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1.  Simple, Defensible Sample Sizes Based on Cost Efficiency 
Biometrics  2008;64(2):577-594.
Summary
The conventional approach of choosing sample size to provide 80% or greater power ignores the cost implications of different sample size choices. Costs, however, are often impossible for investigators and funders to ignore in actual practice. Here, we propose and justify a new approach for choosing sample size based on cost efficiency, the ratio of a study’s projected scientific and/or practical value to its total cost. By showing that a study’s projected value exhibits diminishing marginal returns as a function of increasing sample size for a wide variety of definitions of study value, we are able to develop two simple choices that can be defended as more cost efficient than any larger sample size. The first is to choose the sample size that minimizes the average cost per subject. The second is to choose sample size to minimize total cost divided by the square root of sample size. This latter method is theoretically more justifiable for innovative studies, but also performs reasonably well and has some justification in other cases. For example, if projected study value is assumed to be proportional to power at a specific alternative and total cost is a linear function of sample size, then this approach is guaranteed either to produce more than 90% power or to be more cost efficient than any sample size that does. These methods are easy to implement, based on reliable inputs, and well justified, so they should be regarded as acceptable alternatives to current conventional approaches.
doi:10.1111/j.1541-0420.2008.01004_1.x
PMCID: PMC2769573  PMID: 18482055
Innovation; Peer review; Power; Research funding; Study design
2.  Current sample size conventions: Flaws, harms, and alternatives 
BMC Medicine  2010;8:17.
Background
The belief remains widespread that medical research studies must have statistical power of at least 80% in order to be scientifically sound, and peer reviewers often question whether power is high enough.
Discussion
This requirement and the methods for meeting it have severe flaws. Notably, the true nature of how sample size influences a study's projected scientific or practical value precludes any meaningful blanket designation of <80% power as "inadequate". In addition, standard calculations are inherently unreliable, and focusing only on power neglects a completed study's most important results: estimates and confidence intervals. Current conventions harm the research process in many ways: promoting misinterpretation of completed studies, eroding scientific integrity, giving reviewers arbitrary power, inhibiting innovation, perverting ethical standards, wasting effort, and wasting money. Medical research would benefit from alternative approaches, including established value of information methods, simple choices based on cost or feasibility that have recently been justified, sensitivity analyses that examine a meaningful array of possible findings, and following previous analogous studies. To promote more rational approaches, research training should cover the issues presented here, peer reviewers should be extremely careful before raising issues of "inadequate" sample size, and reports of completed studies should not discuss power.
Summary
Common conventions and expectations concerning sample size are deeply flawed, cause serious harm to the research process, and should be replaced by more rational alternatives.
doi:10.1186/1741-7015-8-17
PMCID: PMC2856520  PMID: 20307281
3.  Selection in Reported Epidemiological Risks: An Empirical Assessment 
PLoS Medicine  2007;4(3):e79.
Background
Epidemiological studies may be subject to selective reporting, but empirical evidence thereof is limited. We empirically evaluated the extent of selection of significant results and large effect sizes in a large sample of recent articles.
Methods and Findings
We evaluated 389 articles of epidemiological studies that reported, in their respective abstracts, at least one relative risk for a continuous risk factor in contrasts based on median, tertile, quartile, or quintile categorizations. We examined the proportion and correlates of reporting statistically significant and nonsignificant results in the abstract and whether the magnitude of the relative risks presented (coined to be consistently ≥1.00) differs depending on the type of contrast used for the risk factor. In 342 articles (87.9%), ≥1 statistically significant relative risk was reported in the abstract, while only 169 articles (43.4%) reported ≥1 statistically nonsignificant relative risk in the abstract. Reporting of statistically significant results was more common with structured abstracts, and was less common in US-based studies and in cancer outcomes. Among 50 randomly selected articles in which the full text was examined, a median of nine (interquartile range 5–16) statistically significant and six (interquartile range 3–16) statistically nonsignificant relative risks were presented (p = 0.25). Paradoxically, the smallest presented relative risks were based on the contrasts of extreme quintiles; on average, the relative risk magnitude was 1.41-, 1.42-, and 1.36-fold larger in contrasts of extreme quartiles, extreme tertiles, and above-versus-below median values, respectively (p < 0.001).
Conclusions
Published epidemiological investigations almost universally highlight significant associations between risk factors and outcomes. For continuous risk factors, investigators selectively present contrasts between more extreme groups, when relative risks are inherently lower.
An evaluation of published articles reporting epidemiological studies found that they almost universally highlight significant associations between risk factors and outcomes.
Editors' Summary
Background.
Medical and scientific researchers use statistical tests to try to work out whether their observations—for example, seeing a difference in some characteristic between two groups of people—might have occurred as a result of chance alone. Statistical tests cannot determine this for sure, rather they can only give a probability that the observations would have arisen by chance. When researchers have many different hypotheses, and carry out many statistical tests on the same set of data, they run the risk of concluding that there are real differences where in fact there are none. At the same time, it has long been known that scientific and medical researchers tend to pick out the findings on which to report in their papers. Findings that are more interesting, impressive, or statistically significant are more likely to be published. This is termed “publication bias” or “selective reporting bias.” Therefore, some people are concerned that the published scientific literature might contain many false-positive findings, i.e., findings that are not true but are simply the result of chance variation in the data. This would have a serious impact on the accuracy of the published scientific literature and would tend to overestimate the strength and direction of relationships being studied.
Why Was This Study Done?
Selective reporting bias has already been studied in detail in the area of randomized trials (studies where participants are randomly allocated to receive an intervention, e.g., a new drug, versus an alternative intervention or “comparator,” in order to understand the benefits or safety of the new intervention). These studies have shown that very many of the findings of trials are never published, and that statistically significant findings are more likely to be included in published papers than nonsignificant findings. However, much medical research is carried out that does not use randomized trial methods, either because that method is not useful to answer the question at hand or is unethical. Epidemiological research is often concerned with looking at links between risk factors and the development of disease, and this type of research would generally use observation rather than experiment to uncover connections. The researchers here were concerned that selective reporting bias might be just as much of a problem in epidemiological research as in randomized trials research, and wanted to study this specifically.
What Did the Researchers Do and Find?
In this investigation, searches were carried out of PubMed, a database of biomedical research studies, to extract epidemiological studies that were published between January 2004 and October 2005. The researchers wanted to specifically look at studies reporting the effect of continuous risk factors and their effect on health or disease outcomes (a continuous risk factor is something like age or glucose concentration in the blood, is a number, and can have any value on a sliding scale). Three hundred and eighty-nine original research studies were found, and the researchers pulled out from the abstracts and full text of these papers the relative risks that were reported along with the results of statistical tests for them. (Relative risk is the chance of getting an outcome, say disease, in one group as compared to another group.) The researchers found that nearly 90% of these studies had one or more statistically significant risks reported in the abstract, but only 43% reported one or more risks that were not statistically significant. When looking at all of the findings reported anywhere in the full text for 50 of these studies, the researchers saw that papers overall reported more statistically significant risks than nonsignificant risks. Finally, it seemed that in the set of papers studied here, the way in which statistical analyses were done produced a bias towards more extreme findings: for datasets showing small relative risks, papers were more likely to report a comparison between extreme subsets of the data so as to report larger relative risks.
What Do These Findings Mean?
These findings suggest that there is a tendency among epidemiology researchers to highlight statistically significant findings and to avoid highlighting nonsignificant findings in their research papers. This behavior may be a problem, because many of these significant findings could in future turn out to be “false positives.” At present, registers exist for researchers to describe ongoing clinical trials, and to set out the outcomes that they plan to analyze for those trials. These registers will go some way towards addressing some of the problems described here, but only for clinical trials research. Registers do not yet exist for epidemiological studies, and therefore it is important that researchers and readers are aware of and cautious about the problem of selective reporting in epidemiological research.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0040079.
Wikipedia entry on publication bias (note: Wikipedia is an internet encyclopedia that anyone can edit)
The International Committee of Medical Journal Editors gives guidelines for submitting manuscripts to its member journals, and includes comments about registration of ongoing studies and the obligation to publish negative studies
ClinicalTrials.gov and the ISRCTN register are two registries of ongoing clinical trials
doi:10.1371/journal.pmed.0040079
PMCID: PMC1808481  PMID: 17341129
4.  How to create innovation by building the translation bridge from basic research into medicinal drugs: an industrial perspective 
Human Genomics  2013;7(1):5.
The global healthcare industry is undergoing substantial changes and adaptations to the constant decline of approved new medical entities. This decrease in internal research productivity is resulting in a major decline of patent-protected sales (patent cliff) of most of the pharmaceutical companies. Three major global adaptive trends as driving forces to cope with these challenges are evident: cut backs of internal research and development jobs in the western hemisphere (Europe and USA), following the market growth potential of Asia by building up internal or external research and development capabilities there and finally, ‘early innovation hunting’ with an increased focus on identifying and investing in very early innovation sources within academia and small start-up companies. Early innovation hunting can be done by different approaches: increased corporate funding, establishment of translational institutions to bridge innovation, increasing sponsored collaborations and formation of technology hunting groups for capturing very early scientific ideas and concepts. This emerging trend towards early innovation hunting demands special adaptations from both the pharmaceutical industry and basic researchers in academia to bridge the translation into new medicines which deliver innovative medicines that matters to the patient. This opinion article describes the different modalities of cross-fertilisation between basic university or publicly funded institutional research and the applied research and development activities within the pharmaceutical industry. Two key factors in this important translational bridge can be identified: preparation of both partnering organisations to open up for new and sometime disruptive ideas and creation of truly trust-based relationships between the different groups allowing long-term scientific collaborations while acknowledging that value-creating differences are an essential factor for successful collaboration building.
doi:10.1186/1479-7364-7-5
PMCID: PMC3608963  PMID: 23496921
Healthcare industry; Corporate venture capital; Open innovation; New frontier science; Translational development; Technology platforms
5.  Publication of Clinical Trials Supporting Successful New Drug Applications: A Literature Analysis 
PLoS Medicine  2008;5(9):e191.
Background
The United States (US) Food and Drug Administration (FDA) approves new drugs based on sponsor-submitted clinical trials. The publication status of these trials in the medical literature and factors associated with publication have not been evaluated. We sought to determine the proportion of trials submitted to the FDA in support of newly approved drugs that are published in biomedical journals that a typical clinician, consumer, or policy maker living in the US would reasonably search.
Methods and Findings
We conducted a cohort study of trials supporting new drugs approved between 1998 and 2000, as described in FDA medical and statistical review documents and the FDA approved drug label. We determined publication status and time from approval to full publication in the medical literature at 2 and 5 y by searching PubMed and other databases through 01 August 2006. We then evaluated trial characteristics associated with publication. We identified 909 trials supporting 90 approved drugs in the FDA reviews, of which 43% (394/909) were published. Among the subset of trials described in the FDA-approved drug label and classified as “pivotal trials” for our analysis, 76% (257/340) were published. In multivariable logistic regression for all trials 5 y postapproval, likelihood of publication correlated with statistically significant results (odds ratio [OR] 3.03, 95% confidence interval [CI] 1.78–5.17); larger sample sizes (OR 1.33 per 2-fold increase in sample size, 95% CI 1.17–1.52); and pivotal status (OR 5.31, 95% CI 3.30–8.55). In multivariable logistic regression for only the pivotal trials 5 y postapproval, likelihood of publication correlated with statistically significant results (OR 2.96, 95% CI 1.24–7.06) and larger sample sizes (OR 1.47 per 2-fold increase in sample size, 95% CI 1.15–1.88). Statistically significant results and larger sample sizes were also predictive of publication at 2 y postapproval and in multivariable Cox proportional models for all trials and the subset of pivotal trials.
Conclusions
Over half of all supporting trials for FDA-approved drugs remained unpublished ≥ 5 y after approval. Pivotal trials and trials with statistically significant results and larger sample sizes are more likely to be published. Selective reporting of trial results exists for commonly marketed drugs. Our data provide a baseline for evaluating publication bias as the new FDA Amendments Act comes into force mandating basic results reporting of clinical trials.
Ida Sim and colleagues investigate the publication status and publication bias of trials submitted to the US Food and Drug Administration (FDA) for a wide variety of approved drugs.
Editors' Summary
Background.
Before a new drug becomes available for the treatment of a specific human disease, its benefits and harms are carefully studied, first in the laboratory and in animals, and then in several types of clinical trials. In the most important of these trials—so-called “pivotal” clinical trials—the efficacy and safety of the new drug and of a standard treatment are compared by giving groups of patients the different treatments and measuring several predefined “outcomes.” These outcomes indicate whether the new drug is more effective than the standard treatment and whether it has any other effects on the patients' health and daily life. All this information is then submitted by the sponsor of the new drug (usually a pharmaceutical company) to the government body responsible for drug approval—in the US, this is the Food and Drug Administration (FDA).
Why Was This Study Done?
After a drug receives FDA approval, information about the clinical trials supporting the FDA's decision are included in the FDA “Summary Basis of Approval” and/or on the drug label. In addition, some clinical trials are described in medical journals. Ideally, all the clinical information that leads to a drug's approval should be publicly available to help clinicians make informed decisions about how to treat their patients. A full-length publication in a medical journal is the primary way that clinical trial results are communicated to the scientific community and the public. Unfortunately, drug sponsors sometimes publish the results only of trials where their drug performed well; as a consequence, trials where the drug did no better than the standard treatment or where it had unwanted side effects remain unpublished. Publication bias like this provides an inaccurate picture of a drug's efficacy and safety relative to other therapies and may lead to excessive prescribing of newer, more expensive (but not necessarily more effective) treatments. In this study, the researchers investigate whether selective trial reporting is common by evaluating the publication status of trials submitted to the FDA for a wide variety of approved drugs. They also ask which factors affect a trial's chances of publication.
What Did the Researchers Do and Find?
The researchers identified 90 drugs approved by the FDA between 1998 and 2000 by searching the FDA's Center for Drug Evaluation and Research Web site. From the Summary Basis of Approval for each drug, they identified 909 clinical trials undertaken to support these approvals. They then searched the published medical literature up to mid-2006 to determine if and when the results of each trial were published. Although 76% of the pivotal trials had appeared in medical journals, usually within 3 years of FDA approval, only 43% of all of the submitted trials had been published. Among all the trials, those with statistically significant results were nearly twice as likely to have been published as those without statistically significant results, and pivotal trials were three times more likely to have been published as nonpivotal trials, 5 years postapproval. In addition, a larger sample size increased the likelihood of publication. Having statistically significant results and larger sample sizes also increased the likelihood of publication of the pivotal trials.
What Do These Findings Mean?
Although the search methods used in this study may have missed some publications, these findings suggest that more than half the clinical trials undertaken to support drug approval remain unpublished 5 years or more after FDA approval. They also reveal selective reporting of results. For example, they show that a pivotal trial in which the new drug does no better than an old drug is less likely to be published than one where the new drug is more effective, a publication bias that could establish an inappropriately favorable record for the new drug in the medical literature. Importantly, these findings provide a baseline for monitoring the effects of the FDA Amendments Act 2007, which was introduced to improve the accuracy and completeness of drug trial reporting. Under this Act, all trials supporting FDA-approved drugs must be registered when they start, and the summary results of all the outcomes declared at trial registration as well as specific details about the trial protocol must be publicly posted within a year of drug approval on the US National Institutes of Health clinical trials site.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0050191.
PLoS Medicine recently published an editorial discussing the FDA Amendment Act and what it means for medical journals: The PLoS Medicine Editors (2008) Next Stop, Don't Block the Doors: Opening Up Access to Clinical Trials Results. PLoS Med 5(7): e160
The US Food and Drug Administration provides information about drug approval in the US for consumers and for health care professionals; detailed information about the process by which drugs are approved is on the Web site of the FDA Center for Drug Evaluation and Research (in English and Spanish)
ClinicalTrials.gov provides information about the US National Institutes of Health clinical trial registry, background information about clinical trials, and a fact sheet detailing the requirements of the FDA Amendments Act 2007 for trial registration
The World Health Organization's International Clinical Trials Registry Platform is working toward international norms and standards for reporting the findings of clinical trials
doi:10.1371/journal.pmed.0050191
PMCID: PMC2553819  PMID: 18816163
6.  Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study 
PLoS Medicine  2013;10(10):e1001538.
Using a microarray-based approach, Michael Levin and colleagues develop a disease risk score to distinguish active from latent tuberculosis, as well as tuberculosis from other diseases, using whole blood samples.
Please see later in the article for the Editors' Summary
Background
A major impediment to tuberculosis control in Africa is the difficulty in diagnosing active tuberculosis (TB), particularly in the context of HIV infection. We hypothesized that a unique host blood RNA transcriptional signature would distinguish TB from other diseases (OD) in HIV-infected and -uninfected patients, and that this could be the basis of a simple diagnostic test.
Methods and Findings
Adult case-control cohorts were established in South Africa and Malawi of HIV-infected or -uninfected individuals consisting of 584 patients with either TB (confirmed by culture of Mycobacterium tuberculosis [M.TB] from sputum or tissue sample in a patient under investigation for TB), OD (i.e., TB was considered in the differential diagnosis but then excluded), or healthy individuals with latent TB infection (LTBI). Individuals were randomized into training (80%) and test (20%) cohorts. Blood transcriptional profiles were assessed and minimal sets of significantly differentially expressed transcripts distinguishing TB from LTBI and OD were identified in the training cohort. A 27 transcript signature distinguished TB from LTBI and a 44 transcript signature distinguished TB from OD. To evaluate our signatures, we used a novel computational method to calculate a disease risk score (DRS) for each patient. The classification based on this score was first evaluated in the test cohort, and then validated in an independent publically available dataset (GSE19491).
In our test cohort, the DRS classified TB from LTBI (sensitivity 95%, 95% CI [87–100]; specificity 90%, 95% CI [80–97]) and TB from OD (sensitivity 93%, 95% CI [83–100]; specificity 88%, 95% CI [74–97]). In the independent validation cohort, TB patients were distinguished both from LTBI individuals (sensitivity 95%, 95% CI [85–100]; specificity 94%, 95% CI [84–100]) and OD patients (sensitivity 100%, 95% CI [100–100]; specificity 96%, 95% CI [93–100]).
Limitations of our study include the use of only culture confirmed TB patients, and the potential that TB may have been misdiagnosed in a small proportion of OD patients despite the extensive clinical investigation used to assign each patient to their diagnostic group.
Conclusions
In our study, blood transcriptional signatures distinguished TB from other conditions prevalent in HIV-infected and -uninfected African adults. Our DRS, based on these signatures, could be developed as a test for TB suitable for use in HIV endemic countries. Further evaluation of the performance of the signatures and DRS in prospective populations of patients with symptoms consistent with TB will be needed to define their clinical value under operational conditions.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Tuberculosis (TB), caused by Mycobacterium tuberculosis, is curable and preventable, but according to the World Health Organization (WHO), in 2011, 8.7 million people had symptoms of TB (usually a productive cough and fever) and 1.4 million people—95% from low- and middle-income countries—died from this infection. Worldwide, TB is also the leading cause of death in people with HIV. For over a century, diagnosis of TB has relied on clinical and radiological features, sputum microscopy, and tuberculin skin testing but all of these tests have major disadvantages, especially in people who are also infected with HIV (HIV/TB co-infection) in whom results are often atypical or falsely negative. Furthermore, current tests cannot distinguish between inactive (latent) and active TB infection. Therefore, there is a need to identify biomarkers that can differentiate TB from other diseases common to African populations, where the burden of the HIV/TB pandemic is greatest.
Why Was This Study Done?
Previous studies have suggested that TB may be associated with specific transcriptional profiles (identified by microarray analysis) in the blood of the infected patient (host), which might make it possible to differentiate TB from other conditions. However, these studies have not included people co-infected with HIV and have included in the differential diagnosis diseases that are unrepresentative of the range of conditions common to African patients. In this study of patients from Malawi and South Africa, the researchers investigated whether blood RNA expression could distinguish TB from other conditions prevalent in African populations and form the basis of a diagnostic test for TB (through a process using transcription signatures).
What Did the Researchers Do and Find?
The researchers recruited patients with suspected TB attending one clinic in Cape Town, South Africa between 2007 and 2010 and in one hospital in Karonga district, Malawi between 2007 and 2009 (the training and test cohorts). Each patient underwent a series of tests for TB (and had a blood test for HIV) and was diagnosed as having TB if there was microbiological evidence confirming the presence of Mycobacterium tuberculosis. At recruitment, each patient also had blood taken for microarray analysis and following this assessment, the researchers selected minimal transcript sets that distinguished TB from latent TB infection and TB from other diseases, even in HIV-infected individuals. In order to help form the basis of a simple, low cost, diagnostic test, the researchers then developed a statistical method for the translation of multiple transcript RNA signatures into a disease risk score, which the researchers then checked using a separate cohort of South African patients (the independent validation cohort).
Using these methods, after screening 437 patients in Malawi and 314 in South Africa, the researchers recruited 273 patients to the Malawi cohort and 311 adults to the South African cohort (the training and test cohorts). Following technical failures, 536 microarray samples were available for analysis. The researchers identified a set of 27 transcripts that could distinguish between TB and latent TB and a set of 44 transcripts that could distinguish TB from other diseases. These multi-transcript signatures were then used to calculate a single value disease risk score for every patient. In the test cohorts, the disease risk score had a high sensitivity (95%) and specificity (90%) for distinguishing TB from latent TB infection (sensitivity is a measure of true positives, correctly identified as such and specificity is a measure of true negatives, correctly identified as such) and for distinguishing TB from other diseases (sensitivity 93% and specificity 88%). In the independent validation cohort, the researchers found that patients with TB could be distinguished from patients with latent TB infection (sensitivity 95% and specificity 94%) and also from patients with other diseases (sensitivity 100% and specificity 96%).
What Do These Findings Mean?
These findings suggest that a distinctive set of RNA transcriptional signatures forming a disease risk score might provide the basis of a diagnostic test that can distinguish active TB from latent TB infection (27 signatures) and also from other diseases (44 signatures), such as pneumonia, that are prevalent in African populations. There is a concern that using transcriptional signatures as a clinical diagnostic tool in resource poor settings might not be feasible because they are complex and costly. The relatively small number of transcripts in the signatures described here may increase the potential for using this approach (transcriptional profiling) as a clinical diagnostic tool using a single blood test. In order to make most use of these findings, there is an urgent need for the academic research community and for industry to develop innovative methods to translate multi-transcript signatures into simple, cheap tests for TB suitable for use in African health facilities.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/ 10.1371/journal.pmed.1001538.
Wikipedia has definitions of tests for gene expression (note that Wikipedia is a free online encyclopedia that anyone can edit; available in several languages)
The National Center for Biotechnology Information has a fact sheet on microarray analysis
MedlinePlus has links to further information about tuberculosis (in English and Spanish)
The World Health Organization has up-to-date information on TB
The Stop TB partnership is working towards tuberculosis elimination; patient stories about tuberculosis/HIV coinfection are available
doi:10.1371/journal.pmed.1001538
PMCID: PMC3805485  PMID: 24167453
7.  Threats to Validity in the Design and Conduct of Preclinical Efficacy Studies: A Systematic Review of Guidelines for In Vivo Animal Experiments 
PLoS Medicine  2013;10(7):e1001489.
Background
The vast majority of medical interventions introduced into clinical development prove unsafe or ineffective. One prominent explanation for the dismal success rate is flawed preclinical research. We conducted a systematic review of preclinical research guidelines and organized recommendations according to the type of validity threat (internal, construct, or external) or programmatic research activity they primarily address.
Methods and Findings
We searched MEDLINE, Google Scholar, Google, and the EQUATOR Network website for all preclinical guideline documents published up to April 9, 2013 that addressed the design and conduct of in vivo animal experiments aimed at supporting clinical translation. To be eligible, documents had to provide guidance on the design or execution of preclinical animal experiments and represent the aggregated consensus of four or more investigators. Data from included guidelines were independently extracted by two individuals for discrete recommendations on the design and implementation of preclinical efficacy studies. These recommendations were then organized according to the type of validity threat they addressed. A total of 2,029 citations were identified through our search strategy. From these, we identified 26 guidelines that met our eligibility criteria—most of which were directed at neurological or cerebrovascular drug development. Together, these guidelines offered 55 different recommendations. Some of the most common recommendations included performance of a power calculation to determine sample size, randomized treatment allocation, and characterization of disease phenotype in the animal model prior to experimentation.
Conclusions
By identifying the most recurrent recommendations among preclinical guidelines, we provide a starting point for developing preclinical guidelines in other disease domains. We also provide a basis for the study and evaluation of preclinical research practice.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
The development process for new drugs is lengthy and complex. It begins in the laboratory, where scientists investigate the causes of diseases and identify potential new treatments. Next, promising interventions undergo preclinical research in cells and in animals (in vivo animal experiments) to test whether the intervention has the expected effect and to support the generalization (extension) of this treatment–effect relationship to patients. Drugs that pass these tests then enter clinical trials, where their safety and efficacy is tested in selected groups of patients under strictly controlled conditions. Finally, the government bodies responsible for drug approval review the results of the clinical trials, and successful drugs receive a marketing license, usually a decade or more after the initial laboratory work. Notably, only 11% of agents that enter clinical testing (investigational drugs) are ultimately licensed.
Why Was This Study Done?
The frequent failure of investigational drugs during clinical translation is potentially harmful to trial participants. Moreover, the costs of these failures are passed onto healthcare systems in the form of higher drug prices. It would be good, therefore, to reduce the attrition rate of investigational drugs. One possible explanation for the dismal success rate of clinical translation is that preclinical research, the key resource for justifying clinical development, is flawed. To address this possibility, several groups of preclinical researchers have issued guidelines intended to improve the design and execution of in vivo animal studies. In this systematic review (a study that uses predefined criteria to identify all the research on a given topic), the authors identify the experimental practices that are commonly recommended in these guidelines and organize these recommendations according to the type of threat to validity (internal, construct, or external) that they address. Internal threats to validity are factors that confound reliable inferences about treatment–effect relationships in preclinical research. For example, experimenter expectation may bias outcome assessment. Construct threats to validity arise when researchers mischaracterize the relationship between an experimental system and the clinical disease it is intended to represent. For example, researchers may use an animal model for a complex multifaceted clinical disease that only includes one characteristic of the disease. External threats to validity are unseen factors that frustrate the transfer of treatment–effect relationships from animal models to patients.
What Did the Researchers Do and Find?
The researchers identified 26 preclinical guidelines that met their predefined eligibility criteria. Twelve guidelines addressed preclinical research for neurological and cerebrovascular drug development; other disorders covered by guidelines included cardiac and circulatory disorders, sepsis, pain, and arthritis. Together, the guidelines offered 55 different recommendations for the design and execution of preclinical in vivo animal studies. Nineteen recommendations addressed threats to internal validity. The most commonly included recommendations of this type called for the use of power calculations to ensure that sample sizes are large enough to yield statistically meaningful results, random allocation of animals to treatment groups, and “blinding” of researchers who assess outcomes to treatment allocation. Among the 25 recommendations that addressed threats to construct validity, the most commonly included recommendations called for characterization of the properties of the animal model before experimentation and matching of the animal model to the human manifestation of the disease. Finally, six recommendations addressed threats to external validity. The most commonly included of these recommendations suggested that preclinical research should be replicated in different models of the same disease and in different species, and should also be replicated independently.
What Do These Findings Mean?
This systematic review identifies a range of investigational recommendations that preclinical researchers believe address threats to the validity of preclinical efficacy studies. Many of these recommendations are not widely implemented in preclinical research at present. Whether the failure to implement them explains the frequent discordance between the results on drug safety and efficacy obtained in preclinical research and in clinical trials is currently unclear. These findings provide a starting point, however, for the improvement of existing preclinical research guidelines for specific diseases, and for the development of similar guidelines for other diseases. They also provide an evidence-based platform for the analysis of preclinical evidence and for the study and evaluation of preclinical research practice. These findings should, therefore, be considered by investigators, institutional review bodies, journals, and funding agents when designing, evaluating, and sponsoring translational research.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001489.
The US Food and Drug Administration provides information about drug approval in the US for consumers and for health professionals; its Patient Network provides a step-by-step description of the drug development process that includes information on preclinical research
The UK Medicines and Healthcare Products Regulatory Agency (MHRA) provides information about all aspects of the scientific evaluation and approval of new medicines in the UK; its My Medicine: From Laboratory to Pharmacy Shelf web pages describe the drug development process from scientific discovery, through preclinical and clinical research, to licensing and ongoing monitoring
The STREAM website provides ongoing information about policy, ethics, and practices used in clinical translation of new drugs
The CAMARADES collaboration offers a “supporting framework for groups involved in the systematic review of animal studies” in stroke and other neurological diseases
doi:10.1371/journal.pmed.1001489
PMCID: PMC3720257  PMID: 23935460
8.  Greater Response to Placebo in Children Than in Adults: A Systematic Review and Meta-Analysis in Drug-Resistant Partial Epilepsy 
PLoS Medicine  2008;5(8):e166.
Background
Despite guidelines establishing the need to perform comprehensive paediatric drug development programs, pivotal trials in children with epilepsy have been completed mostly in Phase IV as a postapproval replication of adult data. However, it has been shown that the treatment response in children can differ from that in adults. It has not been investigated whether differences in drug effect between adults and children might occur in the treatment of drug-resistant partial epilepsy, although such differences may have a substantial impact on the design and results of paediatric randomised controlled trials (RCTs).
Methods and Findings
Three electronic databases were searched for RCTs investigating any antiepileptic drug (AED) in the add-on treatment of drug-resistant partial epilepsy in both children and adults. The treatment effect was compared between the two age groups using the ratio of the relative risk (RR) of the 50% responder rate between active AEDs treatment and placebo groups, as well as meta-regression. Differences in the response to placebo and to active treatment were searched using logistic regression. A comparable approach was used for analysing secondary endpoints, including seizure-free rate, total and adverse events-related withdrawal rates, and withdrawal rate for seizure aggravation. Five AEDs were evaluated in both adults and children with drug-resistant partial epilepsy in 32 RCTs. The treatment effect was significantly lower in children than in adults (RR ratio: 0.67 [95% confidence interval (CI) 0.51–0.89]; p = 0.02 by meta-regression). This difference was related to an age-dependent variation in the response to placebo, with a higher rate in children than in adults (19% versus 9.9%, p < 0.001), whereas no significant difference was observed in the response to active treatment (37.2% versus 30.4%, p = 0.364). The relative risk of the total withdrawal rate was also significantly lower in children than in adults (RR ratio: 0.65 [95% CI 0.43–0.98], p = 0.004 by metaregression), due to higher withdrawal rate for seizure aggravation in children (5.6%) than in adults (0.7%) receiving placebo (p < 0.001). Finally, there was no significant difference in the seizure-free rate between adult and paediatric studies.
Conclusions
Children with drug-resistant partial epilepsy receiving placebo in double-blind RCTs demonstrated significantly greater 50% responder rate than adults, probably reflecting increased placebo and regression to the mean effects. Paediatric clinical trial designs should account for these age-dependent variations of the response to placebo to reduce the risk of an underestimated sample size that could result in falsely negative trials.
In a systematic review of antiepileptic drugs, Philippe Ryvlin and colleagues find that children with drug-resistant partial epilepsy enrolled in trials seem to have a greater response to placebo than adults enrolled in such trials.
Editors' Summary
Background.
Whenever an adult is given a drug to treat a specific condition, that drug will have been tested in “randomized controlled trials” (RCTs). In RCTs, a drug's effects are compared to those of another drug for the same condition (or to a placebo, dummy drug) by giving groups of adult patients the different treatments and measuring how well each drug deals with the condition and whether it has any other effects on the patients' health. However, many drugs given to children have only been tested in adults, the assumption being that children can safely take the same drugs as adults provided the dose is scaled down. This approach to treatment is generally taken in epilepsy, a common brain disorder in children in which disruptions in the electrical activity of part (partial epilepsy) or all (generalized epilepsy) of the brain cause seizures. The symptoms of epilepsy depend on which part of the brain is disrupted and can include abnormal sensations, loss of consciousness, or convulsions. Most but not all patients can be successfully treated with antiepileptic drugs, which reduce or stop the occurrence of seizures.
Why Was This Study Done?
It is increasingly clear that children and adults respond differently to many drugs, including antiepileptic drugs. For example, children often break down drugs differently from adults, so a safe dose for an adult may be fatal to a child even after scaling down for body size, or it may be ineffective because of quicker clearance from the child's body. Consequently, regulatory bodies around the world now require comprehensive drug development programs in children as well as in adults. However, for pediatric trials to yield useful results, the general differences in the treatment response between children and adults must first be determined and then allowed for in the design of pediatric RCTs. In this study, the researchers investigate whether there is any evidence in published RCTs for age-dependent differences in the response to antiepileptic drugs in drug-resistant partial epilepsy.
What Did the Researchers Do and Find?
The researchers searched the literature for reports of RCTs on the effects of antiepileptic drugs in the add-on treatment of drug-resistant partial epilepsy in children and in adults—that is, trials that compared the effects of giving an additional antiepileptic drug with those of giving a placebo by asking what fraction of patients given each treatment had a 50% reduction in seizure frequency during the treatment period compared to a baseline period (the “50% responder rate”). This “systematic review” yielded 32 RCTs, including five pediatric RCTs. The researchers then compared the treatment effect (the ratio of the 50% responder rate in the treatment arm to the placebo arm) in the two age groups using a statistical approach called “meta-analysis” to pool the results of these studies. The treatment effect, they report, was significantly lower in children than in adults. Further analysis indicated that this difference was because more children than adults responded to the placebo. Nearly 1 in 5 children had a 50% reduction in seizure rate when given a placebo compared to only 1 in 10 adults. About a third of both children and adults had a 50% reduction in seizure rate when given antiepileptic drugs.
What Do These Findings Mean?
These findings, although limited by the small number of pediatric trials done so far, suggest that children with drug-resistant partial epilepsy respond more strongly in RCTs to placebo than adults. Although additional studies need to be done to find an explanation for this observation and to discover whether anything similar occurs in other conditions, this difference between children and adults should be taken into account in the design of future pediatric trials on the effects of antiepileptic drugs, and possibly drugs for other conditions. Specifically, to reduce the risk of false-negative results, this finding suggests that it might be necessary to increase the size of future pediatric trials to ensure that the trials have enough power to discover effects of the drugs tested, if they exist.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0050166.
This study is further discussed in a PLoS Medicine Perspective by Terry Klassen and colleagues
The European Medicines Agency provides information about the regulation of medicines for children in Europe
The US Food and Drug Administration Office of Pediatric Therapeutics provides similar information for the US
The UK Medicines and Healthcare products Regulatory Agency also provides information on why medicines need to be tested in children
The MedlinePlus encyclopedia has a page on epilepsy (in English and Spanish)
The US National Institute for Neurological Disorders and Stroke and the UK National Health Service Direct health encyclopedia both provide information on epilepsy for patients (in several languages)
Neuroscience for Kids is an educational Web site prepared by Eric Chudler (University of Washington, Seattle, US) that includes information on epilepsy and a list of links to epilepsy organizations (mainly in English but some sections in other languages as well)
doi:10.1371/journal.pmed.0050166
PMCID: PMC2504483  PMID: 18700812
9.  Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip 
PLoS Genetics  2009;5(5):e1000477.
Genome-wide association studies are revolutionizing the search for the genes underlying human complex diseases. The main decisions to be made at the design stage of these studies are the choice of the commercial genotyping chip to be used and the numbers of case and control samples to be genotyped. The most common method of comparing different chips is using a measure of coverage, but this fails to properly account for the effects of sample size, the genetic model of the disease, and linkage disequilibrium between SNPs. In this paper, we argue that the statistical power to detect a causative variant should be the major criterion in study design. Because of the complicated pattern of linkage disequilibrium (LD) in the human genome, power cannot be calculated analytically and must instead be assessed by simulation. We describe in detail a method of simulating case-control samples at a set of linked SNPs that replicates the patterns of LD in human populations, and we used it to assess power for a comprehensive set of available genotyping chips. Our results allow us to compare the performance of the chips to detect variants with different effect sizes and allele frequencies, look at how power changes with sample size in different populations or when using multi-marker tags and genotype imputation approaches, and how performance compares to a hypothetical chip that contains every SNP in HapMap. A main conclusion of this study is that marked differences in genome coverage may not translate into appreciable differences in power and that, when taking budgetary considerations into account, the most powerful design may not always correspond to the chip with the highest coverage. We also show that genotype imputation can be used to boost the power of many chips up to the level obtained from a hypothetical “complete” chip containing all the SNPs in HapMap. Our results have been encapsulated into an R software package that allows users to design future association studies and our methods provide a framework with which new chip sets can be evaluated.
Author Summary
Genome-wide association studies are a powerful and now widely-used method for finding genetic variants that increase the risk of developing particular diseases. These studies are complex and must be planned carefully in order to maximize the probability of finding novel associations. The main design choices to be made relate to sample sizes and choice of commercially available genotyping chip and are often constrained by cost, which can currently be as much as several million dollars. No comprehensive comparisons of chips based on their power for different sample sizes or for fixed study cost are currently available. We describe in detail a method for simulating large genome-wide association samples that accounts for the complex correlations between SNPs due to LD, and we used this method to assess the power of current genotyping chips. Our results highlight the differences between the chips under a range of plausible scenarios, and we demonstrate how our results can be used to design a study with a budget constraint. We also show how genotype imputation can be used to boost the power of each chip and that this method decreases the differences between the chips. Our simulation method and software for comparing power are being made available so that future association studies can be designed in a principled fashion.
doi:10.1371/journal.pgen.1000477
PMCID: PMC2688469  PMID: 19492015
10.  Robotic-Assisted Minimally Invasive Surgery for Gynecologic and Urologic Oncology 
Executive Summary
Objective
An application was received to review the evidence on the ‘The Da Vinci Surgical System’ for the treatment of gynecologic malignancies (e.g. endometrial and cervical cancers). Limitations to the current standard of care include the lack of trained physicians on minimally invasive surgery and limited access to minimally invasive surgery for patients. The potential benefits of ‘The Da Vinci Surgical System’ include improved technical manipulation and physician uptake leading to increased surgeries, and treatment and management of these cancers.
The demand for robotic surgery for the treatment and management of prostate cancer has been increasing due to its alleged benefits of recovery of erectile function and urinary continence, two important factors of men’s health. The potential technical benefits of robotic surgery leading to improved patient functional outcomes are surgical precision and vision.
Clinical Need
Uterine and cervical cancers represent 5.4% (4,400 of 81,700) and 1.6% (1,300 of 81,700), respectively, of incident cases of cancer among female cancers in Canada. Uterine cancer, otherwise referred to as endometrial cancer is cancer of the lining of the uterus. The most common treatment option for endometrial cancer is removing the cancer through surgery. A surgical option is the removal of the uterus and cervix through a small incision in the abdomen using a laparoscope which is referred to as total laparoscopic hysterectomy. Risk factors that increase the risk of endometrial cancer include taking estrogen replacement therapy after menopause, being obese, early age at menarche, late age at menopause, being nulliparous, having had high-dose radiation to the pelvis, and use of tamoxifen.
Cervical cancer occurs at the lower narrow end of the uterus. There are more treatment options for cervical cancer compared to endometrial cancer, however total laparoscopic hysterectomy is also a treatment option. Risk factors that increase the risk for cervical cancer are multiple sexual partners, early sexual activity, infection with the human papillomavirus, and cigarette smoking, whereas barrier-type of contraception as a risk factor decreases the risk of cervical cancer.
Prostate cancer is ranked first in men in Canada in terms of the number of new cases among all male cancers (25,500 of 89,300 or 28.6%). The impact on men who develop prostate cancer is substantial given the potential for erectile dysfunction and urinary incontinence. Prostate cancer arises within the prostate gland, which resides in the male reproductive system and near the bladder. Radical retropubic prostatectomy is the gold standard treatment for localized prostate cancer. Prostate cancer affects men above 60 years of age. Other risk factors include a family history of prostate cancer, being of African descent, being obese, consuming a diet high in fat, physical inactivity, and working with cadium.
The Da Vinci Surgical System
The Da Vinci Surgical System is a robotic device. There are four main components to the system: 1) the surgeon’s console, where the surgeon sits and views a magnified three-dimensional image of the surgical field; 2) patient side-cart, which sits beside the patient and consists of three instrument arms and one endoscope arm; 3) detachable instruments (endowrist instruments and intuitive masters), which simulate fine motor human movements. The hand movements of the surgeon’s hands at the surgeon’s console are translated into smaller ones by the robotic device and are acted out by the attached instruments; 4) three-dimensional vision system: the camera unit or endoscope arm. The main advantages of use of the robotic device are: 1) the precision of the instrument and improved dexterity due to the use of “wristed” instruments; 2) three-dimensional imaging, with improved ability to locate blood vessels, nerves and tissues; 3) the surgeon’s console, which reduces fatigue accompanied with conventional laparoscopy surgery and allows for tremor-free manipulation. The main disadvantages of use of the robotic device are the costs including instrument costs ($2.6 million in US dollars), cost per use ($200 per use), the costs associated with training surgeons and operating room personnel, and the lack of tactile feedback, with the trade-off being increased visual feedback.
Research Questions
For endometrial and cervical cancers,
1. What is the effectiveness of the Da Vinci Surgical System vs. laparoscopy and laparotomy for women undergoing any hysterectomy for the surgical treatment and management of their endometrial and cervical cancers?
2. What are the incremental costs of the Da Vinci Surgical System vs. laparoscopy and laparotomy for women undergoing any hysterectomy for the surgical treatment and management of their endometrial and cervical cancers?
For prostate cancer,
3. What is the effectiveness of robotically-assisted radical prostatectomy using the Da Vinci Surgical System vs. laparoscopic radical prostatectomy and retropubic radical prostatectomy for the surgical treatment and management of prostate cancer?
4. What are the incremental costs of robotically-assisted radical prostatectomy using the Da Vinci Surgical System vs. laparoscopic radical prostatectomy and retropubic radical prostatectomy for the surgical treatment and management of prostate cancer?
Research Methods
Literature Search
Search Strategy
A literature search was performed on May 12, 2010 using OVID MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, OVID EMBASE, Wiley Cochrane, CINAHL, Centre for Reviews and Dissemination/International Agency for Health Technology Assessment for studies published from January 1, 2000 until May 12, 2010. Abstracts were reviewed by a single reviewer and, for those studies meeting the eligibility criteria, full-text articles were obtained. Reference lists were also examined for any additional relevant studies not identified through the search. Articles with unknown eligibility were reviewed with a second clinical epidemiologist, then a group of epidemiologists until consensus was established. The quality of evidence was assessed as high, moderate, low or very low according to GRADE methodology.
Inclusion Criteria
English language articles (January 1, 2000-May 12, 2010)
Journal articles that report on the effectiveness or cost-effectiveness for the comparisons of interest using a primary data source (e.g. obtained in a clinical setting)
Journal articles that report on the effectiveness or cost-effectiveness for the comparisons of interest using a secondary data source (e.g. hospital- or population-based registries)
Study design and methods must be clearly described
Health technology assessments, systematic reviews, randomized controlled trials, non-randomized controlled trials and/or cohort studies, case-case studies, regardless of sample size, cost-effectiveness studies
Exclusion Criteria
Duplicate publications (with the more recent publication on the same study population included)
Non-English papers
Animal or in-vitro studies
Case reports or case series without a referent or comparison group
Studies on long-term survival which may be affected by treatment
Studies that do not examine the cancers (e.g. advanced disease) or outcomes of interest
Outcomes of Interest
For endometrial and cervical cancers,
Primary outcomes:
Morbidity factors
- Length of hospitalization
- Number of complications*
Peri-operative factors
- Operation time
- Amount of blood loss*
- Number of conversions to laparotomy*
Number of lymph nodes recovered
For prostate cancer,
Primary outcomes:
Morbidity factors
- Length of hospitalization
- Amount of morphine use/pain*
Peri-operative factors
- Operation time
- Amount of blood loss*
- Number of transfusions*
- Duration of catheterization
- Number of complications*
- Number of anastomotic strictures*
Number of lymph nodes recovered
Oncologic factors
- Proportion of positive surgical margins
Long-term outcomes
- Urinary continence
- Erectile function
Summary of Findings
Robotic use for gynecologic oncology compared to:
Laparotomy: benefits of robotic surgery in terms of shorter length of hospitalization and less blood loss. These results indicate clinical effectiveness in terms of reduced morbidity and safety, respectively, in the context of study design limitations.
The beneficial effect of robotic surgery was shown in pooled analysis for complications, owing to increased sample size.
More work is needed to clarify the role of complications in terms of safety, including improved study designs, analysis and measurement.
Laparoscopy: benefits of robotic surgery in terms of shorter length of hospitalization, less blood loss and fewer conversions to laparotomy likely owing to the technical difficulty of conventional laparoscopy, in the context of study design limitations.
Clinical significance of significant findings for length of hospitalizations and blood loss is low.
Fewer conversions to laparotomy indicate clinical effectiveness in terms of reduced morbidity.
Robotic use for urologic oncology, specifically prostate cancer, compared to:
Retropubic surgery: benefits of robotic surgery in terms of shorter length of hospitalization and less blood loss/fewer individuals requiring transfusions. These results indicate clinical effectiveness in terms of reduced morbidity and safety, respectively, in the context of study design limitations. There was a beneficial effect in terms of decreased positive surgical margins and erectile dysfunction. These results indicate clinical effectiveness in terms of improved cancer control and functional outcomes, respectively, in the context of study design limitations.
Surgeon skill had an impact on cancer control and functional outcomes.
The results for complications were inconsistent when measured as either total number of complications, pain management or anastomosis. There is some suggestion that robotic surgery is safe with respect to less post-operative pain management required compared to retropubic surgery, however improved study design and measurement of complications need to be further addressed.
Clinical significance of significant findings for length of hospitalizations is low.
Laparoscopy: benefits of robotic surgery in terms of less blood loss and fewer individuals requiring transfusions likely owing to the technical difficulty of conventional laparoscopy, in the context of study design limitations.
Clinical significance of significant findings for blood loss is low.
The potential link between less blood loss, improved visualization and improved functional outcomes is an important consideration for use of robotics.
All studies included were observational in nature and therefore the results must be interpreted cautiously.
Economic Analysis
The objective of this project was to assess the economic impact of robotic-assisted laparoscopy (RAL) for endometrial, cervical, and prostate cancers in the province of Ontario.
A budget impact analysis was undertaken to report direct costs associated with open surgery (OS), endoscopic laparoscopy (EL) and robotic-assisted laparoscopy (RAL) based on clinical literature review outcomes, to report a budget impact in the province based on volumes and costs from administrative data sets, and to project a future impact of RAL in Ontario. A cost-effectiveness analysis was not conducted because of the low quality evidence from the clinical literature review.
Hospital costs were obtained from the Ontario Case Costing Initiative (OCCI) for the appropriate Canadian Classification of Health Intervention (CCI) codes restricted to selective ICD-10 diagnostic codes after consultation with experts in the field. Physician fees were obtained from the Ontario Schedule of Benefits (OSB) after consultation with experts in the field. Fees were costed based on operation times reported in the clinical literature for the procedures being investigated. Volumes of procedures were obtained from the Ministry of Health and Long-Term Care (MOHLTC) administrative databases.
Direct costs associated with RAL, EL and OS included professional fees, hospital costs (including disposable instruments), radiotherapy costs associated with positive surgical margins in prostate cancer and conversion to OS in gynecological cancer. The total cost per case was higher for RAL than EL and OS for both gynecological and prostate cancers. There is also an acquisition cost associated with RAL. After conversation with the only supplier in Canada, hospitals are looking to spend an initial 3.6M to acquire the robotic surgical system
Previous volumes of OS and EL procedures were used to project volumes into Years 1-3 using a linear mathematical expression. Burden of OS and EL hysterectomies and prostatectomies was calculated by multiplying the number of cases for that year by the cost/case of the procedure.
The number of procedures is expected to increase in the next three years based on historical data. RAL is expected to capture this market by 65% after consultation with experts. If it’s assumed that RAL will capture the current market in Ontario by 65%, the net impact is expected to be by Year 3, 3.1M for hysterectomy and 6.7M for prostatectomy procedures respectively in the province.
RAL has diffused in the province with four surgical systems in place in Ontario, two in Toronto and two in London. RAL is a more expensive technology on a per case basis due to more expensive robot specific instrumentation and physician labour reflected by increased OR time reported in the clinical literature. There is also an upfront cost to acquire the machine and maintenance contract. RAL is expected to capture the market at 65% with project net impacts by Year 3 of 3.1M and 6.7M for hysterectomy and prostatectomy respectively.
PMCID: PMC3382308  PMID: 23074405
11.  Lipoprotein Particle Profiles Mark Familial and Sporadic Human Longevity 
PLoS Medicine  2006;3(12):e495.
Background
Genetic and biochemical studies have indicated an important role for lipid metabolism in human longevity. Ashkenazi Jewish centenarians and their offspring have large low-density lipoprotein (LDL) and high-density lipoprotein (HDL) particles as compared with control individuals. This profile also coincided with a lower prevalence of disease. Here, we investigate whether this observation can be confirmed for familial longevity in an outbred European population and whether it can be extended to sporadic longevity in the general population.
Methods and Findings
NMR-measured lipoprotein profiles were analyzed in 165 families from the Leiden Longevity Study, consisting of 340 long-lived siblings (females >91 y, males >89 y), 511 of their offspring, and 243 partners of the offspring. Offspring had larger (21.3 versus 21.1 nm; p = 0.020) and fewer (1,470 versus 1,561 nmol/l; p = 0.011) LDL particles than their same-aged partners. This effect was even more prominent in the long-lived siblings (p < 10−3) and could be pinpointed to a reduction specifically in the concentration of small LDL particles. No differences were observed for HDL particle phenotypes. The mean LDL particle sizes in 259 90-y-old singletons from a population-based study were similar to those in the long-lived siblings and thus significantly larger than in partners of the offspring, suggesting that the relevance of this phenotype extends beyond familial longevity. A low concentration of small LDL particles was associated with better overall health among both long-lived siblings (p = 0.003) and 90-y-old singletons (p = 0.007).
Conclusions
Our study indicates that LDL particle profiles mark both familial and sporadic human longevity already in middle age.
Offspring of families from the Leiden Longevity Study had larger and fewer LDL particles than same-aged partners, suggesting that even in middle age LDL particle profiles are associated with longevity.
Editors' Summary
Background.
It is not clear why some people go on to live longer than others do. Some studies have shown that close relatives of long-lived people are themselves more likely to live for a long time; these findings suggest that there is probably a genetic basis for long life. However, the actual mechanisms involved have not yet been worked out. Some genes coding for proteins involved in fat metabolism, such as APOE, APOB, and CETP, have been associated with long life, suggesting a link between the way fat gets metabolized and the aging process. One study that supports this idea found that the children of 100-year-old people had larger lipoprotein particles (assemblies of proteins and fats that carry cholesterol and triglycerides in the blood) than similarly aged control individuals. However, studies such as this are very prone to “false positive” findings and therefore need to be backed up by confirmatory evidence. In addition, the previous study was performed in a very specific population (Ashkenazi Jewish people), and it is important to find out whether the findings are also true in other populations.
Why Was This Study Done?
The research group carrying out this study wanted to address several distinct questions to do with the genetics of aging. Firstly, they wanted to see if they could confirm previous findings associating large lipoprotein particles with longer life, but looking at people who were more representative of the general European population and not from a genetically isolated population. Secondly, they wanted to see whether this association applied to only long-lived people whose family members were also long-lived, or to long-lived people in general. Finally, they wanted to find out if the large lipoprotein particles were associated with better health.
What Did the Researchers Do and Find?
In the study, the researchers looked at long-lived people from across The Netherlands whose relatives were also long-lived. For this, they recruited 340 men aged over 89 and women aged over 91 into the study, all of whom had at least one similarly long-lived sister or brother. Their children (511 individuals), and the partners of their children (243 people), were also recruited into the study, with the partners acting as “controls.” The researchers also studied 259 people who had just turned 90 years old; these people were included to see whether particular characteristics of lipoproteins existed in long-lived people whose longevity did not run in families. All the participants gave blood samples, and the researchers then measured the size and amount of different lipoprotein particles in these samples. Two types of lipoprotein particles were looked at: low-density lipoprotein (LDL, often termed “bad cholesterol”) and high-density lipoprotein (HDL, sometimes called “good cholesterol”). The researchers found that the children from the long-lived people had larger and fewer LDL particles than their partners (the “control” individuals) just like their long-lived parents. Thus even though the children were not long-lived themselves, LDL particles marked the fact that they have a higher chance of becoming long-lived in the future. Similar changes in LDL particles were found for long-lived people whose relatives were not also long-lived. Interestingly, simply the level of cholesterol—the classical risk factor for cardiovascular disease—did not appear to play a role. Thus it seems that it is not the amount of cholesterol that is important in longevity but how it is packaged. Better health status was also associated with a lower proportion of small LDL particles in the blood, supporting these findings. No characteristics of the HDL particles seemed to be associated with longevity.
What Do These Findings Mean?
These findings confirm those from a previous study in Ashkenazi Jewish people that suggested that the size of LDL particles in the blood was associated with long life. The nature of this association is not clear; some studies indicated that small LDL particles increase the risk of cardiovascular disease but small LDL particles may also be harmless themselves and reflect the efficiency of other processes causally related to aging.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0030495.
Wikipedia chapter on senescence (biology of aging) (note that Wikipedia is a free Internet encyclopedia that anyone can edit)
US National Institute on Aging provides information on healthy aging, details of publicly funded research into aging, and other resources for the public
Help the Aged information on research into aging
doi:10.1371/journal.pmed.0030495
PMCID: PMC1716190  PMID: 17194192
12.  Voluntary Medical Male Circumcision: A Framework Analysis of Policy and Program Implementation in Eastern and Southern Africa 
PLoS Medicine  2011;8(11):e1001133.
Kim Dickson and colleagues analyze the progress made by 13 priority countries toward scale-up of medical male circumcision programs, finding that the most successful programs involve country ownership of the program and have sustained leadership at all levels.
Background
Following confirmation of the effectiveness of voluntary medical male circumcision (VMMC) for HIV prevention, the World Health Organization and the Joint United Nations Programme on HIV/AIDS issued recommendations in 2007. Less than 5 y later, priority countries are at different stages of program scale-up. This paper analyzes the progress towards the scale-up of VMMC programs. It analyzes the adoption of VMMC as an additional HIV prevention strategy and explores the factors may have expedited or hindered the adoption of policies and initial program implementation in priority countries to date.
Methods and Findings
VMMCs performed in priority countries between 2008 and 2010 were recorded and used to classify countries into five adopter categories according to the Diffusion of Innovations framework. The main predictors of VMMC program adoption were determined and factors influencing subsequent scale-up explored. By the end of 2010, over 550,000 VMMCs had been performed, representing approximately 3% of the target coverage level in priority countries. The “early adopter” countries developed national VMMC policies and initiated VMMC program implementation soon after the release of the WHO recommendations. However, based on modeling using the Decision Makers' Program Planning Tool (DMPPT), only Kenya appears to be on track towards achievement of the DMPPT-estimated 80% coverage goal by 2015, having already achieved 61.5% of the DMPPT target. None of the other countries appear to be on track to achieve their targets. Potential predicators of early adoption of male circumcision programs include having a VMMC focal person, establishing a national policy, having an operational strategy, and the establishment of a pilot program.
Conclusions
Early adoption of VMMC policies did not necessarily result in rapid program scale-up. A key lesson is the importance of not only being ready to adopt a new intervention but also ensuring that factors critical to supporting and accelerating scale-up are incorporated into the program. The most successful program had country ownership and sustained leadership to translate research into a national policy and program.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Every year, more than 2.5 million people (mostly in sub-Saharan Africa) become infected with HIV, the virus that causes AIDS. There is no cure for HIV/AIDS and no HIV vaccine. Consequently, global efforts to combat HIV/AIDS are concentrating on evidence-based prevention strategies such as voluntary medical male circumcision (VMMC). Circumcision—the removal of the foreskin, a loose fold of skin that covers the head of the penis—reduced HIV transmission through sexual intercourse by 60% in men in trials undertaken in sub-Saharan Africa, so in 2007, the World Health Organization (WHO) and the Joint United Nations Programme on HIV/AIDS (UNAIDS) recommended implementation of VMMC programs in countries with a generalized HIV epidemic and low levels of male circumcision. They also identified 13 countries in southern and eastern Africa as high priority countries for rapid VMMC scale-up. Mathematical modeling suggests that 20.3 million circumcisions by 2015 and 8.4 million circumcisions between 2016 and 2025 are needed to reach 80% VMMC coverage in these countries. If this coverage is achieved, it will avert about 3.4 million new HIV infections through 2025.
Why Was This Study Done?
Despite convincing evidence that VMMC is an effective, cost-saving intervention in the fight against HIV/AIDS, national VMMC scale-up programs in the priority countries are currently at very different stages. A better understanding of the challenges faced by these programs would help countries still in the early stages of VMMC scale-up implement their national programs and would facilitate implementation of other HIV prevention strategies. In this study, the researchers use the Diffusion of Innovations (DOI) theory to analyze progress towards VMMC scale-up in the priority countries and to identify the factors that may have expedited or hindered program scale-up. This theory seeks to explain how, why, and at what rate new ideas and technology spread through cultures. It posits that a few individuals (“innovators”) adopt new ideas before they become mainstream ideas. A few more individuals—the “early adopters”—follow the innovators. The “early majority” is the next group to adopt the innovation, followed by the “late majority” and the “laggards.”
What Did the Researchers Do and Find?
The researchers used the annual number of VMMCs performed in the priority countries since 2008 to classify the countries into DOI adopter categories. They calculated a total scale-up score for each country based on six key elements of program scale-up (such as whether and when a VMMC policy had been approved). Finally, they analyzed the association between the DOI adopter category and the scores for the individual scale-up elements to determine which elements predict adoption and VMMC scale-up. By the end of 2010, about 560,000 VMMCs had been completed, less than 3% of the target coverage for the priority countries. Kenya, the only DOI innovator country, had completed nearly two-thirds of the VMMCs needed to reach its target coverage and was the only country on track to reach its target. The early adopters (South Africa, Zambia, and Swaziland) had initiated VMMC program scale-up soon after the release of the 2007 recommendations and had started VMMC scale-up pilot programs in 2008 but were far from achieving their VMMC targets. Having a VMMC focal person, establishing a national policy, having an operational strategy, and establishing a pilot program all predicted early adoption of VMMC scale-up.
What Do These Findings Mean?
These findings show that, three years after the WHO/UNAIDS recommendation to integrate VMMC into comprehensive HIV prevention programs, VMMC scale-up activities had been initiated in all the priority countries but that progress towards the 80% coverage target was variable and generally poor. Importantly, they show that early adoption of VMMC as a national program had not necessarily resulted in rapid program scale-up. Although these findings may not be generalizable to other settings, they suggest that countries endeavoring to scale up VMMC (or other HIV prevention strategies) must not only be ready to adopt VMMC but must also ensure that all the factors critical to supporting and accelerating scale-up are incorporated into the scale-up program. Finally, these findings show that the most successful national programs are those that involve country ownership of the program and that have sustained leadership at all levels to facilitate the translation of research into national policies and programs.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001133.
This study is part of a PLoS Collection of articles on VMMC (http://www.ploscollections.org/VMMC2011) and is further discussed in a PLoS Medicine Review Article by Hankins et al. (http://dx.doi.org/10.1371/journal.pmed.1001127)
Information is available from WHO, UNAIDS, and PEPFAR on all aspects of HIV/AIDS
NAM/aidsmap provides basic information about HIV/AIDS, summaries of recent research findings on HIV care and treatment, and information on male circumcision for the prevention of HIV transmission
Information is available from Avert, an international AIDS charity on many aspects of HIV/AIDS, including information on aspects of HIV prevention, and on HIV/AIDS in Africa (in English and Spanish)
The Clearinghouse on Male Circumcision, a resource provided by WHO, UNAIDS, and other international bodies, provides information and tools for VMMC policy development and program implementation
Wikipedia has a page on Diffusion of Innovations theory (note: Wikipedia is a free online encyclopedia that anyone can edit; available in several languages)
Personal stories about living with HIV/AIDS are available through Avert, through NAM/aidsmap, and through the charity website Healthtalkonline
doi:10.1371/journal.pmed.1001133
PMCID: PMC3226465  PMID: 22140368
13.  Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA 
eLife  2013;2:e00780.
Eukaryotes have two types of spliceosomes, comprised of either major (U1, U2, U4, U5, U6) or minor (U11, U12, U4atac, U6atac; <1%) snRNPs. The high conservation of minor introns, typically one amidst many major introns in several hundred genes, despite their poor splicing, has been a long-standing enigma. Here, we discovered that the low abundance minor spliceosome’s catalytic snRNP, U6atac, is strikingly unstable (t½<2 hr). We show that U6atac level depends on both RNA polymerases II and III and can be rapidly increased by cell stress-activated kinase p38MAPK, which stabilizes it, enhancing mRNA expression of hundreds of minor intron-containing genes that are otherwise suppressed by limiting U6atac. Furthermore, p38MAPK-dependent U6atac modulation can control minor intron-containing tumor suppressor PTEN expression and cytokine production. We propose that minor introns are embedded molecular switches regulated by U6atac abundance, providing a novel post-transcriptional gene expression mechanism and a rationale for the minor spliceosome’s evolutionary conservation.
DOI: http://dx.doi.org/10.7554/eLife.00780.001
eLife digest
The central dogma of biology states that genetic material, DNA, is transcribed into RNA, which is then translated into proteins. However, the genes of many organisms have stretches of non-coding DNA that interrupt the sequences that code for protein. These non-coding sequences, which are called introns, must be removed, and the remaining sequences—which are called exons—must then be joined together to produce a messenger RNA (mRNA) transcript that is ready to be translated into protein.
The process of removing the introns and joining the exons is called splicing, and it is carried out by a molecular machine called the spliceosome. However, in addition to containing typical (‘major’) introns, several hundred human genes also contain a single ‘minor’ intron, and a minor spliceosome is needed to remove it. Minor introns occur in many highly conserved genes, but they are often inefficiently spliced. This means that the resulting mRNA transcripts may not be translated into proteins—which is puzzling given that these proteins perform important roles within the cell.
The major and minor spliceosomes are composed of proteins and small non-coding RNA molecules (which, as their name suggests, are never translated in cells). Now Younis et al. shed new light on the minor spliceosome by showing that a small non-coding RNA molecule known as U6atac, which catalyzes the removal of introns by the minor spliceosome, is highly unstable in human cells. This means that U6atac is a limiting factor for the splicing of minor introns—a process that is already limited by the very low abundance of the minor spliceosome under normal conditions. However, Younis et al. found that this bottleneck could be relieved by halting the degradation of U6atac. Experiments showed that U6atac can be stabilized by a key signaling molecule, a protein kinase (called p38MAPK), which is activated in response to stress. The resulting higher levels of U6atac promoted splicing of the introns in its target mRNA transcripts, and also modulated various signaling pathways in the cells.
Together, these results imply that the minor spliceosome is used as a valve that can help cells to adapt to stress and other changes. Moreover, by helping to translate mRNA transcripts that are already present in cells, it enables proteins to be produced rapidly in response to stress, bypassing the need for a fresh round of transcription.
DOI: http://dx.doi.org/10.7554/eLife.00780.002
doi:10.7554/eLife.00780
PMCID: PMC3728624  PMID: 23908766
snRNA; U6atac; splicing; gene regulation; Human
14.  Angiotensin-Converting Enzyme I/D Polymorphism and Preeclampsia Risk: Evidence of Small-Study Bias 
PLoS Medicine  2006;3(12):e520.
Background
Inappropriate activation of the renin–angiotensin system may play a part in the development of preeclampsia. An insertion/deletion polymorphism within the angiotensin-I converting enzyme gene (ACE-I/D) has shown to be reliably associated with differences in angiotensin-converting enzyme (ACE) activity. However, previous studies of the ACE-I/D variant and preeclampsia have been individually underpowered to detect plausible genotypic risks.
Methods and Findings
A prospective case-control study was conducted in 1,711 unrelated young pregnant women (665 preeclamptic and 1,046 healthy pregnant controls) recruited from five Colombian cities. Maternal blood was obtained to genotype for the ACE-I/D polymorphism. Crude and adjusted odds ratio (OR) and 95% confidence interval (CI) using logistic regression models were obtained to evaluate the strength of the association between ACE-I/D variant and preeclampsia risk. A meta-analysis was then undertaken of all published studies to February 2006 evaluating the ACE-I/D variant in preeclampsia. An additive model (per-D-allele) revealed a null association between the ACE-I/D variant and preeclampsia risk (crude OR = 0.95 [95% CI, 0.81–1.10]) in the new case-control study. Similar results were obtained after adjusting for confounders (adjusted per-allele OR = 0.90 [95% CI, 0.77–1.06]) and using other genetic models of inheritance. A meta-analysis (2,596 cases and 3,828 controls from 22 studies) showed a per-allele OR of 1.26 (95% CI, 1.07–1.49). An analysis stratified by study size showed an attenuated OR toward the null as study size increased.
Conclusions
It is highly likely that the observed small nominal increase in risk of preeclampsia associated with the ACE D-allele is due to small-study bias, similar to that observed in cardiovascular disease. Reliable assessment of the origins of preeclampsia using a genetic approach may require the establishment of a collaborating consortium to generate a dataset of adequate size.
The observed small increase in risk of preeclampsia associated with theACE D-allele is likely to be due to small-study bias, a similar result to that observed in cardiovascular disease.
Editors' Summary
Background.
Preeclampsia is a common condition affecting pregnant women worldwide; it is defined as the presence of increased blood pressure, together with protein in the urine. Although in many women preeclampsia may never result in symptoms, other women may experience headaches, problems with their vision, swollen ankles and feet, and other problems. Sometimes, preeclampsia progresses to eclampsia, in which potentially life-threatening seizures result. The causes of preeclampsia are not well understood, but several factors are known to contribute to the risk. These factors include diabetes, high blood pressure prior to pregnancy, obesity, and first pregnancy. There is also the possibility that preeclampsia has, at least in part, a genetic basis; the condition is more likely among women whose relatives have also had it. However, no definite genetic cause has yet been confirmed.
Why Was This Study Done?
A common variant in one particular gene, ACE, which codes for the angiotensin-1 converting enzyme, has been linked with preeclampsia in a number of different studies. The protein encoded by ACE is involved in controlling blood pressure and the balance of fluid and salts in the blood. However, many of the studies supposedly linking ACE and preeclampsia were done on very few participants. Small studies are more likely to generate “false positive” findings. Therefore, a group of investigators from Colombia and the UK wanted to find out whether they could reproduce the supposed link between the ACE gene variant and preeclampsia in a large study, and also to see whether the previous studies could have been “false positives.”
What Did the Researchers Do and Find?
These investigators carried out a case-control study. This means that women with preeclampsia (“cases”) were recruited, and compared with women similar in all other respects but who did not have preeclampsia (“controls”). In total 1,711 pregnant women from five Colombian cities were studied, of whom 665 had preeclampsia and 1,046 did not. Blood was taken from each participant and used for DNA sequencing of the ACE gene. The investigators then did a statistical comparison to see whether there was any association between preeclampsia and possession of a particular variant of the ACE gene. The results showed that there was no such association. Then, the investigators did a literature search to find all previous studies that had examined a possible link between variants of the ACE gene and preeclampsia. They found 22 studies reporting data obtained from 6,424 women (these figures include the results from the investigators' own case-control study described here). The data from all of these studies were then put together into a combined analysis. This combined analysis did suggest a small increase in the risk of preeclampsia in women with one particular variant in the ACE gene. However, this result was more likely in studies with small numbers of participants. Furthermore, the earliest studies done were most likely to show an effect, with the supposed link disappearing as more and more data were collected.
What Do These Findings Mean?
The findings presented here suggest that “small study bias” may explain the discrepancy between the results of the case-control study and the combined analysis. That is, studies involving few participants are less reliable and more likely to produce false-positive results. Therefore, it is possible that the proposed link between ACE gene variants and preeclampsia is a spurious one. The investigators propose that in future, collaborative research networks will be needed to carry out rigorous research on the genetics of preeclampsia. Such initiatives will help to overcome the problem of bias that can arise from small studies.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0030520.
Information for patients from NHS Direct (UK National Health Service) about preeclampsia
Medical encyclopedia entry on preeclampsia from MedLine Plus, supplied by the US National Library of Medicine
Information from the World Health Organization and Pan American Health Organization on maternal health in the Americas
doi:10.1371/journal.pmed.0030520
PMCID: PMC1716194  PMID: 17194198
15.  Surveillance of Infection Severity: A Registry Study of Laboratory Diagnosed Clostridium difficile 
PLoS Medicine  2012;9(7):e1001279.
Iryna Schlackow and colleagues investigated whether electronic systems providing early warning of changing severity of infectious conditions can be established using routinely collected laboratory hospital data. They showed that for Clostridium difficile infection, these systems perform better than those monitoring mortality.
Background
Changing clinical impact, as virulent clones replace less virulent ones, is a feature of many pathogenic bacterial species and can be difficult to detect. Consequently, innovative techniques monitoring infection severity are of potential clinical value.
Methods and Findings
We studied 5,551 toxin-positive and 20,098 persistently toxin-negative patients tested for Clostridium difficile infection between February 1998 and July 2009 in a group of hospitals based in Oxford, UK, and investigated 28-day mortality and biomarkers of inflammation (blood neutrophil count, urea, and creatinine concentrations) collected at diagnosis using iterative sequential regression (ISR), a novel joinpoint-based regression technique suitable for serial monitoring of continuous or dichotomous outcomes. Among C. difficile toxin-positive patients in the Oxford hospitals, mean neutrophil counts on diagnosis increased from 2003, peaked in 2006–2007, and then declined; 28-day mortality increased from early 2006, peaked in late 2006–2007, and then declined. Molecular typing confirmed these changes were likely due to the ingress of the globally distributed severe C. difficile strain, ST1. We assessed the generalizability of ISR-based severity monitoring in three ways. First, we assessed and found strong (p<0.0001) associations between isolation of the ST1 severe strain and higher neutrophil counts at diagnosis in two unrelated large multi-centre studies, suggesting the technique described might be useful elsewhere. Second, we assessed and found similar trends in a second group of hospitals in Birmingham, UK, from which 5,399 cases were analysed. Third, we used simulation to assess the performance of this surveillance system given the ingress of future severe strains under a variety of assumptions. ISR-based severity monitoring allowed the detection of the severity change years earlier than mortality monitoring.
Conclusions
Automated electronic systems providing early warning of the changing severity of infectious conditions can be established using routinely collected laboratory hospital data. In the settings studied here these systems have higher performance than those monitoring mortality, at least in C. difficile infection. Such systems could have wider applicability for monitoring infections presenting in hospital.
Editor's Summary
Background
The ability of bacteria to cause infection and disease (that is, their virulence) is in part determined by bacterial genetic makeup. At any time, there is a great deal of genetic diversity within common kinds of bacteria, which naturally generate new variants all the time. Sometimes organisms arise with a genetic makeup that causes more severe infection in humans and even death. For example, in 2005, spread of a particularly virulent strain (called 027/ST1) of the toxin-producing bacterium Clostridium difficile caused a global epidemic of C. difficile infection.
Why Was This Study Done?
In health care settings, general methods of detecting changing virulence to enable the early recognition, control, and optimal management of increasingly severe infections would be highly beneficial. Changing virulence of a bacterial infection is often measured using death rates, but only a small proportion of those with infection die from it, so this may not be the most sensitive method of monitoring. Consequently, in this study the researchers investigated whether the changing virulence of C. difficile infection could be tracked by using common clinical measurements (white blood cell count, neutrophil count, blood urea, and creatinine concentrations, which reflect how unwell patients are) as the basis of an infection-severity surveillance scheme.
What Did the Researchers Do and Find?
The researchers examined all C. difficile toxin tests obtained from the microbiological lab serving hospitals in Oxford, UK, between February 1, 1998 and August 1, 2009. They also identified all inpatients aged over 18 years with a positive C. difficile test when admitted to hospitals over this time, examined their laboratory blood tests, and noted recorded deaths. The researchers used patients with C. difficile toxin-negative samples as a control group. To further validate their analysis, the researchers also undertook a similar analysis in a hospital in another UK city (Birmingham).
The researchers used statistical models to estimate changes in potential biomarkers (neutrophils, creatinine, and urea) with reference to the C. difficile 2005 global epidemic and post-infection death rates. The researchers used another statistical model (an iterative sequential regression technique) to estimate how soon any changes in biomarker/mortality trends would have been detected. Finally, to evaluate these severity-monitoring techniques, the researchers performed two simulation studies in which they assumed a more severe strain of C. difficile was introduced into a hospital.
Using these methods, the researchers found that in patients who were positive for C. difficile toxin, average neutrophil counts on diagnosis increased from 2003, peaked in 2006–2007, and then declined. They also found that 28-day deaths from C. difficile infection increased from early 2006, peaked in late 2006–2007, and then declined. Furthermore, laboratory tests (molecular typing) confirmed these changes were likely due to the severe C. difficile strain. The simulation model derived from the observed data suggested the performance of biomarker-based detection was notably higher than that of monitoring deaths post-infection.
What Do These Findings Mean?
These findings suggest that passively monitoring the severity of infection using routinely measured clinical biomarkers is feasible and can potentially detect important shifts in the virulence of human pathogens, such as C. difficile. Furthermore, such a surveillance system is superior to, and has obvious advantages over, monitoring deaths from infection — provided biomarker data is available. It could be used to provide an early trigger for more detailed investigations of patient characteristics, complemented by studies of bacterial genetic makeup, with the aim of tailoring policy and optimizing treatment of infection. Although this study monitored only one bacterial species, as changes in virulence are common to most human pathogens, this surveillance of severity technique could be applied to other organisms.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001279.
Wikipedia provides information about bacterial virulence (note that Wikipedia is a free online encyclopedia that anyone can edit; available in several languages)
The World Health Organization provides the latest news on infection outbreaks and epidemics
The Centers for Disease Control and Prevention provide information on C. difficile for health professionals and patients
Trends in C. difficile disease in England and Wales are reported by the Health Protection Agency
doi:10.1371/journal.pmed.1001279
PMCID: PMC3409138  PMID: 22859914
16.  Costs of Recruiting Couples to a Clinical Trial 
Multiple barriers contribute to the slow recruitment of participants to research studies, which in turn extends the time required to translate promising scientific discoveries into proven therapeutic interventions. A small but growing literature is developing on the extraordinary costs of recruiting participants to studies, and thereby demonstrating that underestimating the cost of participant recruitment can contribute to these recruitment problems. These recruitment challenges and costs are exacerbated when the participants’ study eligibility is determined by relatively narrowly defined illness parameters. Recruitment challenges are further compounded when dyads (two individuals engaged in a sociologically significant relationship, such as husbands and wives, siblings or extended families) must be recruited to an illness-focused study. For these latter groups, there are no data to guide researchers in how to anticipate those participant recruitment costs.
This paper describes the staff costs for a variety of strategies used to recruit participants to a randomized supportive care study for couples who were within 18 months of a prostate cancer diagnosis. Pegged to the value of the U.S. dollar for the period, the average cost of staff time was $288 per recruited and enrolled dyad, plus a promised additional $100 incentive for study retention. Within the strategies used, the staff costs per recruited dyad ranged from $ 152 to $1,688. Accrual per strategy ranged from zero to 107 enrolled couples. When asked for secondary sources of information about the study, many participants reported more than one source of study referral, reflective of the multifaceted recruitment strategies deployed. In spite of innovative, culturally competent, and broad based recruitment methods, attainment of a diverse sample was difficult to accomplish in this study. Having estimates of the actual cost of recruiting dyads to research studies can help investigators prepare realistic study budgets.
doi:10.1016/j.cct.2006.11.006
PMCID: PMC2819400  PMID: 17218166
Clinical trials; Cost; Couples; Diversity; Dyads; Prostate Cancer; Recruitment; Recruitment strategies
17.  Statistics in Brief: The Importance of Sample Size in the Planning and Interpretation of Medical Research 
The increasing volume of research by the medical community often leads to increasing numbers of contradictory findings and conclusions. Although the differences observed may represent true differences, the results also may differ because of sampling variability as all studies are performed on a limited number of specimens or patients. When planning a study reporting differences among groups of patients or describing some variable in a single group, sample size should be considered because it allows the researcher to control for the risk of reporting a false-negative finding (Type II error) or to estimate the precision his or her experiment will yield. Equally important, readers of medical journals should understand sample size because such understanding is essential to interpret the relevance of a finding with regard to their own patients. At the time of planning, the investigator must establish (1) a justifiable level of statistical significance, (2) the chances of detecting a difference of given magnitude between the groups compared, ie, the power, (3) this targeted difference (ie, effect size), and (4) the variability of the data (for quantitative data). We believe correct planning of experiments is an ethical issue of concern to the entire community.
doi:10.1007/s11999-008-0346-9
PMCID: PMC2493004  PMID: 18566874
18.  Cancer Screening: A Mathematical Model Relating Secreted Blood Biomarker Levels to Tumor Sizes  
PLoS Medicine  2008;5(8):e170.
Background
Increasing efforts and financial resources are being invested in early cancer detection research. Blood assays detecting tumor biomarkers promise noninvasive and financially reasonable screening for early cancer with high potential of positive impact on patients' survival and quality of life. For novel tumor biomarkers, the actual tumor detection limits are usually unknown and there have been no studies exploring the tumor burden detection limits of blood tumor biomarkers using mathematical models. Therefore, the purpose of this study was to develop a mathematical model relating blood biomarker levels to tumor burden.
Methods and Findings
Using a linear one-compartment model, the steady state between tumor biomarker secretion into and removal out of the intravascular space was calculated. Two conditions were assumed: (1) the compartment (plasma) is well-mixed and kinetically homogenous; (2) the tumor biomarker consists of a protein that is secreted by tumor cells into the extracellular fluid compartment, and a certain percentage of the secreted protein enters the intravascular space at a continuous rate. The model was applied to two pathophysiologic conditions: tumor biomarker is secreted (1) exclusively by the tumor cells or (2) by both tumor cells and healthy normal cells. To test the model, a sensitivity analysis was performed assuming variable conditions of the model parameters. The model parameters were primed on the basis of literature data for two established and well-studied tumor biomarkers (CA125 and prostate-specific antigen [PSA]). Assuming biomarker secretion by tumor cells only and 10% of the secreted tumor biomarker reaching the plasma, the calculated minimally detectable tumor sizes ranged between 0.11 mm3 and 3,610.14 mm3 for CA125 and between 0.21 mm3 and 131.51 mm3 for PSA. When biomarker secretion by healthy cells and tumor cells was assumed, the calculated tumor sizes leading to positive test results ranged between 116.7 mm3 and 1.52 × 106 mm3 for CA125 and between 27 mm3 and 3.45 × 105 mm3 for PSA. One of the limitations of the study is the absence of quantitative data available in the literature on the secreted tumor biomarker amount per cancer cell in intact whole body animal tumor models or in cancer patients. Additionally, the fraction of secreted tumor biomarkers actually reaching the plasma is unknown. Therefore, we used data from published cell culture experiments to estimate tumor cell biomarker secretion rates and assumed a wide range of secretion rates to account for their potential changes due to field effects of the tumor environment.
Conclusions
This study introduced a linear one-compartment mathematical model that allows estimation of minimal detectable tumor sizes based on blood tumor biomarker assays. Assuming physiological data on CA125 and PSA from the literature, the model predicted detection limits of tumors that were in qualitative agreement with the actual clinical performance of both biomarkers. The model may be helpful in future estimation of minimal detectable tumor sizes for novel proteomic biomarker assays if sufficient physiologic data for the biomarker are available. The model may address the potential and limitations of tumor biomarkers, help prioritize biomarkers, and guide investments into early cancer detection research efforts.
Sanjiv Gambhir and colleagues describe a linear one-compartment mathematical model that allows estimation of minimal detectable tumor sizes based on blood tumor biomarker assays.
Editors' Summary
Background.
Cancers—disorganized masses of cells that can occur in any tissue—develop when cells acquire genetic changes that allow them to grow uncontrollably and to spread around the body (metastasize). If a cancer (tumor) is detected when it is small, surgery can often provide a cure. Unfortunately, many cancers (particularly those deep inside the body) are not detected until they are large enough to cause pain or other symptoms by pressing against surrounding tissue. By this time, it may be impossible to remove the original tumor surgically and there may be metastases scattered around the body. In such cases, radiotherapy and chemotherapy can sometimes help, but the outlook for patients whose cancers are detected late is often poor. Consequently, researchers are trying to develop early detection tests for different types of cancer. Many tumors release specific proteins—“cancer biomarkers”—into the blood and the hope is that it might be possible to find sets of blood biomarkers that detect cancers when they are still small and thus save many lives.
Why Was This Study Done?
For most biomarkers, it is not known how the amount of protein detected in the blood relates to tumor size or how sensitive the assays for biomarkers must be to improve patient survival. In this study, the researchers develop a “linear one-compartment” mathematical model to predict how large tumors need to be before blood biomarkers can be used to detect them and test this model using published data on two established cancer biomarkers—CA125 and prostate-specific antigen (PSA). CA125 is used to monitor the progress of patients with ovarian cancer after treatment; ovarian cancer is rarely diagnosed in its early stages and only one-fourth of women with advanced disease survive for 5 y after diagnosis. PSA is used to screen for prostate cancer and has increased the detection of this cancer in its early stages when it is curable.
What Did the Researchers Do and Find?
To develop a model that relates secreted blood biomarker levels to tumor sizes, the researchers assumed that biomarkers mix evenly throughout the patient's blood, that cancer cells secrete biomarkers into the fluid that surrounds them, that 0.1%–20% of these secreted proteins enter the blood at a continuous rate, and that biomarkers are continuously removed from the blood. The researchers then used their model to calculate the smallest tumor sizes that might be detectable with these biomarkers by feeding in existing data on CA125 and on PSA, including assay detection limits and the biomarker secretion rates of cancer cells growing in dishes. When only tumor cells secreted the biomarker and 10% of the secreted biomarker reach the blood, the model predicted that ovarian tumors between 0.11 mm3 (smaller than a grain of salt) and nearly 4,000 mm3 (about the size of a cherry) would be detectable by measuring CA125 blood levels (the range was determined by varying the amount of biomarker secreted by the tumor cells and the assay sensitivity); for prostate cancer, the detectable tumor sizes ranged from similar lower size to about 130 mm3 (pea-sized). However, healthy cells often also secrete small quantities of cancer biomarkers. With this condition incorporated into the model, the estimated detectable tumor sizes (or total tumor burden including metastases) ranged between grape-sized and melon-sized for ovarian cancers and between pea-sized to about grapefruit-sized for prostate cancers.
What Do These Findings Mean?
The accuracy of the calculated tumor sizes provided by the researchers' mathematical model is limited by the lack of data on how tumors behave in the human body and by the many assumptions incorporated into the model. Nevertheless, the model predicts detection limits for ovarian and prostate cancer that broadly mirror the clinical performance of both biomarkers. Somewhat worryingly, the model also indicates that a tumor may have to be very large for blood biomarkers to reveal its presence, a result that could limit the clinical usefulness of biomarkers, especially if they are secreted not only by tumor cells but also by healthy cells. Given this finding, as more information about how biomarkers behave in the human body becomes available, this model (and more complex versions of it) should help researchers decide which biomarkers are likely to improve early cancer detection and patient outcomes.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0050170.
The US National Cancer Institute provides a brief description of what cancer is and how it develops and a fact sheet on tumor markers; it also provides information on all aspects of ovarian and prostate cancer for patients and professionals, including information on screening and testing (in English and Spanish)
The UK charity Cancerbackup also provides general information about cancer and more specific information about ovarian and prostate cancer, including the use of CA125 and PSA for screening and follow-up
The American Society of Clinical Oncology offers a wide range of information on various cancer types, including online published articles on the current status of cancer diagnosis and management from the educational book developed by the annual meeting faculty and presenters. Registration is mandatory, but information is free
doi:10.1371/journal.pmed.0050170
PMCID: PMC2517618  PMID: 18715113
19.  Eurocan plus report: feasibility study for coordination of national cancer research activities 
Summary
The EUROCAN+PLUS Project, called for by the European Parliament, was launched in October 2005 as a feasibility study for coordination of national cancer research activities in Europe. Over the course of the next two years, the Project process organized over 60 large meetings and countless smaller meetings that gathered in total over a thousand people, the largest Europe–wide consultation ever conducted in the field of cancer research.
Despite a strong tradition in biomedical science in Europe, fragmentation and lack of sustainability remain formidable challenges for implementing innovative cancer research and cancer care improvement. There is an enormous duplication of research effort in the Member States, which wastes time, wastes money and severely limits the total intellectual concentration on the wide cancer problem. There is a striking lack of communication between some of the biggest actors on the European scene, and there are palpable tensions between funders and those researchers seeking funds.
It is essential to include the patients’ voice in the establishment of priority areas in cancer research at the present time. The necessity to have dialogue between funders and scientists to establish the best mechanisms to meet the needs of the entire community is evident. A top priority should be the development of translational research (in its widest form), leading to the development of effective and innovative cancer treatments and preventive strategies. Translational research ranges from bench–to–bedside innovative cancer therapies and extends to include bringing about changes in population behaviours when a risk factor is established.
The EUROCAN+PLUS Project recommends the creation of a small, permanent and independent European Cancer Initiative (ECI). This should be a model structure and was widely supported at both General Assemblies of the project. The ECI should assume responsibility for stimulating innovative cancer research and facilitating processes, becoming the common voice of the cancer research community and serving as an interface between the cancer research community and European citizens, patients’ organizations, European institutions, Member States, industry and small and medium enterprises (SMEs), putting into practice solutions aimed at alleviating barriers to collaboration and coordination of cancer research activities in the European Union, and dealing with legal and regulatory issues. The development of an effective ECI will require time, but this entity should be established immediately. As an initial step, coordination efforts should be directed towards the creation of a platform on translational research that could encompass (1) coordination between basic, clinical and epidemiological research; (2) formal agreements of co–operation between comprehensive cancer centres and basic research laboratories throughout Europe and (3) networking between funding bodies at the European level.
The European Parliament and its instruments have had a major influence in cancer control in Europe, notably in tobacco control and in the implementation of effective population–based screening. To make further progress there is a need for novelty and innovation in cancer research and prevention in Europe, and having a platform such as the ECI, where those involved in all aspects of cancer research can meet, discuss and interact, is a decisive development for Europe.
Executive Summary
Cancer is one of the biggest public health crises facing Europe in the 21st century—one for which Europe is currently not prepared nor preparing itself. Cancer is a major cause of death in Europe with two million casualties and three million new cases diagnosed annually, and the situation is set to worsen as the population ages.
These facts led the European Parliament, through the Research Directorate-General of the European Commission, to call for initiatives for better coordination of cancer research efforts in the European Union. The EUROCAN+PLUS Project was launched in October 2005 as a feasibility study for coordination of national cancer research activities. Over the course of the next two years, the Project process organized over 60 large meetings and countless smaller meetings that gathered in total over a thousand people. In this respect, the Project became the largest Europe-wide consultation ever conducted in the field of cancer research, implicating researchers, cancer centres and hospitals, administrators, healthcare professionals, funding agencies, industry, patients’ organizations and patients.
The Project first identified barriers impeding research and collaboration in research in Europe. Despite a strong tradition in biomedical science in Europe, fragmentation and lack of sustainability remain the formidable challenges for implementing innovative cancer research and cancer care improvement. There is an enormous duplication of research effort in the Member States, which wastes time, wastes money and severely limits the total intellectual concentration on the wide cancer problem. There is a striking lack of communication between some of the biggest actors on the European scene, and there are palpable tensions between funders and those researchers seeking funds.
In addition, there is a shortage of leadership, a multiplicity of institutions each focusing on its own agenda, sub–optimal contact with industry, inadequate training, non–existent career paths, low personnel mobility in research especially among clinicians and inefficient funding—all conspiring against efficient collaboration in cancer care and research. European cancer research today does not have a functional translational research continuum, that is the process that exploits biomedical research innovations and converts them into prevention methods, diagnostic tools and therapies. Moreover, epidemiological research is not integrated with other types of cancer research, and the implementation of the European Directives on Clinical Trials 1 and on Personal Data Protection 2 has further slowed the innovation process in Europe. Furthermore, large inequalities in health and research exist between the EU–15 and the New Member States.
The picture is not entirely bleak, however, as the European cancer research scene presents several strengths, such as excellent basic research and clinical research and innovative etiological research that should be better exploited.
When considering recommendations, several priority dimensions had to be retained. It is essential that proposals include actions and recommendations that can benefit all Member States of the European Union and not just States with the elite centres. It is also essential to have a broader patient orientation to help provide the knowledge to establish cancer control possibilities when we exhaust what can be achieved by the implementation of current knowledge. It is vital that the actions proposed can contribute to the Lisbon Strategy to make Europe more innovative and competitive in (cancer) research.
The Project participants identified six areas for which consensus solutions should be implemented in order to obtain better coordination of cancer research activities. The required solutions are as follows. The proactive management of innovation, detection, facilitation of collaborations and maintenance of healthy competition within the European cancer research community.The establishment of an exchange portal of information for health professionals, patients and policy makers.The provision of guidance for translational and clinical research including the establishment of a translational research platform involving comprehensive cancer centres and cancer research centres.The coordination of calls and financial management of cancer research projects.The construction of a ‘one–stop shop’ as a contact interface between the industry, small and medium enterprises, scientists and other stakeholders.The support of greater involvement of healthcare professionals in translational research and multidisciplinary training.
In the course of the EUROCAN+PLUS consultative process, several key collaborative projects emerged between the various groups and institutes engaged in the consultation. There was a collaboration network established with Europe’s leading Comprehensive Cancer Centres; funding was awarded for a closer collaboration of Owners of Cancer Registries in Europe (EUROCOURSE); there was funding received from FP7 for an extensive network of leading Biological Resource Centres in Europe (BBMRI); a Working Group identified the special needs of Central, Eastern and South–eastern Europe and proposed a remedy (‘Warsaw Declaration’), and the concept of developing a one–stop shop for dealing with academia and industry including the Innovative Medicines Initiative (IMI) was discussed in detail.
Several other dimensions currently lacking were identified. There is an absolute necessity to include the patients’ voice in the establishment of priority areas in cancer research at the present time. It was a salutary lesson when it was recognized that all that is known about the quality of life of the cancer patient comes from the experience of a tiny proportion of cancer patients included in a few clinical trials. The necessity to have dialogue between funders and scientists to establish the best mechanisms to meet the needs of the entire community was evident. A top priority should be the development of translational research (in its widest form) and the development of effective and innovative cancer treatments and preventative strategies in the European Union. Translational research ranges from bench-to-bedside innovative cancer therapies and extends to include bringing about changes in population behaviours when a risk factor is established.
Having taken note of the barriers and the solutions and having examined relevant examples of existing European organizations in the field, it was agreed during the General Assembly of 19 November 2007 that the EUROCAN+PLUS Project had to recommend the creation of a small, permanent and neutral ECI. This should be a model structure and was widely supported at both General Assemblies of the project. The proposal is based on the successful model of the European Molecular Biology Organisation (EMBO), and its principal aims include providing a forum where researchers from all backgrounds and from all countries can meet with members of other specialities including patients, nurses, clinicians, funders and scientific administrators to develop priority programmes to make Europe more competitive in research and more focused on the cancer patient.
The ECI should assume responsibility for: stimulating innovative cancer research and facilitating processes;becoming the common voice of the cancer research community and serving as an interface between the cancer research community and European citizens, patients’ and organizations;European institutions, Member States, industry and small and medium enterprises;putting into practice the aforementioned solutions aimed at alleviating barriers and coordinating cancer research activities in the EU;dealing with legal and regulatory issues.
Solutions implemented through the ECI will lead to better coordination and collaboration throughout Europe, more efficient use of resources, an increase in Europe’s attractiveness to the biomedical industry and better quality of cancer research and education of health professionals.
The Project considered that European legal instruments currently available were inadequate for addressing many aspects of the barriers identified and for the implementation of effective, lasting solutions. Therefore, the legal environment that could shelter an idea like the ECI remains to be defined but should be done so as a priority. In this context, the initiative of the European Commission for a new legal entity for research infrastructure might be a step in this direction. The development of an effective ECI will require time, but this should be established immediately. As an initial step, coordination efforts should be directed towards the creation of a platform on translational research that could encompass: (1) coordination between basic, clinical and epidemiological research; (2) formal agreements of co-operation between comprehensive cancer centres and basic research laboratories throughout Europe; (3) networking between funding bodies at the European level. Another topic deserving immediate attention is the creation of a European database on cancer research projects and cancer research facilities.
Despite enormous progress in cancer control in Europe during the past two decades, there was an increase of 300,000 in the number of new cases of cancer diagnosed between 2004 and 2006. The European Parliament and its instruments have had a major influence in cancer control, notably in tobacco control and in the implementation of effective population–based screening. To make further progress there is a need for novelty and innovation in cancer research and prevention in Europe, and having a platform such as the ECI, where those involved in all aspects of cancer research can meet, discuss and interact, is a decisive development for Europe.
doi:10.3332/ecancer.2011.84
PMCID: PMC3234055  PMID: 22274749
20.  Representation and Misrepresentation of Scientific Evidence in Contemporary Tobacco Regulation: A Review of Tobacco Industry Submissions to the UK Government Consultation on Standardised Packaging 
PLoS Medicine  2014;11(3):e1001629.
Selda Ulucanlar and colleagues analyze submissions by two tobacco companies to the UK government consultation on standardized packaging.
Please see later in the article for the Editors' Summary
Background
Standardised packaging (SP) of tobacco products is an innovative tobacco control measure opposed by transnational tobacco companies (TTCs) whose responses to the UK government's public consultation on SP argued that evidence was inadequate to support implementing the measure. The government's initial decision, announced 11 months after the consultation closed, was to wait for ‘more evidence’, but four months later a second ‘independent review’ was launched. In view of the centrality of evidence to debates over SP and TTCs' history of denying harms and manufacturing uncertainty about scientific evidence, we analysed their submissions to examine how they used evidence to oppose SP.
Methods and Findings
We purposively selected and analysed two TTC submissions using a verification-oriented cross-documentary method to ascertain how published studies were used and interpretive analysis with a constructivist grounded theory approach to examine the conceptual significance of TTC critiques. The companies' overall argument was that the SP evidence base was seriously flawed and did not warrant the introduction of SP. However, this argument was underpinned by three complementary techniques that misrepresented the evidence base. First, published studies were repeatedly misquoted, distorting the main messages. Second, ‘mimicked scientific critique’ was used to undermine evidence; this form of critique insisted on methodological perfection, rejected methodological pluralism, adopted a litigation (not scientific) model, and was not rigorous. Third, TTCs engaged in ‘evidential landscaping’, promoting a parallel evidence base to deflect attention from SP and excluding company-held evidence relevant to SP. The study's sample was limited to sub-sections of two out of four submissions, but leaked industry documents suggest at least one other company used a similar approach.
Conclusions
The TTCs' claim that SP will not lead to public health benefits is largely without foundation. The tools of Better Regulation, particularly stakeholder consultation, provide an opportunity for highly resourced corporations to slow, weaken, or prevent public health policies.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Every year, about 6 million people die from tobacco-related diseases and, if current trends continue, annual tobacco-related deaths will increase to more than 8 million by 2030. To reduce this loss of life, national and international bodies have drawn up various conventions and directives designed to implement tobacco control measures such as the adoption of taxation policies aimed at reducing tobacco consumption and bans on tobacco advertising, promotion, and sponsorship. One innovative but largely unused tobacco control measure is standardised packaging of tobacco products. Standardised packaging aims to prevent the use of packaging as a marketing tool by removing all brand imagery and text (other than name) and by introducing packs of a standard shape and colour that include prominent pictorial health warnings. Standardised packaging was first suggested as a tobacco control measure in 1986 but has been consistently opposed by the tobacco industry.
Why Was This Study Done?
The UK is currently considering standardised packaging of tobacco products. In the UK, Better Regulation guidance obliges officials to seek the views of stakeholders, including corporations, on the government's cost and benefit estimates of regulatory measures such as standardised packaging and on the evidence underlying these estimates. In response to a public consultation about standardised packaging in July 2013, which considered submissions from several transnational tobacco companies (TTCs), the UK government announced that it would wait for the results of the standardised packaging legislation that Australia adopted in December 2012 before making its final decision about this tobacco control measure. Parliamentary debates and media statements have suggested that doubt over the adequacy of the evidence was the main reason for this ‘wait and see’ decision. Notably, TTCs have a history of manufacturing uncertainty about the scientific evidence related to the harms of tobacco. Given the centrality of evidence to the debate about standardised packaging, in this study, the researchers analyse submissions made by two TTCs, British American Tobacco (BAT) and Japan Tobacco International (JTI), to the first UK consultation on standardised packaging (a second review is currently underway and will report shortly) to examine how TTCs used evidence to oppose standardised packaging.
What Did the Researchers Do and Find?
The researchers analysed sub-sections of two of the four TTC submissions (those submitted by BAT and JTI) made to the public consultation using verification-oriented cross-documentary analysis, which compared references made to published sources with the original sources to ascertain how these sources had been used, and interpretative analysis to examine the conceptual significance of TTC critiques of the evidence on standardised packaging. The researchers report that the companies' overall argument was that the evidence base in support of standardised packaging was seriously flawed and did not warrant the introduction of such packaging. The researchers identified three ways in which the TTC reports misrepresented the evidence base. First, the TTCs misquoted published studies, thereby distorting the main messages of these studies. For example, the TTCs sometimes omitted important qualifying information when quoting from published studies. Second, the TTCs undermined evidence by employing experts to review published studies for methodological rigor and value in ways that did not conform to normal scientific critique approaches (‘mimicked scientific critique’). So, for example, the experts considered each piece of evidence in isolation for its ability to support standardised packaging rather than considering the cumulative weight of the evidence. Finally, the TTCs engaged in ‘evidential landscaping’. That is, they promoted research that deflected attention from standardised packaging (for example, research into social explanations of smoking behaviour) and omitted internal industry research on the role of packaging in marketing.
What Do These Findings Mean?
These findings suggest that the TTC critique of the evidence in favour of standardised packaging that was presented to the UK public consultation on this tobacco control measure is highly misleading. However, because the researchers' analysis only considered subsections of the submissions from two TTCs, these findings may not be applicable to the other submissions or to other TTCs. Moreover, their analysis only considered the efforts made by TTCs to influence public health policy and not the effectiveness of these efforts. Nevertheless, these findings suggest that the claim of TTCs that standardised packaging will not lead to public health benefits is largely without foundation. More generally, these findings highlight the possibility that the tools of Better Regulation, particularly stakeholder consultation, provide an opportunity for wealthy corporations to slow, weaken, or prevent the implementation of public health policies.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001629.
The World Health Organization provides information about the dangers of tobacco (in several languages) and an article about first experiences with Australia's tobacco plain packaging law; for information about the tobacco industry's influence on policy, see the 2009 World Health Organization report ‘Tobacco industry interference with tobacco control’
A UK parliamentary briefing on standardised packaging of tobacco products, a press release about the consultation, and a summary report of the consultation are available; the ideas behind the UK's Better Regulation guidance are described in a leaflet produced by the Better Regulation Task Force
Cancer Research UK (CRUK) has a web page with information on standardised packaging and includes videos
Wikipedia has a page on standardised packaging of tobacco products (note: Wikipedia is a free online encyclopaedia that anyone can edit; available in several languages)
The UK Centre for Tobacco Control Studies is a network of UK universities that undertakes original research, policy development, advocacy, and teaching and training in the field of tobacco control
TobaccoTactics.org, an online resource managed by the University of Bath, provides up-to-date information on the tobacco industry and the tactics it uses to influence tobacco regulation
SmokeFree, a website provided by the UK National Health Service, offers advice on quitting smoking and includes personal stories from people who have stopped smoking
Smokefree.gov, from the US National Cancer Institute, offers online tools and resources to help people quit smoking
doi:10.1371/journal.pmed.1001629
PMCID: PMC3965396  PMID: 24667150
21.  Procedures and Criteria for the regulation of innovative non-medicinal technologies into the benefit catalogue of solidly financed health care insurances 
Because great interest in an efficient range of effective medicinal innovations and achievements has arisen, many countries have introduced procedures to regulate the adoption of innovative non-medicinal technologies into the benefit catalogue of solidly financed health care insurances. With this as a background, this report will describe procedures for the adoption of innovative non-medicinal technologies by solidly financed health care insurances in Germany, England, Australia and Switzerland. This report was commissioned by the German Agency for Health Technology Assessment at the German Institute for Medical Documentation and Information.
In order to find the relevant literature and information, systematic literature research, a hand search and a written survey were carried out. All the selected documents (chosen according to defined criteria for inclusion and exclusion) were qualitatively evaluated, summarized and presented on a chart using a framework developed for this purpose.
All the countries in this report require that some innovative non-medicinal technologies undergo evaluation by a central governing body. This evaluation is a prerequisite for adoption into the benefit catalogue. The process of evaluation can differ (e. g. the people and institutions concerned, the division of the synthesis of evidence and overall evaluation, processing the evidence). Similarities do exist, such as the size and composition of the governing bodies or the overreaching criteria according to which institutions must make their recommendations. This is how all the countries examined in this report determine how the benefits and effectiveness of the innovations, as well as their cost-effectiveness, can be chosen as criteria for the evaluation.
Furthermore, there are many criteria which differ from country to country (social and ethical aspects, possible effects on the health system, etc.) and which are also relevant to an evaluation. The preferred types of clinical studies for these evaluations are randomized controlled trials. However, all institutions do allow for other types of evidence (e. g. expert opinion) when no other study types of a higher evidence level are available. In addition, all the countries are willing to allow unpublished or confidential information (e. g. from manufacturers) to be included in an evaluation.
It is important to remember that the decisions made by the central governing bodies do not necessarily become conditions for the introduction of innovative non-medicinal technologies. There is a host of other requirements which determine how these innovations can be introduced. This means that a large number of non-medicinal technologies make it into the medical care system via these other decision-making processes. Often, these innovations are unevaluated and differ from region to region.
Every country has established a system of observation and registration for medicinal products. These systems are meant to document any incidents with the innovations and to confer responsibility on certain organizations. All in all, no country has a central authority which systematically investigates the effects of newly introduced innovative non-medicinal technologies on medical care in general. However, Australia and England both carry out a review of innovations in some areas (e. g. by means of special commissions).
In principle, the starting point for improving regulations of innovative non-medicinal technologies lies in the extension of transparency, the shortening of decision-making time (especially the central decision-making processes), the further development of evaluation methods, more flexibility and increased capacity in the governing bodies’ decision-making processes and also, if needed, in the creation of a single authority to act as contact for people who are interested in introducing an innovation into the benefit catalogue.
More research is required, especially in the area of decentralized decision-makers and how they actually decide whether or not to introduce innovative technologies into the core care system (methods, criteria, etc.). In view of this, it would also be interesting to see how the application of innovations actually happens in practice once their adoption has been approved by the corresponding governing bodies.
PMCID: PMC3011333  PMID: 21289947
22.  Does Raising Type 1 Error Rate Improve Power to Detect Interactions in Linear Regression Models? A Simulation Study 
PLoS ONE  2013;8(8):e71079.
Introduction
Statistical interactions are a common component of data analysis across a broad range of scientific disciplines. However, the statistical power to detect interactions is often undesirably low. One solution is to elevate the Type 1 error rate so that important interactions are not missed in a low power situation. To date, no study has quantified the effects of this practice on power in a linear regression model.
Methods
A Monte Carlo simulation study was performed. A continuous dependent variable was specified, along with three types of interactions: continuous variable by continuous variable; continuous by dichotomous; and dichotomous by dichotomous. For each of the three scenarios, the interaction effect sizes, sample sizes, and Type 1 error rate were varied, resulting in a total of 240 unique simulations.
Results
In general, power to detect the interaction effect was either so low or so high at α = 0.05 that raising the Type 1 error rate only served to increase the probability of including a spurious interaction in the model. A small number of scenarios were identified in which an elevated Type 1 error rate may be justified.
Conclusions
Routinely elevating Type 1 error rate when testing interaction effects is not an advisable practice. Researchers are best served by positing interaction effects a priori and accounting for them when conducting sample size calculations.
doi:10.1371/journal.pone.0071079
PMCID: PMC3745431  PMID: 23976980
23.  Primary Prevention of Cannabis Use: A Systematic Review of Randomized Controlled Trials 
PLoS ONE  2013;8(1):e53187.
A systematic review of primary prevention was conducted for cannabis use outcomes in youth and young adults. The aim of the review was to develop a comprehensive understanding of prevention programming by assessing universal, targeted, uni-modal, and multi-modal approaches as well as individual program characteristics. Twenty-eight articles, representing 25 unique studies, identified from eight electronic databases (EMBASE, MEDLINE, CINAHL, ERIC, PsycINFO, DRUG, EBM Reviews, and Project CORK), were eligible for inclusion. Results indicated that primary prevention programs can be effective in reducing cannabis use in youth populations, with statistically significant effect sizes ranging from trivial (0.07) to extremely large (5.26), with the majority of significant effect sizes being trivial to small. Given that the preponderance of significant effect sizes were trivial to small and that percentages of statistically significant and non-statistically significant findings were often equivalent across program type and individual components, the effectiveness of primary prevention for cannabis use should be interpreted with caution. Universal multi-modal programs appeared to outperform other program types (i.e, universal uni-modal, targeted multi-modal, targeted unimodal). Specifically, universal multi-modal programs that targeted early adolescents (10–13 year olds), utilised non-teacher or multiple facilitators, were short in duration (10 sessions or less), and implemented boosters sessions were associated with large median effect sizes. While there were studies in these areas that contradicted these results, the results highlight the importance of assessing the interdependent relationship of program components and program types. Finally, results indicated that the overall quality of included studies was poor, with an average quality rating of 4.64 out of 9. Thus, further quality research and reporting and the development of new innovative programs are required.
doi:10.1371/journal.pone.0053187
PMCID: PMC3543459  PMID: 23326396
24.  Configuring Balanced Scorecards for Measuring Health System Performance: Evidence from 5 Years' Evaluation in Afghanistan 
PLoS Medicine  2011;8(7):e1001066.
Anbrasi Edward and colleagues report the results of a balanced scorecard performance system used to examine 29 key performance indicators over a 5-year period in Afghanistan, between 2004 and 2008.
Background
In 2004, Afghanistan pioneered a balanced scorecard (BSC) performance system to manage the delivery of primary health care services. This study examines the trends of 29 key performance indicators over a 5-year period between 2004 and 2008.
Methods and Findings
Independent evaluations of performance in six domains were conducted annually through 5,500 patient observations and exit interviews and 1,500 provider interviews in >600 facilities selected by stratified random sampling in each province. Generalized estimating equation (GEE) models were used to assess trends in BSC parameters. There was a progressive improvement in the national median scores scaled from 0–100 between 2004 and 2008 in all six domains: patient and community satisfaction of services (65.3–84.5, p<0.0001); provider satisfaction (65.4–79.2, p<0.01); capacity for service provision (47.4–76.4, p<0.0001); quality of services (40.5–67.4, p<0.0001); and overall vision for pro-poor and pro-female health services (52.0–52.6). The financial domain also showed improvement until 2007 (84.4–95.7, p<0.01), after which user fees were eliminated. By 2008, all provinces achieved the upper benchmark of national median set in 2004.
Conclusions
The BSC has been successfully employed to assess and improve health service capacity and service delivery using performance benchmarking during the 5-year period. However, scorecard reconfigurations are needed to integrate effectiveness and efficiency measures and accommodate changes in health systems policy and strategy architecture to ensure its continued relevance and effectiveness as a comprehensive health system performance measure. The process of BSC design and implementation can serve as a valuable prototype for health policy planners managing performance in similar health care contexts.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Traditionally, the performance of a health system (the complete network of health care agencies, facilities, and providers in a defined geographical region) has been measured in terms of health outcomes: how many people have been treated, how many got better, and how many died. But, nowadays, with increased demand for improved governance and accountability, policy makers are seeking comprehensive performance measures that show in detail how innovations designed to strengthen health systems are affecting service delivery and health outcomes. One such performance measure is the “balanced scorecard,” an integrated management and measurement tool that enables organizations to clarify their vision and strategy and translate them into action. The balanced scorecard—essentially a list of key performance indicators and performance benchmarks in several domains—was originally developed for industry but is now becoming a popular strategic management tool in the health sector. For example, balanced scorecards have been successfully integrated into the Dutch and Italian public health care systems.
Why Was This Study Done?
Little is known about the use of balanced scorecards in the national public health care systems of developing countries but the introduction of performance management into health system reform in fragile states in particular (developing countries where the state fails to perform the fundamental functions necessary to meet its citizens' basic needs and expectations) could help to promote governance and leadership, and facilitate essential policy changes. One fragile state that has introduced the balanced scorecard system for public health care management is Afghanistan, which emerged from decades of conflict in 2002 with some of the world's worst health indicators. To deal with an extremely high burden of disease, the Ministry of Public Health (MOPH) designed a Basic Package of Health Services (BPHS), which is delivered by nongovernmental organizations and MOPH agencies. In 2004, the MOPH introduced the National Health Service Performance Assessment (NHSPA), an annual country-wide assessment of service provision and patient satisfaction and pioneered a balanced scorecard, which uses data collected in the NHSPA, to manage the delivery of primary health care services. In this study, the researchers examine the trends between 2004 and 2008 of the 29 key performance indicators in six domains included in this balanced scorecard, and consider the potential and limitations of the scorecard as a management tool to measure and improve health service delivery in Afghanistan and other similar countries.
What Did the Researchers Do and Find?
Each year of the study, a random sample of 25 facilities (district hospitals and comprehensive and basic health centers) in 28 of Afghanistan's 34 provinces was chosen (one province did not have functional facilities in 2004 and the other five missing provinces were inaccessible because of ongoing conflicts). NHSPA surveyors collected approximately 5,000 patient observations, 5,000 exit interviews with patients or their caregivers, and 1,500 health provider interviews by observing consultations involving five children under 5 years old and five patients over 5 years old in each facility. The researchers then used this information to evaluate the key performance indicators in the balanced scorecard and a statistical method called generalized estimating equation modeling to assess trends in these indicators. They report that there was a progressive improvement in national average scores in all six domains (patients and community satisfaction with services, provider satisfaction, capacity for service provision, quality of services, overall vision for pro-poor and pro-female health services, and financial systems) between 2004 and 2008.
What Do These Findings Mean?
These findings suggest that the balanced scorecard was successfully used to improve health system capacity and service delivery through performance benchmarking over the 5-year study period. Importantly, the use of the balanced scorecard helped to show the effects of investments, facilitate policy change, and create a more evidence-based decision-making culture in Afghanistan's primary health care system. However, the researchers warn that the continuing success of the balanced scorecard in Afghanistan will depend on its ability to accommodate changes in health systems policy. Furthermore, reconfigurations of the scorecard are needed to include measures of the overall effectiveness and efficiency of the health system such as mortality rates. More generally, the researchers conclude that the balanced scorecard offers a promising measure of health system performance that could be used to examine the effectiveness of health care strategies and innovations in other fragile and developing countries.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001066.
A 2010 article entitled An Afghan Success Story: The Balanced Scorecard and Improved Health Services in The Globe, a newsletter produced by the Department of International Health at the John Hopkins Bloomberg School of Public Health, provides a detailed description of the balanced scorecard used in this study
Wikipedia has a page on health systems and on balanced scorecards (note that Wikipedia is a free online encyclopedia that anyone can edit; available in several languages)
The World Health Organization country profile of Afghanistan provides information on the country's health system and burden of disease (in several languages)
doi:10.1371/journal.pmed.1001066
PMCID: PMC3144209  PMID: 21814499
25.  Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies 
PLoS ONE  2010;5(9):e12336.
High-throughput post-genomic studies are now routinely and promisingly investigated in biological and biomedical research. The main statistical approach to select genes differentially expressed between two groups is to apply a t-test, which is subject of criticism in the literature. Numerous alternatives have been developed based on different and innovative variance modeling strategies. However, a critical issue is that selecting a different test usually leads to a different gene list. In this context and given the current tendency to apply the t-test, identifying the most efficient approach in practice remains crucial. To provide elements to answer, we conduct a comparison of eight tests representative of variance modeling strategies in gene expression data: Welch's t-test, ANOVA [1], Wilcoxon's test, SAM [2], RVM [3], limma [4], VarMixt [5] and SMVar [6]. Our comparison process relies on four steps (gene list analysis, simulations, spike-in data and re-sampling) to formulate comprehensive and robust conclusions about test performance, in terms of statistical power, false-positive rate, execution time and ease of use. Our results raise concerns about the ability of some methods to control the expected number of false positives at a desirable level. Besides, two tests (limma and VarMixt) show significant improvement compared to the t-test, in particular to deal with small sample sizes. In addition limma presents several practical advantages, so we advocate its application to analyze gene expression data.
doi:10.1371/journal.pone.0012336
PMCID: PMC2933223  PMID: 20838429

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