GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data

<p>Abstract</p> <p>Background</p> <p>One-dimensional (1-D) electrophoretic data obtained using the cDNA-AFLP method have attracted great interest for the identification of differentially expressed transcript-derived fragments (TDFs). However, high-throughput analysis of the cDNA-AFLP data is currently limited by the need for labor-intensive visual evaluation of multiple electropherograms. We would like to have high-throughput ways of identifying such TDFs.</p> <p>Results</p> <p>We describe a method, GOGOT, which automatically detects the differentially expressed TDFs in a set of time-course electropherograms. Analysis by GOGOT is conducted as follows: correction of fragment lengths of TDFs, alignment of identical TDFs across different electropherograms, normalization of peak heights, and identification of differentially expressed TDFs using a special statistic. The output of the analysis is a highly reduced list of differentially expressed TDFs. Visual evaluation confirmed that the peak alignment was performed perfectly for the TDFs by virtue of the correction of peak fragment lengths before alignment in step 1. The validity of the automated ranking of TDFs by the special statistic was confirmed by the visual evaluation of a third party.</p> <p>Conclusion</p> <p>GOGOT is useful for the automated detection of differentially expressed TDFs from cDNA-AFLP temporal electrophoretic data. The current algorithm may be applied to other electrophoretic data and temporal microarray data.</p

^{31}P and ^{75}As NMR evidence for a residual density of states at zero energy in superconducting BaFe_2(As_{0.67}P_{0.33})_2

^{31}P and ^{75}As NMR measurements were performed in superconducting BaFe_2(As_{0.67}P_{0.33})_2 with T_c = 30 K. The nuclear-spin-lattice relaxation rate T_1^{-1} and the Knight shift in the normal state indicate the development of antiferromagnetic fluctuations, and T_1^{-1} in the superconducting (SC) state decreases without a coherence peak just below T_c, as observed in (Ba_{1-x}K_{x})Fe_2As_2. In contrast to other iron arsenide superconductors, the T_1^{-1} \propto T behavior is observed below 4K, indicating the presence of a residual density of states at zero energy. Our results suggest that strikingly different SC gaps appear in BaFe_2(As_{1-x}P_{x})_2 despite a comparable T_c value, an analogous phase diagram, and similar Fermi surfaces to (Ba_{1-x}K_{x})Fe_2As_2.Comment: 4 pages, 5 figure

ROKU: a novel method for identification of tissue-specific genes

BACKGROUND: One of the important goals of microarray research is the identification of genes whose expression is considerably higher or lower in some tissues than in others. We would like to have ways of identifying such tissue-specific genes. RESULTS: We describe a method, ROKU, which selects tissue-specific patterns from gene expression data for many tissues and thousands of genes. ROKU ranks genes according to their overall tissue specificity using Shannon entropy and detects tissues specific to each gene if any exist using an outlier detection method. We evaluated the capacity for the detection of various specific expression patterns using synthetic and real data. We observed that ROKU was superior to a conventional entropy-based method in its ability to rank genes according to overall tissue specificity and to detect genes whose expression pattern are specific only to objective tissues. CONCLUSION: ROKU is useful for the detection of various tissue-specific expression patterns. The framework is also directly applicable to the selection of diagnostic markers for molecular classification of multiple classes

Randomized Group-Greedy Method for Large-Scale Sensor Selection Problems

The randomized group-greedy method and its customized method for large-scale sensor selection problems are proposed. The randomized greedy sensor selection algorithm is applied straightforwardly to the group-greedy method, and a customized method is also considered. In the customized method, a part of the compressed sensor candidates is selected using the common greedy method or other low-cost methods. This strategy compensates for the deterioration of the solution due to compressed sensor candidates. The proposed methods are implemented based on the D- and E-optimal design of experiments, and numerical experiments are conducted using randomly generated sensor candidate matrices with potential sensor locations of 10,000--1,000,000. The proposed method can provide better optimization results than those obtained by the original group-greedy method when a similar computational cost is spent as for the original group-greedy method. This is because the group size for the group-greedy method can be increased as a result of the compressed sensor candidates by the randomized algorithm. Similar results were also obtained in the real dataset. The proposed method is effective for the E-optimality criterion, in which the objective function that the optimization by the common greedy method is difficult due to the absence of submodularity of the objective function. The idea of the present method can improve the performance of all optimizations using a greedy algorithm

Increased [¹⁸F]FMISO accumulation under hypoxia by multidrug-resistant protein 1 inhibitors

BACKGROUND: [¹⁸F]Fluoromisonidazole ([¹⁸F]FMISO) is a PET imaging probe widely used for the detection of hypoxia. We previously reported that [¹⁸F]FMISO is metabolized to the glutathione conjugate of the reduced form in hypoxic cells. In addition, we found that the [¹⁸F]FMISO uptake level varied depending on the cellular glutathione conjugation and excretion ability such as enzyme activity of glutathione-S-transferase and expression levels of multidrug resistance-associated protein 1 (MRP1, an efflux transporter), in addition to the cellular hypoxic state. In this study, we evaluated whether MRP1 activity affected [¹⁸F]FMISO PET imaging. METHODS: FaDu human pharyngeal squamous cell carcinoma cells were pretreated with MRP1 inhibitors (cyclosporine A, lapatinib, or MK-571) for 1 h, incubated with [¹⁸F]FMISO for 4 h under hypoxia, and their radioactivity was then measured. FaDu tumor-bearing mice were intravenously injected with [¹⁸F]FMISO, and PET/CT images were acquired at 4 h post-injection (1st PET scan). Two days later, the same mice were pretreated with MRP1 inhibitors (cyclosporine A, lapatinib, or MK-571) for 1 h, and PET/CT images were acquired (2nd PET scan). RESULTS: FaDu cells pretreated with MRP1 inhibitors exhibited significantly higher radioactivity than those without inhibitor treatment (cyclosporine A: 6.91 ± 0.27, lapatinib: 10.03 ± 0.47, MK-571: 10.15 ± 0.44%dose/mg protein, p < 0.01). In the in vivo PET study, the SUVmean ratio in tumors [calculated as after treatment (2nd PET scan)/before treatment of MRP1 inhibitors (1st PET scan)] of the mice treated with MRP1 inhibitors was significantly higher than those of control mice (cyclosporine A: 2.6 ± 0.7, lapatinib: 2.2 ± 0.7, MK-571: 2.2 ± 0.7, control: 1.2 ± 0.2, p < 0.05). CONCLUSION: In this study, we revealed that MRP1 inhibitors increase [¹⁸F]FMISO accumulation in hypoxic cells. This suggests that [¹⁸F]FMISO-PET imaging is affected by MRP1 inhibitors independent of the hypoxic state

Data-Driven Sensor Selection Method Based on Proximal Optimization for High-Dimensional Data With Correlated Measurement Noise

The present paper proposes a data-driven sensor selection method for a high-dimensional nondynamical system with strongly correlated measurement noise. The proposed method is based on proximal optimization and determines sensor locations by minimizing the trace of the inverse of the Fisher information matrix under a block-sparsity hard constraint. The proposed method can avoid the difficulty of sensor selection with strongly correlated measurement noise, in which the possible sensor locations must be known in advance for calculating the precision matrix for selecting sensor locations. The problem can be efficiently solved by the alternating direction method of multipliers, and the computational complexity of the proposed method is proportional to the number of potential sensor locations when it is used in combination with a low-rank expression of the measurement noise model. The advantage of the proposed method over existing sensor selection methods is demonstrated through experiments using artificial and real datasets

Study of the factors related to atrial fibrillation after coronary artery bypass grafting: A search for a marker to predict the occurrence of atrial fibrillation before surgical intervention

ObjectiveAtrial fibrillation after cardiac surgery is a frequent complication. In this study we studied various factors in addition to trying to identify a marker that would predict the potential for atrial fibrillation before surgical intervention to prevent its occurrence.MethodsWe targeted 234 cases in which isolated coronary artery bypass grafting had been performed. The items for study included age, EuroSCORE, and maximum values of creatine phosphokinase–MB, troponin I, and angiotensin II after surgical intervention and preoperative values of atrial natriuretic peptide, brain natriuretic peptide, and C-reactive protein. As fibrotic markers, we measured levels of the sialylated carbohydrate antigen KL-6 in the blood, hyaluronic acid, and pyridinoline cross-linked carboxyterminal telepeptide of type I collagen C. At the time of surgical intervention, a section of the right atrium was extracted, and atrial natriuretic peptide, the sialylated carbohydrate antigen KL-6, hyaluronic acid, and pyridinoline cross-linked telopeptide of type I collagen levels were measured.ResultsAtrial fibrillation was observed in 73 (31.2%) cases, and preoperative factors that showed statistically significant differences in the occurrence of atrial fibrillation included age, EuroSCORE, and preoperative values of atrial natriuretic peptide, angiotensin II, the sialylated carbohydrate antigen KL-6, hyaluronic acid, and pyridinoline cross-linked telopeptide of type I collagen in the blood. As for intraoperative and postoperative factors, statistically significant differences were observed in the postoperative maximum of angiotensin II, atrial natriuretic peptide of the right atrium, the sialylated carbohydrate antigen KL-6, hyaluronic acid, and pyridinoline cross-linked telopeptide of type I collagen levels.ConclusionThe fibrosis of tissue associated with age is believed to be closely related to the occurrence of atrial fibrillation after coronary artery bypass grafting. This study suggests that the preoperative values of atrial natriuretic peptide, angiotensin II, the sialylated carbohydrate antigen KL-6, hyaluronic acid, and pyridinoline cross-linked telopeptide of type I collagen in the blood are useful as a new index for the occurrence of atrial fibrillation after coronary artery bypass grafting

Electrical storm after cardiac resynchronization therapy in a patient with nonischemic cardiomyopathy: Signal-averaged vector-projected 187-channel electrocardiogram-based risk stratification for lethal arrhythmia

AbstractWe describe treatment of atrial flutter and electrical storm presenting as incessant ventricular tachycardia (VT) after implantation of a cardiac resynchronization therapy defibrillator (CRT-D) in a patient with dilated cardiomyopathy. No prior arrhythmic event had occurred. Our treatment strategy, including amiodarone administration, was guided in part by signal-averaged vector-projected 187-channel electrocardiogram (SAVP-ECG)-based risk stratification for ventricular arrhythmia. Corrected recovery time (RTc) dispersion and Tpeak-end dispersion were used to evaluate transmural dispersion of repolarization. RTc and Tpeak-end dispersion increased during the period of electrical storm. Values were improved 2 years after CRT-D implantation, and the amiodarone was discontinued. The VT has not recurred despite discontinuation of the antiarrhythmic agent. SAVP-ECG-based risk stratification for ventricular arrhythmia proved useful for the management of antiarrhythmic therapy