Filter-wrapper combination and embedded feature selection for gene expression data

Biomedical and bioinformatics datasets are generally large in terms of their number of features - and include redundant and irrelevant features, which affect the effectiveness and efficiency of classification of these datasets. Several different features selection methods have been utilised in various fields, including bioinformatics, to reduce the number of features. This study utilised Filter-Wrapper combination and embedded (LASSO) feature selection methods on both high and low dimensional datasets before classification was performed. The results illustrate that the combination of filter and wrapper feature selection to create a hybrid form of feature selection provides better performance than using filter only. In addition, LASSO performed better on high dimensional data

Origin for the enhanced copper spin echo decay rate in the pseudogap regime of the multilayer high-T_c cuprates

We report measurements of the anisotropy of the spin echo decay for the inner layer Cu site of the triple layer cuprate, Hg_0.8Re_0.2Ba_2Ca_2Cu_3O_8 (T_c=126 K) in the pseudogap T regime below T_pg ~ 170 K and the corresponding analysis for their interpretation. As the field alignment is varied, the shape of the decay curve changes from Gaussian (H_0 \parallel c) to single exponential (H_0 \perp c). The latter characterizes the decay caused by the fluctuations of adjacent Cu nuclear spins caused by their interactions with electron spins. The angular dependence of the second moment (T_{2M}^{-2} \equiv ) deduced from the decay curves indicates that T_{2M}^{-2} for H_0 \parallel c, which is identical to T_{2G}^{-2} (T_{2G} is the Gaussian component), is substantially enhanced, as seen in the pseudogap regime of the bilayer systems. Comparison of T_{2M}^{-2} between H_0 \parallel c and H_0 \perp c indicates that this enhancement is caused by electron spin correlations between the inner and the outer CuO_2 layers. These results provide the answer to the long-standing controversy regarding the opposite T dependences of (T_1T)^{-1} and T_{2G}^{-2} in the pseudogap regime of bi- and trilayer systems.Comment: 4 pages, 4 figure

Thermal Properties of Heavy Fermion Compound YbP

Low-temperature specific heat and its field-dependence up to 16 T was measured in a stoichiometric single crystal of YbP. A sharp peak was observed at {\it T}$_{\rm N}$ = 0.53 K in zero magnetic field. Application of external field seems to induce a new magnetic phase above 11 T. The field dependence of the transition temperature in the high-field phase is different from that of the low field phase. The linear coefficient of the electronic specific heat is estimated as 120 mJ/mole K$^{2}$ from low temperature specfic heat, suggesting heavy Fermion state in YbP.Comment: to be published in J.Phys.Soc.Jpn on May, 200

Signatures of low-scale string models at the LHC

Low-scale string models, in which the string scale M_s is of the order of TeV with large extra dimensions, can solve the problems of scale hierarchy and non-renormalizable quantum gravity in the standard model. String excited states of the standard model particles are possibly observed as resonances in the dijet invariant mass distribution at the LHC. There are two properties to distinguish whether the resonances are due to low-scale string or some other "new physics". One is a characteristic angular distribution in dijet events at the resonance due to spin degeneracy of string excited states, and the other is an appearance of the second resonance at a characteristic mass of second string excited states. We investigate a possibility to observe these evidences of low-scale string models by Monte Carlo simulations with a reference value of M_s = 4 TeV at sqrt{s} = 14 TeV. It is shown that spin degeneracy at the dijet resonance can be observed by looking the chi-distribution with integrated luminosity of 20 fb^-1. It is shown that the second resonance can be observed at rather close to the first resonance in the dijet invariant mass distribution with integrated luminosity of 50 fb^-1. These are inevitable signatures of low-scale string models.Comment: 21 pages, 8 figure

A switchable controlled-NOT gate in a spin-chain NMR quantum computer

A method of switching a controlled-NOT gate in a solid-stae NMR quantum computer is presented. Qubits of I=1/2 nuclear spins are placed periodically along a quantum spin chain (1-D antiferromagnet) having a singlet ground state with a finite spin gap to the lowest excited state caused by some quantum effect. Irradiation of a microwave tuned to the spin gap energy excites a packet of triplet magnons at a specific part of the chain where control and target qubits are involved. The packet switches on the Suhl-Nakamura interaction between the qubits, which serves as a controlled NOT gate. The qubit initialization is achieved by a qubit initializer consisting of semiconducting sheets attached to the spin chain, where spin polarizations created by the optical pumping method in the semiconductors are transferred to the spin chain. The scheme allows us to separate the initialization process from the computation, so that one can optimize the computation part without being restricted by the initialization scheme, which provides us with a wide selection of materials for a quantum computer.Comment: 8 pages, 5 figure

N-Terminal Prolactin-Derived Fragments, Vasoinhibins, Are Proapoptoptic and Antiproliferative in the Anterior Pituitary

The anterior pituitary is under a constant cell turnover modulated by gonadal steroids. In the rat, an increase in the rate of apoptosis occurs at proestrus whereas a peak of proliferation takes place at estrus. At proestrus, concomitant with the maximum rate of apoptosis, a peak in circulating levels of prolactin is observed. Prolactin can be cleaved to different N-terminal fragments, vasoinhibins, which are proapoptotic and antiproliferative factors for endothelial cells. It was reported that a 16 kDa vasoinhibin is produced in the rat anterior pituitary by cathepsin D. In the present study we investigated the anterior pituitary production of N-terminal prolactin-derived fragments along the estrous cycle and the involvement of estrogens in this process. In addition, we studied the effects of a recombinant vasoinhibin, 16 kDa prolactin, on anterior pituitary apoptosis and proliferation. We observed by Western Blot that N-terminal prolactin-derived fragments production in the anterior pituitary was higher at proestrus with respect to diestrus and that the content and release of these prolactin forms from anterior pituitary cells in culture were increased by estradiol. A recombinant preparation of 16 kDa prolactin induced apoptosis (determined by TUNEL assay and flow cytometry) of cultured anterior pituitary cells and lactotropes from ovariectomized rats only in the presence of estradiol, as previously reported for other proapoptotic factors in the anterior pituitary. In addition, 16 kDa prolactin decreased forskolin-induced proliferation (evaluated by BrdU incorporation) of rat total anterior pituitary cells and lactotropes in culture and decreased the proportion of cells in S-phase of the cell cycle (determined by flow cytometry). In conclusion, our study indicates that the anterior pituitary production of 16 kDa prolactin is variable along the estrous cycle and increased by estrogens. The antiproliferative and estradiol-dependent proapoptotic actions of this vasoinhibin may be involved in the control of anterior pituitary cell renewal

Up-regulation of multiple proteins and biological processes during maxillary expansion in rats

<p>Abstract</p> <p>Background</p> <p>Maxillary expansion (ME) is a common practice in orthodontics that aims to increase the constricted maxillary arch width. Relapse often occurs, however, and better treatment strategies are needed. In order to develop a more effective method, this study was designed to further examine the process of tissue remodeling during ME, to identify the changes in expression of several proteins of interest, and to clarify the molecular mechanism responsible for tissue remodeling.</p> <p>Methods</p> <p>Male Wistar rats were randomly divided into control and ME groups. The rats were euthanized at various intervals over 11 days, and the dissected palates were prepared for histological examination. The structure of the midpalatal sutures changed little during the first three days. Proteins from samples in the ground midpalatal tissues obtained on the third day were subjected to two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. Validation of protein expression was performed by Western blot analyses.</p> <p>Results</p> <p>From day 5, chondrocytes in the inner layer of suture cartilage and osteoblasts at the end of the suture cartilage began to proliferate, and the skeletal matrix increased later adjacent to the cartilage in the ME group. Comparative proteomic analysis showed increases in 22 protein spots present in the ME group. The changes in three proteins closely related to osteogenesis (parathyroid hormone, osteoprotegerin and vimentin) were confirmed by Western blotting.</p> <p>Conclusion</p> <p>Many proteins are over-expressed during ME, and they may play an important role in the remodeling process.</p

Identification of a biomarker panel for colorectal cancer diagnosis

<p>Abstract</p> <p>Background</p> <p>Malignancies arising in the large bowel cause the second largest number of deaths from cancer in the Western World. Despite progresses made during the last decades, colorectal cancer remains one of the most frequent and deadly neoplasias in the western countries.</p> <p>Methods</p> <p>A genomic study of human colorectal cancer has been carried out on a total of 31 tumoral samples, corresponding to different stages of the disease, and 33 non-tumoral samples. The study was carried out by hybridisation of the tumour samples against a reference pool of non-tumoral samples using Agilent Human 1A 60-mer oligo microarrays. The results obtained were validated by qRT-PCR. In the subsequent bioinformatics analysis, gene networks by means of Bayesian classifiers, variable selection and bootstrap resampling were built. The consensus among all the induced models produced a hierarchy of dependences and, thus, of variables.</p> <p>Results</p> <p>After an exhaustive process of pre-processing to ensure data quality--lost values imputation, probes quality, data smoothing and intraclass variability filtering--the final dataset comprised a total of 8, 104 probes. Next, a supervised classification approach and data analysis was carried out to obtain the most relevant genes. Two of them are directly involved in cancer progression and in particular in colorectal cancer. Finally, a supervised classifier was induced to classify new unseen samples.</p> <p>Conclusions</p> <p>We have developed a tentative model for the diagnosis of colorectal cancer based on a biomarker panel. Our results indicate that the gene profile described herein can discriminate between non-cancerous and cancerous samples with 94.45% accuracy using different supervised classifiers (AUC values in the range of 0.997 and 0.955).</p