Measuring the functional sequence complexity of proteins

<p>Abstract</p> <p>Background</p> <p>Abel and Trevors have delineated three aspects of sequence complexity, Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC) observed in biosequences such as proteins. In this paper, we provide a method to measure functional sequence complexity.</p> <p>Methods and Results</p> <p>We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families. Considerations were made in determining how the measure can be used to correlate functionality when relating to the whole molecule and sub-molecule. In the experiment, we show that when the proposed measure is applied to the aligned protein sequences of ubiquitin, 6 of the 7 highest value sites correlate with the binding domain.</p> <p>Conclusion</p> <p>For future extensions, measures of functional bioinformatics may provide a means to evaluate potential evolving pathways from effects such as mutations, as well as analyzing the internal structural and functional relationships within the 3-D structure of proteins.</p

Clinical significance of frizzled homolog 3 protein in colorectal cancer patients

2013-2014 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

The effects of ocular magnification on Spectralis spectral domain optical coherence tomography scan length

Purpose The purpose of this study was to assess the effects of incorporating individual ocular biometry measures of corneal curvature, refractive error, and axial length on scan length obtained using Spectralis spectral domain optical coherence tomography (SD-OCT). Methods Two SD-OCT scans were acquired for 50 eyes of 50 healthy participants, first using the Spectralis default keratometry (K) setting followed by incorporating individual mean-K values. Resulting scan lengths were compared to predicted scan lengths produced by image simulation software, based on individual ocular biometry measures including axial length. Results Axial length varied from 21.41 to 29.04 mm. Spectralis SD-OCT scan lengths obtained with default-K ranged from 5.7 to 7.3 mm, and with mean-K from 5.6 to 7.6 mm. We report a stronger correlation of simulated scan lengths incorporating the subject’s mean-K value (ρ = 0.926, P < 0.0005) compared to Spectralis default settings (ρ = 0.663, P < 0.0005). Conclusions Ocular magnification appears to be better accounted for when individual mean-K values are incorporated into Spectralis SD-OCT scan acquisition versus using the device’s default-K setting. This must be considered when taking area measurements and lateral measurements parallel to the retinal surface

Neuroprotective effect of Lycium barbarum in rat chronic ocular hypertension model via immunomodulation of macrophages/microglia

Abstract of Poster presentationSociety of Neurosciences, Hong Kong, 2005. In Neurosignals, 2006, v. 15 n. 3, p. 145-146, poster no. P-8/2

Chemical pathology case conference - Renal function tests

Glomerular filtration rate (GFR) is the best index for assessing the overall renal function but it can only be determined indirectly. Measurement of serum creatinine is the simplest and the most widely used method for GFR assessment. Correct interpretation of serum creatinine levels requires knowledge about the age, sex, muscle mass and physiological states of individual patients and factors that may interfere with laboratory measurements. Determination of creatinine clearance (CrCl) using 24-hour urine sample is also used for GFR assessment. CrCl can overestimate GFR because of the renal tubular secretion of creatinine. Under or over collection of 24-hour urine can cause significant errors in CrCl calculations. The Cockcroft & Gault formula and the abbreviated MDRD equation can provide additional information to serum creatinine level alone. Understanding their limitations is required for accurate application of these equations in clinical practice. Numerous disease processes and pharmaceutical agents have primary and secondary effects on the kidneys. A stepwise investigative approach is required to delineate the underlying cause of renal impairment. Physical examination, routine laboratory tests and some basic radiological examinations help divide the cause of renal impairment into prerenal, renal and postrenal forms. This information is very useful in guiding appropriate management and further investigations.link_to_subscribed_fulltex

Hotspot KRAS exon 2 mutations in CD166 positive colorectal cancer and colorectal adenoma cells

2017-2018 > Academic research: refereed > Publication in refereed journal201809 bcmaVersion of RecordPublishe