Determination of the minimum number of microarray experiments for discovery of gene expression patterns

BACKGROUND: One type of DNA microarray experiment is discovery of gene expression patterns for a cell line undergoing a biological process over a series of time points. Two important issues with such an experiment are the number of time points, and the interval between them. In the absence of biological knowledge regarding appropriate values, it is natural to question whether the behaviour of progressively generated data may by itself determine a threshold beyond which further microarray experiments do not contribute to pattern discovery. Additionally, such a threshold implies a minimum number of microarray experiments, which is important given the cost of these experiments. RESULTS: We have developed a method for determining the minimum number of microarray experiments (i.e. time points) for temporal gene expression, assuming that the span between time points is given and the hierarchical clustering technique is used for gene expression pattern discovery. The key idea is a similarity measure for two clusterings which is expressed as a function of the data for progressive time points. While the experiments are underway, this function is evaluated. When the function reaches its maximum, it indicates the set of experiments reach a saturated state. Therefore, further experiments do not contribute to the discrimination of patterns. CONCLUSION: The method has been verified with two previously published gene expression datasets. For both experiments, the number of time points determined with our method is less than in the published experiments. It is noted that the overall approach is applicable to other clustering techniques

A new hybrid approach to human error probability quantification-applications in maritime operations

Human Reliability Analysis (HRA) has always been an essential research issue in safety critical systems. Cognitive Reliability Error Analysis Method (CREAM), as a well-known second generation HRA method is capable of conducting both retrospective and prospective analysis, thus being widely used in many sectors. However, the needs of addressing the use of a deterministic approach to configure common performance conditions (CPCs) and the assignment of the same importance to all the CPCs in a traditional CREAM method reveal a significant research gap to be fulfilled. This paper describes a modified CREAM methodology based on an Evidential Reasoning (ER) approach and a Decision Making Trial and Evaluation Laboratory (DEMATEL) technique for making human error probability quantification in CREAM rational. An illustrative case study associated with maritime operations is presented. The proposed method is validated by sensitivity analysis and the quantitative analysis result is verified through comparing the real data collected from Shanghai coastal waters. Its main contribution lies in that it for the first time addresses the data incompleteness in HEP, given that the previous relevant studies mainly focus on the fuzziness in data. The findings will provide useful insights for quantitative assessment of seafarers' errors to reduce maritime risks due to human errors

Can social capital be transferred cross the boundary of the real and virtual worlds? An empirical investigation of Twitter

Author name used in this publication: He, Wei.2011-2012 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Dynamic response of a cracked atomic force microscope cantilever used for nanomachining

The vibration behavior of an atomic force microscope [AFM] cantilever with a crack during the nanomachining process is studied. The cantilever is divided into two segments by the crack, and a rotational spring is used to simulate the crack. The two individual governing equations of transverse vibration for the cracked cantilever can be expressed. However, the corresponding boundary conditions are coupled because of the crack interaction. Analytical expressions for the vibration displacement and natural frequency of the cracked cantilever are obtained. In addition, the effects of crack flexibility, crack location, and tip length on the vibration displacement of the cantilever are analyzed. Results show that the crack occurs in the AFM cantilever that can significantly affect its vibration response

Specific involvement of atypical PKCζ/PKMζ in spinal persistent nociceptive processing following peripheral inflammation in rat.

BACKGROUND: Central sensitization requires the activation of various intracellular signalling pathways within spinal dorsal horn neurons, leading to a lowering of activation threshold and enhanced responsiveness of these cells. Such plasticity contributes to the manifestation of chronic pain states and displays a number of features of long-term potentiation (LTP), a ubiquitous neuronal mechanism of increased synaptic strength. Here we describe the role of a novel pathway involving atypical PKCζ/PKMζ in persistent spinal nociceptive processing, previously implicated in the maintenance of late-phase LTP. RESULTS: Using both behavioral tests and in vivo electrophysiology in rats, we show that inhibition of this pathway, via spinal delivery of a myristoylated protein kinase C-ζ pseudo-substrate inhibitor, reduces both pain-related behaviors and the activity of deep dorsal horn wide dynamic range neurons (WDRs) following formalin administration. In addition, Complete Freund's Adjuvant (CFA)-induced mechanical and thermal hypersensitivity was also reduced by inhibition of PKCζ/PKMζ activity. Importantly, this inhibition did not affect acute pain or locomotor behavior in normal rats and interestingly, did not inhibited mechanical allodynia and hyperalgesia in neuropathic rats. Pain-related behaviors in both inflammatory models coincided with increased phosphorylation of PKCζ/PKMζ in dorsal horn neurons, specifically PKMζ phosphorylation in formalin rats. Finally, inhibition of PKCζ/PKMζ activity decreased the expression of Fos in response to formalin and CFA in both superficial and deep laminae of the dorsal horn. CONCLUSIONS: These results suggest that PKCζ, especially PKMζ isoform, is a significant factor involved in spinal persistent nociceptive processing, specifically, the manifestation of chronic pain states following peripheral inflammation

Onset Rivalry: Brief Presentation Isolates an Early Independent Phase of Perceptual Competition

When the left and right eyes are simultaneously presented with different images, observers typically report exclusive awareness of only one image. This phenomenon is termed binocular rivalry, reflecting the fact that the dominant image alternates every few seconds in a cycle of perceptual competition that continues indefinitely. Despite the apparent continuity in perceptual switching, we now demonstrate that the initial “onset” period is fundamentally different to all subsequent rivalry epochs. Using brief intermittent presentations, rivalry dominance shows strong biases such that the same target is perceived with each successive stimulus onset. These biases remain consistent within any given location, but vary across the visual field in a distribution that is stable over multiple weeks but highly idiosyncratic across observers. If the presentation exceeds ∼1sec at any location, however, the very different and much more balanced alternations of sustained binocular rivalry become apparent. These powerful onset biases are observed with brief intermittent presentations at a single location or with continual smooth motion of the targets. Periods of adaptation to one of the rivaling targets induced local switches in dominance to the non-adapted target. However, these effects were generally limited to the spatial site of adaptation and had less influence over each subsequent cycle of the target. We conclude that onset rivalry is independent of sustained rivalry and cannot be explained by local regions of monocular dominance or memory of past perceptual history, but rather reflects low-level, spatially localized factors that are stable over periods of weeks. These findings suggest that brief presentation paradigms are inappropriate for their current use in studies of the mechanisms underlying sustained rivalry. However, brief presentations are ideal for investigating early stages of perceptual competition

8-Hydroxy-(S)-3-methyl-1-oxoisochromane-5-carboxylic acid(5-carboxymellein)

The molecules of the title compound, C11H10O5, are linked by a hydrogen bond involving the acid H and the carbonyl O atom of the dihydroisocoumarin unit into a linear chain running along the b axis of the monoclinic unit cell

7,8-dihydroxy-3-methyl-10-oxo-1H,10H-pyrano[4,3-b]chromene-9-carboxylic acid

The structure of the title compound, anhydrofulvic acid, C14H10O7, a yellow acidic metabolite isolated from Paecilomyces sp. was determined by X-ray analysis. The chromone ring system is essentially planar, with the carboxylic acid group coplanar with the ring