The transcription factor encyclopedia

Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field.

Framingham risk score and alternatives for prediction of coronary heart disease in older adults

Background Guidelines for the prevention of coronary heart disease (CHD) recommend use of Framingham-based risk scores that were developed in white middle-aged populations. It remains unclear whether and how CHD risk prediction might be improved among older adults. We aimed to compare the prognostic performance of the Framingham risk score (FRS), directly and after recalibration, with refit functions derived from the present cohort, as well as to assess the utility of adding other routinely available risk parameters to FRS. Methods Among 2193 black and white older adults (mean age, 73.5 years) without pre-existing cardiovascular disease from the Health ABC cohort, we examined adjudicated CHD events, defined as incident myocardial infarction, CHD death, and hospitalization for angina or coronary revascularization. Results During 8-year follow-up, 351 participants experienced CHD events. The FRS poorly discriminated between persons who experienced CHD events vs. not (C-index: 0.577 in women; 0.583 in men) and underestimated absolute risk prediction by 51% in women and 8% in men. Recalibration of the FRS improved absolute risk prediction, particulary for women. For both genders, refitting these functions substantially improved absolute risk prediction, with similar discrimination to the FRS. Results did not differ between whites and blacks. The addition of lifestyle variables, waist circumference and creatinine did not improve risk prediction beyond risk factors of the FRS. Conclusions The FRS underestimates CHD risk in older adults, particularly in women, although traditional risk factors remain the best predictors of CHD. Re-estimated risk functions using these factors improve accurate estimation of absolute risk.

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease

Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.

Executive Reorganization: Building a State Government That Worked for People -- Tom Harrison, Diana Dowling & Sheena Wilson ���In the Crucible of Change���

One of the primary accomplishments of Governor Forrest Anderson in 1969-71 was the reorganization of the Executive Branch of Montana government, something that had been attempted six different times between 1919 and 1962 as state government had grown from twenty agencies to almost 200 uncontrolled boards, bureaus and commissions. The chaotic structure of the executive branch disempowered governors of both parties and empowered the private corporations and organizations that were the power structure of Montana. With remarkable political acumen, Governor Anderson figured out how to get that near impossible job done. Central to his efforts was the creation of an Executive Reorganization Commission, including eight legislators and the Governor, the adoption of a Constitutional Amendment that limited the executive branch to no more than twenty departments under the Governor, and the timely completion of a massive research effort to delineate the actual structure of the twenty departments. That story is told in this episode by three major players in the effort, all involved directly with the Executive Reorganization Commission: Tom Harrison, Diana Dowling and Sheena Wilson. Their recollections reflect an insider���s perspective of this significant accomplishment that helped change Montana ���In the Crucible of Change.��� Tom Harrison is a former Republican State Representative and State Senator from Helena, who was a member of the Executive Reorganization Commission. As Majority Leader in the Montana House of Representatives in 1971, he was the primary sponsor of the House���s executive reorganization bill and helped shepherd the Senate���s version to passage. Harrison was the Republican candidate for Attorney General in 1976 after which he practiced private law for 3 more decades. He served in the Montana Army National Guard for almost 34 years, rising to the rank of Colonel in the position of Judge Advocate General. He was a founding Director of Federal Defenders of Montana (legal representation for indigents accused within the Federal Judicial System); appointed Chairman of the original Montana State Fund (workers' compensation insurance) by Gov. Stephens; served as President of the Montana Trial Lawyers Association, Helena Kiwanis Club and St. Peter's Community Hospital Foundation, as well as Chairman and Director of AAA MountainWest; and was a founder, first Chairman and Director of the Valley Bank of Helena for over 25 years. Diana Dowling was an attorney for the Executive Reorganization Commission and helped draft the legislation that was passed. She also worked for Governor Forrest Anderson and for the 1972 Constitutional Convention where she prepared and directed publication of official explanation of the new Constitution that was mailed to all Montana voters. Diana was Executive Director of the Montana Bar Association and for 20 years held various legal positions with the Montana Legislative Council. For 12 years she was a commissioner on the National Conference of Commissioners on Uniform State Laws and for 7 years was a member of Montana State Board of Bar Examiners. Diana was the first director of the Montana Lottery, an adjunct professor at both Carroll College and the UM Law School, and an administrative officer for Falcon Press Publishing Co. Diana is currently - and intends to continue being - a perpetual college student. Sheena Wilson came fresh out of the University of Montana to become a Research Assistant for the Executive Reorganization Commission. Later she worked for seven years as a field representative in Idaho and Montana for the Mountain Plains Family Education Program, for thirteen years with Congressman Pat Williams as Executive Assistant in Washington and Field Assistant here in Montana, owned and managed a Helena restaurant for seven years, worked as Executive Assistant for State Auditor John Morrison and was Deputy Chief of Staff for Governor Brian Schweitzer his full 8 years in the Governorship. Though currently ���retired���, Sheena serves on the Montana Board of Investments, the Public Employees Retirement Board and the Capitol Complex Advisory Council and is a partner in a dry-land wheat farm in Teton County that was homesteaded by her great uncle.

Light-cone Wilson loop in classical lattice gauge theory

The transverse broadening of an energetic jet passing through a non-Abelian plasma is believed to be described by the thermal expectation value of a light-cone Wilson loop. In this exploratory study, we measure the light-cone Wilson loop with classical lattice gauge theory simulations. We observe, as suggested by previous studies, that there are strong interactions already at short transverse distances, which may lead to more efficient jet quenching than in leading-order perturbation theory. We also verify that the asymptotics of the Wilson loop do not change qualitatively when crossing the light cone, which supports arguments in the literature that infrared contributions to jet quenching can be studied with dimensionally reduced simulations in the space-like domain. Finally we speculate on possibilities for full four-dimensional lattice studies of the same observable, perhaps by employing shifted boundary conditions in order to simulate ensembles boosted by an imaginary velocity.

Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies.

A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS). True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a "cosmopolitan" tagging approach to capture the genetic diversity across approximately 2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions.