Comparison of pattern detection methods in microarray time series of the segmentation clock.

While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data (tens of thousands of profiles) associated with a certain level of noise remains a challenge. A microarray time series was recently generated to study the transcriptional program of the mouse segmentation clock, a biological oscillator associated with the periodic formation of the segments of the body axis. A method related to Fourier analysis, the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset, leading to the identification of a novel set of cyclic genes associated with the segmentation clock. Here, we applied to the same microarray time series dataset four distinct mathematical methods to identify significant patterns in gene expression profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron test and Stable persistence, and are based on different conceptual frameworks that are either hypothesis- or data-driven. Some of the methods, unlike Fourier transforms, are not dependent on the assumption of periodicity of the pattern of interest. Remarkably, these methods identified blindly the expression profiles of known cyclic genes as the most significant patterns in the dataset. Many candidate genes predicted by more than one approach appeared to be true positive cyclic genes and will be of particular interest for future research. In addition, these methods predicted novel candidate cyclic genes that were consistent with previous biological knowledge and experimental validation in mouse embryos. Our results demonstrate the utility of these novel pattern detection strategies, notably for detection of periodic profiles, and suggest that combining several distinct mathematical approaches to analyze microarray datasets is a valuable strategy for identifying genes that exhibit novel, interesting transcriptional patterns.

Mid-term results and factors affecting outcome of a metal-backed unicompartmental knee design: a case series.

BACKGROUND: Controversies exist regarding the indications for unicompartmental knee arthroplasty. The objective of this study is to report the mid-term results and examine predictors of failure in a metal-backed unicompartmental knee arthroplasty design. METHODS: At a mean follow-up of 60 months, 80 medial unicompartmental knee arthroplasties (68 patients) were evaluated. Implant survivorship was analyzed using Kaplan-Meier method. The Knee Society objective and functional scores and radiographic characteristics were compared before surgery and at final follow-up. A Cox proportional hazard model was used to examine the association of patient's age, gender, obesity (body mass index > 30 kg/m2), diagnosis, Knee Society scores and patella arthrosis with failure. RESULTS: There were 9 failures during the follow up. The mean Knee Society objective and functional scores were respectively 49 and 48 points preoperatively and 95 and 92 points postoperatively. The survival rate was 92% at 5 years and 84% at 10 years. The mean age was younger in the failure group than the non-failure group (p < 0.01). However, none of the factors assessed was independently associated with failure based on the results from the Cox proportional hazard model. CONCLUSION: Gender, pre-operative diagnosis, preoperative objective and functional scores and patellar osteophytes were not independent predictors of failure of unicompartmental knee implants, although high body mass index trended toward significance. The findings suggest that the standard criteria for UKA may be expanded without compromising the outcomes, although caution may be warranted in patients with very high body mass index pending additional data to confirm our results. LEVEL OF EVIDENCE: IV.

HPLC-ESI-MS method development for the elucidation of nicardipine degradation products

Purpose: Nicardipine is a member of a family of calcium channel blockers named dihydropiridines that are known to be photolabile and may cause phototoxicity. It is therefore vital to develop analytical method which can study the photodegradation of nicardipine. Method: Forced acid degradation of nicardipine was conducted by heating 12 ml of 1 mg/ml nicardipine with 3 ml of 2.5 M HCl for two hours. A gradient HPLC medthod was developed using Agilent Technologies 1200 series quaternary system. Separation was achieved with a Hichrome (250 x 4.6 mm) 5 μm C18 reversed phase column and mobile phase composition of 70% A(100%v/v water) and 30% B(99%v/v acetonitrile + 1%v/v formic acid) at time zero, composition of A and B was then charged to 60%v/v A;40%v/v B at 10minutes, 50%v/v A; 50%v/v B at 30minutes and 70%v/v A; 30%v/v B at 35minutes. 20μl of 0.8mg/ml of nicardipine degradation was injected at room temperature (25oC). The gradient method was transferred onto a HPLC-ESI-MS system (HP 1050 series - AQUAMAX mass detector) and analysis conducted with an acid degradation concentration of 0.25mg/ml and 20μl injection volume. ESI spectra were acquired in positive ionisation mode with MRM 0-600 m/z. Results: Eleven nicardipine degradation products were detected in the HPLC analysis and the resolution (RS) between the respective degradants where 1.0, 1.2, 6.0, 0.4, 1.7, 3.7, 1.8, 1.0, and 1.7 respectively. Nine degradation products were identified in the ESI spectra with the respective m/z ratio; 171.0, 166.1, 441.2, 423.2, 455.2, 455.2, 331.1, 273.1, and 290.1. The possible molecular formulae for each degradants were ambiguously determined. Conclusion: A sensitive and specific method was developed for the analysis of nicardipine degradants. Method enables detection and quantification of nicardipine degradation products that can be used for the study of the kinetics of nicardipine degradation processes.

Improved Equivalent Frame Analysis Method for Flat Plate Structures in Vicinity of Edge Columns

This paper proposes a modification to the ACI 318-02 equivalent frame method of analysis of reinforced concrete flat plate exterior panels. Two existing code methods were examined: ACI 318 and BS 8110. The derivation of the torsional stiffness of the edge strip as proposed by ACI 318 is examined and a more accurate estimate of this value is proposed, based on both theoretical analysis and experimental results. A series of 1/3-scale models of flat plate exterior panels have been tested. Unique experimental results were obtained by measuring strains in reinforcing bars at approximately 200 selected locations in the plate panel throughout the entire loading history. The measured strains were used to calculate curvature and, hence, bending moments; these were used along with moments in the columns to assess the accuracy of the equivalent frame methods. The proposed method leads to a more accurate prediction of the moments in the plate at the column front face, at the panel midspan, and in the edge column. Registered Subscribers: View the full article. This document is available as a free download to qualified members. An electronic (PDF) version is available for purchase and download. Click on the Order Now button to continue with the download.

A comparative study of the synthesis of 3-substituted catechols using an enzymatic and a chemoenzymatic method

A series of cis-dihydrodiol metabolites, available from the bacterial dioxygenase-catalysed oxidation of monosubstituted benzene substrates using Pseudomonas putida UV4, have been converted to the corresponding catechols using both a heterogeneous catalyst (Pd/C) and a naphthalene cis-diol dehydrogenase enzyme present in whole cells of the recombinant strain Escherichia coli DH5 alpha(pUC129: nar B). A comparative study of the merits of both routes to 3-substituted catechols has been carried out and the two methods have been found to be complementary. A similarity in mechanism for catechol formation under both enzymatic and chemoenzymatic conditions, involving regioselective oxidation of the hydroxyl group at C-1, has been found using deuterium labelled toluene cis-dihydrodiols. The potential, of combining a biocatalytic step (dioxygenase-catalysed cis-dihydroxylation) with a chemocatalytic step (Pd/C-catalysed dehydrogenation), into a one-pot route to catechols, from the parent substituted benzene substrates, has been realised.

Convergence acceleration of the doubly periodic Green's function for the analysis of thin wire arrays

A method is proposed to accelerate the evaluation of the Green's function of an infinite double periodic array of thin wire antennas. The method is based on the expansion of the Green's function into series corresponding to the propagating and evanescent waves and the use of Poisson and Kummer transformations enhanced with the analytic summation of the slowly convergent asymptotic terms. Unlike existing techniques the procedure reported here provides uniform convergence regardless of the geometrical parameters of the problem or plane wave excitation wavelength. In addition, it is numerically stable and does not require numerical integration or internal tuning parameters, since all necessary series are directly calculated in terms of analytical functions. This means that for nonlinear problem scenarios that the algorithm can be deployed without run time intervention or recursive adjustment within a harmonic balance engine. Numerical examples are provided to illustrate the efficiency and accuracy of the developed approach as compared with the Ewald method for which these classes of problems requires run time splitting parameter adaptation.

Developing a simple, rapid method for identifying and monitoring jellyfish aggregations from the air

Within the marine environment, aerial surveys have historically centred on apex predators, such as pinnipeds, cetaceans and sea birds. However, it is becoming increasingly apparent that the utility of this technique may also extend to subsurface species such as pre-spawning fish stocks and aggregations of jellyfish that occur close to the surface. In light of this, we tested the utility of aerial surveys to provide baseline data for 3 poorly understood scyphozoan jellyfish found throughout British and Irish waters: Rhizostoma octopus, Cyanea capillata and Chrysaora hysoscella. Our principal objectives were to develop a simple sampling protocol to identify and quantify surface aggregations, assess their consistency in space and time, and consider the overall applicability of this technique to the study of gelatinous zooplankton. This approach provided a general understanding of range and relative abundance for each target species, with greatest suitability to the study of R. octopus. For this species it was possible to identify and monitor extensive, temporally consistent and previously undocumented aggregations throughout the Irish Sea, an area spanning thousands of square kilometres. This finding has pronounced implications for ecologists and fisheries managers alike and, moreover, draws attention to the broad utility of aerial surveys for the study of gelatinous aggregations beyond the range of conventional ship-based techniques.

NON-GAUSSIAN STATISTICS OF OIL PRICING TIME-SERIES: A CASE STUDY

The stochastic nature of oil price fluctuations is investigated over a twelve-year period, borrowing feedback from an existing database (USA Energy Information Administration database, available online). We evaluate the scaling exponents of the fluctuations by employing different statistical analysis methods, namely rescaled range analysis (R/S), scale windowed variance analysis (SWV) and the generalized Hurst exponent (GH) method. Relying on the scaling exponents obtained, we apply a rescaling procedure to investigate the complex characteristics of the probability density functions (PDFs) dominating oil price fluctuations. It is found that PDFs exhibit scale invariance, and in fact collapse onto a single curve when increments are measured over microscales (typically less than 30 days). The time evolution of the distributions is well fitted by a Levy-type stable distribution. The relevance of a Levy distribution is made plausible by a simple model of nonlinear transfer. Our results also exhibit a degree of multifractality as the PDFs change and converge toward to a Gaussian distribution at the macroscales.

The impact of a PCR assay for candidemia on antifungal drug prescribing in critical care: an interrupted time series pilot study.

Objective To evaluate the feasibility of conducting a definitive study to assess the impact of introducing a rapid PCR-based test for candidemia on antifungal drug prescribing. Method Prospective, single centre, interrupted time series study consisting of three periods of six months' duration. The assay was available during the second period, during which the PCR assay was available for routine use by physicians Monday–Friday with guaranteed 24-h turnaround time. For each period total antifungal drug use, expressed as treatment-days, was recorded and an adjustment was made to exclude estimated use for proven candidemia. Also, during the intervention period, antifungal prescribing decisions for up to 72 h after each PCR result became available were recorded as either concordant or discordant with that result. Results While overall antifungal use remained relatively stable throughout, after adjustment for candidemia, there was a 38% reduction in use following introduction of the PCR test; however, this was nonsignificant at the 95% level. During the intervention period overall concordance between the PCR result and prescribing decisions was 84%. Conclusions The PCR assay for candidemia was requested, prescribing decisions were generally concordant with the results produced and there was an apparent decrease in antifungal prescription, although this was sustained even after withdrawal of the intervention; these findings should be more thoroughly evaluated in a larger trial.

Nonlinear time series prediction based on a power-law noise model

In this paper we investigate the influence of a power-law noise model, also called noise, on the performance of a feed-forward neural network used to predict time series. We introduce an optimization procedure that optimizes the parameters the neural networks by maximizing the likelihood function based on the power-law model. We show that our optimization procedure minimizes the mean squared leading to an optimal prediction. Further, we present numerical results applying method to time series from the logistic map and the annual number of sunspots demonstrate that a power-law noise model gives better results than a Gaussian model.

Identification of dyes on ancient Chinese paper samples using the subtracted shifted Raman spectroscopy method

The Stein Collection in the British Library contains the Diamond Sutra, the world's oldest, dated, printed document. The paper of the Diamond Sutra and other documents from the Stein collection is believed to be dyed yellow by a natural extract, called huangbo, from the bark of Phellodendron amurense, which contains three major yellow chromophores: berberine, palmatine, and jatrorrhizine, Conservation of these documents requires definite information on the chemical composition of the dyes but no suitable, completely noninvasive analytical method is known. Here we report resonance Raman studies of a series of prate dyes, of plant materials and extracts, and of dyed ancient and modern paper samples. Resonance Raman spectroscopy is used to enhance the spectra of the dyes over the signals from the paper matrixes in which they are held. The samples an give resonance Raman spectra which are dominated by intense fluorescence, but by using SSRS (subtracted shifted Raman spectroscopy) we have obtained reliable spectra of the pure dyes, native bark from the Phellodendron amurense, modern paper dyed with huangbo extracted from this bark, and ancient paper samples. For both ancient paper samples whose pigment bands were detected, the relative intensities of the bands due to berberine and palmatine suggest that the ancient paper is richer in berberine than its modern counterpart, This is the first nondestructive in situ method for detection of these pigments in manuscripts, and as such has considerable potential benefit for the treatment of irreplaceable documents that are believed to be dyed with huangbo but documents on which conservation work cannot proceed without definite identification of the chemical compounds that they contain.

Moving Object Scanning Apparatus and Method

Apparatus for scanning a moving object includes a visible waveband sensor oriented to collect a series of images of the object as it passes through a field of view. An image processor uses the series of images to form a composite image. The image processor stores image pixel data for a current image and predecessor image in the series. It uses information in the current image and its predecessor to analyse images and derive likelihood measures indicating probabilities that current image pixels correspond to parts of the object. The image processor estimates motion between the current image and its predecessor from likelihood weighted pixels. It generates the composite image from frames positioned according to respective estimates of object image motion. Image motion may alternatively be detected be a speed sensor such as Doppler radar sensing object motion directly and providing image timing signals