A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS

Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that permits the detection of segmental changes in DNA copy number that span thousands of basepairs across the genome. Genome-wide association studies (GWAS) may simultaneously screen for copy number-phenotype and SNP-phenotype associations as part of the analytic strategy. However, genome-wide array analyses are particularly susceptible to batch effects as the logistics of preparing DNA and processing thousands of arrays often involves multiple laboratories and technicians, or changes over calendar time to the reagents and laboratory equipment. Failure to adjust for batch effects can lead to incorrect inference and requires inefficient post-hoc quality control procedures that exclude regions that are associated with batch. Our work extends previous model-based approaches for copy number estimation by explicitly modeling batch effects and using shrinkage to improve locus-specific estimates of copy number uncertainty. Key features of this approach include the use of diallelic genotype calls from experimental data to estimate batch- and locus-specific parameters of background and signal without the requirement of training data. We illustrate these ideas using a study of bipolar disease and a study of chromosome 21 trisomy. The former has batch effects that dominate much of the observed variation in quantile-normalized intensities, while the latter illustrates the robustness of our approach to datasets where as many as 25% of the samples have altered copy number. Locus-specific estimates of copy number can be plotted on the copy-number scale to investigate mosaicism and guide the choice of appropriate downstream approaches for smoothing the copy number as a function of physical position. The software is open source and implemented in the R package CRLMM available at Bioconductor (http:www.bioconductor.org).

Substitutions due to antiretroviral toxicity or contraindication in the first 3 years of antiretroviral therapy in a large South African cohort

INTRODUCTION: The patterns and reasons for antiretroviral therapy (ART) drug substitutions are poorly described in resource-limited settings. METHODS: Time to and reason for drug substitution were recorded in treatment-naive adults receiving ART in two primary care treatment programmes in Cape Town. The cumulative proportion of patients having therapy changed because of toxicity was described for each drug, and associations with these changes were explored in multivariate models. RESULTS: Analysis included 2,679 individuals followed for a median of 11 months. Median CD4+ T-cell count at baseline was 85 cells/microl. Mean weight was 59 kg, mean age was 32 years and 71% were women. All started non-nucleoside reverse transcriptase inhibitor-based ART (60% on efavrienz) and 75% started on stavudine (d4T). After 3 years, 75% remained in care on-site, of whom 72% remained on their initial regimen. Substitutions due to toxicity of nevirapine (8% by 3 years), efavirenz (2%) and zidovudine (8%) occurred early. Substitutions on d4T occurred in 21% of patients by 3 years, due to symptomatic hyperlactataemia (5%), lipodystrophy (9%) or peripheral neuropathy (6%), and continued to accumulate over time. Those at greatest risk of hyperlactataemia or lipodystrophy were women on ART > or =6 months, weighing > or =75 kg at baseline. DISCUSSION: A high proportion of adult patients are able to tolerate their initial ART regimen for up to 3 years. In most instances treatment-limiting toxicities occur early, but continue to accumulate over time in patients on d4T. Whilst awaiting other treatment options, the risks of known toxicities could be minimized through early identification of patients at the highest risk.

Concentration- and time-dependent effects of the synthetic estrogen, 17alpha-ethinylestradiol, on reproductive capabilities of the zebrafish, Danio rerio

Partial or full life-cycle tests are needed to assess the potential of endocrine-disrupting compounds (EDCs) to adversely affect development and reproduction of fish. Small fish species such as zebrafish, Danio rerio, are under consideration as model organisms for appropriate test protocols. The present study examines how reproductive effects resulting from exposure of zebrafish to the synthetic estrogen 17alpha-ethinylestradiol (EE2) vary with concentration (0.05 to 10 ng EE2 L(-1), nominal), and with timing/duration of exposure (partial life-cycle, full life-cycle, and two-generation exposure). Partial life-cycle exposure of the parental (F1) generation until completion of gonad differentiation (0-75 d postfertilization, dpf) impaired juvenile growth, time to sexual maturity, adult fecundity (egg production/female/day), and adult fertilization success at 1.1 ng EE2 L(-1) and higher. Lifelong exposure of the F1 generation until 177 dpf resulted in lowest observed effect concentrations (LOECs) for time to sexual maturity, fecundity, and fertilization success identical to those of the developmental test (0-75 dpf), but the slope of the concentration-response curve was steeper. Reproduction of zebrafish was completely inhibited at 9.3 ng EE2 L(-1), and this was essentially irreversible as a 3-mo depuration restored fertilization success to only a very low rate. Accordingly, elevated endogenous vitellogenin (VTG) synthesis and degenerative changes in gonad morphology persisted in depurated zebrafish. Full life-cycle exposure of the filial (F2) generation until 162 dpf impaired growth, delayed onset of spawning and reduced fecundity and fertilization success at 2.0 ng EE2 L(-1). In conclusion, results show that the impact of estrogenic agents on zebrafish sexual development and reproductive functions as well as the reversibility of effects, varies with exposure concentration (reversibility at < or = 1.1 ng EE2 L(-1) and irreversibility at 9.3 ng EE2 L(-1)), and between partial and full life-cycle exposure (exposure to 10 ng EE2 L(-1) during critical period exerted no permanent effect on sexual differentiation, but life-cycle exposure did).

Effect of intensive lipid lowering with atorvastatin on renal function in patients with coronary heart disease: the Treating to New Targets (TNT) study

BACKGROUND AND OBJECTIVES: Data suggest that atorvastatin may be nephroprotective. This subanalysis of the Treating to New Targets study investigated how intensive lipid lowering with 80 mg of atorvastatin affects renal function when compared with 10 mg in patients with coronary heart disease. DESIGN, SETTING, PARTICIPANTS, ; MEASUREMENTS: A total of 10,001 patients with coronary heart disease and LDL cholesterol levels of <130 mg/dl were randomly assigned to double-blind therapy with 10 or 80 mg/d atorvastatin. Estimated GFR using the Modification of Diet in Renal Disease equation was compared at baseline and at the end of follow-up in 9656 participants with complete renal data. RESULTS: Mean estimated GFR at baseline was 65.6 +/- 11.4 ml/min per 1.73 m2 in the 10-mg group and 65.0 +/- 11.2 ml/min per 1.73 m2 in the 80-mg group. At the end of follow-up (median time to final creatinine measurement 59.5 months), mean change in estimated GFR showed an increase of 3.5 +/- 0.14 ml/min per 1.73 m2 with 10 mg and 5.2 +/- 0.14 ml/min per 1.73 m2 with 80 mg (P < 0.0001 for treatment difference). In the 80-mg arm, estimated GFR improved to > or = 60 ml/min per 1.73 m2 in significantly more patients and declined to < 60 ml/min per 1.73 m2 in significantly fewer patients than in the 10-mg arm. CONCLUSIONS: The expected 5-yr decline in renal function was not observed. Estimated GFR improved in both treatment groups but was significantly greater with 80 mg than with 10 mg, suggesting this benefit may be dosage related.

Predictors of optimal viral suppression in patients switched to abacavir, lamivudine, and zidovudine: the Swiss HIV Cohort Study

OBJECTIVE: To investigate predictors of continued HIV RNA viral load suppression in individuals switched to abacavir (ABC), lamivudine (3TC) and zidovudine (ZDV) after successful previous treatment with a protease inhibitor or non-nucleoside reverse transcriptase inhibitor-based combination antiretroviral therapy. DESIGN AND METHODS: An observational cohort study, which included individuals in the Swiss HIV Cohort Study switching to ABC/3TC/ZDV following successful suppression of viral load. The primary endpoint was time to treatment failure defined as the first of the following events: two consecutiveviral load measurements > 400 copies/ml under ABC/3TC/ZDV, one viral load measurement > 400 copies/ml and subsequent discontinuation of ABC/3TC/ZDV within 3 months, AIDS or death. RESULTS: We included 495 individuals; 47 experienced treatment failure in 1459 person-years of follow-up [rate = 3.22 events/100 person-years; 95% confidence interval (95% CI), 2.30-4.14]. Of all failures, 62% occurred in the first year after switching to ABC/3TC/ZDV. In a Cox regression analysis, treatment failure was independently associated with earlier exposure to nucleoside reverse transcriptase inhibitor (NRTI) mono or dual therapy [hazard ratio (HR), 8.02; 95% CI, 4.19-15.35) and low CD4 cell count at the time of the switch (HR, 0.66; 95% CI, 0.51-0.87 by +100 cells/microl up to 500 cells/microl). In patients without earlier exposure to mono or dual therapy, AIDS prior to switch to simplified maintenance therapy was an additional risk factor. CONCLUSIONS: The failure rate was low in patients with suppressed viral load and switch to ABC/3TC/ZDV treatment. Patients with earlier exposure to mono or dual NRTI therapy, low CD4 cell count at time of switch, or AIDS are at increased risk of treatment failure, limiting the use of ABC/3TC/ZDV in these patient groups.

Adding cetuximab to capecitabine plus oxaliplatin (XELOX) in first-line treatment of metastatic colorectal cancer: a randomized phase II trial of the Swiss Group for Clinical Cancer Research SAKK

BACKGROUND: To determine the activity and tolerability of adding cetuximab to the oxaliplatin and capecitabine (XELOX) combination in first-line treatment of metastatic colorectal cancer (MCC). PATIENTS AND METHODS: In a multicenter two-arm phase II trial, patients were randomized to receive oxaliplatin 130 mg/m(2) on day 1 and capecitabine 1000 mg/m(2) twice daily on days 1-14 every 3 weeks alone or in combination with standard dose cetuximab. Treatment was limited to a maximum of six cycles. RESULTS: Seventy-four patients with good performance status entered the trial. Objective partial response rates after external review and radiological confirmation were 14% and 41% in the XELOX and in the XELOX + Cetuximab arm, respectively. Stable disease has been observed in 62% and 35% of the patients, with 76% disease control in both arms. Cetuximab led to skin rash in 65% of the patients. The median overall survival was 16.5 months for arm A and 20.5 months for arm B. The median time to progression was 5.8 months for arm A and 7.2 months for arm B. CONCLUSION: Differences in response rates between the treatment arms indicate that cetuximab may improve outcome with XELOX. The correct place of the cetuximab, oxaliplatin and fluoropyrimidine combinations in first-line treatment of MCC has to be assessed in phase III trials.

Characterization of legacy organic carbon in a culturally eutrophic lake : the role of the historic carbon deposition in the time course and extent of lake recovery

The time course of lake recovery after a reduction in external loading of nutrients is often controlled by conditions in the sediment. Remediation of eutrophication is hindered by the presence of legacy organic carbon deposits, that exert a demand on the terminal electron acceptors of the lake and contribute to problems such as internal nutrient recycling, absence of sediment macrofauna, and flux of toxic metal species into the water column. Being able to quantify the timing of a lake’s response requires determination of the magnitude and lability, i.e., the susceptibility to biodegradation, of the organic carbon within the legacy deposit. This characterization is problematic for organic carbon in sediments because of the presence of different fractions of carbon, which vary from highly labile to refractory. The lability of carbon under varied conditions was tested with a bioassay approach. It was found that the majority of the organic material found in the sediments is conditionally-labile, where mineralization potential is dependent on prevailing conditions. High labilities were noted under oxygenated conditions and a favorable temperature of 30 °C. Lability decreased when oxygen was removed, and was further reduced when the temperature was dropped to the hypolimnetic average of 8° C . These results indicate that reversible preservation mechanisms exist in the sediment, and are able to protect otherwise labile material from being mineralized under in situ conditions. The concept of an active sediment layer, a region in the sediments in which diagenetic reactions occur (with nothing occurring below it), was examined through three lines of evidence. Initially, porewater profiles of oxygen, nitrate, sulfate/total sulfide, ETSA (Electron Transport System Activity- the activity of oxygen, nitrate, iron/manganese, and sulfate), and methane were considered. It was found through examination of the porewater profiles that the edge of diagenesis occurred around 15-20 cm. Secondly, historical and contemporary TOC profiles were compared to find the point at which the profiles were coincident, indicating the depth at which no change has occurred over the (13 year) interval between core collections. This analysis suggested that no diagenesis has occurred in Onondaga Lake sediment below a depth of 15 cm. Finally, the time to 99% mineralization, the t99, was viewed by using a literature estimate of the kinetic rate constant for diagenesis. A t99 of 34 years, or approximately 30 cm of sediment depth, resulted for the slowly decaying carbon fraction. Based on these three lines of evidence , an active sediment layer of 15-20 cm is proposed for Onondaga Lake, corresponding to a time since deposition of 15-20 years. While a large legacy deposit of conditionally-labile organic material remains in the sediments of Onondaga Lake, it becomes clear that preservation, mechanisms that act to shield labile organic carbon from being degraded, protects this material from being mineralized and exerting a demand on the terminal electron acceptors of the lake. This has major implications for management of the lake, as it defines the time course of lake recovery following a reduction in nutrient loading.

Plackett and Burman analysis to select effective compiler optimizations

Compiler optimizations help to make code run faster at runtime. When the compilation is done before the program is run, compilation time is less of an issue, but how do on-the-fly compilation and optimization impact the overall runtime? If the compiler must compete with the running application for resources, the running application will take more time to complete. This paper investigates the impact of specific compiler optimizations on the overall runtime of an application. A foldover Plackett and Burman design is used to choose compiler optimizations that appear to contribute to shorter overall runtimes. These selected optimizations are compared with the default optimization levels in the Jikes RVM. This method selects optimizations that result in a shorter overall runtime than the default O0, O1, and O2 levels. This shows that careful selection of compiler optimizations can have a significant, positive impact on overall runtime.

Non-invasive measurement of steroids in fish-holding water: important considerations when applying the procedure to behaviour studies

Fish behaviourists are increasingly turning to non-invasive measurement of steroid hormones in holding water, as opposed to blood plasma. When some of us met at a workshop in Faro, Portugal, in September, 2007, we realised that there were still many issues concerning the application of this procedure that needed resolution, including: Why do we measure release rates rather than just concentrations of steroids in the water? How does one interpret steroid release rates when dealing with fish of different sizes? What are the merits of measuring conjugated as well as free steroids in water? In the ‘static’ sampling procedure, where fish are placed in a separate container for a short period of time, does this affect steroid release—and, if so, how can it be minimised? After exposing a fish to a behavioural stimulus, when is the optimal time to sample? What is the minimum amount of validation when applying the procedure to a new species? The purpose of this review is to attempt to answer these questions and, in doing so, to emphasize that application of the non-invasive procedure requires more planning and validation than conventional plasma sampling. However, we consider that the rewards justify the extra effort.

Using PSA to guide timing of androgen deprivation in patients with T0-4 N0-2 M0 prostate cancer not suitable for local curative treatment (EORTC 30891)

OBJECTIVE: EORTC trial 30891 compared immediate versus deferred androgen-deprivation therapy (ADT) in T0-4 N0-2 M0 prostate cancer (PCa). Many patients randomly assigned to deferred ADT did not require ADT because they died before becoming symptomatic. The question arises whether serum prostate-specific antigen (PSA) levels may be used to decide when to initiate ADT in PCa not suitable for local curative treatment. METHODS: PSA data at baseline, PSA doubling time (PSADT) in patients receiving no ADT, and time to PSA relapse (>2 ng/ml) in patients whose PSA declined to <2 ng/ml within the first year after immediate ADT were analyzed in 939 eligible patients randomly assigned to immediate (n=468) or deferred ADT (n=471). RESULTS: In both arms, patients with a baseline PSA>50 ng/ml were at a>3.5-fold higher risk to die of PCa than patients with a baseline PSA12 mo. Time to PSA relapse after response to immediate ADT correlated significantly with baseline PSA, suggesting that baseline PSA may also reflect disease aggressiveness. CONCLUSIONS: Patients with a baseline PSA>50 ng/ml and/or a PSADT<12 mo were at increased risk to die from PCa and might have benefited from immediate ADT, whereas patients with a baseline PSA<50 ng/ml and a slow PSADT (>12 mo) were likely to die of causes unrelated to PCa, and thus could be spared the burden of immediate ADT.

To stent or not to stent perioperatively the ureteroileal anastomosis of ileal orthotopic bladder substitutes and ileal conduits? Results of a prospective randomized trial

PURPOSE: We evaluated the impact of stenting the ureteroileal anastomosis on its competence, upper urinary tract dilatation, gastrointestinal recovery, metabolic parameters and patency rate after cystectomy with ileal bladder substitution or ileal conduit. MATERIALS AND METHODS: A total of 54 patients (37 with an ileal bladder substitute and 17 with an ileal conduit) were prospectively randomized into 2 groups, with (29) or without (25) perioperative stenting of the ureteroileal anastomosis. In all cases an end-to-side ureteroileal refluxing anastomosis was performed. The stents were removed after 5 to 10 days. The parameters assessed postoperative days 1, 3 and 7 were creatinine concentration from the wound drains, upper urinary tract dilatation, time to bowel function recovery, serum creatinine, as well as urea and incidence of metabolic acidosis. RESULTS: Median patient age was 68 years (range 45 to 85). Urine leak on postoperative day 1 was more frequent in those anastomoses without stents, and on postoperative days 3 and 7 the values were comparable. Stenting of the ureteroileal anastomosis resulted in significantly decreased early postoperative upper urinary tract dilatation, improved recovery of bowel function and decreased metabolic acidosis. In either group no patient had clinical evidence of ureteroileal anastomotic stricture during the early postoperative period. Three patients with perioperative stenting required surgical or endoscopic treatment for a stricture of the ureteroileal anastomosis during the 12-month followup. CONCLUSIONS: Stenting of the ureteroileal anastomosis allows for significantly less frequent incidence of early postoperative dilatation of the pelvicaliceal system, bowel activity resumes significantly earlier and metabolic acidosis is significantly less frequent.

Self-reported non-adherence to antiretroviral therapy repeatedly assessed by two questions predicts treatment failure in virologically suppressed patients

BACKGROUND: The aim of this study was to explore the predictive value of longitudinal self-reported adherence data on viral rebound. METHODS: Individuals in the Swiss HIV Cohort Study on combined antiretroviral therapy (cART) with RNA <50 copies/ml over the previous 3 months and who were interviewed about adherence at least once prior to 1 March 2007 were eligible. Adherence was defined in terms of missed doses of cART (0, 1, 2 or >2) in the previous 28 days. Viral rebound was defined as RNA >500 copies/ml. Cox regression models with time-independent and -dependent covariates were used to evaluate time to viral rebound. RESULTS: A total of 2,664 individuals and 15,530 visits were included. Across all visits, missing doses were reported as follows: 1 dose 14.7%, 2 doses 5.1%, >2 doses 3.8% taking <95% of doses 4.5% and missing > or =2 consecutive doses 3.2%. In total, 308 (11.6%) patients experienced viral rebound. After controlling for confounding variables, self-reported non-adherence remained significantly associated with the rate of occurrence of viral rebound (compared with zero missed doses: 1 dose, hazard ratio [HR] 1.03, 95% confidence interval [CI] 0.72-1.48; 2 doses, HR 2.17, 95% CI 1.46-3.25; >2 doses, HR 3.66, 95% CI 2.50-5.34). Several variables significantly associated with an increased risk of viral rebound irrespective of adherence were identified: being on a protease inhibitor or triple nucleoside regimen (compared with a non-nucleoside reverse transcriptase inhibitor), >5 previous cART regimens, seeing a less-experienced physician, taking co-medication, and a shorter time virally suppressed. CONCLUSIONS: A simple self-report adherence questionnaire repeatedly administered provides a sensitive measure of non-adherence that predicts viral rebound.

USING AUTO- AND CROSS-CORRELATIONS FROM SEISMIC NOISE TO MONITOR VELOCITY CHANGES AT VILLARRICA VOLCANO, CHILE

We used the Green's functions from auto-correlations and cross-correlations of seismic ambient noise to monitor temporal velocity changes in the subsurface at Villarrica volcano in the Southern Andes of Chile. Campaigns were conducted from March to October 2010 and February to April 2011 with 8 broadband and 6 short-period stations, respectively. We prepared the data by removing the instrument response, normalizing with a root-mean-square method, whitening the spectra, and filtering from 1 to 10 Hz. This frequency band was chosen based on the relatively high background noise level in that range. Hour-long auto- and cross-correlations were computed and the Green's functions stacked by day and total time. To track the temporal velocity changes we stretched a 24 hour moving window of correlation functions from 90% to 110% of the original and cross correlated them with the total stack. All of the stations' auto-correlations detected what is interpreted as an increase in velocity in 2010, with an average increase of 0.13%. Cross-correlations from station V01, near the summit, to the other stations show comparable changes that are also interpreted as increases in velocity. We attribute this change to the closing of cracks in the subsurface due either to seasonal snow loading or regional tectonics. In addition to the common increase in velocity across the stations, there are excursions in velocity on the same order lasting several days. Amplitude decreases as the station's distance from the vent increases suggesting these excursions may be attributed to changes within the volcanic edifice. In at least two occurrences the amplitudes at stations V06 and V07, the stations farthest from the vent, are smaller. Similar short temporal excursions were seen in the auto-correlations from 2011, however, there was little to no increase in the overall velocity.

EVALUATION OF THE EVOLVING STRESS FIELD OF THE YELLOWSTONE VOLCANIC PLATEAU FROM 1988 TO 2010 FROM EARTHQUAKE FIRST MOTIONS INVERSION

Within the Yellowstone National Park, Wyoming, the silicic Yellowstone volcanic field is one of the most active volcanic systems all over the world. Although the last rhyolite eruption occurred around 70,000 years ago, Yellowstone is still believed to be volcanically active, due to high hydrothermal and seismic activity. The earthquake data used in this study cover the period of time between 1988 and 2010. Earthquake relocations and a set of 369 well-constrained, double-couple, focal mechanism solutions were computed. Events were grouped according to location and time to investigate trends in faulting. The majority of the events has oblique, normal-faulting solutions. The overall direction of extension throughout the 0.64 Ma Yellowstone caldera looks nearly ENE, consistently with the direction of alignments of volcanic vents within the caldera, but detailed study revealed spatial and temporal variations. Stress-field solutions for different areas and time periods were calculated from earthquake focal mechanism inversion. A well-resolved rotation of σ3 was found, from NNE-SSW near the Hebgen Lake fault zone, to ENE-WSW near Norris Junction. In particular, the σ3 direction changed throughout the years in the Norris Junction area, from being ENE-WSW, as calculated in the study by Waite and Smith (2004), to NNE-SSW, while the other σ3 directions are mostly unchanged over time. The Yellowstone caldera was subject to periods of net uplift and subsidence over the past century, explained in previous studies as caused by expanding or contracting sills, at different depths. Based on the models used to explain these deformation periods, we investigated the relationship between variability in aseismic deformation and seismic activity and faulting styles. Focal mechanisms and P and T axes were divided into temporal and depth intervals, in order to identify spatial or temporal trends in deformation. The presence of “chocolate tablet” structures, with composite dilational faults, was identified in many stages of the deformation history both in the Norris Geyser Basin area and inside the caldera. Strike-slip component movement was found in a depth interval below a contracting sill, indicating the movement of magma towards the caldera.

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.