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1.  Causal Inference in Public Health 
Causal inference has a central role in public health; the determination that an association is causal indicates the possibility for intervention. We review and comment on the long-used guidelines for interpreting evidence as supporting a causal association and contrast them with the potential outcomes framework that encourages thinking in terms of causes that are interventions. We argue that in public health this framework is more suitable, providing an estimate of an action’s consequences rather than the less precise notion of a risk factor’s causal effect. A variety of modern statistical methods adopt this approach. When an intervention cannot be specified, causal relations can still exist, but how to intervene to change the outcome will be unclear. In application, the often-complex structure of causal processes needs to be acknowledged and appropriate data collected to study them. These newer approaches need to be brought to bear on the increasingly complex public health challenges of our globalized world.
doi:10.1146/annurev-publhealth-031811-124606
PMCID: PMC4079266  PMID: 23297653
causation; causal modeling; causal framework; epidemiology
2.  Phase II Study of Risk-Adapted Therapy of Newly Diagnosed, Aggressive Non-Hodgkin Lymphoma Based on Midtreatment FDG-PET Scanning 
In newly diagnosed aggressive non-Hodgkin lymphoma (NHL), a positive midtreatment fluorine-18 fluorodeoxyglucose positron emission tomography (PET) scan often carries a poor prognosis, with reported 2-year event-free survival (EFS) rates of 0% to 30% after standard therapy. To determine the outcome of early treatment intensification for midtreatment PET-positive disease, a phase II trial of risk-adapted therapy was conducted. Fifty-nine newly diagnosed patients, 98% with B cell lymphoma, had PET/CT performed after 2 or 3 cycles of first-line chemotherapy. Those with negative PET on semiquantitative visual interpretation completed standard therapy. Those with positive PET received platinum-based salvage chemotherapy, high-dose therapy, and autologous stem cell transplantation (ASCT). Midtreatment PET was positive in 33 (56%); 28 received ASCT with an actuarial 2-year EFS of 75% (95% confidence interval, 60%–93%). On intention-to-treat analysis, 2-year EFS was 67% (53%–86%) in all PET-positive patients and 89% (77%–100%) in PET-negative patients. No association was found between the International Prognostic Index category and the midtreatment PET result. The favorable outcome achieved here in historically poor-risk patients warrants further, more definitive investigation of treatment modification based on early PET scanning.
doi:10.1016/j.bbmt.2008.11.026
PMCID: PMC4020440  PMID: 19167684
Lymphoma; Positron emission tomography (PET); Prognosis; Autologous stem cell transplantation
3.  An epigenetic marker panel for detection of lung cancer using cell-free serum DNA 
PURPOSE
We investigated the feasibility of detecting aberrant DNA methylation of some novel and known genes in the serum of lung cancer patients.
EXPERIMENTAL DESIGN
To determine the analytical sensitivity, we examined the tumor and the matched serum DNA for aberrant methylation of fifteen gene promoters from 10 patients with primary lung tumors by using Quantitative methylation specific PCR. We then tested this 15 gene set to identify the more useful DNA methylation changes in the serum of a limited number of lung cancer patients and controls. In an independent set, we tested the six most promising genes (APC, CDH1, MGMT, DCC, RASSF1A and AIM) for further elucidation of the diagnostic application of this panel of markers.
RESULTS
Promoter hypermethylation of at least one of the genes studied was detected in all 10 lung primary tumors. In majority of cases, aberrant methylation in serum DNA was accompanied by methylation in the matched tumor samples. In the independent set, using a single gene that had 100% specificity (DCC), 35.5% (95% CI 25%, 47%) of the 76 lung cancer patients were correctly identified. For patients without methylated DCC, addition of a logistic regression score that was based on the five remaining genes improved sensitivity from 35.5% to 75% (95% CI: 64%, 84%) but decreased the specificity from 100% to 73% (95% CI:54%, 88%).
CONCLUSION
This approach needs to be evaluated in a larger test set to determine the role of this gene set in early detection and surveillance of lung cancer.
doi:10.1158/1078-0432.CCR-10-3436
PMCID: PMC3131425  PMID: 21610147
DNA methylation/epigenetics; serum; lung cancer
4.  RNAi mediated silencing of Nrf2 gene expression in non-small cell lung cancer inhibits tumor growth and increases efficacy of chemotherapy 
Cancer research  2008;68(19):7975-7984.
Nuclear factor erythroid-2 related factor-2 (Nrf2) is a redox-sensitive transcription factor that regulates the expression of electrophile and xenobiotic detoxification enzymes and efflux proteins, which confer cytoprotection against oxidative stress and apoptosis in normal cells. Loss of function mutations in the Nrf2 inhibitor, Kelch-like ECH-associated protein (Keap1), results in constitutive activation of Nrf2 function in non-small-cell lung cancer (NSCLC). In this study, we demonstrate that constitutive activation of Nrf2 in lung cancer cells promotes tumorigenicity and contributes to chemoresistance by upregulation of glutathione, thioredoxin and the drug efflux pathways involved in detoxification of electrophiles and broad spectrum of drugs. RNAi-mediated reduction of Nrf2 expression in lung cancer cells induces generation of reactive oxygen species, suppresses tumor growth and results in increased sensitivity to chemotherapeutic drug induced cell death in vitro and in vivo. Inhibiting Nrf2 expression using naked siRNA duplexes in combination with carboplatin significantly inhibits tumor growth in a subcutaneous model of lung cancer. Thus, targeting Nrf2 activity in lung cancers, particularly those with Keap1 mutations, could be a promising strategy to inhibit tumor growth and circumvent chemoresistance.
doi:10.1158/0008-5472.CAN-08-1401
PMCID: PMC3070411  PMID: 18829555
Nrf2; Keap1; lung cancer; drug resistance; ROS; RNAi
6.  Purpose and Benefits of Early Phase Cancer Trials: What Do Oncologists Say? What Do Patients Hear? 
Cancer patients overestimate benefits of early phase trials but studies have not reported what oncologists say to patients about trials. We audiotaped oncologists talking to cancer patients about Phase I or II trials and interviewed patients about the purpose and expected outcomes of trials presented to them. Oncologists gave mixed messages, saying Phase I trials measure safety and dosing, yet referring to trials as treatment with uncertain therapeutic effects. Seventeen percent of Phase I respondents said the trial’s purpose related to safety/dosing (p = 0.017); 17% of Phase I respondents said the purpose was “to cure my cancer.” Patients may find it important to believe trials offer significant benefit. Oncologists, while respecting patients’ hopes, should be precise in their language, particularly regarding Phase I trials, distinguishing early stages of research from treatment.
doi:10.1525/jer.2008.3.3.57
PMCID: PMC2861824  PMID: 19385771
cancer; ethics; research; informed consent; Phase I; Phase II; therapeutic misconception
7.  Considering Usual Medical Care in Clinical Trial Design 
PLoS Medicine  2009;6(9):e1000111.
Liza Dawson and colleagues discuss the scientific and ethical issues associated with choosing clinical trial designs when there is no consensus on what constitutes usual care.
doi:10.1371/journal.pmed.1000111
PMCID: PMC2746285  PMID: 19787044
8.  TIMP3 Promoter Methylation is an Independent Prognostic Factor for Bladder Cancer 
The Journal of urology  2007;179(2):743-747.
Purpose
Tissue inhibitor of metalloproteinases-3 (TIMP-3) is one of four members of a family of proteins that were originally classified according to their ability to inhibit matrix metalloproteinases (MMP). We analyzed TIMP-3 methylation in 175 urine sediment DNA samples from bladder cancer patients with well characterized clinicopathological parameters including patient outcome.
Materials and methods
We examined urine sediment DNA for aberrant methylation of 9 genes including TIMP-3 by quantitative fluorogenic real-time PCR.
Results
Using an optimal cutoff value by Taqman quantitation, we found that the risk of death was statistically significantly higher in patients with higher TIMP-3 and ARF methylation (hazard ratio [HR] =1.99, 95% confidence interval [CI] =1.12 to 3.27; p= 0.01 and HR=1.66, 95% CI=1.00 to 2.76; p=0.05 respectively) than in patients without/lower TIMP3 and ARF methylation in urine. A significant correlation was also seen between risk of death and stage 3 tumor (HR=2.73, 95% CI=1.58 to 4.72; p=0.003 and the presence of metastasis (HR=3.32, 95% CI=1.98 to 5.57; p=0.0001). Multivariate analysis subsequently revealed that TIMP-3 methylation was an independent prognostic factor for bladder cancer survival with stage and metastasis (p=0.001 and 0.02 respectively).
Conclusion
These results suggest that TIMP-3 promoter methylation could be a clinically applicable marker for bladder cancer progression.
doi:10.1016/j.juro.2007.09.019
PMCID: PMC2674621  PMID: 18082200
9.  Bayesian Communication 
Abstract Objective: To develop a model for Bayesian communication to enable readers to make reported data more relevant by including their prior knowledge and values.
Background: To change their practice, clinicians need good evidence, yet they also need to make new technology applicable to their local knowledge and circumstances. Availability of the Web has the potential for greatly affecting the scientific communication process between research and clinician. Going beyond format changes and hyperlinking, Bayesian communication enables readers to make reported data more relevant by including their prior knowledge and values. This paper addresses the needs and implications for Bayesian communication.
Formulation: Literature review and development of specifications from readers', authors', publishers', and computers' perspectives consistent with formal requirements for Bayesian reasoning.
Results: Seventeen specifications were developed, which included eight for readers (express prior knowledge, view effect size and variability, express threshold, make inferences, view explanation, evaluate study and statistical quality, synthesize multiple studies, and view prior beliefs of the community), three for authors (protect the author's investment, publish enough information, make authoring easy), three for publishers (limit liability, scale up, and establish a business model), and two for computers (incorporate into reading process, use familiar interface metaphors). A sample client-only prototype is available at http://omie.med.jhmi.edu/bayes .
Conclusion: Bayesian communication has formal justification consistent with the needs of readers and can best be implemented in an online environment. Much research must be done to establish whether the formalism and the reality of readers' needs can meet.
PMCID: PMC61428  PMID: 10833162
10.  Prevention of Thromboembolism in Atrial Fibrillation 
OBJECTIVE
Appropriate use of drugs to prevent thromboembolism in patients with atrial fibrillation (AF) involves comparing the patient's risk of stroke and risk of hemorrhage. This review summarizes the evidence regarding the efficacy of these medications.
METHODS
We conducted a meta-analysis of randomized controlled trials of drugs used to prevent thromboembolism in adults with nonpostoperative AF. Articles were identified through the Cochrane Collaboration's CENTRAL database and MEDLINE until May 1998.
MAIN RESULTS
Eleven articles met criteria for inclusion in this review. Warfarin was more efficacious than placebo for primary stroke prevention (aggregate odds ratio [OR] of stroke =0.30, 95% confidence interval [CI] 0.19, 0.48), with moderate evidence of more major bleeding (OR 1.90; 95% CI 0.89, 4.04). Aspirin was inconclusively more efficacious than placebo for stroke prevention (OR 0.56, 95% CI 0.19, 1.65), with inconclusive evidence regarding more major bleeds (OR 0.81, 95% CI 0.37, 1.77). For primary prevention, assuming a baseline risk of 45 strokes per 1,000 patient-years, warfarin could prevent 30 strokes at the expense of only 6 additional major bleeds. Aspirin could prevent 17 strokes, without increasing major hemorrhage. In direct comparison, there was evidence suggesting fewer strokes among patients on warfarin than among patients on aspirin (aggregate OR 0.64, 95% CI 0.43, 0.96), with only suggestive evidence for more major hemorrhage (OR 1.60, 95% CI 0.77,3.35). However, in younger patients, with a mean age of 65 years, the absolute reduction in stroke rate with warfarin compared with aspirin was low (5.5 per 1,000 person-years) compared with an older group (15 per 1,000 person-years).
CONCLUSION
In general, the evidence strongly supports warfarin for patients with AF at average or greater risk of stroke. Aspirin may prove to be useful in subgroups with a low risk of stroke, although this is not definitively supported by the evidence.
doi:10.1046/j.1525-1497.2000.04329.x
PMCID: PMC1495320  PMID: 10632835
atrial fibrillation; warfarin; anticoagulation; stroke; aspirin
11.  Statistical Reviewing Policies of Medical Journals 
OBJECTIVE
To describe the current policies regarding statistical review of clinical research in biomedical journals.
DESIGN
Cross-sectional survey.
PARTICIPANTS
Editors of biomedical journals that publish original clinical research.
MEASUREMENTS
General policies on statistical review, types of persons used for statistical reviewing, compensation of statistical reviewers, percentage of articles subject to such review, percentage of time statistical review makes an important difference, journal circulation, and selectivity.
MAIN RESULTS
Of 171 journals, 114 (67%) responded to the survey. About one third of journals had policies that guaranteed statistical review for all accepted manuscripts. In approximately half of the journals, articles were sent for statistical review at the discretion of the editor. There was some evidence that statistical review policies differed between journals of different circulation size. In journals in the top quartile of circulation (>25,000) the probability of definitely having a statistical review before an acceptance decision was 52%, but it was only 27% in journals in the lower three quartiles (p = .09). The probability of a statistical consultant on staff ranged from 31% in the bottom quarter, to 58% in the middle two, to 82% in the highest quarter (p < .001). Editors judged that statistical review resulted in an important change in a manuscript about half of the time.
CONCLUSIONS
Except in the largest circulation medical journals, the probability of formal methodologic review of original clinical research is fairly low. As readers and researchers depend on the journals to assess the validity of the statistical methods and logic used in published reports, this is potentially a serious problem. This situation may exist because the cost of such statistical review can be considerable, and because finding appropriate reviewers can be difficult. It may also exist partly because editors or publishers may not regard such review as important. The professions of medical publishing, statistics, epidemiology, and other quantitative disciplines should work together to address this problem.
doi:10.1046/j.1525-1497.1998.00227.x
PMCID: PMC1497035  PMID: 9824521
medical journals; statistical review

Results 1-11 (11)