DNA sensing by amplifying the number of near-infrared emitting, oligonucleotide-encapsulated silver clusters

A bifunctional oligonucleotide integrates in situ synthesis of a fluorogenic silver cluster with recognition of a target DNA sequence. With the template C(3)AC(3)AC(3)GC(3)A, a complex forms with 10 silver atoms that possesses electronic transitions in the near-infrared and that is detected at nanomolar concentrations using diode laser excitation. Pendant to this cluster encoding region, the recognition component binds a target DNA strand through hybridization, and decoupling of these two regions of the composite sensor renders a modular sensor for specific oligonucleotides. A target is detected using a quencher strand that bridges the cluster template and recognition components and disturbs cluster binding, as indicated by static quenching. Competitive displacement of the quencher by the target strand restores the favored cluster environment, and our key finding is that this exchange enhances emission through a proportional increase in the number of emissive clusters. DNA detection is also accomplished in serum-containing buffers by taking advantage of the high brightness of this fluorophore and the inherently low endogenous background in the near-infrared spectral region. Cluster stability in this biological environment is enhanced by supplementing the solutions with Ag(+).     

A Stereo‐Matching Technique for Recovering 3D Information from Underwater Inspection Imagery

Underwater inspections stand to gain from using stereo imaging systems to collect three‐dimensional measurements. Although many stereo‐matching algorithms have been devised to solve the correspondence problem, that is, find the same points in multiple images, these algorithms often perform poorly when applied to images of underwater scenes due to the poor visibility and the complex underwater light field. This article presents a new stereo‐matching algorithm, called PaLPaBEL (Pyramidal Loopy Propagated BELief) that is designed to operate on challenging imagery. At its core, PaLPaBEL is a semiglobal method based on a loopy belief propagation message passing algorithm applied on a Markov random field. A pyramidal scheme is adopted that enables wide disparity ranges and high‐resolution images to be handled efficiently. For performance evaluation, PaLPaBEL is applied to underwater stereo images captured under various visibility conditions in a laboratory setting, and to synthetic imagery created in a virtual underwater environment. The technique is also demonstrated on stereo images obtained from a real‐world inspection. The successful results indicate that PaLPaBEL is well suited for underwater application and has value as a tool for the cost‐effective inspection of marine structures.     

Perception of safety of cyclists in Dublin City

In recent years, cycling has been recognized and is being promoted as a sustainable mode of travel. The perception of cycling as an unsafe mode of travel is a significant obstacle in increasing the mode share of bicycles in a city. Hence, it is important to identify and analyze the factors which influence the safety experiences of the cyclists in an urban signalized multi-modal transportation network. Previous researches in the area of perceived safety of cyclists primarily considered the influence of network infrastructure and operation specific variables and are often limited to specific locations within the network. This study explores the factors that are expected to be important in influencing the perception of safety among cyclists but were never studied in the past. These factors include the safety behavior of existing cyclists, the users of other travel modes and their attitude toward cyclists, facilities and network infrastructures applicable to cycling as well as to other modes in all parts of an urban transportation network. A survey of existing cyclists in Dublin City was conducted to gain an insight into the different aspects related to the safety experience of cyclists. Ordered Logistic Regression (OLR) and Principal Component Analysis (PCA) were used in the analysis of survey responses. This study has revealed that respondents perceive cycling as less safe than driving in Dublin City. The new findings have shown that the compliance of cyclists with the rules of the road increase their safety experience, while the reckless and careless attitudes of drivers are exceptionally detrimental to their perceived safety. The policy implications of the results of analysis are discussed with the intention of building on the reputation of cycling as a viable mode of transportation among all network users.     

Optical sensing by transforming chromophoric silver clusters in DNA nanoreactors

Bifunctional DNA oligonucleotides serve as templates for chromophoric silver clusters and as recognition sites for target DNA strands, and communication between these two components is the basis of an oligonucleotide sensor. Few-atom silver clusters exhibit distinct electronic spectra spanning the visible and near-infrared region, and they are selectively synthesized by varying the base sequence of the DNA template. In these studies, a 16-base cluster template is adjoined with a 12-base sequence complementary to the target analyte, and hybridization induces structural changes in the composite sensor that direct the conversion between two spectrally and stoichiometrically distinct clusters. Without its complement, the sensor strand selectively harbors ~7 Ag atoms that absorb at 400 nm and fold the DNA host. Upon association of the target with its recognition site, the sensor strand opens to expose the cluster template that has the binding site for ~11 Ag atoms, and absorption at 720 nm with relatively strong emission develops in lieu of the violet absorption. Variations in the length and composition of the recognition site and the cluster template indicate that these types of dual-component sensors provide a general platform for near-infrared-based detection of oligonucleotides in challenging biological environments.     

Fault diagnosis in discrete time hybrid systems - A case study

A method of analysing diagnosability of discrete time hybrid systems (DTHS), which are similar to the simple n-rate timed automata [R. Alur, C. Courcoubetis, T.A. Henzinger, P. Ho, Hybrid automata: an algorithmic approach to the specification and verification of hybrid systems, in: Hybrid Systems, LNCS 736, Springer Verlag, 1993, pp. 209-229], has been proposed. A state based fault modeling formalism is used. The properties of the DTHS model, under measurement limitations due to inadequacy or non-availability of sensors, are discussed. A definition of diagnosability for DTHS models has been adopted from the one proposed in [M. Sampath, R. Sengupta, S. Lafortune, K. Sinnamohideen, D. Teneketzis, Diagnosability of discrete-event systems, IEEE Transactions on Automatic Control 40 (9) (1995) 1555-1575] for discrete-event system (DES) models. Based on the measurement limited DTHS models, an algorithm for construction of a diagnoser is presented. It is next demonstrated through an example of a chemical reaction chamber that the diagnosability condition (over the diagnoser), which has been shown to be necessary and sufficient for DES diagnosability, fails to hold for many systems. This is so because the abstraction employed in DES modeling obliterates an important feature of the transitions namely fairness. Exploiting the explicit continuous dynamics of the DTHS models, the fairness of transitions is identified and used to demonstrate diagnosability. The diagnosability condition over the diagnoser is suitably modified to encompass the situations typified by the example.     

Effects of Varying MBE Growth Conditions on Layered Zn-Se-Te Structures

We report the effects of varying growth parameters on the photoluminescence (PL) and time-resolved photoluminescence (TRPL) emission from layered Zn-Se:Te structures with submonolayer quantities of ZnTe grown by a combination of migration-enhanced epitaxy (MEE) and molecular beam epitaxy (MBE). Dependences on Te effusion cell temperature (T _{Te source}) and “wait time” (duration for which all shutters are closed, t _all-off) are investigated to show that these parameters contribute towards changing the size and/or composition of the quantum dots (QDs). Optical studies showed that increasing T _{Te source} resulted in the formation of larger QDs. Increasing t _all-off from 0 s to 3 s contributed towards the formation of larger QDs, while further increasing t _all-off to 9 s led to desorption of Te adatoms which resulted in smaller QDs. These parameters are easy to control, and thus understanding their effects should help us to gain better control towards obtaining high-quality QDs.