A Bayesian Whittaker–Henderson smoother for general‐purpose and sample‐based spectral baseline estimation and peak extraction

Raman spectroscopy is a well‐established technique that allows both chemical and structural analysis of materials. Raman spectra are often complex and extracting meaningful information is easily hindered by spectral interferences; one of the most significant sources being variations in background. Raman spectra have diverse sources of background making it hard to eliminate them or theoretically to predict the form of the baseline, which frequently varies between samples. Although many different methods for baseline removal have been proposed, most require some form of user input. User input is also subjective and consequently less reproducible than automated methods and variations in baseline subtraction can distort peak heights leading to erroneous results. We present a Bayesian Whittaker–Henderson smoother for spectral baseline estimation and peak extraction. It is a generalisation of the Whittaker–Henderson smoother, a regularised regression algorithm. We introduce hierarchical priors for model parameters of the smoother and propose a global aligner for consistent peak extraction across multiple spectra. We show that this novel smoother significantly outperforms several existing smoothers. Copyright © 2012 John Wiley & Sons, Ltd.     

Enhancement in SERS intensity with hierarchical nanostructures by bimetallic deposition approach

We investigate the plasmonic enhancement arising from bimetallic (Au/Ag) hierarchical structure and address the fundamental issues relating to the design of multilayered nanostructures for surface‐enhanced Raman scattering (SERS) spectroscopy. SERS‐active nanosphere arrays with Ag underlayer and Au overlayer were systematically constructed, with the thickness of each layer altered from 40 to 320 nm. The SERS responses of the resultant bimetallic structures were measured with 2‐naphthalenethiol dye as the test sample. The results confirm the dependency of SERS enhancement on the thickness ratio (Au : Ag). Compared with Au‐arrays, our optimized bimetallic structures, which exhibit nanoprotrusions on the nanospheres, were found to be 2.5 times more SERS enhancing, approaching the enhancement factor of an Ag‐array. The elevated SERS is attributed to the formation of effective hot‐spots associated with increased roughness of the outer Au film, resulting from subsequent sputtering of Au granules on a roughened Ag surface. The morphology and reflectance studies suggest that the SERS hot‐spots are distributed at the junctions of interconnected nanospheres and over the nanosphere surface, depending on the thickness ratio between the Au and Ag layers. We show that, by varying the thickness ratio, it is possible to optimize the SERS enhancement factor without significantly altering the operating plasmon resonance wavelength, which is dictated solely by the size of the underlying nanospheres template. In addition, our bimetallic substrates show long‐term stability compared with previously reported Ag‐arrays, whose SERS efficiency drops by 60% within a week because of oxidation. These findings demonstrate the potential of using such a bimetallic configuration to morphologically optimize any SERS substrate for sensing applications that demand huge SERS enhancement and adequate chemical stability. Copyright © 2011 John Wiley & Sons, Ltd.     

Direct observation of multiple pathways of single-stranded DNA stretching

We observed multiple pathways of stretching single-stranded polydeoxynucleotides, poly(dA). Poly(dA) has been shown to undergo unique transitions under mechanical force, and such transitions were attributed to the stacking characteristics of poly(dA). Using single-molecule manipulation studies, we found that poly(dA) has two stretching pathways at high forces. The previously observed pathway has a free energy that is less than what is expected of single-stranded DNA with a random sequence, indicating the existence of a novel conformation of poly(dA) at large extensions. We also observed stepwise transitions between the two pathways by pulling the molecule with constant force, and found that the transitions are cooperative. These results suggest that the unique mechanical property of poly(dA) may play an important role in biological processes such as gene expression.     

Rational Design of Carboxyl Groups Perpendicularly Attached to a Graphene Sheet: A Platform for Enhanced Biosensing Applications

Graphene oxide (GO)‐based materials offer great potential for biofunctionalization with applications ranging from biosensing to drug delivery. Such biofunctionalization utilizes specific functional groups, typically a carboxyl moiety, as anchoring points for biomolecule. However, due to the fact that the exact chemical structure of GO is still largely unknown and poorly defined (it was postulated to consist of various oxygen‐containing groups, such as epoxy, hydroxyl, carboxyl, carbonyl, and peroxy in varying ratios), it is challenging to fabricate highly biofunctionalized GO surfaces. The predominant anchoring sites (i.e., carboxyl groups) are mainly present as terminal groups on the edges of GO sheets and thus account for only a fraction of the oxygen‐containing groups on GO. Herein, we suggest a direct solution to the long‐standing problem of limited abundance of carboxyl groups on GO; GO was first reduced to graphene and consequently modified with only carboxyl groups grafted perpendicularly to its surface by a rational synthesis using free‐radical addition of isobutyronitrile with subsequent hydrolysis. Such grafted graphene oxide can contain a high amount of carboxyl groups for consequent biofunctionalization, at which the extent of grafting is limited only by the number of carbon atoms in the graphene plane; in contrast, the abundance of carboxyl groups on “classical” GO is limited by the amount of terminal carbon atoms. Such a graphene platform embedded with perpendicularly grafted carboxyl groups was characterized in detail by X‐ray photoelectron spectroscopy, cyclic voltammetry, and electrochemical impedance spectroscopy, and its application was exemplified with single‐nucleotide polymorphism detection. It was found that the removal of oxygen functionalities after the chemical reduction enhanced the electron‐transfer rate of the graphene. More importantly, the introduction of carboxyl groups promoted a more efficient immobilization of DNA probes on the electrode surface and improved the performance of graphene as a biosensor in comparison to GO. The proposed material can be used as a universal platform for biomolecule immobilization to facilitate rapid and sensitive detection of DNA or proteins for point‐of‐care investigations. Such reactive carboxyl groups grafted perpendicularly on GO holds promise for a highly efficient tailored biofunctionalization for applications in biosensing or drug delivery.     

Determination of in situ speciation of manganese in treated acid mine drainage water by using multiple diffusive gradients in thin films devices

Acid mine drainage (AMD) is a serious environmental problem that creates acidic solution with high Mn concentrations. The speciation of residual Mn from AMD after an active treatment involving the addition of a neutralizing agent can reliably evaluate the treatment efficiency and provide knowledge of the Mn species being inputted into the environment. The aim of this study was to evaluate the in situ lability and speciation of Mn using the diffusive gradients in thin films (DGT) technique with treated drainage water from a uranium mine (TAMD). DGT devices with different binding phases (Chelex-100 and P81 and DE81membranes) were used to perform the in situ speciation of Mn.     

Reactivity of Iminophosphoranes. Formation of the Piperazine Ring

Reaction of 3-azidopropyl methanesulfonate with triphenylphosphine produced the 1,4-bis(triphenyl-phosphino)piperazine 5 by intermolecular cyclization, instead of formation azidine derivatives by an intramolecular pathway. Structural formulation of 5 was achieved by both spectral and X-ray crystal analysis. Hydrolysis of 5 under basic condition gives piperazine, whereas reaction of lithium diphenylphosphide with 5 produced 1,2-bis(diphenyl-phosphino)ethane (dppe) exclusively.     

Top‐Down and Bottom‐Up Approaches in Engineering 1 T Phase Molybdenum Disulfide (MoS2): Towards Highly Catalytically Active Materials

The metallic 1 T phase of MoS₂ has been widely identified to be responsible for the improved performances of MoS₂ in applications including hydrogen evolution reactions and electrochemical supercapacitors. To this aim, various synthetic methods have been reported to obtain 1 T phase‐rich MoS₂. Here, the aim is to evaluate the efficiencies of the bottom‐up (hydrothermal reaction) and top‐down (chemical exfoliation) approaches in producing 1 T phase MoS₂. It is established in this study that the 1 T phase MoS₂ produced through the bottom‐up approach contains a high proportion of 1 T phase and demonstrates excellent electrochemical and electrical properties. Its performance in the hydrogen evolution reaction and electrochemical supercapacitors also surpassed that of 1 T phase MoS₂ produced through a top‐down approach.     

Speech coding in the auditory nerve: V. Vowels in background noise

Responses of auditory-nerve fibers to steady-state, two-formant vowels in low-pass background noise (S/N = 10 dB) were obtained in anesthetized cats. For fibers over a wide range of characteristic frequencies (CFs), the peaks in discharge rate at the onset of the vowel stimuli were nearly eliminated in the presence of noise. In contrast, strong effects of noise on fine time patterns of discharge were limited to CF regions that are far from the formant frequencies. One effect is a reduction in the amplitude of the response component at the fundamental frequency in the high-CF regions and for CFs between F1 and F2 when the formants are widely separated. A reduction in the amplitude of the response components at the formant frequencies, with concomitant increase in components near CF or low-frequency components occurs in CF regions where the signal-to-noise ratio is particularly low. The processing schemes that were effective for estimating the formant frequencies and fundamental frequency of vowels in quiet generally remain adequate in moderate-level background noise. Overall, the discharge patterns contain many cues for distinctions among the vowel stimuli, so that the central processor should be able to identify the different vowels, consistent with psychophysical performance at moderate signal-to-noise ratios.