We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally.

The development of a highly parallel enzyme logic sensing concept employing a novel encoding scheme for the determination of multiple pathophysiological conditions is reported. The new concept multiplexes a contingent of enzyme-based logic gates to yield a distinct 'injury code' corresponding to a unique pathophysiological state as prescribed by a truth table. The new concept is illustrated using an array of NAND and AND gates to assess the biomedical significance of numerous biomarker inputs including creatine kinase, lactate dehydrogenase, norepinephrine, glutamate, alanine transaminase, lactate, glucose, glutathione disulfide, and glutathione reductase to assess soft-tissue injury, traumatic brain injury, liver injury, abdominal trauma, hemorrhagic shock, and oxidative stress. Under the optimal conditions, physiological and pathological levels of these biomarkers were detected through either optical or electrochemical techniques by monitoring the level of the outputs generated by each of the six logic gates. By establishing a pathologically meaningful threshold for each logic gate, the absorbance and amperometric assays tendered the diagnosis in a digitally encoded 6-bit word, defined as an 'injury code'. This binary 'injury code' enabled the effective discrimination of 64 unique pathological conditions to offer a comprehensive high-fidelity diagnosis of multiple injury conditions. Such processing of relevant biomarker inputs and the subsequent multiplexing of the logic gate outputs to yield a comprehensive 'injury code' offer significant potential for the rapid and reliable assessment of varied and complex forms of injury in circumstances where access to a clinical laboratory is not viable. While the new concept of parallel and multiplexed enzyme logic gates is illustrated here in connection to multi-injury diagnosis, it could be readily extended to a wide range of practical medical, industrial, security and environmental applications.

The design and characterization of a microneedle array-based carbon paste electrode towards minimally invasive electrochemical sensing are described. Arrays consisting of 3 × 3 pyramidal microneedle structures, each with an opening of 425 µm, were loaded with a metallized carbon paste transducer. The renewable nature of carbon paste electrodes enables the convenient packing of hollow non-planar microneedles with pastes that contain assorted catalysts and biocatalysts. Smoothing the surface results in good microelectrode-to-microelectrode uniformity. Optical and scanning electron micrographs shed useful insights into the surface morphology at the microneedle apertures. The attractive performance of the novel microneedle electrode arrays is illustrated in vitro for the low-potential detection of hydrogen peroxide at rhodium-dispersed carbon paste microneedles and for lactate biosensing by the inclusion of lactate oxidase in the metallized carbon paste matrix. Highly repeatable sensing is observed following consecutive cycles of packing/unpacking the carbon paste. The operational stability of the array is demonstrated as well as the interference-free detection of lactate in the presence of physiologically relevant levels of ascorbic acid, uric acid, and acetaminophen. Upon addressing the biofouling effects associated with on-body sensing, the microneedle carbon paste platform would be attractive for the subcutaneous electrochemical monitoring of a number of physiologically relevant analytes.

The incorporation of amperometric sensors into clothing through direct screen-printing onto the textile substrate is described. Particular attention is given to electrochemical sensors printed directly on the elastic waist of underwear that offers tight direct contact with the skin. The textile-based printed carbon electrodes have a well-defined appearance with relatively smooth conductor edges and no apparent defects or cracks. Convenient voltammetric and chronoamperometric measurements of 0-3 mM ferrocyanide, 0-25 mM hydrogen peroxide, and 0-100 muM NADH have been documented. The favorable electrochemical behavior is maintained under folding or stretching stress, relevant to the deformation of clothing. The electrochemical performance and tolerance to mechanical stress are influenced by the physical characteristics of the textile substrate. The results indicate the potential of textile-based screen-printed amperometric sensors for future healthcare, sport or military applications. Such future applications would benefit from tailoring the ink composition and printing conditions to meet the specific requirements of the textile substrate.

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A multi-enzyme biocatalytic cascade processing simultaneously five biomarkers characteristic of traumatic brain injury (TBI) and soft tissue injury (STI) was developed. The system operates as a digital biosensor based on concerted function of 8 Boolean AND logic gates, resulting in the decision about the physiological conditions based on the logic analysis of complex patterns of the biomarkers. The system represents the first example of a multi-step/multi-enzyme biosensor with the built-in logic for the analysis of complex combinations of biochemical inputs. The approach is based on recent advances in enzyme-based biocomputing systems and the present paper demonstrates the potential applicability of biocomputing for developing novel digital biosensor networks.

This study examines the influence of textile substrates upon the behavior of wearable screen-printed electrodes and demonstrates the attractive sensing properties of these sensors towards the detection of nitroaromatic explosives. Compared to electrodes printed on common cotton or polyester substrates, GORE-TEX-based electrochemical sensors display reproducible background cyclic voltammograms, reflecting the excellent water-repellant properties of the GORE-TEX fabric. The wetting properties of different printed textile electrodes are elucidated using contact angle measurements. The influence of laundry washing and mechanical stress is explored. The GORE-TEX-based printed electrodes exhibit favorable detection of 2,4-dinitrotoluene (DNT) and 2,4,6-trinitrotoluene (TNT) explosives, including rapid detection of DNT vapor.

Our results showed a high overall incidence (32.6%) of three-rooted mandibular first molars in Taiwanese individuals. CBCT could be a valuable tool for identifying an extra distolingual root in mandibular first molars.