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

Cesaro mean distribution of group automata starting from measures with summable decay

Consider a finite Abelian group (G,+), with |G|=p^r, p a prime number, and F: G^N -> G^N the cellular automaton given by {F(x)}_n= A x_n + B x_{n+1} for any n in N, where A and B are integers relatively primes to p. We prove that if P is a translation invariant probability measure on G^Z determining a chain with complete connections and summable decay of correlations, then for any w= (w_i:i<0) the Cesaro mean distribution of the time iterates of the automaton with initial distribution P_w --the law P conditioned to w on the left of the origin-- converges to the uniform product measure on G^N. The proof uses a regeneration representation of P

Sensitive SQUID magnetometry for studying nano-magnetism

The superconducting quantum interference device (SQUID) magnetometer is one of the most sensitive experimental techniques to magnetically characterize samples with high sensitivity. Here we present a detailed discussion of possible artifacts and pitfalls characteristic for commercial SQUID magnetometers. This includes intrinsic artifacts which stem from the inherent design of the magnetometer as well as potential issues due to the user. We provide some guidelines how to avoid and correct these, which is of particular importance when the proper magnetization of nano-scale objects shall be established in cases where its response is dwarfed by that of the substrate it comes with, a situation frequently found in the field of nano-magnetism.Comment: 18 pages PRB style, 13 figures (1st and 3rd wrongly reproduced, ???

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

The Effects of Bilingual Placement and Middle School Transition on the Sense of School Belonging in Hispanic Students

Because bilingual programs provide a secure environment likely to promote school belonging, it was hypothesized that Hispanic students in a bilingual program would experience higher belonging than those in regular education and that they would experience a steeper drop in belonging at the transition to middle school. Participants were 277 Hispanic and White elementary and middle school students who were followed longitudinally from grade 4 to 6. Structural Equation Modeling (SEM) was used to compare the mean levels of school belonging across groups and measure the change in school belonging at the transition. Results suggested that Hispanic students both in bilingual and in regular education had higher belonging than White students and that groups did not differ in their change in belonging at the transition to middle school

03-06 "Free Trade, Corn, and the Environment: Environmental Impacts of US – Mexico Corn Trade Under NAFTA"

The North American Free Trade Agreement (NAFTA) had a profound impact on corn trade between the United States and Mexico. Negotiated tariff reductions and the Mexican government’s decision not to charge some tariffs to which it was entitled resulted in a doubling of US corn exports to Mexico. This paper examines the environmental implications of this change on both sides of the border.

Chaos in Glassy Systems from a TAP Perspective

We discuss level crossing of the free-energy of TAP solutions under variations of external parameters such as magnetic field or temperature in mean-field spin-glass models that exhibit one-step Replica-Symmetry-Breaking (1RSB). We study the problem through a generalized complexity that describes the density of TAP solutions at a given value of the free-energy and a given value of the extensive quantity conjugate to the external parameter. We show that variations of the external parameter by any finite amount can induce level crossing between groups of TAP states whose free-energies are extensively different. In models with 1RSB, this means strong chaos with respect to the perturbation. The linear-response induced by extensive level crossing is self-averaging and its value matches precisely with the disorder-average of the non self-averaging anomaly computed from the 2nd moment of thermal fluctuations between low-lying, almost degenerate TAP states. We present an analytical recipe to compute the generalized complexity and test the scenario on the spherical multi-$p$ spin models under variation of temperature.Comment: 12 pages, 2 figure