Integrated Geophysical Investigation of the St. James Fault Complex: A Case Study

We noninvasively detected the characteristics and location of a regional fault in an area of poor bedrock exposure complicated by karst weathering features in the subsurface. Because this regional fault is associated with sinkhole formation, its location is important for hazard avoidance. The bedrock lithologies on either side of the fault trace are similar; hence, we chose an approach that capitalized on the complementary strengths of very low frequency (VLF) electromagnetic, resistivity, and gravity methods. VLF proved most useful as a first-order reconnaissance tool, allowing us to define a narrow target area for further geophysical exploration. Fault-related epikarst was delineated using resistivity. Ultimately, a high-resolution gravity survey and subsequent inverse modeling using the results of the resistivity survey helped to further constrain the location and approximate orientation of the fault. The combined results indicated that the location of the fault trace needed to be adjusted 53 m south of the current published location and was consistent with a north-dipping thrust fault. Additionally, a gravity low south of the fault trace agreed with the location of conductive material from the resistivity and VLF surveys. We interpreted these anomalies to represent enhanced epikarst in the fault footwall. We clearly found that a staged approach involving a progression of methods beginning with a reconnaissance VLF survey, followed by high-resolution gravity and electrical resistivity surveys, can be used to characterize a fault and fault-related karst in an area of poor bedrock surface exposure.

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

Genome-wide association studies and candidate gene studies in ulcerative colitis have identified 18 susceptibility loci. We conducted a meta-analysis of six ulcerative colitis genome-wide association study datasets, comprising 6,687 cases and 19,718 controls, and followed up the top association signals in 9,628 cases and 12,917 controls. We identified 29 additional risk loci (P < 5 × 10(-8)), increasing the number of ulcerative colitis-associated loci to 47. After annotating associated regions using GRAIL, expression quantitative trait loci data and correlations with non-synonymous SNPs, we identified many candidate genes that provide potentially important insights into disease pathogenesis, including IL1R2, IL8RA-IL8RB, IL7R, IL12B, DAP, PRDM1, JAK2, IRF5, GNA12 and LSP1. The total number of confirmed inflammatory bowel disease risk loci is now 99, including a minimum of 28 shared association signals between Crohn's disease and ulcerative colitis.

Design, conduct, and analysis of a multicenter, pharmacogenomic, biomarker study in matched patients with severe sepsis treated with or without drotrecogin Alfa (activated)

A genomic biomarker identifying patients likely to benefit from drotrecogin alfa (activated) (DAA) may be clinically useful as a companion diagnostic. This trial was designed to validate biomarkers (improved response polymorphisms (IRPs)). Each IRP (A and B) contains two single nucleotide polymorphisms that were associated with a differential DAA treatment effect.

Celecoxib plus hormone therapy versus hormone therapy alone for hormone-sensitive prostate cancer: first results from the STAMPEDE multiarm, multistage, randomised controlled trial

Long-term hormone therapy alone is standard care for metastatic or high-risk, non-metastatic prostate cancer. STAMPEDE--an international, open-label, randomised controlled trial--uses a novel multiarm, multistage design to assess whether the early additional use of one or two drugs (docetaxel, zoledronic acid, celecoxib, zoledronic acid and docetaxel, or zoledronic acid and celecoxib) improves survival in men starting first-line, long-term hormone therapy. Here, we report the preplanned, second intermediate analysis comparing hormone therapy plus celecoxib (arm D) with hormone therapy alone (control arm A).

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.

Evidence of viral adaptation to HLA class I-restricted immune pressure in chronic hepatitis C virus infection

Cellular immune responses are an important correlate of hepatitis C virus (HCV) infection outcome. These responses are governed by the host's human leukocyte antigen (HLA) type, and HLA-restricted viral escape mutants are a critical aspect of this host-virus interaction. We examined the driving forces of HCV evolution by characterizing the in vivo selective pressure(s) exerted on single amino acid residues within nonstructural protein 3 (NS3) by the HLA types present in two host populations. Associations between polymorphisms within NS3 and HLA class I alleles were assessed in 118 individuals from Western Australia and Switzerland with chronic hepatitis C infection, of whom 82 (69%) were coinfected with human immunodeficiency virus. The levels and locations of amino acid polymorphisms exhibited within NS3 were remarkably similar between the two cohorts and revealed regions under functional constraint and selective pressures. We identified specific HCV mutations within and flanking published epitopes with the correct HLA restriction and predicted escaped amino acid. Additional HLA-restricted mutations were identified that mark putative epitopes targeted by cell-mediated immune responses. This analysis of host-virus interaction reveals evidence of HCV adaptation to HLA class I-restricted immune pressure and identifies in vivo targets of cellular immune responses at the population level.

Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.

Governor Tom Judge: Early Years - The Path to Becoming Montana's 18th Governor -- Sidney Armstrong, Larry Pettit & Kent Kleinkopf “In the Crucible of Change”

The dramatic period of progressive change in Montana that is documented "In the Crucible of Change" series really exploded with the election of Governors Forrest Anderson and Tom Judge. Anderson's single term saw the dispatching of the sales tax as an issue for a long period, the reorganization of the executive branch of state government and the revision of Montana's Constitution. As a former legislator, county attorney, Supreme Court justice, and Attorney General, Anderson brought unmatched experience to the governorship when elected. Tom Judge, although much younger (elected MT’s youngest governor at age 38 immediately following Anderson), also brought serious experience to the governorship: six years as a MT State Representative, two years as a MT State Senator, four years is Lieutenant Governor and significant business experience. The campaign and election of John F. Kennedy in 1960 spurred other young Americans to service, including Tom Judge. First elected in 1960, he rose rapidly through MT’s political-governmental hierarchy until he took over the governorship in time to implement many of the changes started in Governor Anderson’s term. But as a strong progressive leader in his own right, Governor Judge sponsored and implemented significant advancements of his own for Montana. Those accomplishments, however, are the subject of other films in this series. This film deals with Tom Judge’s early years – his rise to the governorship from when he returned home after college at Notre Dame and newspaper experience in Kentucky to his actual election in November 1972. That story is discussed in this episode by three major players in the effort, all directly involved in Tom Judge’s early years and path to the governorship: Sidney Armstrong, Larry Pettit and Kent Kleinkopf. Their recollections of the early Tom Judge and the period of his advancement to the governorship provide an insider’s perspective of the growth of this significant leader of the important period of progressive change documented “In the Crucible of Change.” Sidney Armstrong, President of Sidney Armstrong Consulting, serves on the board and as the Executive Director of the Greater Montana Foundation. Formerly Executive Director of the Montana Community Foundation (MCF), she has served on national committees and participated in national foundation initiatives. While at MCF, she worked extensively with MT Governors Racicot and Martz on the state charitable endowment tax credit and other endowed philanthropy issues. A member of MT Governor Thomas L. Judge’s staff in the 1970s, she was also part of Governor Brian Schweitzer’s 2004 Transition Team, continuing to serve as a volunteer advisor during his term. In the 1980s, Sidney also worked for the MT State AFL-CIO and the MT Democratic Party as well as working two sessions with the MT Senate as Assistant Secretary of the Senate and aide to the President. A Helena native, and great granddaughter of pioneer Montanans, Sidney has served on numerous nonprofit boards, and is currently a board member for the Montana History Foundation. Recently she served on the board of the Holter Museum of Art and was a Governor’s appointee to the Humanities Montana board. She is a graduate of the International School of Geneva, Switzerland and the University of Montana. Armstrong's Irish maternal immigrant great-grandparents, Thomas and Maria Cahill Cooney, came to Virginia City, MT in a covered wagon in 1865, looking for gold. Eventually, they settled on the banks of the Missouri River outside Helena as ranchers. She also has roots in Butte, MT, where her journalist father's family, both of whom were newspaper people, lived. Her father, Richard K. O’Malley, is also the author of a well-known book about Butte, Mile High, Mile Deep, recently re-published by Russell Chatham. She is the mother of four and the grandmother of eight. Dr. Lawrence K. Pettit (Larry Pettit) (b. 5/2/1937) has had a dual career in politics and higher education. In addition to being Montana’s first Commissioner of Higher Education (the subject of another film in this series); Pettit, of Lewistown, served as legislative assistant to U.S. Senators James E. Murray and Lee Metcalf, campaign manager, head of transition team and assistant to Montana Governor Thomas L. Judge; taught political science at The Pennsylvania State University (main campus), was chair of political science at Montana State University, Deputy Commissioner for Academic Programs at the Texas Higher Education Coordinating Board, Chancellor of the University System of South Texas (since merged with Texas A&M University), President of Southern Illinois University, and President of Indiana University of Pennsylvania from where he retired in 2003. He has served as chair of the Commission on Leadership for the American Council on Education, president of the National Association of (University) System Heads, and on many national and state boards and commissions in higher education. Pettit is author of “If You Live by the Sword: Politics in the Making and Unmaking of a University President.” More about Pettit is found at http://www.lawrencekpettit.com… Kent Kleinkopf of Missoula is co-founder of a firm with a national scope of business that specializes in litigation consultation, expert vocational testimony, and employee assistance programs. His partner (and wife of 45 years) Kathy, is an expert witness in the 27 year old business. Kent received a BA in History/Education from the University of Idaho and an MA in Economics from the University of Utah. The Kleinkopfs moved to Helena, MT in 1971 where he was Assistant to the Commissioner of State Lands (later Governor) Ted Schwinden. In early 1972 Kent volunteered full time in Lt. Governor Tom Judge’s campaign for Governor, driving the Lt. Governor extensively throughout Montana. After Judge was elected governor, Kent briefly joined the staff of Governor Forrest Anderson, then in 1973 transitioned to Judge’s Governor’s Office staff, where he became Montana’s first “Citizens’ Advocate.” In that capacity he fielded requests for assistance from citizens with concerns and information regarding State Agencies. While on the Governor’s staff, Kent continued as a travel aide with the governor both in Montana and nationally. In 1977 Kent was appointed Director of the MT Department of Business Regulation. That role included responsibility as Superintendent of Banking and Chairman of the State Banking Board, where Kent presided over the chartering of many banks, savings and loans, and credit unions. In 1981 the Kleinkopfs moved to Missoula and went into the business they run today. Kent was appointed by Governor Brian Schweitzer to the Board of the Montana Historical Society in 2006, was reappointed and continues to serve. Kathy and Kent have a daughter and son-in-law in Missoula.