MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects.

MINTbase is a repository that comprises nuclear and mitochondrial tRNA-derived fragments (\u27tRFs\u27) found in multiple human tissues. The original version of MINTbase comprised tRFs obtained from 768 transcriptomic datasets. We used our deterministic and exhaustive tRF mining pipeline to process all of The Cancer Genome Atlas datasets (TCGA). We identified 23 413 tRFs with abundance of ≥ 1.0 reads-per-million (RPM). To facilitate further studies of tRFs by the community, we just released version 2.0 of MINTbase that contains information about 26 531 distinct human tRFs from 11 719 human datasets as of October 2017. Key new elements include: the ability to filter tRFs on-the-fly by minimum abundance thresholding; the ability to filter tRFs by tissue keywords; easy access to information about a tRF\u27s maximum abundance and the datasets that contain it; the ability to generate relative abundance plots for tRFs across cancer types and convert them into embeddable figures; MODOMICS information about modifications of the parental tRNA, etc. Version 2.0 of MINTbase contains 15x more datasets and nearly 4x more distinct tRFs than the original version, yet continues to offer fast, interactive access to its contents. Version 2.0 is available freely at http://cm.jefferson.edu/MINTbase/

Probabilistic Prediction of Chaotic Time Series Using Similarity of Attractors and LOOCV Predictable Horizons for Obtaining Plausible Predictions

This paper presents a method for probabilistic prediction of chaotic time series. So far, we have developed several model selection methods for chaotic time series prediction, but the methods cannot estimate the predictable horizon of predicted time series. Instead of using model selection methods employing the estimation of mean square prediction error (MSE), we present a method to obtain a probabilistic prediction which provides a prediction of time series and the estimation of predictable horizon. The method obtains a set of plausible predictions by means of using the similarity of attractors of training time series and the time series predicted by a number of learning machines with different parameter values, and then obtains a smaller set of more plausible predictions with longer predictable horizons estimated by LOOCV (leave-one-out cross-validation) method. The effectiveness and the properties of the present method are shown by means of analyzing the result of numerical experiments.22nd International Conference, ICONIP 2015, November 9-12, 2015, Istanbul, Turke

Potential role of IGF-1 in parathyroid hormone-related renal growth induced by high protein diet in uninephrectomized rats

Potential role of IGF-1 in parathyroid hormone-related renal growth induced by high protein diet in uninephrectomized rats. Recent studies indicate that parathyroidectomy (PTX) prevents the progression of kidney damage due to high protein diet in the subtotal nephrectomized rat model of chronic renal failure. Associated with this protection, the difference in the renal “compensatory” growth induced by high (HPr) as compared to normal protein diet (NPr) is completely abolished by PTX. To understand the physiological mechanism responsible for this protection, the changes in both circulating level and kidney content of IGF-1, a growth factor capable of influencing renal “compensatory” growth, was analyzed after unilateral nephrectomy (UNX). In UNX rats, HPr as compared to NPr diet given for five days significantly increased the kidney/body weight ratio (0.48 ± 0.01%, N = 11 vs. 0.44 ± 0.01%, N = 11, P < 0.005) and the plasma level of IGF-1 (365 ± 10 ng/ml vs. 306 ± 10 ng/ml, P < 0.001). In UNX rats fed HPr, PTX completely abolished the renal “compensatory” growth (0.38 ± 0.02%, N = 7, P < 0.001) and the increased plasma level of IGF-1 (246 ± 14 ng/ml, N=7,P < 0.001). In PTX-UNX rats treated with physiological doses of 1,25-dihydroxyvitamin D3 which nearly normalized the calcemia, the renal growth and the increased plasma level of IGF-1 induced by HPr were restored towards those recorded in SHAM-UNX rats fed the HPr diet. Similar effects were observed in PTX-UNX rats in which the plasma calcium concentration was increased by the chronic administration of a retinoid derivative, used as an agent where the calcemie effect is essentially mediated by a stimulation of bone resorption. There was a positive significant correlation between the change in kidney growth in response to UNX and the plasma level of IGF-1 (r = 0.685, P < 0.001). The kidney IGF-1 content was affected neither by the protein intake nor by the PTH status. In rats with an intact renal mass and fed NPr diet, chronic administration of bovine PTH did not alter the plasma IGF-1 concentration. In these animals, both the increase of the plasma IGF-1 level under HPr diet and the blunting effect of PTX thereon were similar to the response observed in UNX animals. There was, however, no significant change in the kidney/body weight ratios in response to HPr diet. In conclusion, the results of the present study provide evidence that calciotropic hormones such as PTH and 1,25-dihydroxyvitamin D3 and/or the associated change in extracellular calcium concentration modulate the effect of protein intake on hepatic production of IGF-1. In rats with a reduced renal mass, the elevation in the circulating level of IGF-1 is likely responsible for the increased “compensatory” growth of remaining nephrons, which is associated with an acceleration of renal function deterioration induced by high protein diet

The Insulin receptor catalyzes the tyrosine phosphorylation o Caveolin 1

Our previous studies revealed that insulin stimulates the tyrosine phosphorylation of caveolin in 3T3L1 adipocytes. To explore the mechanisms involved in this event, we evaluated the association of the insulin receptor with caveolin. The receptor was detected in a Triton-insoluble low density fraction, co-sedimenting with caveolin and flotillin on sucrose density gradients. We also detected the receptor in caveolin-enriched rosette structures by immunohistochemical analysis of plasma membrane sheets from 3T3L1 adipocytes. Insulin stimulated the phosphorylation of caveolin-1 on Tyr14. This effect of the hormone was not blocked by overexpression of mutant forms of the Cbl-associated protein that block the translocation of phospho-Cbl to the caveolin-enriched, lipid raft microdomains. Moreover, this phosphorylation event was also unaffected by inhibitors of the MAPK and phosphatidylinositol 3-kinase pathways. Although previous studies demonstrated that the Src family kinase Fyn was highly enriched in caveolae, an inhibitor of this kinase had no effect on insulin-stimulated caveolin phosphorylation. Interestingly, overexpression of a mutant form of caveolin that failed to interact with the insulin receptor did not undergo phosphorylation. Taken together, these data indicate that the insulin receptor directly catalyzes the tyrosine phosphorylation of caveolin. Previous article in issu

Landau Model for Commensurate-Commensurate Phase Transitions in Uniaxial Improper Ferroelectric Crystals

We propose the Landau model for lock-in phase transitions in uniaxially modulated improper ferroelectric incommensurate-commensurate systems of class I. It includes Umklapp terms of third and fourth order and secondary order parameter representing the local polarization. The corresponding phase diagram has the structure of harmless staircase, with the allowed wave numbers obeying the Farey tree algorithm. Among the stable commensurate phases only those with periods equal to odd number of lattice constants have finite macroscopic polarizations. These results are in excellent agreement with experimental findings in some A2BX4 compounds.Comment: 9 pages, 5 figures, revtex, to be published in Journal of Physics: Cond. Matter as a Letter to the Edito

Efficient room-temperature magnetization direction detection by means of the enhanced anomalous Nernst effect in a Weyl ferromagnet

Spintronic phenomena exhibiting a longitudinal resistance change under magnetization reversal are a quite novel feature in nanoscience, which has been intensively studied in hopes of realizing all-electrical magnetization direction detection devices, where no reference ferromagnetic layer is required. However, cryogenic temperatures and/or high magnetic fields have been required to achieve noticeable effects. Here, the high heat-to-charge conversion efficiency of the Heusler alloy Weyl semimetal Co₂MnGa is exploited in single layer nanoscaled wires at room temperature to produce at least two orders of magnitude enhancement of the resistance change ratio, when compared with conventional ferromagnets. Such resistance change under magnetization reversal is consistently explained through temperature distribution simulations and direct thermoelectric measurements of the large anomalous Nernst effect (ANE) in this topologically nontrivial material. Although many reports consider ANE signals as perturbations or undesired artifacts, we demonstrate that they are dominant in this system and can be seized for nonvolatile memory readout, as shown in a prototype device. These results open up new horizons of using enhanced thermoelectric voltages in novel materials for magnetization direction detection in any system where significant temperature gradients exist

Continued-fraction expansion of eigenvalues of generalized evolution operators in terms of periodic orbits

A new expansion scheme to evaluate the eigenvalues of the generalized evolution operator (Frobenius-Perron operator) $H_{q}$ relevant to the fluctuation spectrum and poles of the order-$q$ power spectrum is proposed. The ``partition function'' is computed in terms of unstable periodic orbits and then used in a finite pole approximation of the continued fraction expansion for the evolution operator. A solvable example is presented and the approximate and exact results are compared; good agreement is found.Comment: CYCLER Paper 93mar00

Chromosomal Aberrations in Normal and AT Cells Exposed to High Dose of Low Dose Rate Irradiation

Ataxia telangiectasia (A-T) is a human autosomally recessive syndrome characterized by cerebellar ataxia, telangiectases, immune dysfunction, and genomic instability, and high rate of cancer incidence. A-T cell lines are abnormally sensitive to agents that induce DNA double strand breaks, including ionizing radiation. The diverse clinical features in individuals affected by A-T and the complex cellular phenotypes are all linked to the functional inactivation of a single gene (AT mutated). It is well known that cells deficient in ATM show increased yields of both simple and complex chromosomal aberrations after high-dose-rate irradiation, but, less is known on how cells respond to low-dose-rate irradiation. It has been shown that AT cells contain a large number of unrejoined breaks after both low-dose-rate irradiation and high-dose-rate irradiation, however sensitivity for chromosomal aberrations at low-dose-rate are less often studied. To study how AT cells respond to low-dose-rate irradiation, we exposed confluent normal and AT fibroblast cells to up to 3 Gy of gamma-irradiation at a dose rate of 0.5 Gy/day and analyzed chromosomal aberrations in G0 using fusion PCC (Premature Chromosomal Condensation) technique. Giemsa staining showed that 1 Gy induces around 0.36 unrejoined fragments per cell in normal cells and around 1.35 fragments in AT cells, whereas 3Gy induces around 0.65 fragments in normal cells and around 3.3 fragments in AT cells. This result indicates that AT cells can rejoin breaks less effectively in G0 phase of the cell cycle? compared to normal cells. We also analyzed chromosomal exchanges in normal and AT cells after exposure to 3 Gy of low-dose-rate rays using a combination of G0 PCC and FISH techniques. Misrejoining was detected in the AT cells only? When cells irradiated with 3 Gy were subcultured and G2 chromosomal aberrations were analyzed using calyculin-A induced PCC technique, the yield of unrejoined breaks decreased in both normal and AT cells and misrejoined breaks increased in both cell lines. The present study suggests that AT cells begin to rejoin breaks when a certain number of breaks are accumulated and an increased number of exchanges were observed in G0 AT cells, which is similar situation after high-dose-rate irradiation

Investigation of the thermal tolerance of silicon-based lateral spin valves

Improvement in the thermal tolerance of Si-based spin devices is realized by employing thermally stable nonmagnetic (NM) electrodes. For Au/Ta/Al electrodes, intermixing between Al atoms and Au atoms occurs at approximately 300 °C, resulting in the formation of a Au/Si interface. The Au–Si liquid phase is formed and diffuses mainly along an in-plane direction between the Si and AlN capping layers, eventually breaking the MgO layer of the ferromagnetic (FM) metal/MgO electrodes, which is located 7 µm away from the NM electrodes. By changing the layer structure of the NM electrode from Au/Ta/Al to Au/Ta, the thermal tolerance is clearly enhanced. Clear spin transport signals are obtained even after annealing at 400 °C. To investigate the effects of Mg insertion in FM electrodes on thermal tolerance, we also compare the thermal tolerance among Fe/Co/MgO, Fe/Co/Mg/MgO and Fe/Co/MgO/Mg contacts. Although a highly efficient spin injection has been reported by insertion of a thin Mg layer below or above the MgO layer, these thermal tolerances decrease obviously