Cavity-enhanced spectroscopies for applications of remote sensing, chemical kinetics and detection of radical species

This thesis describes applications of cavity enhanced spectroscopy towards applications of remote sensing, chemical kinetics and detection of transient radical molecular species. Both direct absorption spectroscopy and cavity ring-down spectroscopy are used in this work. Frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) was utilized for measurements of spectral lineshapes of O₂ and CO₂ for obtaining laboratory reference data in support of NASA’s OCO-2 mission. FS-CRDS is highly sensitive (> 10 km absorption path length) and precise (> 10000:1 SNR), making it ideal to study subtle non-Voigt lineshape effects. In addition, these advantages of FS-CRDS were further extended for measuring kinetic isotope effects: A dual-wavelength variation of FS-CRDS was used for measuring precise D/H and ¹³C/¹²C methane isotope ratios (sigma>0.026%) for the purpose of measuring the temperature dependent kinetic isotope effects of methane oxidation with O(¹D) and OH radicals. Finally, direct absorption spectroscopic detection of the trans-DOCO radical via a frequency combs spectrometer was conducted in collaboration with professor Jun Ye at JILA/University of Colorado.

Detection of specific bacteria in water: implications of survival strategy

It is widely recognised that conventional culture techniques may underestimate true viable bacterial numbers by several orders of magnitude. The basis of this discrepancy is that a culture in or on media of high nutrient concentration is highly selective (either through ”nutrient shock” or failure to provide vital co-factors) and decreases apparent diversity; thus it is unrepresentative of the natural community. In addition, the non-culturable but viable state (NCBV) is a strategy adopted by some bacteria as a response to environmental stress. The basis for the non-culturable state is that cells placed in conditions present in the environment cannot be recultured but can be shown to maintain their viability. Consequently, these cells would not be detected by standard water quality techniques that are based on culture. In the case of pathogens, it may explain outbreaks of disease in populations that have not come into contact with the pathogen. However, the NCBV state is difficult to attribute, due to the failure to distinguish between NCBV and non-viable cells. This article will describe experiences with the fish pathogen Aeromonas salmonicida subsp. salmonicida and the application of molecular techniques for its detection and physiological analysis.

MCBoost: Multiple classifier boosting for perceptual co-clustering of images and visual features

We present a new co-clustering problem of images and visual features. The problem involves a set of non-object images in addition to a set of object images and features to be co-clustered. Co-clustering is performed in a way that maximises discrimination of object images from non-object images, thus emphasizing discriminative features. This provides a way of obtaining perceptual joint-clusters of object images and features. We tackle the problem by simultaneously boosting multiple strong classifiers which compete for images by their expertise. Each boosting classifier is an aggregation of weak-learners, i.e. simple visual features. The obtained classifiers are useful for object detection tasks which exhibit multimodalities, e.g. multi-category and multi-view object detection tasks. Experiments on a set of pedestrian images and a face data set demonstrate that the method yields intuitive image clusters with associated features and is much superior to conventional boosting classifiers in object detection tasks.

Graphene SOI CMOS sensors for detection of PPB levels of NO2 in air

There is considerable demand for sensors that are capable of detecting ultra-low concentrations (sub-PPM) of toxic gases in air. Of particular interest are NO2 and CO that are exhaust products of internal combustion engines. Electrochemical (EC) sensors are widely used to detect these gases and offer the advantages of low power, good selectivity and temporal stability. However, EC sensors are large (1 cm3), hand-made and thus expensive ($25). Consequently, they are unsuitable for the low-cost automotive market that demands units for less than $10. One alternative technology is SnO2 or WO3 resistive gas sensors that are fabricated in volume today using screen-printed films on alumina substrates and operate at 400°C. Unfortunately, they suffer from several disadvantages: power consumption is high 200 mW; reproducibility of the sensing element is poor; and cross-sensitivity is high. © 2013 IEEE.

A novel method to construct a third-generation biosensor: self-assembling gold nanoparticles on thiol-functionalized poly(styrene-co-acrylic acid) nanospheres

A novel method for fabrication of horseradish peroxidase (HRP) biosensor has been developed by self-assembling gold nanoparticles on thiol-functionalized poly(styrene-co-acrylic acid) (St-co-AA) nanospheres. At first, a cleaned gold electrode was immersed in thiol-functionalized poly(St-co-AA) nanosphere latex prepared by emulsifier-free emulsion polymerization of St with AA and function with dithioglycol to assemble the nanospheres, then gold nanoparticles were chemisorbed onto the thiol groups. Finally, horseradish peroxi- dase was immobilized on the surface of the gold nanoparticles. The sensor displayed an excellent electrocatalytical response to reduction of H2O2 without the aid of an electron mediator. The sensor was highly sensitive to hydrogen peroxide with a detection limit of 4.0 mumol l(-1), and the linear range was from 10.0 mumol l(-1) to 7.0 mmol l(-1). The biosensor retained more than 97.8% of its original activity after 60 days of use. Moreover, the Studied biosensor exhibited good current repeatability and good fabrication reproducibility.

Assemble of poly(aniline-co-o-aminobenzenesulfonic acid) three-dimensional tubal net-works onto ITO electrode and its application for the direct electrochemistry and electrocatalytic behavior of cytochrome c

Stable electroactive film of poly(aniline-co-o-aminobenzenesulfonic acid) three-dimensional tubal net-works was assembled on indium oxide glass (ITO) successfully, and the cytochrome c was immobilized on the matrix by the electrostatic interactions. The adsorbed cytochrome c showed a good electrochemical activity with a pair of well-defined redox waves in pH 6.2 phosphate buffer solution, and the adsorbed protein showed more faster electron transfer rate (12.9 s(-1)) on the net-works matrix than those of on inorganic porous or even nano-materials reported recently. The immobilized cytochrome c exhibited a good electrocatalytic activity and amperometric response (2 s) for the reduction of hydrogen peroxide (H2O2). The detection limit for H2O2 was 1.5 mu M, and the linear range was from 3 mu M to 1 mM. Poly(aniline-co-o-aminobenzenesulfonic acid) three-dimensional tubal net-works was proved to be a good matrix for protein immobilization and biosensor preparation.

Self-assembling gold nanoparticles on thiol-functionalized poly(styrene-co-acrylic acid) nanospheres for fabrication of a mediatorless biosensor

A novel strategy to construct a sensitive mediatorless sensor of H2O2 was described. At first, a cleaned gold electrode was immersed in thiol-functionalized poly(styrene-co-acrylic acid) (St-co-AA) nanosphere latex prepared by emulsifier-free emulsion polymerization St with AA and function with dithioglycol to assemble the nanospheres, then gold nanoparticles were chemisorbed onto the thiol groups and formed monolayers on the surface of poly(St-co-AA) nanospheres. Finally, horseradish peroxidase (HRP) was immobilized on the surface of the gold nanoparticles. The sensor displayed an excellent electrocatalytical response to reduction of H2O2 without the aid of an electron mediator. The biosensor showed a linear range of 8.0 mu mol L-1-7.0 mmol L-1 with a detection limit of 4.0 mu mol L-1. The biosensor retained more than 97.8% of its original activity after 60 days' storage. Moreover, the studied biosensor exhibited good current reproducibility and good fabrication reproducibility.

Assembly of the transition metal substituted polyoxometalates ZnW11M(H2O)O-39(n-) (M = Mn, Cu, Fe, Co, Cr, Ni, Zn) on 4-aminobenzoic acid modified glassy carbon electrode and their electrochemical study

Through layer-by-layer assembly, a series of undecatungstozincates monosubstituted by first-row transition metals, ZnW11M(H2O)O-39(n-) (M=Cr, Mn, Fe, Co, Ni, Cu. or Zn) were first successfully immobilized on a 4-aminobenzoic acid modified glassy carbon electrode surface. The electrochemical behaviors of these polyoxometalates were investigated. They exhibit some special properties in the films different from those in homogeneous aqueous solution. The Cu-centered reaction mechanism in the ZnW11Cu multilayer film was described. The electrocatalytic behaviors of these multilayer film electrodes to the reduction of H2O2 and BrO3- were comparatively studied.

A chemiluminescence optical fiber glucose biosensor based on co-immobilizing glucose oxidase and horseradish peroxidase in a sol-gel film

An optical fiber bienzyme sensor based on the luminol chemiluminescent reaction was developed and demonstrated to be sensitive to glucose. Glucose oxidase (GOD) and horseradish peroxidase (HRP) were co-immobilized by microencapsulation in a sol-gel film derived from tetraethyl orthosilicate(TEOS). The calibration plots for glucose were established by the optical fiber glucose sensor fabricated by attaching the bienzyme silica gel onto the glass window of the fiber bundle. The linear range was 0.2-2 mmol/L and the detection limit was approximately 0.12 mmol/L. The relative standard deviation was 5.3% (n = 6). The proposed biosensor was applied to glucose assay in ofloxacin injection successfully.

Determination of amines using 2-(11H-benzo[a]carbazol-11-yl) ethyl chloroformate (BCEC-Cl) as labeling reagent by HPLC with fluorescence detection and identification with APCI/MS

A pre-column derivatization method for the sensitive determination of amines using a labeling reagent 2-(11H-benzo[a]-carbazol-11-yl) ethyl chloroformate (BCEC-Cl) followed by high-performance, liquid chromatography with fluorescence detection has been developed. Identification of derivatives was carried out by LC/APCI/MS in positive-ion mode. The chromophore of 1,2-benzo-3,4-dihydrocarbazole-9-ethyl chloroformate (BCEOC-Cl) reagent was replaced by 2-(11H-benzo[a]-carbazol-11-yl) ethyl functional group, which resulted in a sensitive fluorescence derivatizing reagent BCEC-Cl. BCEC-Cl could easily and quickly label amines. Derivatives were stable enough to be efficiently analyzed by HPLC and showed an intense protonated molecular ion corresponding m/z [M+ H](+) under APCI/MS in positive-ion mode. The collision-induced dissociation of the protonated molecular ion formed characteristic fragment ions at m/z 261.8 and m/z 243.8 corresponding to the cleavages of CH2O-CO and CH2-OCO bonds. Studies on derivatization demonstrated excellent derivative yields over the pH 9.0-10.0. Maximal yields close to 100% were observed with three- to four-fold molar reagent excess. In addition, the detection responses for BCEC-derivatives were compared to those obtained using 1,2-benzo-3,4-dihydrocarbazole-9-ethyl chloroformate (BCEOC-Cl) and 9-fluorenyl methylchloroformate, (FMOC-Cl) as labeling reagents. The ratios I-BCEC/I-BCEOC = 1.94-2.17 and I-BCEC/I-FMOC = 1.04-2.19 for fluorescent (FL) responses (here, I was relative fluorescence intensity). Separation of the derivatized amines had been optimized on reversed-phase Eclipse XDB-C-8 column. Detection limits calculated from 0.50 pmol injection, at a signal-to-noise ratio of 3, were 1.77-14.4 fmol. The relative standard deviations for within-day determination (n = 11) were 1.84-2.89% for the tested amines. The mean intra- and inter-assay precision for all amines levels were < 3.64% and 2.52%, respectively. The mean recoveries ranged from 96.6% to 107.1% with their standard deviations in the range of 0.8-2.7. Excellent linear responses were observed with coefficients of > 0.9996. (C) 2006 Elsevier B.V. All rights reserved.

Design and implementation of robust systems for secure malware detection

Malicious software (malware) have significantly increased in terms of number and effectiveness during the past years. Until 2006, such software were mostly used to disrupt network infrastructures or to show coders’ skills. Nowadays, malware constitute a very important source of economical profit, and are very difficult to detect. Thousands of novel variants are released every day, and modern obfuscation techniques are used to ensure that signature-based anti-malware systems are not able to detect such threats. This tendency has also appeared on mobile devices, with Android being the most targeted platform. To counteract this phenomenon, a lot of approaches have been developed by the scientific community that attempt to increase the resilience of anti-malware systems. Most of these approaches rely on machine learning, and have become very popular also in commercial applications. However, attackers are now knowledgeable about these systems, and have started preparing their countermeasures. This has lead to an arms race between attackers and developers. Novel systems are progressively built to tackle the attacks that get more and more sophisticated. For this reason, a necessity grows for the developers to anticipate the attackers’ moves. This means that defense systems should be built proactively, i.e., by introducing some security design principles in their development. The main goal of this work is showing that such proactive approach can be employed on a number of case studies. To do so, I adopted a global methodology that can be divided in two steps. First, understanding what are the vulnerabilities of current state-of-the-art systems (this anticipates the attacker’s moves). Then, developing novel systems that are robust to these attacks, or suggesting research guidelines with which current systems can be improved. This work presents two main case studies, concerning the detection of PDF and Android malware. The idea is showing that a proactive approach can be applied both on the X86 and mobile world. The contributions provided on this two case studies are multifolded. With respect to PDF files, I first develop novel attacks that can empirically and optimally evade current state-of-the-art detectors. Then, I propose possible solutions with which it is possible to increase the robustness of such detectors against known and novel attacks. With respect to the Android case study, I first show how current signature-based tools and academically developed systems are weak against empirical obfuscation attacks, which can be easily employed without particular knowledge of the targeted systems. Then, I examine a possible strategy to build a machine learning detector that is robust against both empirical obfuscation and optimal attacks. Finally, I will show how proactive approaches can be also employed to develop systems that are not aimed at detecting malware, such as mobile fingerprinting systems. In particular, I propose a methodology to build a powerful mobile fingerprinting system, and examine possible attacks with which users might be able to evade it, thus preserving their privacy. To provide the aforementioned contributions, I co-developed (with the cooperation of the researchers at PRALab and Ruhr-Universität Bochum) various systems: a library to perform optimal attacks against machine learning systems (AdversariaLib), a framework for automatically obfuscating Android applications, a system to the robust detection of Javascript malware inside PDF files (LuxOR), a robust machine learning system to the detection of Android malware, and a system to fingerprint mobile devices. I also contributed to develop Android PRAGuard, a dataset containing a lot of empirical obfuscation attacks against the Android platform. Finally, I entirely developed Slayer NEO, an evolution of a previous system to the detection of PDF malware. The results attained by using the aforementioned tools show that it is possible to proactively build systems that predict possible evasion attacks. This suggests that a proactive approach is crucial to build systems that provide concrete security against general and evasion attacks.

Co-acquisition of hyperpolarised 13C and 15N NMR spectra

Recent developments in dynamic nuclear polarisation now allow significant enhancements to be generated in the cryo solid state and transferred to the liquid state for detection at high resolution. We demonstrate that the Ardenkjaer-Larsen method can be extended by taking advantage of the properties of the trityl radicals used. It is possible to hyperpolarise 13C and 15N simultaneously in the solid state, and to maintain these hyperpolarisations through rapid dissolution into the liquid state. We demonstrate the almost simultaneous measurement of hyperpolarised 13C and hyperpolarised 15N NMR spectra. The prospects for further improvement of the method using contemporary technology are also discussed.

Detection of Emerging and Re-Emerging Pathogens in Surface Waters Close to an Urban Area

Current knowledge about the spread of pathogens in aquatic environments is scarce probably because bacteria, viruses, algae and their toxins tend to occur at low concentrations in water, making them very difficult to measure directly. The purpose of this study was the development and validation of tools to detect pathogens in freshwater systems close to an urban area. In order to evaluate anthropogenic impacts on water microbiological quality, a phylogenetic microarray was developed in the context of the EU project µAQUA to detect simultaneously numerous pathogens and applied to samples from two different locations close to an urban area located upstream and downstream of Rome in the Tiber River. Furthermore, human enteric viruses were also detected. Fifty liters of water were collected and concentrated using a hollow-fiber ultrafiltration approach. The resultant concentrate was further size-fractionated through a series of decreasing pore size filters. RNA was extracted from pooled filters and hybridized to the newly designed microarray to detect pathogenic bacteria, protozoa and toxic cyanobacteria. Diatoms as indicators of the water quality status, were also included in the microarray to evaluate water quality. The microarray results gave positive signals for bacteria, diatoms, cyanobacteria and protozoa. Cross validation of the microarray was performed using standard microbiological methods for the bacteria. The presence of oral-fecal transmitted human enteric-viruses were detected using q-PCR. Significant concentrations of Salmonella, Clostridium, Campylobacter and Staphylococcus as well as Hepatitis E Virus (HEV), noroviruses GI (NoGGI) and GII (NoGII) and human adenovirus 41 (ADV 41) were found in the Mezzocammino site, whereas lower concentrations of other bacteria and only the ADV41 virus was recovered at the Castel Giubileo site. This study revealed that the pollution level in the Tiber River was considerably higher downstream rather than upstream of Rome and the downstream location was contaminated by emerging and re-emerging pathogens.