strains, comprised of new Australasian thraustochytrids (AMCQS5-5 and S7) and standard cultures (AH-2 and S31). Unsupervised hierarchical cluster analysis (UHCA) indicated close similarities between S7 and AH-7 strains, with AMCQS5-5 being distinctly different. UHCA correlation conformed well to the fatty acid profiles, indicating the type of fatty acids as a critical factor in chemotaxonomic discrimination of these thraustochytrids and also revealing the distinctively high polyunsaturated fatty acid content as key identity of AMCQS5-5. Partial least squares discriminant analysis using cross-validation approach between two replicate datasets was demonstrated to be a powerful classification method leading to models of high robustness and 100% predictive accuracy for strain identification. The results emphasized the exceptional S-FTIR capability to perform real-time in vivo measurement of single live cells directly within their original medium, providing unique information on cell variability among the population of each isolate and evidence of spontaneous lipid peroxidation that could lead to deeper understanding of lipid production and oxidation in thraustochytrids for single-cell oil development.

Graphene nanodots-encaged porous gold electrode fabricated via ion beam sputtering deposition for electrochemical analysis of heavy metal ions

All rights reserved. A graphene nanodots-encaged porous gold electrode via ion beam sputtering deposition (IBSD) for electrochemical sensing is presented. The electrodes were fabricated using Au target, and a composite target of Al and graphene, which were simultaneously sputtered onto glass substrates by Ar ion beam, followed with hydrochloric acid corrosion. The as-prepared graphene nanodots-encaged porous gold electrodes were then used for the analysis of heavy metal ions, e.g. Cu2+ and Pb2+ by Osteryoung square wave voltammetry (OSWV). These porous electrodes exhibited enhanced detection range for the heavy metal ions due to the entrapped graphene nanodots in 3-D porous structure. In addition, it was also found that when the thickness of porous electrode reached 40 nm the detection sensitivity came into saturation. The linear detection range is 0.009-4 μM for Cu2+ and 0.006-2.5 μM for Pb2+. Good reusability and repeatability were also observed. The formation mechanism and 3-D structure of the porous electrode were also investigated using scanning electron microscope (SEM), transmission electron microscope (TEM) and X-ray photoelectron spectra (XPS). This graphene entrapped 3-D porous structure may envision promising applications in sensing devices.