Predicting the subcellular location of apoptosis proteins based on recurrence quantification analysis and the Hilbert Huang transform

Apoptosis proteins play an important role in the development and homeostasis of an organism. The elucidation of the subcellular locations and functions of these proteins is helpful for understanding the mechanism of programmed cell death. In this paper, the recurrent quantification analysis, Hilbert-Huang transform methods, the maximum relevance and minimum redundancy method and support vector machine are used to predict the subcellular location of apoptosis proteins. The validation of the jackknife test suggests that the proposed method can improve the prediction accuracy of the subcellular location of apoptosis proteins and its application may be promising in other fields.

A clinical analysis of risk factor with lymph node metastatic recurrence in patients with N0 esophageal cancer after Ivor-Lewis Esophagectomy

Objective To investigate the risk factors with lymph node metastatic recurrence in patients with N0 esophageal cancer after Ivor-Lewis Esophagectomy. Methods The subjects were 82 patients with pN0 esophagea cancer who underwent Ivor-Lewis esophagectomy from January 2001 to January 2005. By using RT-PCR,VEGF C mRNA was detected in tumor issues,and Mucin (MUC1) mRNA was detected in lymph nodes. The Kaplan-Meier method was used to calculate the survival

Characterization of various structures in gas-solid fluidized beds by recurrence quantification analysis

Gas-solid fluidized beds are widely considered as nonlinear and chaotic dynamic systems. Pressure fluc- tuations were measured in a fluidized bed of 0.15 m in diameter and were analyzed using multiple approaches： discrete Fourier transform （DFT）, discrete wavelet transform （DWT）, and nonlinear recur- rence quantification analysis （RQA）. Three different methods proposed that the complex dynamics of a fluidized bed system can be presented as macro, meso and micro structures. It was found from DFT and DWT that a minimum in wide band energy with an increase in the velocity corresponds to the transition between macro structures and finer structures of the fluidization system. Corresponding transition veloc- ity occurs at gas velocities of 0.3, 0.5 and 0.6 m]s for sands with mean diameters of 150, 280 and 490/~m, respectively. DFT, DWT, and RQA could determine frequency range of0-3.125 Hz for macro, 3. ! 25-50 Hz for meso, and 50-200 Hz for micro structures. The RQA showed that the micro structures have the least periodicity and consequently their determinism and laminarity are the lowest. The results show that a combination of DFT, DWT, and RQA can be used as an effective approach to characterize multi-scale flow behavior in gas-solid fluidized beds.

Hidden Sequence Repeats: Additional Evidence for the Origin of TIM-Barrel Family

Most proteins adopt an approximate structural symmetry. However, they have no symmetry detectable in their sequences and it is unclear for most of these proteins whether their structural symmetry originates from duplication. As one of the six popular folds (super-folds) possessing an approximate structural symmetry, the triosephosphate isomerase barrel (TIM-barrel) domain has been widely studied. Using modified recurrent quantification analysis of primary sequences, we identified the same 2-, 3-, and 4-fold symmetry pattern as their tertiary structures. This result indicates that the symmetry in tertiary structure is coded by symmetry in the primary sequence and that the TIM-barrel adopts a 2-, 3-, or 4-fold repeat pattern during evolution. This discovery will be useful for understanding the evolutionary mechanisms of this protein family and the symmetry pattern that may be a clue into the ancient origin of duplication of half-barrels or the β a unit.

Automatic Assessment of Expanded Disability Status Scale (EDSS) in Multiple Sclerosis Using a Decision Tree

The expanded disability status scale (EDSS) is frequently used to classify the patients with multiple sclerosis (MS). We presented in this paper a novel method to automatically assess the EDSS score from posturologic data (center of pres-sure signals) using a decision tree. Two groups of participants (one for learning and the other for test) with EDSS rang-ing from 0 to 4.5 performed our balance experiment with eyes closed. Two linear measures (the length and the surface) and twelve non-linear measures (the recurrence rate, the Shannon entropy, the averaged diagonal line length and the trapping time for the position, the instantaneous velocity and the instantaneous acceleration of the center of pressure respectively) were calculated for all the participants. Several decision trees were constructed with learning data and tested with test data. By comparing clinical and estimated EDSS scores in the test group, we selected one decision tree with five measures which revealed a 75% of agreement. The results have signified that our tree model is able to auto-matically assess the EDSS scores and that it is possible to distinguish the EDSS scores by using linear and non-linear postural sway measures.

Analysis of correlative factors in peptic ulcer recurrence in the elderly

Objective To analyze the correlative factors of peptic ulcer recurrence in the elderly.Methods From January to December 2009,169 elderly patients(≥60 years old)with peptic ulcer delected by edoscopy were enrolled,whose treatment and usage of medication were analyzed.Data of treatment and recurrence in 3-year follow-up were recorded.Mann-Whitney rank sum test

Efficacy of treatment for pterygium by autologous conjunctival transplantation and mitomycin C

Background The recurrence of pterygium after surgery is high. A variety of adjunctive treatment approaches have been developed to improve the clinical efficacy and many related articles have been published. This study aimed to determine the risk for postoperative pterygium recurrence comparing autologous conjunctival transplantation （ACT） versus mitomycin C （MMC）. Methods Relevant literature published until December 2010 in Medline, Embase, Cochrane, Cochrane library, Science Citation Index, and Google Scholar were searched. Qualified random clinical trial （RCT） studies on the comparison of recurrence rate of pterygium after ACT and MMC treatment were included in this study. Results Eight RCTs with 663 eyes entered the final analysis. The recurrent rate of pterygium was 8.7% （30/343） for ACT and 18.75% （60/320） for MMC. Using fixed-effect meta analysis, we found that the recurrence was significantly lower after ACT than MMC treatment （odds ratio （OR）=0.40, 95% confidence index （C/）, 0.25-0.63, P 〈0.0001）. In sensitivity analyses, we employed random-effects model and excluded studies of low quality or studies in which MMC was administrated after the operation. All the sensitivity analyses confirmed that ACT led to lower recurrence rates than MMC. Sub-group analysis revealed that the recurrence rate was 20.2% （20/99） and 27.65% （26/94） for conjunctival autograft （CA） and MMC respectively, and no significant difference in the recurrence rate was detected （OR=0.65, 95% CI 0.33-1.28, P=0.22）. However, we found that conjunctival limbal autograft （CLA） had lower recurrence rate than MMC （OR=0.26, 95% CI 0.14-0.48, P=0.0001）.

Multiscale characterization of nanoparticles in a magnetically assisted fluidized bed

Pressure fluctuations of a fluidized bed of nanoparticles were measured during the fluidization of nanoparticles with and without a magnetic field at a frequency of 50 Hz.Recurrence quantification analysis(RQA)and wavelet transform were used to determine the frequency range of various flow structures in the bed at three scales.The frequency ranges of the macro-,meso-,and micro-structures were determined to be 0-49Hz,49-781 Hz,and 781+Hz,respectively.Comparison of the determinisms of the sub-signals with and without the external field revealed that in the presence the field,breakage of larger agglomerates occurs faster than re-agglomeration of small agglomerates into larger ones.The power spectral density function of the pressure fluctuations indicated that with an external magnetic field,the power and the frequency range of the pressure signal of macro-structures do not change noticeably.However,the power of the meso-structure signal increases and its frequency range is widened toward higher frequencies,confirming that the number of small bubbles and agglomerates increase in the bed.ln addition,the energy of signal analysis indicated that the external field significantly increases the share of meso-structures in the bed,confirming the RQA results.

Finding Chaos in Finnish GDP

The goal of this paper is to analyze the Finnish gross domestic product(GDP) and to find chaos in the Finnish GDP. We chose Finland where data has been available since 1975, because we needed the longest time series possible. At first we estimated the time delay and the embedding dimension, which is needed for the Lyapunov exponent estimation and for the phase space reconstruction.Subsequently, we computed the largest Lyapunov exponent, which is one of the important indicators of chaos. Then we calculated the 0-1 test for chaos. Finally we computed the Hurst exponent by rescaled range analysis and by dispersional analysis. The Hurst exponent is a numerical estimate of the predictability of a time series. In the end, we executed a recurrent analysis and displayed recurrence plots of detrended GDP time series. The results indicated that chaotic behaviors obviously exist in GDP.