Detection and use of QTL for complex traits in multiple environments.

QTL mapping methods for complex traits are challenged by new developments in marker technology, phenotyping platforms, and breeding methods. In meeting these challenges, QTL mapping approaches will need to also acknowledge the central roles of QTL by environment interactions (QEI) and QTL by trait interactions in the expression of complex traits like yield. This paper presents an overview of mixed model QTL methodology that is suitable for many types of populations and that allows predictive modeling of QEI, both for environmental and developmental gradients. Attention is also given to multi-trait QTL models which are essential to interpret the genetic basis of trait correlations. Biophysical (crop growth) model simulations are proposed as a complement to statistical QTL mapping for the interpretation of the nature of QEI and to investigate better methods for the dissection of complex traits into component traits and their genetic controls.

Sparse Representation Based Acoustic Rangefinders: From Sensor Platforms to Mobile Devices

Acoustic rangerfinders are a promising technology for accurate proximity detection, a critical requirement for many emerging mobile computing applications. While state-of-the-art systems deliver robust ranging performance, the computational intensiveness of their detection mechanism expedites the energy depletion of the associated devices that are typically powered by batteries. The contribution of this article is fourfold. First, it outlines the common factors that are important for ranging. Second, it presents a review of acoustic rangers and identifies their potential problems. Third, it explores the design of an information processing framework based on sparse representation that could potentially address existing challenges, especially for mobile devices. Finally, it presents mu-BeepBeep: a low energy acoustic ranging service for mobile devices, and empirically evaluates its benefits.

Plasmonic Lipid Bilayer Membranes for Enhanced Detection Sensitivity of Biolabeling Fluorophores

Plasmonics based sensing, using the surface plasmon resonance of metal nanoparticles, has been effectively demonstrated in various applications. Extending this methodology to cell and artificial lipid bilayer membranes is extremely beneficial in enhancing the sensitivity of the detection of binding and cellular transport of molecules across such membranes. Here, the creation of an artificial plasmonic biomembrane template is demonstrated and used to show the enhanced detection sensitivity of certain widely used biomarker molecules. The efficacy of these templates is explained in terms of the ability of the hydrophobic polymer grafted gold nanoparticles used to organize, penetrate, and fluidize the membranes. The enhancement of photoluminescence of the dye molecules used occurs over a reasonably large spectral range as compared to the plasmon resonance of gold nanoparticles. The results could, possibly, be extended to cellular membranes with relevant modifications, as well as to the detection of any other biological molecule appropriately labeled with fluorescent dye molecules, and demonstrate the versatility of these plasmonic bioinspired platforms as potential biochemical sensors.

DNA-Mediated Charge Transport Devices for Protein Detection

Detection of biologically relevant targets, including small molecules, proteins, DNA, and RNA, is vital for fundamental research as well as clinical diagnostics. Sensors with biological elements provide a natural foundation for such devices because of the inherent recognition capabilities of biomolecules. Electrochemical DNA platforms are simple, sensitive, and do not require complex target labeling or expensive instrumentation. Sensitivity and specificity are added to DNA electrochemical platforms when the physical properties of DNA are harnessed. The inherent structure of DNA, with its stacked core of aromatic bases, enables DNA to act as a wire via DNA-mediated charge transport (DNA CT). DNA CT is not only robust over long molecular distances of at least 34 nm, but is also especially sensitive to anything that perturbs proper base stacking, including DNA mismatches, lesions, or DNA-binding proteins that distort the π-stack. Electrochemical sensors based on DNA CT have previously been used for single-nucleotide polymorphism detection, hybridization assays, and DNA-binding protein detection. Here, improvements to (i) the structure of DNA monolayers and (ii) the signal amplification with DNA CT platforms for improved sensitivity and detection are described.

First, improvements to the control over DNA monolayer formation are reported through the incorporation of copper-free click chemistry into DNA monolayer assembly. As opposed to conventional film formation involving the self-assembly of thiolated DNA, copper-free click chemistry enables DNA to be tethered to a pre-formed mixed alkylthiol monolayer. The total amount of DNA in the final film is directly related to the amount of azide in the underlying alkylthiol monolayer. DNA monolayers formed with this technique are significantly more homogeneous and lower density, with a larger amount of individual helices exposed to the analyte solution. With these improved monolayers, significantly more sensitive detection of the transcription factor TATA binding protein (TBP) is achieved.

Using low-density DNA monolayers, two-electrode DNA arrays were designed and fabricated to enable the placement of multiple DNA sequences onto a single underlying electrode. To pattern DNA onto the primary electrode surface of these arrays, a copper precatalyst for click chemistry was electrochemically activated at the secondary electrode. The location of the secondary electrode relative to the primary electrode enabled the patterning of up to four sequences of DNA onto a single electrode surface. As opposed to conventional electrochemical readout from the primary, DNA-modified electrode, a secondary microelectrode, coupled with electrocatalytic signal amplification, enables more sensitive detection with spatial resolution on the DNA array electrode surface. Using this two-electrode platform, arrays have been formed that facilitate differentiation between well-matched and mismatched sequences, detection of transcription factors, and sequence-selective DNA hybridization, all with the incorporation of internal controls.

For effective clinical detection, the two working electrode platform was multiplexed to contain two complementary arrays, each with fifteen electrodes. This platform, coupled with low density DNA monolayers and electrocatalysis with readout from a secondary electrode, enabled even more sensitive detection from especially small volumes (4 μL per well). This multiplexed platform has enabled the simultaneous detection of two transcription factors, TBP and CopG, with surface dissociation constants comparable to their solution dissociation constants.

With the sensitivity and selectivity obtained from the multiplexed, two working electrode array, an electrochemical signal-on assay for activity of the human methyltransferase DNMT1 was incorporated. DNMT1 is the most abundant human methyltransferase, and its aberrant methylation has been linked to the development of cancer. However, current methods to monitor methyltransferase activity are either ineffective with crude samples or are impractical to develop for clinical applications due to a reliance on radioactivity. Electrochemical detection of methyltransferase activity, in contrast, circumvents these issues. The signal-on detection assay translates methylation events into electrochemical signals via a methylation-specific restriction enzyme. Using the two working electrode platform combined with this assay, DNMT1 activity from tumor and healthy adjacent tissue lysate were evaluated. Our electrochemical measurements revealed significant differences in methyltransferase activity between tumor tissue and healthy adjacent tissue.

As differential activity was observed between colorectal tumor tissue and healthy adjacent tissue, ten tumor sets were subsequently analyzed for DNMT1 activity both electrochemically and by tritium incorporation. These results were compared to expression levels of DNMT1, measured by qPCR, and total DNMT1 protein content, measured by Western blot. The only trend detected was that hyperactivity was observed in the tumor samples as compared to the healthy adjacent tissue when measured electrochemically. These advances in DNA CT-based platforms have propelled this class of sensors from the purely academic realm into the realm of clinically relevant detection.

An Optically recombined laser interferometer for gravitational wave detection

Kilometer scale interferometers for the detection of gravitational waves are currently under construction by the LIGO (Laser Interferometer Gravitational-wave Observatory) and VIRGO projects. These interferometers will consist of two Fabry-Perot cavities illuminated by a laser beam which is split in half by a beam splitter. A recycling mirror between the laser and the beam splitter will reflect the light returning from the beam splitter towards the laser back into the interferometer. The positions of the optical components in these interferometers must be controlled to a small fraction of a wavelength of the laser light. Schemes to extract signals necessary to control these optical components have been developed and demonstrated on the tabletop. In the large scale gravitational wave detectors the optical components must be suspended from vibration isolation platforms to achieve the necessary isolation from seismic motion. These suspended components present a new class of problems in controlling the interferometer, but also provide more exacting test of interferometer signal and noise models.

This thesis discusses the first operation of a suspended-mass Fabry-Perot-Michelson interferometer, in which signals carried by the optically recombined beams are used to detect and control all important mirror displacements. This interferometer uses an optical configuration and signal extraction scheme that is planned for the full scale LIGO interferometers with the simplification of the removal of the recycling mirror. A theoretical analysis of the performance that is expected from such an interferometer is presented and the experimental results are shown to be in generally good agreement.

Optimized vertical carbon nanotube forests for multiplex surface-enhanced raman scattering detection

The highly sensitive and molecule-specific technique of surface-enhanced Raman spectroscopy (SERS) generates high signal enhancements via localized optical fields on nanoscale metallic materials, which can be tuned by manipulation of the surface roughness and architecture on the submicrometer level. We investigate gold-functionalized vertically aligned carbon nanotube forests (VACNTs) as low-cost straightforward SERS nanoplatforms. We find that their SERS enhancements depend on their diameter and density, which are systematically optimized for their performance. Modeling of the VACNT-based SERS substrates confirms consistent dependence on structural parameters as observed experimentally. The created nanostructures span over large substrate areas, are readily configurable, and yield uniform and reproducible SERS enhancement factors. Further fabricated micropatterned VACNTs platforms are shown to deliver multiplexed SERS detection. The unique properties of CNTs, which can be synergistically utilized in VACNT-based substrates and patterned arrays, can thus provide new generation platforms for SERS detection. © 2012 American Chemical Society.

Sensory information and associative cues used in food detection by wild vervet monkeys.

Understanding animals' spatial perception is a critical step toward discerning their cognitive processes. The spatial sense is multimodal and based on both the external world and mental representations of that world. Navigation in each species depends upon its evolutionary history, physiology, and ecological niche. We carried out foraging experiments on wild vervet monkeys (Chlorocebus pygerythrus) at Lake Nabugabo, Uganda, to determine the types of cues used to detect food and whether associative cues could be used to find hidden food. Our first and second set of experiments differentiated between vervets' use of global spatial cues (including the arrangement of feeding platforms within the surrounding vegetation) and/or local layout cues (the position of platforms relative to one another), relative to the use of goal-object cues on each platform. Our third experiment provided an associative cue to the presence of food with global spatial, local layout, and goal-object cues disguised. Vervets located food above chance levels when goal-object cues and associative cues were present, and visual signals were the predominant goal-object cues that they attended to. With similar sample sizes and methods as previous studies on New World monkeys, vervets were not able to locate food using only global spatial cues and local layout cues, unlike all five species of platyrrhines thus far tested. Relative to these platyrrhines, the spatial location of food may need to stay the same for a longer time period before vervets encode this information, and goal-object cues may be more salient for them in small-scale space.

Pterin detection using surface-enhanced Raman spectroscopy incorporating a straightforward silver colloid-based synthesis technique

Optical techniques toward the realization of sensitive and selective biosensing platforms have received considerable attention in recent times. Techniques based on interferometry, surface plasmon resonance, and waveguides have all proved popular, while spectroscopy in particular offers much potential. Raman spectroscopy is an information-rich technique in which the vibrational frequencies reveal much about the structure of a compound, but it is a weak process and offers poor sensitivity. In response to this problem, surface-enhanced Raman scattering (SERS) has received much attention, due to significant increases in sensitivity instigated by bringing the sample into contact with an enhancing substrate. Here we discuss a facile and rapid technique for the detection of pterins using SERS-active colloidal silver suspensions. Pterins are a family of biological compounds that are employed in nature in color pigmentation and as facilitators in metabolic pathways. In this work, small volumes of xanthopterin, isoxanthopterin, and 7,8-dihydrobiopterin have been examined while adsorbed to silver colloids. Limits of detection have been examined for both xanthopterin and isoxanthopterin using a 10-s exposure to a 12 mW 532 nm laser, which, while showing a trade-off between scan time and signal intensity, still provides the opportunity for the investigation of simultaneous detection of both pterins in solution. (C) 2011 Society of Photo-Optical Instrumentation Engineers (SPIE). [DOI: 10.1117/1.3600658]

Android Malware Detection Using Parallel Machine Learning Classifiers

Mobile malware has continued to grow at an alarming rate despite on-going mitigation efforts. This has been much more prevalent on Android due to being an open platform that is rapidly overtaking other competing platforms in the mobile smart devices market. Recently, a new generation of Android malware families has emerged with advanced evasion capabilities which make them much more difficult to detect using conventional methods. This paper proposes and investigates a parallel machine learning based classification approach for early detection of Android malware. Using real malware samples and benign applications, a composite classification model is developed from parallel combination of heterogeneous classifiers. The empirical evaluation of the model under different combination schemes demonstrates its efficacy and potential to improve detection accuracy. More importantly, by utilizing several classifiers with diverse characteristics, their strengths can be harnessed not only for enhanced Android malware detection but also quicker white box analysis by means of the more interpretable constituent classifiers.

Defocused transmission spectroscopy: a potential detection of sodium in the atmosphere of WASP-12b

We report on a pilot study of a novel observing technique, defocussed transmission spectroscopy, and its application to the study of exoplanet atmospheres using ground-based platforms. Similar to defocussed photometry, defocussed transmission spectroscopy has an added advantage over normal spectroscopy in that it reduces systematic errors due to flat-fielding, PSF variations, slit-jaw imperfections and other effects associated with ground-based observations. For one of the planetary systems studied, WASP-12b, we report a tentative detection of additional Na absorption of 0.12+/-0.03[+0.03]% during transit using a 2A wavelength mask. After consideration of a systematic that occurs mid-transit, it is likely that the true depth is actually closer to 0.15%. This is a similar level of absorption reported in the atmosphere of HD209458b (0.135+/-0.017%, Snellen et al. 2008). Finally, we outline methods that will improve the technique during future observations, based on our findings from this pilot study.

A New Android Malware Detection Method Using Bayesian Classification

Mobile malware has been growing in scale and complexity as smartphone usage continues to rise. Android has surpassed other mobile platforms as the most popular whilst also witnessing a dramatic increase in malware targeting the platform. A worrying trend that is emerging is the increasing sophistication of Android malware to evade detection by traditional signature-based scanners. As such, Android app marketplaces remain at risk of hosting malicious apps that could evade detection before being downloaded by unsuspecting users. Hence, in this paper we present an effective approach to alleviate this problem based on Bayesian classification models obtained from static code analysis. The models are built from a collection of code and app characteristics that provide indicators of potential malicious activities. The models are evaluated with real malware samples in the wild and results of experiments are presented to demonstrate the effectiveness of the proposed approach.

A quantitative TaqMan PCR assay for the detection of Mycoplasma suis

Aim: To develop a TaqMan probe-based, highly sensitive and specific quantitative PCR (qPCR) assay for the detection and quantification of Mycoplasma suis in the blood of pigs. Methods and Results: Primers and probes specific to Myc. suis 16S rRNA gene were designed. The qPCR assay`s specificity, detection limit, intra- and inter-assay variability were evaluated and its performance was compared with a Myc. suis conventional PCR assay (cPCR). Blood of two experimentally infected pigs, 40 Indiana pigs, 40 Brazilian sows and 28 peccaries were tested. The assay detected as few as ten copies of Myc. suis plasmids and was 100-fold more sensitive than the cPCR. No cross-reactivity with nontarget pig mycoplasmas was observed. An average of 1.62 x 10(11) and 2.75 x 10(8) target copies ml(-1) of blood were detected in the acutely and chronically infected pigs, respectively. Three (7.5%) pigs and 32 (80.0%) sows were positive while all peccaries were negative for Myc. suis. Conclusion: The developed qPCR assay is highly sensitive and specific for Myc. suis detection and quantification. Significance and Impact of the Study: TaqMan qPCR is an accurate and quick test for detection of Myc. suis infected pigs, which can be used on varied instrumentation platforms.

Direct determination of Al, As, Cu, Fe, Mn, and Ni in fuel ethanol by simultaneous GFAAS using integrated platforms pretreated with W-Rh permanent modifier together with Pd plus Mg modifier

A method is proposed for the simultaneous determination of Al, As, Cu, Fe, Mn, and Ni in fuel ethanol by electrothermal atomic absorption spectrometry (ETAAS) using W-Rh permanent modifier together with Pd(NO3)(2) + Mg(NO3)(2) conventional modifier. The integrated platform of a transversely heated graphite atomizer (THGA) was treated with tungsten, followed by rhodium, forming a deposit containing 250 mug W + 200 mug Rh. A 500-muL, volume of fuel ethanol was diluted with 500 muL, of 0.14 mol L-1 HNO3 in an autosampler cup of the spectrometer. Then, 20 muL, of the diluted ethanol was introduced into the pretreated graphite platform followed by the introduction of 5 mug Pd(NO3)(2) + 3 mug Mg(NO3)(2). The injection of this modifier was required to improve arsenic and iron recoveries in fuel ethanol. Calibrations were carried out using multi-element reference solutions prepared in diluted ethanol (1 + 1, v/v) acidified to 0. 14 mol L-1 HNO3. The pyrolysis and atomization temperatures of the heating program were 1200degreesC and 2200degreesC, respectively, which were obtained with multielement reference solutions in acidic diluted ethanol (1 + 1, v/v; 0. 14 mol L-1 HNO3). The characteristic masses for the simultaneous determination in ethanol fuel were 78 pg Al, 33 pg As, 10 pg Cu, 14 pg Fe, 7 pg Mn, and 24 pg Ni. The lifetime of the pretreated tube was about 700 firings. The detection limits (D.L.) were 1.9 mug L-1 Al, 2.9 mug L-1 As, 0.57 mug L-1.Cu, 1.3 mug L-1 Fe, 0.40 mug L-1 Mn, and 1.3 mug L-1 Ni. The relative standard deviations (n = 12) were 4%, 4%, 3%, 1.5%, 1.2%, and 2.2% for Al, As, Cu, Fe, Mn, and Ni, respectively. The recoveries of Al, As, Cu, Fe, Mn, and Ni added to the fuel ethanol samples varied from 81% to 95%, 80% to 98%, 97% to 109%, 85% to 107%, 98% to 106% and 97% to 103%, respectively. Accuracy was checked for the Al, As, Cu, Fe, Mn, and Ni determination in 10 samples purchased at a local gas station in Araraquara-SP City, Brazil. A paired t-test showed that at the 95% confidence level the results were in agreement with those obtained by single-element ETAAS.

Dendrimers/TiO2 nanoparticles layer-by-layer films as extended gate FET for pH detection

The layer-by-layer (LbL) technique combined with field-effect transistor (FET) based sensors has enabled the production of pH-sensitive platforms with potential application in biosensors. A variation of the FET architecture, so called separative extended gate FET (SEGFET) devices, are promise as an alternative to conventional ion sensitive FET (ISFET). SEGFET configuration exhibits the advantage of combining the field-effect concept with organic and inorganic materials directly adsorbed on the extended gate, allowing the test of new pH-sensitive materials in a simple and low cost way. In this communication, poly(propylene imine) dendrimer (PPI) and TiO2 nanoparticles (TiO2-np) were assembled onto gold-covered substrates via layer-by-layer technique to produce a low cost SEGFET pH sensor. The sensor presented good pH sensitivity, ca. 57 mV pH(-1), showing that our strategy has potential advantages to fabricate low cost pH-sensing membranes. (C) 2012 Elsevier B.V. All rights reserved.

Cooperative communication and distributed detection in wireless sensor networks

Recent progress in microelectronic and wireless communications have enabled the development of low cost, low power, multifunctional sensors, which has allowed the birth of new type of networks named wireless sensor networks (WSNs). The main features of such networks are: the nodes can be positioned randomly over a given field with a high density; each node operates both like sensor (for collection of environmental data) as well as transceiver (for transmission of information to the data retrieval); the nodes have limited energy resources. The use of wireless communications and the small size of nodes, make this type of networks suitable for a large number of applications. For example, sensor nodes can be used to monitor a high risk region, as near a volcano; in a hospital they could be used to monitor physical conditions of patients. For each of these possible application scenarios, it is necessary to guarantee a trade-off between energy consumptions and communication reliability. The thesis investigates the use of WSNs in two possible scenarios and for each of them suggests a solution that permits to solve relating problems considering the trade-off introduced. The first scenario considers a network with a high number of nodes deployed in a given geographical area without detailed planning that have to transmit data toward a coordinator node, named sink, that we assume to be located onboard an unmanned aerial vehicle (UAV). This is a practical example of reachback communication, characterized by the high density of nodes that have to transmit data reliably and efficiently towards a far receiver. It is considered that each node transmits a common shared message directly to the receiver onboard the UAV whenever it receives a broadcast message (triggered for example by the vehicle). We assume that the communication channels between the local nodes and the receiver are subject to fading and noise. The receiver onboard the UAV must be able to fuse the weak and noisy signals in a coherent way to receive the data reliably. It is proposed a cooperative diversity concept as an effective solution to the reachback problem. In particular, it is considered a spread spectrum (SS) transmission scheme in conjunction with a fusion center that can exploit cooperative diversity, without requiring stringent synchronization between nodes. The idea consists of simultaneous transmission of the common message among the nodes and a Rake reception at the fusion center. The proposed solution is mainly motivated by two goals: the necessity to have simple nodes (to this aim we move the computational complexity to the receiver onboard the UAV), and the importance to guarantee high levels of energy efficiency of the network, thus increasing the network lifetime. The proposed scheme is analyzed in order to better understand the effectiveness of the approach presented. The performance metrics considered are both the theoretical limit on the maximum amount of data that can be collected by the receiver, as well as the error probability with a given modulation scheme. Since we deal with a WSN, both of these performance are evaluated taking into consideration the energy efficiency of the network. The second scenario considers the use of a chain network for the detection of fires by using nodes that have a double function of sensors and routers. The first one is relative to the monitoring of a temperature parameter that allows to take a local binary decision of target (fire) absent/present. The second one considers that each node receives a decision made by the previous node of the chain, compares this with that deriving by the observation of the phenomenon, and transmits the final result to the next node. The chain ends at the sink node that transmits the received decision to the user. In this network the goals are to limit throughput in each sensor-to-sensor link and minimize probability of error at the last stage of the chain. This is a typical scenario of distributed detection. To obtain good performance it is necessary to define some fusion rules for each node to summarize local observations and decisions of the previous nodes, to get a final decision that it is transmitted to the next node. WSNs have been studied also under a practical point of view, describing both the main characteristics of IEEE802:15:4 standard and two commercial WSN platforms. By using a commercial WSN platform it is realized an agricultural application that has been tested in a six months on-field experimentation.