HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).
Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.
Conclusions: HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes

Platelet kinetics in the pulmonary microcirculation in vivo assessed by intravital microscopy

Growing evidence supports the substantial pathophysiological impact of platelets on the development of acute lung injury. Methods for studying these cellular mechanisms in vivo are not present yet. The aim of this study was to develop a model enabling the quantitative analysis of platelet kinetics and platelet-endothelium interaction within consecutive segments of the pulmonary microcirculation in vivo. New Zealand White rabbits were anesthetized and ventilated. Autologous platelets were separated from blood and labeled ex vivo with rhodamine 6G. After implantation of a thoracic window, microhemodynamics and kinetics of platelets were investigated by intravital microscopy. Velocities of red blood cells (RBCs) and platelets were measured in arterioles, capillaries and venules, and the number of platelets adhering to the microvascular endothelium was counted. Kinetics of unstimulated platelets was compared with kinetics of thrombin-activated platelets. Velocity of unstimulated platelets was comparable to RBC velocity in all vessel segments. Unstimulated platelets passed the pulmonary microcirculation without substantial platelet-endothelial interaction. In contrast, velocity of activated platelets was decreased in all vascular segments indicating platelet margination and temporal platelet-endothelium interaction. Thrombin-activated platelets adhered to arteriolar endothelium; in capillaries and venules adherence of platelets was increased 8-fold and 13-fold, respectively. In conclusion, using intravital microscopy platelet kinetics were directly analyzed in the pulmonary microcirculation in vivo for the first time. In contrast to leukocytes, no substantial platelet-endothelium interaction occurs in the pulmonary microcirculation without any further stimulus. In response to platelet activation, molecular mechanisms enable adhesion of platelets in arterioles and venules as well as retention of platelets within capillaries. Copyright (C) 2002 S. Karger AG, Basel

Multimodal Supervised Exercise Training Is Effective in Improving Long Term Walking Performance in Patients with Symptomatic Lower Extremity Peripheral Artery Disease.

This study aimed to evaluate the effect of a multimodal supervised exercise training (SET) program on walking performance for 12 months in patients with symptomatic lower extremity peripheral artery disease (PAD). Consecutive patients with Fontaine stage II PAD participating in the SET program of our hospital were retrospectively investigated. Walking performance, assessed using a treadmill with measures of the pain-free and maximal walking distance (PFWD, MWD, respectively), and 6 min walking distance (6MWD), were tested before and following SET, as well as at 6 and 12 months after SET completion. Ninety-three symptomatic patients with PAD (65.0 ± 1.1 y) were included in the study. Following SET, the walking performance significantly improved (PFWD: +145%, p ≤ 0.001; MWD: +97%, p ≤ 0.001; 6MWD: +15%, p ≤ 0.001). At 6 months, PFWD (+257%, p ≤ 0.001), MWD (+132%, p ≤ 0.001), and 6MWD (+11%, p ≤ 0.001) remained significantly improved compared with the pre-SET condition. At 12 months, PFWD (+272%, p ≤ 0.001), MWD (+130%, p ≤ 0.001), and 6MWD (+11%, p ≤ 0.001) remained significantly improved compared with the pre-training condition. The walking performance remained significantly improved in both women and men for up to 12 months (p ≤ 0.001). Multimodal SET is effective at improving walking performance in symptomatic patients with PAD, with improvements lasting up to 12 months

Large deviations for a damped telegraph process

In this paper we consider a slight generalization of the damped telegraph process in Di Crescenzo and Martinucci (2010). We prove a large deviation principle for this process and an asymptotic result for its level crossing probabilities (as the level goes to infinity). Finally we compare our results with the analogous well-known results for the standard telegraph process

Magnetic interaction of Co ions near the {10\bar{1}0} ZnO surface

Co-doped ZnO is the prototypical dilute magnetic oxide showing many of the characteristics of ferromagnetism. The microscopic origin of the long range order however remains elusive, since the conventional mechanisms for the magnetic interaction, such as super-exchange and double exchange, fail either at the fundamental or at a quantitative level. Intriguingly, there is a growing evidence that defects both in point-like or extended form play a fundamental role in driving the magnetic order. Here we explore one of such possibilities by performing {\it ab initio} density functional theory calculations for the magnetic interaction of Co ions at or near a ZnO \{10$\bar{1}$0\} surface. We find that extended surface states can hybridize with the $e$-levels of Co and efficiently mediate the magnetic order, although such a mechanism is effective only for ions placed in the first few atomic planes near the surface. We also find that the magnetic anisotropy changes at the surface from an hard-axis easy-plane to an easy axis, with an associated increase of its magnitude. We then conclude that clusters with high densities of surfacial Co ions may display blocking temperatures much higher than in the bulk

Historical vintage descriptions from Luxembourg - an indicator for the climatic conditions in the past?

Verbal vintage descriptions in a historical wine chronicle (809-1904) of the Luxembourgish winegrowing region were assigned to five wine quality and three wine quantity classes. To calibrate models describing the impact of the seasonal heat consumption on wine quality and quantity, instrumental records from Luxembourg-City in a reference period (1854-1885) and the associated vintage quality and quantity classes were correlated. Dummy regression models showed, that in the reference period the wine quality classes assigned were significantly correlated with the annual modified heliothermic index values (representing the heat consumption) (R2adj.= 0.55, p = 0.0002); whereas, the incorporation of the wine quantity as additional predictor variable did not significantly improve model output. Based on linear correlations between annual thermal conditions and wine quality descriptions, average April-September temperatures were reconstructed for the period 1200-1904. Running averages calculated using LOESS smoothing showed that periods with cooler and warmer climatic conditions alternated in the past centuries. Even though a precise reconstruction of the annual temperature conditions solely based on vintage descriptions is not possible due to the broad set of potentially interfering effects, long-term climatic trends described in the literature such as the Medieval Climate Optimum and the Little Ice Age could be retrieved

Chaos and Universality in a Four-Dimensional Spin Glass

We present a finite size scaling analysis of Monte Carlo simulation results on a four dimensional Ising spin glass. We study chaos with both coupling and temperature perturbations, and find the same chaos exponent in each case. Chaos is investigated both at the critical temperature and below where it seems to be more efficient (larger exponent). Dimension four seems to be above the critical dimension where chaos with temperature is no more present in the critical region. Our results are consistent with the Gaussian and bimodal coupling distributions being in the same universality class.Comment: 11 pages, including 6 postscript figures. Latex with revtex macro

Disorder chaos in spin glasses

We investigate numerically disorder chaos in spin glasses, i.e. the sensitivity of the ground state to small changes of the random couplings. Our study focuses on the Edwards-Anderson model in d=1,2,3 and in mean-field. We find that in all cases, simple scaling laws, involving the size of the system and the strength of the perturbation, are obeyed. We characterize in detail the distribution of overlap between ground states and the geometrical properties of flipped spin clusters in both the weak and strong chaos regime. The possible relevance of these results to temperature chaos is discussed.Comment: 7 pages, 8 figures, replaced with accepted versio