bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of Fluoroneplanocin A
Authors: Jeong Lak Shin , Tosh Dilip K. , Choi Won Jun , Pal Shantana
Published: October 2008

Fluoroneplanocin A, designed as a potent mechanism‐based irreversible inhibitor of S‐adenosylhomocysteine hydrolase (SAH), is synthesized from D‐ribose via a key D‐cyclopentenone intermediate. This intermediate is synthesized using a stereoselective Grignard reaction, a ring‐closing metathesis (RCM) reaction, and oxidative rearrangement as key steps. Curr. Protoc. Nucleic Acid Chem. 34:14.6.1‐14.6.18. © 2008 by John Wiley & Sons, Inc.
Matrix Metalloproteinases
Authors: Birkedal‐Hansen Henning , Yamada Susan , Windsor Jack , Pollard Anne Havernose , Lyons Guy , Stetler‐Stevenson William , Birkedal‐Hansen Bente
Published: October 2008

Matrix metalloproteinases are a class of enzymes that play an important role in the remodeling of the extracellular matrix in development and cancer metastasis. This unit describes a set of methods—cell‐mediated dissolution of type‐1 collagen fibrils, direct and reverse zymography, enzyme capture based on α2‐macroglobulin and TIMP‐1 and ‐2, and demonstration of cryptic thiol groups in metalloproteinase precursors—that are used to characterize the functions of matrix metalloproteinases and their inhibitors. Curr. Protoc. Cell Biol. 40:10.8.1‐10.8.23. © 2008 by John Wiley & Sons, Inc.
Use of Hyaluronan‐Derived Hydrogels for Three‐Dimensional Cell Culture and Tumor Xenografts
Authors: Serban Monica A. , Scott Anna , Prestwich Glenn D.
Published: October 2008

The practice of in vitro three‐dimensional (3‐D) cell culture has lagged behind the realization that classical two‐dimensional (2‐D) culture on plastic surfaces fails to mirror normal cell biology. Biologically, a complex network of proteins and proteoglycans that constitute the extracellular matrix (ECM) surrounds every cell. To recapitulate the normal cellular behavior, scaffolds (ECM analogs) that reconstitute the essential biological cues are required. This unit describes the 3‐D cell culture and tumor engineering applications of Extracel, a novel semisynthetic ECM (sECM), based on cross‐linked derivatives of hyaluronan and gelatin. A simplified cell encapsulation and pseudo‐3‐D culturing (on top of hydrogels) protocol is provided. In addition, the use of this sECM as a vehicle to obtain tumor xenografts with improved take rates and tumor growth is presented. These engineered tumors can be used to evaluate anticancer therapies under physiologically relevant conditions. Curr. Protoc. Cell Biol. 40:10.14.1‐10.14.21. © 2008 by John Wiley & Sons, Inc.
Analysis of Endocytic Trafficking by Single‐Cell Fluorescence Ratio Imaging
Authors: Barriere Herve , Lukacs Gergely L.
Published: October 2008

The post‐endocytic sorting of internalized membrane proteins plays a critical role in numerous physiological processes, including receptor desensitization, degradation of non‐native plasma membrane proteins, and cell surface retrieval of receptors from early endosomes upon ligand dissociation. Here, we describe a fluorescence ratiometric image analysis (FRIA) method used to determine the post‐endocytic fate and transport kinetics of transmembrane proteins based on the pH measurement of internalized cargo‐containing compartments in living cells. The method relies on the notion that the pH of a cargo‐containing transport vesicle (vesicular pH, pHv) could be taken as an indicator of its identity, considering that endocytic organelles (e.g., sorting endosome, recycling endosome, late endosome/MVB, and lysosome) have characteristic pHv. The pH‐sensitive FITC‐conjugated secondary antibody is attached to the cargo via a primary antibody, recognizing the cargo extracellular domain. The pHv is determined by single‐cell FRIA. Internalized cargo colocalization with organellar markers, as well as pHv measurement of recycling endosome, lysosome, and the TGN are discussed to validate the technique and facilitate data interpretation. Curr. Protoc. Cell Biol. 40:15.13.1‐15.13.21. © 2008 by John Wiley & Sons, Inc.
Making Giant Unilamellar Vesicles via Hydration of a Lipid Film
Authors: Manley Suliana , Gordon Vernita D.
Published: October 2008

This unit describes protocols for making giant unilamellar vesicles (GUVs) based on rehydration of dried lipid films. These model membranes are useful for determining the impact of membrane and membrane‐binding components on lipid bilayer stiffness and phase behavior. Due to their large size, they are especially amenable to studies using fluorescence and light microscopy, and may also be manipulated for mechanical measurements with optical traps or micropipets. In addition to their use in encapsulation, GUVs have proven to be useful model systems for studying many cellular processes, including tubulation, budding, and fusion, as well as peptide insertion. The introduction of enzymes or proteins can result in reorganization, leading to such diverse behavior as vesicle aggregation, fusion, and fission. Curr. Protoc. Cell Biol. 40:24.3.1‐24.3.13. © 2008 by John Wiley & Sons, Inc.
Exploring Biological Networks with Cytoscape Software
Authors: Yeung Natalie , Cline Melissa S. , Kuchinsky Allan , Smoot Michael E. , Bader Gary D.
Published: October 2008

Cytoscape is a free software package for visualizing, modeling, and analyzing molecular and genetic interaction networks. As a key feature, Cytoscape enables biologists to determine and analyze the interconnectivity of a list of genes or proteins. This unit explains how to use Cytoscape to load and navigate biological network information and view mRNA expression profiles and other functional genomics and proteomics data in the context of the network obtained for genes of interest. Additional analyses that can be performed with Cytoscape are also discussed. Curr. Protoc. Bioinform. 23:8.13.1‐8.13.20. © 2008 by John Wiley & Sons, Inc.
PharmGKB: An Integrated Resource of Pharmacogenomic Data and Knowledge
Authors: Gong Li , Owen Ryan P. , Gor Winston , Altman Russ B. , Klein Teri E.
Published: October 2008

The PharmGKB is a publicly available online resource that aims to facilitate understanding how genetic variation contributes to variation in drug response. It is not only a repository of pharmacogenomics primary data, but it also provides fully curated knowledge including drug pathways, annotated pharmacogene summaries, and relationships among genes, drugs, and diseases. This unit describes how to navigate the PharmGKB Web site to retrieve detailed information on genes and important variants, as well as their relationship to drugs and diseases. It also includes protocols on our drug‐centered pathway, annotated pharmacogene summaries, and our Web services for downloading the underlying data. Workflow on how to use PharmGKB to facilitate design of the pharmacogenomic study is also described in this unit. Curr. Protoc. Bioinform. 23:14.7.1‐14.7.17. © 2008 by John Wiley & Sons, Inc.
Endothelial Differentiation of Embryonic Stem Cells
Authors: Blancas Alicia A. , Lauer Nicholas E. , McCloskey Kara E.
Published: October 2008

Vascular progenitor cells derived from stem cells could potentially lead to a variety of clinically relevant applications, including cell‐based therapies and tissue engineering. Here, we describe methods for isolating purified proliferating populations of vascular endothelial cells from mouse embryonic stem cells (mESC) using Flk‐1 positive sorted cells, VEGF supplementation, and a rigorous manual selection technique required for endothelial cell purification and expansion. Using this in vitro derivation procedure, it is possible to obtain millions of cells at various stages of differentiation, with the potential for up to 25 population doublings. Curr. Protoc. Stem Cell Biol. 6:1F.5.1‐1F.5.19. © 2008 by John Wiley & Sons, Inc.
Hematopoietic Differentiation of Human Embryonic Stem Cells by Cocultivation with Stromal Layers
Authors: Hill Katherine L. , Kaufman Dan S.
Published: October 2008

Human embryonic stem (hES) cells are of remarkable interest both for the utility of these cells for studying basic human developmental biology and as a potential source for novel therapeutics. Here, we provide detailed methodologies of one of the first systems used to mediate differentiation of hES cells—stromal cell coculture. Use of stromal cells adds the ability to manipulate aspects of the developmental niche that support differentiation into a defined lineage. These methods will allow efficient and reproducible development of hematopoietic progenitor cells, as well as potentially mature hematopoietic cells that are suitable for subsequent in vitro and in vivo studies. Curr. Protoc. Stem Cell Biol. 6:1F.6.1‐1F.6.12. © 2008 by John Wiley & Sons, Inc.
Isolating, Expanding, and Infecting Human and Rodent Fetal Neural Progenitor Cells
Authors: Ebert Allison D. , McMillan Erin L. , Svendsen Clive N.
Published: October 2008

Neural progenitor cells have tremendous utility for understanding basic developmental processes, disease modeling, and therapeutic intervention. The protocols described in this unit provide detailed information to isolate and expand human and rodent neural progenitor cells in culture for several months as floating aggregates (termed neurospheres) or plated cultures. Detailed protocols for cryopreservation, neural differentiation, exogenous gene expression using lentivirus, and transplantation into the rodent nervous system are also described. Curr. Protoc. Stem Cell Biol. 6:2D.2.1‐2D.2.16. © 2008 by John Wiley & Sons, Inc.
Good Clinical Practice (
GCP
)
Authors: Barr David B.
Published: October 2008

Good Clinical Practices (GCPs) are international ethical and quality standards for the design, conduct, performance, monitoring, auditing, analysis, recording, reporting, and regulation of clinical investigations. Clinical investigations are experiments in which a medical product such as a drug is administered or dispensed to, or used involving, one or more human subjects. These standards provide assurance that the rights and confidentiality of the trial subjects are protected and that the data and reported results are credible and accurate.
Randomization Schedule
Authors: Kuznetsova Olga M.
Published: October 2008

The randomization schedule is used in a clinical trial to assign subjects randomly to one of the treatment regimens studied in the trial. Randomization helps to make the treatment groups comparable in baseline characteristics (both measured and not measured) and thus lessen the potential for bias in the evaluation of the treatments. It also allows causal inference with respect to intervention effects. The schedule is generated prior to the trial start and provides the list of treatment assignments by subject number (allocation number). In a stratified trial, a range of allocation numbers is designated for each stratum, and a separate randomization schedule is provided for each stratum. Subjects randomized into the trial are assigned allocation numbers in order of entry in their respective randomization stratum and receive the corresponding treatment.
Gold Standard
Authors: Agin Marilyn A.
Published: October 2008

In economics, the gold standard refers to a monetary standard under which the currency of a country is equal in value to and redeemable by a certain quantity of gold. Today, informal usage of the term “gold standard” has expanded beyond economics to denote a practice or principle that is a model of excellence with which things of the same class can be compared.
Phase 2/3 Trials
Authors: Liu Qing
Published: October 2008

Seamless phase 2/3 combination designs (or phase 2/3 designs) hold great promise to bring optimal treatment to patients early and more efficiently. The concept is to combine traditional phase 2 and phase 3 trials seamlessly in operation and inferentially in statistical analysis. As phase 2/3 designs cover a large area of clinical applications, it is not possible to provide comprehensive details for all different clinical applications in this article. Rather, the focus is on providing general descriptions of phase 2/3 designs and their legal foundations under the framework of Title 21 Part 312 of Code of Federal Regulations and Section 355 (b) of the Federal Food, Drug, and Cosmetic Act. This legal framework also provides the basis for correcting misrepresentations of phase 2/3 combination designs found in the literature. Various aspects and underlying principles are discussed in depth with highlights on current difficulties and future challenges to statistical inference.
Chemistry, Manufacturing and Controls (
CMC
)
Authors: Schmuff Norman R. , Lin David T.
Published: October 2008

This article describes general expectations and issues related to the Quality (also known as Chemistry, Manufacturing and Controls) section of Investigational New Drug (IND) (see Investigational New Drug Application (IND) article) applications filed with the U.S. Food and Drug Administration's (FDA's) Center for Drug Evaluation and Research (CDER) (see CDER article). Only brief mention will be made to FDA's Center for Biologics Evaluation and Research (CBER) (see CBER article) and other regulatory authorities (see Ministry of Health and Welfare (Japan, now known as the MHLW),
Medicines Control Agency
(United Kingdom, now known as the MHRA), and
EMEA
(European Union) articles). For determining whether INDs are required for clinical studies, see the Investigational New Drug Application (IND) article.
Crossover Design
Authors: Kenward Michael G.
Published: October 2008

In a crossover design, each subject is randomized to a sequence of treatments with the aim of comparing the effect of an individual treatment assignment. Such trials are restricted to fairly stable conditions and treatments with reversible effects. When within‐subject dependence of the outcome is high, such designs can be much more efficient than a parallel‐group study with the same number of subjects. However, because randomization applies to the sequences, not the individual treatments, the justification for the analysis of data from such trials depends more on model‐based assumptions than a typical parallel‐group study. The most commonly used crossover design is the so‐called two‐period, two‐treatment design, in which subjects are randomized to one of two sequences, A then B or B then A. Provided it can be assumed that the consequences of treatment allocation in the first period does not bias the treatment comparison in the second period (carryover), the analysis of such trials is very simple. It turns out that in most trials there will be very little information in the data on possible carryover, and therefore no useful statistical procedure exists either for its assessment or for adjustment for it. As a consequence, prior knowledge and adequate washout periods need to be used to justify the analysis in such settings. Higher order designs with more than two periods and more than two sequences exist for both the two‐treatment setting and for more than two treatments. Efficient designs can be constructed that allow adjustment for carryover, but only when it is expressed in particular, limited, mathematical forms. Data from crossover designs are examples of conventional repeated measures and analyses can be taken from the range of tools available for these, both with continuous and discrete outcomes.
Alpha‐Spending Function
Authors: DeMets David L. , Lan K. K. Gordon
Published: October 2008

Randomized clinical trials are typically monitored periodically for early evidence of convincing benefit or of potential harm for both scientific and ethical reasons by a data monitoring committee. After increments in the number of patients randomized or in the number of observed events, interim statistical analyses may be conducted to evaluate emerging results. This process may be referred to as a group sequential design. However, repeated analysis of accumulating data with conventional statistical testing can lead to substantially increased Type I or false positive error rates. The alpha spending function provides a flexible approach to control the Type I error while allowing the data monitoring committee to review the data as needed without having to specifya prioriwhen and how many such interim analyses will be conducted. Other earlier group sequential methods had these somewhat restrictive requirements. This alpha spending function approach can be applied to several spending functions that approximate some of these earlier methods.
Bootstrap
Authors: Hesterberg Tim
Published: October 2008

This article provides an introduction to the bootstrap. The bootstrap provides statistical inferences—standard error and bias estimates, confidence intervals, and hypothesis tests—without assumptions such as normal distributions or equal variances. As such, bootstrap methods can be remarkably more accurate than classic inferences based on normal ortdistributions. The bootstrap uses the same basic procedure regardless of the statistic being calculated, without requiring the use of application‐specific formulae.

This article may provide two big surprises for many readers. The first is that the bootstrap shows that commontconfidence intervals are woefully inaccurate when populations are skewed, with one‐sided coverage levels off by factors of two or more, even for very large samples. The second is that the number of bootstrap samples required is much larger than generally realized.
Query Management: The Route to a Quality Database
Authors: Hauser Larry A. , Morrow Ellen
Published: October 2008

The success of a clinical trial depends on the quality and integrity of the results captured in the database. If data stored in the database are incorrect, conclusions of analyses may also be incorrect. The purpose of the query management process is to achieve a high‐quality database to be used for additional analysis and reporting, whether for a regulatory filing or a peer‐reviewed publication. This task is accomplished by first identifying any data that seem questionable for accuracy or completeness and then taking steps to address the inconsistency. This article focuses on query management for a paper‐based study processed from a case report form, as well as data captured at the investigator site via an electronic data capture (EDC) system. EDC offers several key advantages, with potential for improved efficiencies and reduced time to database lock. Therefore, it is at a tipping point in its adoption, with nearly half of all new Phase I–III studies forecast to use EDC by the end of 2007. Future trends are projected to take the technology a step further with eSource (without a paper source), which results in even greater changes from the traditional roles that Data Management, the clinical monitor, and the investigator staff have historically played.
Identifying the Most Successful Dose (MSD) in Dose‐Finding Studies
Authors: O'Quigley John , Zohar Sarah
Published: October 2008

From a range of candidate doses, the MSD (most successful dose) is the dose at which the overall success rate—the product of the rate of seeing nontoxicities together with the rate of tumor response—is the highest. Among different algorithms designed to achieve this goal, the one closest to optimal (SIM) is the approach described in O'Quigley et al. (2001). This approach has been extended to the cancer setting by Ivanova (2003) and Zohar and O'Quigley (2006).
Change/Percent Change From Baseline
Authors: Vickers Andrew J.
Published: October 2008

Many clinical trials involve baseline and follow‐up assessment of a continuous outcome, such as pain, blood pressure, or weight. Different methods are available to analyze the results of such trials, which include between‐group two‐sample comparisons of the follow‐up measure, change score or percentage change, and linear regression of treatment on the follow‐up measure with the baseline measure as a covariate [analysis of covariance (ANCOVA)]. Each method provides a statistic that may have greater or less clinical applicability, depending on the particular trial involved. ANCOVA has greatest statistical power irrespective of the correlation between baseline and follow‐up measure, the nature of the treatment effect (shift or ratio), whether the control group also experiences change, and the distribution of the follow‐up measure. ANCOVA has additional advantages including control for chance baseline differences and incorporation of randomization strata as covariates. If trials results are best expressed in terms other than ANCOVA, such as a percentage change, then the preferred approach is to analyze the trial using ANCOVA and then convert the results into statistics that can be readily understood by clinicians.
AIDSClinical Trials Group (ACTG)
Authors: Andersen Janet W.
Published: October 2008

The AIDS Clinical Trials Group (ACTG) is the largest Network conducting therapeutic clinical trials in AIDS and HIV, with active clinical sites in the United States, South America, Haiti, Africa, India, and Thailand. The ultimate goal of the ACTG is to identify drugs and other treatment modalities that will result in the successful control of HIV in infected persons.
ASCOTTrial
Authors: Mehlsen Jesper
Published: October 2008

The Anglo Scandinavian Cardiac Outcomes Trial (ASCOT) had two main objectives. The first objective was to determine and compare the effects of an amlodipine‐based therapy with an atenolol‐based therapy in hypertensive patients with mild‐to‐moderate risk of developing cardiovascular events (ASCOT‐BPLA). The second objective was in those patients with a serum cholesterol level at or below average to evaluate the possible beneficial effects on cardiovascular events of a statin compared with placebo (ASCOT‐LLA). ASCOT‐LLA was terminated prematurely after a mean observational period of 3.3 years because of a highly significant reduction in the primary endpoint of CHD events compared with placebo. ASCOT‐BPLA was also terminated prematurely after a mean observational period of 5.5 years because of significantly higher all cause mortality in the atenolol‐based treatment arm compared with the amlodipine‐based arm.
Physicians' Health Study (PHS)
Authors: Gaziano J. Michael , Hennekens Charles H.
Published: October 2008

The United States Physicians' Health Study I was a landmark randomized trial of primary prevention because it was conducted entirely by mail, used a prerandomization run‐in, collected prerandomization blood specimens, used a 2 × 2 factorial design to test two hypotheses, had very high compliance to the assigned treatments, and had virtually complete morbidity and mortality data after 12 years of treatment and follow‐up. PHS I was funded by the National Institutes of Health and enrolled 22,071 male physicians aged 40 to 84 years at baseline in 1982. This randomized, double‐blind, placebo‐controlled trial tested primarily the effects of aspirin on cardiovascular disease and beta carotene on cancer. After 5 years of treatment and follow‐up, based on the unanimous recommendation of the independent Data and Safety Monitoring Board, the randomized aspirin component was terminated early mainly because of the emergence of a statistically extreme (P < 0.00001) 44% reduction in first myocardial infarction among those assigned to aspirin. After 12 years of treatment and follow‐up, the beta carotene arm ended on schedule and produced no significant overall evidence of benefit or harm either on cancer or cardiovascular disease.
Data Monitoring Committee
Authors: Ellenberg Susan
Published: October 2008

Data Monitoring Committees, also known as Data and Safety Monitoring Boards, are often established as a component of clinical trial oversight to review interim data of the ongoing trial so that safety concerns or problematic operational issues can be identified rapidly and corrective measures can be undertaken. Such committees may be independent of the trial sponsor and investigator to ensure recommendations are as objective as possible and unaffected by conflicts of interest. Federal funding and regulatory agencies have issued policy documents concerning the establishment and operation of Data Monitoring Committees, but substantial variation exists in committee processes.
The Center for Biologics Evaluation and Research
Authors: King Barney
Published: October 2008

Overview of the Center for Biologics Evaluation and Research (CBER) of the FDA. CBER's primary responsibility is the regulation of biologics products. The article briefly describes the history of biologics regulation, the regulatory authority behind the regulation, the types of products regulated by CBER, the general organization of the Center, and a gemera, a description of the approval process for biologics.
Wei‐Lin‐Weissfeld Method for Multiple Times to Events
Authors: Signorovitch James E. , Wei Lee‐Jen
Published: October 2008

Subjects followed in a longitudinal study can often experience multiple clinical events of interest at different times. The events could be of different types, for example, the onset times for various opportunistic infections in HIV‐infected patients, or multiple recurrences of the same type of event, such as recurrent superficial bladder tumors in cancer patients. This article describes the Wei–Lin–Weissfeld (WLW) method for analyzing multivariate failure time data that develop in such settings.
Maximum Tolerable Dose (
MTD
)
Authors: Chevret Sylvie
Published: October 2008

The “Maximum Tolerable Dose” (MTD), also known as the “Maximum Tolerated Dose” or the “Maximally Tolerated Dose”, is defined as the dose that produces an “acceptable” level of toxicity or that, if exceeded, would put animals or patients at “unacceptable” risk for toxicity. Besides determining animal toxicology, establishing the MTD is the main objective of Phase I clinical trials, mostly in cancer and HIV treatment in which relatively high doses of drugs are usually chosen to achieve the greatest possible beneficial antitumor effect. Definition of the MTD usually relies on the sample, as MTD is defined as the dose level at which more than two patients over six experienced dose‐limiting toxicity (DLT). More recently, the MTD has been defined as the dose that produces a certain frequency of DLT within the treated patient population. In this framework, the MTD is estimated from the data using Bayes or maximum likelihood inference. In all these designs, the MTD is established for one initial administration or treatment course of a cytotoxic experimental agent, ignoring efficacy. To address these issues, the maximum tolerated schedule and the most successful dose have been proposed to be used rather than a conventional MTD. Finally, the concept of MTD that uses toxicity as a surrogate endpoint for efficacy in cytotoxic Phase I trials has been also controversial. Interests in alternatives to MTD have gained recently when dealing with new cytostatic agents that may produce relatively minimal organ toxicity, compared with standard cytotoxics. New optimal doses should be defined in the near future.
Adverse Event Evaluation
Authors: McNair Lindsay A.
Published: October 2008

Although much of the focus in clinical trials is on the evaluation of the efficacy of an intervention or pharmaceutical product, the appropriate collection and assessment of safety data is a critical part of any clinical study. In early stage trials, the primary objective of the study may be the assessment of safety (or the identification of a maximum tolerated dose). For the assessment of safety data, several key factors must be collected for any adverse event. It is important to ensure that every adverse event—regardless of apparent association with the study or the intervention–is recorded. For each event, it is then important to collect the timing of the event, the relationship to the intervention, the severity, the expectedness, the intervention required, and the outcome. All of this information will initially be used to determine whether the event requires expedited reporting to regulatory agencies or safety monitoring committees, and later, it will be used to understand fully the safety profile of the intervention or investigational product.
Factor Analysis: Confirmatory
Authors: Byrne Barbara M.
Published: October 2008

The intent of this article is to present an introductory overview of the basic concepts and testing procedures associated with confirmatory factor analysis (CFA). Working from a hypothesized four‐factor structure of a nonacademic self‐concept (SC), as measured by 32 items from the Self Description Questionnaire, readers are introduced to both a graphical and a structural equation specification of this CFA model, followed by a review of the related procedures involved in its testing, estimation, and evaluation, together with the interpretation of results. Important issues and caveats associated with the testing of CFA models are also briefly addressed.
Women's Health Initiative: Statistical Aspects and Selected Early Results
Authors: Prentice Ross L. , Anderson Garnet L.
Published: October 2008

An overview is provided of the women's health initiative clinical trial and observational study of 161 808 postmenopausal women in the age range 50 to 79. The clinical trial includes 68 132 women in a partial factorial design having four intervention comparisons: a low‐fat eating pattern among 48 835 women; a hormone therapy trial of 0.625 mg per day of conjugated equine estrogen among 10 739 women who were posthysterectomy at baseline; a hormone therapy trial of this same estrogen plus 2.5 mg per day of medroxyprogesterone acetate among 16 608 women with uterus at baseline; and a calcium (1000 mg/day) plus vitamin D (400 international units/day) trial among 36 282 women. Each CT component had its specified primary and secondary hypotheses, along with an overriding emphasis on overall health benefits versus risks. A so‐called global index was defined for each CT component as the earliest occurrence of a set of clinical outcomes plausibly affected by the intervention, or death from other causes. Specialized data management communication, quality assurance, and data monitoring procedures were established to support this large and complex research program. Some detail is provided on the results of the combined hormone trial component, which was stopped early in 2002 when the external Data and Safety Monitoring Board judged that overall health risks exceeded benefits over an average follow‐up period in excess of five years.
Confounding
Authors: Greenland Sander
Published: October 2008

The word
confounding
has been used to refer to at least three distinct concepts. In the oldest usage, confounding is a
bias
in estimating causal effects (
see
Causation
). This bias is sometimes informally described as a mixing of effects of extraneous factors (called
confounders
) with the effect of interest. This usage predominates in nonexperimental research, especially in epidemiology and sociology. In a second and more recent usage, confounding is a synonym for noncollapsibility (
see
Collapsibility
), although this usage is often limited to situations in which the parameter of interest is a causal effect. In a third usage, originating in the
experimental‐design
literature, confounding refers to inseparability of main effects and
interactions
under a particular design. The term
aliasing
is also sometimes used to refer to the latter concept; this usage is common in the
analysis of variance
literature.
Correlation
Authors: Armitage Peter
Published: October 2008

In a loose sense, two variables are correlated if changes in one tend to be accompanied by changes in the other. More specifically, correlation implies a linear relationship with superimposed random variation. The product–moment correlation coefficient was introduced by Galton and greatly exploited by Karl Pearson. Its square is the proportion of the variance of one variable “explained” by linear regression on a second variable. Standard tests are described in the article. An important extension is to intraclass correlation for measurements on individuals falling into groups, which measures the association between individuals in the same group.
Data Mining
Authors: Hand David J.
Published: October 2008

Data mining seeks unexpected, interesting, or valuable structures in large data sets. There are two distinct classes of data mining tool, modeling, and pattern discovery. Difficulties arise in coping with data distortion and errors. The tools of data mining hold great promise for scientific and medical advance, but many theoretical questions remain open.
Fisher's Exact Test
Authors: Routledge Rick
Published: October 2008

Fisher's exact test can be used to assess the significance of a difference between the proportions in the two groups. In particular, it provides a widely applicable way to assess the results of simple, completely randomized experiments leading to two‐by‐two contingency tables with small frequency counts, However, it has low power, especially when the standardP‐value is used. The power can be increased considerably through either using the mid‐Pvalue, or carefully constructing a test based, at least in part, on a binomial model.
Hazard Rate
Authors: Gail Mitchell H.
Published: October 2008

The hazard rate is defined and related to other quantities used in epidemiology and survival analysis.
Interaction Model
Authors: Kreiner Svend
Published: October 2008

Loglinear models that describe association patterns among categorical variables are sometimes calledinteraction models. Graphical interaction models are useful for portraying conditional independence and indicating when an association remains the same after collapsing over a variable. This article discusses a “Separation theorem” that describes how conditional independence patterns are maintained by conditioning on a certain subset of variables as indicated by an interaction graph. Collapsibility issues are also discussed.
Paired

t

Test
Authors: Hsu Henry , Lachenbruch Peter A.
Published: October 2008

This is used to compare mean differences between treatments when the observations have been obtained in pairs. The difference between the paired values is assumed to be normally distributed, and the null hypothesis that the expectation is zero is tested by Student's
t
test. The robustness properties are discussed, as is the asymptotic relative efficiency of nonparametric alternatives.
Proportions, Inferences, and Comparisons
Authors: Connor Jason T. , Imrey Peter B.
Published: October 2008

This article selectively reviews asymptotic, exact, and Bayesian methods for inference about one proportion, or for comparing two proportions from separate samples. For a single proportion, interval estimation is emphasized, and coverage properties of Wald, Jeffreys, Wilson, Agresti–Coull, and Clopper–Pearson (exact) confidence intervals are compared. Hypothesis testing is also discussed, primarily in the context of inverting interval estimates. For comparing proportions between two samples, we consider tests including the power‐divergence family (which incorporates all asymptotic tests commonly used); both conditional and unconditional exact tests; Bayesian tests; and several interval estimates. Some general aspects of power computation and sample size determination are discussed briefly in both contexts.
Eligibility and Exclusion Criteria
Authors: Foulkes Mary A.
Published: October 2008

Design characteristics of a clinical trial, such as eligibility and exclusion criteria, are broadly influential in the conduct, interpretation, and impact of trials. The research objectives, the intended inference or generalization of results, the balance of factors affecting the trial recruitment and conduct, all impact the determination of eligibility and exclusion criteria. Clinical contraindications, regulatory and ethical considerations also relate to this determination.
Placebos
Authors: Holbrook Anne , Goldsmith Charles H. , Leung Mova
Published: October 2008

Placebos have a long and controversial history in clinical research and in practice. In this chapter, we review the meaning, the pharmacology, effectiveness, safety, influences on, and ethical issues involving placebos. Various international guidelines for the use of placebos in research are available and evolving. We then suggest novel factorial designs to allow a full assessment of efficacy and safety of a new therapy while minimizing patient exposure to placebo alone.
Screening, Models of
Authors: Stevenson Chris
Published: October 2008

This article describes models for disease screening and how they have developed in recent years. The discussion focuses on screening for cancer, because most of the methodological advances in screening design and evaluation have concerned cancer screening. The first part of the article describes the characteristics of these models and illustrates them with a discussion of a simple screening model. The second part describes the development, strengths, and weaknesses of the two main types of screening model—analytic and simulation models—with a particular focus on microsimulation models. The third part discusses model fitting and validation, and the final part briefly describes models for diseases other than cancer—in particular, models for screening for infectious diseases—and discusses the current state and possible future directions for models of disease screening.
Clinical Trials, Early Cancer and Heart Disease
Authors: Schneiderman Marvin A. , Gehan Edmund A.
Published: October 2008

Early developments in controlled clinical trials at the National Institutes of Health (NIH) took place mainly at the National Cancer Institute (NCI) and what was then the National Heart Institute (NHI) (subsequently the National Heart, Lung, and Blood Institute (NHLBI))beginning in the 1950s. This article reviews the developments from the early 1950s to the late 1960s at both institutes, summarizing the early efforts in clinical trials, the organizations set up to conduct and monitor the clinical trials, and the developments in statistical methodology that have formed the basis for conducting many of the present day randomized controlled trials. The early history of clinical trials at these institutes has been reviewed in more detail at NCI by Gehan & Schneiderman and at NHLBI by Halperin et al.
Hemoglobin Kenya composed of α‐ and (Aγβ)‐fusion‐globin chains, associated with hereditary persistence of fetal hemoglobin
Authors: Wilcox Ibifiri , Boettger Kevin , Greene Lance , Malek Anita , Davis Lance , Steinberg Martin H. , Luo Hong‐Yuan , Chui David H.K.
Published: October 2008

Hb Kenya is made up of two normal α‐globin chains and two Aγβ‐fusion globin chains. The latter are the product of an Aγβ‐hybrid globin gene formed as a result of misalignment during meiosis and nonhomologous crossing over. It is associated with a deletion of 22.7 kb including the δ‐globin gene, between the Aγ‐ and β‐globin genes. Hb Kenya is found in Kenyans and Ugandans. Heterozygotes have moderately increased Hb F, and this mutation has been known as an (Aγβ)+ hereditary persistence of fetal hemoglobin (HPFH). Compound heterozygotes for Hb Kenya/Hb S are thought to be asymptomatic, but reports of long term follow‐up of these patients are lacking. The correct identification of Hb Kenya is sometimes problematic. In cation exchange high performance liquid chromatography, Hb Kenya elutes in similar position as Hb A2, Hb Lepore, Hb E, and several other variant hemoglobins. Definitive diagnosis that is necessary for proper patient management is best done by DNA‐based gap‐PCR tests. Am. J. Hematol, 2009. © 2008 Wiley‐Liss, Inc.
The proteasome inhibitor, bortezomib suppresses primary myeloma and stimulates bone formation in myelomatous and nonmyelomatous bones in vivo
Authors: Pennisi Angela , Li Xin , Ling Wen , Khan Sharmin , Zangari Maurizio , Yaccoby Shmuel
Published: October 2008

Multiple myeloma (MM), a hematologic malignancy of terminally differentiated plasma cells is closely associated with induction of osteolytic bone disease, induced by stimulation of osteoclastogenesis and suppression of osteoblastogenesis. The ubiquitin‐proteasome pathway regulates differentiation of bone cells and MM cell growth. The proteasome inhibitor, bortezomib, is a clinical potent antimyeloma agent. The main goal of this study was to investigate the effect of bortezomib on myeloma‐induced bone resorption and tumor growth in SCID‐rab mice engrafted with MM cells from 16 patients. Antimyeloma response of bortezomib, which was evident in >50% of 16 experiments and resembled clinical response, was associated with significant increased bone mineral density (BMD) and osteoblast numbers, and reduced osteoclast numbers in myelomatous bones. This bone anabolic effect, which was also visualized on X‐ray radiographs and confirmed by static and dynamic histomorphometric analyses, was unique to bortezomib and was not observed in hosts responding to melphalan, a chemotherapeutic drug widely used to treat MM. Bortezomib also increased BMD and osteoblasts number and reduced osteoclasts number in nonmyelomatous implanted bones. In vitro bortezomib directly suppressed human osteoclast formation and promoted maturation of osteoblasts. We conclude that bortezomib promotes bone formation in myelomatous and nonmyelomatous bones by simultaneously inhibiting osteoclastogenesis and stimulating osteoblastogenesis. As clinical and experimental studies indicate that bone disease is both a consequence and necessity of MM progression our results suggest and that bortezomib's effects on bone remodeling contribute to the antimyeloma efficacy of this drug. Am. J. Hematol., 2009. © 2008 Wiley‐Liss, Inc.
High CD8+ lymphocyte dose in the autograft predicts early absolute lymphocyte count recovery after peripheral hematopoietic stem cell transplantation
Authors: Atta Elias Hallack , de Azevedo Alexandre Mello , Maiolino Angelo , Coelho Cláudia Júlia Bruzzi Porto , Sarcinelli Silvia Maria Patiño , de Alvarenga Máximo Cláudia , Marra Vera Lúcia Neves
Published: October 2008

Early lymphocyte recovery (ELR) after autologous peripheral hematopoietic stem cell transplantation (ASCT) is an independent predictor for survival in patients with hematological and non‐hematological cancers. Sixty‐five ASCT for hematological cancers were retrospectively analyzed to identify the factors associated with ELR and to assess the impact of different mobilization regimens on the pre‐collection absolute lymphocyte count (ALC). The CD8+ lymphocyte dose in the autograft and the pre‐mobilization ALC were independently associated with ELR (P < 0.001 and P = 0.008, respectively). CD8+ lymphocyte doses higher than 0.1 × 109/kg were strongly associated with ELR [P < 0.001, odds ratio 25.22, 95% confidence interval (CI) 4.98–127.69] and this cutoff may be used to predict ELR (P = 0.001, area under the curve 0.75, 95% CI 0.62–0.88). Mobilization with granulocyte colony‐stimulating factor (G‐CSF) alone, the pre‐collection ALC and the number of apheresis sessions were independently associated with the CD8+ lymphocyte dose (P = 0.04, P = 0.001, and P < 0.001, respectively). The number of aphereses was the variable with the strongest correlation to the CD8+ lymphocyte dose (rs = 0.68, P < 0.001). Median pre‐mobilization ALC was higher than pre‐collection ALC in the subgroup of patients without ELR mobilized with chemotherapy followed by G‐CSF (1090 vs. 758 lymphocytes/μL; P < 0.001). This reduction was not significant in the subgroup with ELR mobilized with chemotherapy plus G‐CSF (1920 vs. 1539/μL, respectively; P = 0.23). These results suggest that the CD8+ lymphocyte dose in the autograft is critical for ELR after ASCT and also demonstrates that mobilization with chemotherapy followed by G‐CSF significantly decreases the pre‐collection ALC, especially in patients with low pre‐mobilization ALC. Am. J. Hematol, 2009. © 2008 Wiley‐Liss, Inc.
Apolipoprotein E genotype is related to nitric oxide production in platelets
Authors: Marcourakis Tania , Bahia Valéria S. , Kawamoto Elisa M. , Munhoz Carolina D. , Gorjão Renata , Artes Rinaldo , Kok Fernando , Caramelli Paulo , Nitrini Ricardo , Curi Rui , Scavone Cristoforo
Published: October 2008

The presence of the ε4 allele of apolipoprotein E (APOE) is considered a risk factor for sporadic Alzheimer's disease (AD). Our recent data demonstrated that the systemic modulation of oxidative stress in platelets and erythrocytes is disrupted in aging and AD. In this study, the relationship between APOE genotype and oxidative stress markers, both in AD patients and controls, was evaluated. The AD group showed an increase in the content of thiobarbituric acid‐reactive substances (TBARS) and in the activities of nitric oxide synthase (NOS) and Na, K‐ATPase, when compared to controls. Both groups had a similar cGMP content and superoxide dismutase activity. APOE ε4 allele carriers showed higher NOS activity than non‐carriers. These results suggest a possible influence of APOE genotype on nitric oxide (NO) production that might enhance the effects of age‐related specific factor(s) associated with neurodegenerative disorders. Copyright © 2008 John Wiley & Sons, Ltd.
Soy lecithin supplementation alters macrophage phagocytosis and lymphocyte response to concanavalin A: a study in alloxan‐induced diabetic rats
Authors: Miranda Dalva T. S. Z. , Batista Vanessa G. , Grando Fernanda C. C. , Paula Fernanda M. , Felício Caroline A. , Rubbo Gabriella F. S. , Fernandes Luiz C. , Curi Rui , Nishiyama Anita
Published: October 2008

Dietary soy lecithin supplementation decreases hyperlipidemia and influences lipid metabolism. Although this product is used by diabetic patients, there are no data about the effect of soy lecithin supplementation on the immune system. The addition of phosphatidylcholine, the main component of lecithin, to a culture of lymphocytes has been reported to alter their function. If phosphatidylcholine changes lymphocyte functions in vitro as previously shown, then it could also affect immune cells in vivo. In the present study, the effect of dietary soy lecithin on macrophage phagocytic capacity and on lymphocyte number in response to concanavalin A (ConA) stimulation was investigated in non‐diabetic and alloxan‐induced diabetic rats. Supplementation was carried out daily with 2 g kg−1 b.w. lecithin during 7 days. After that, blood was drawn from fasting rats and peritoneal macrophages and mesenteric lymph node lymphocytes were collected to determine the phospholipid content. Plasma triacylglycerol (TAG), total and HDL cholesterol and glucose levels were also determined. Lymphocytes were stimulated by ConA. The MTT (3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide) dye reduction method and flow cytometry were employed to evaluate lymphocyte metabolism and cell number, respectively. Soy lecithin supplementation significantly increased both macrophage phagocytic capacity (+29%) in non‐diabetic rats and the lymphocyte number in diabetic rats (+92%). It is unlikely that plasma lipid levels indirectly affect immune cells, since plasma cholesterol, TAG, or phospholipid content was not modified by lecithin supplementation. In conclusion, lymphocyte and macrophage function were altered by lecithin supplementation, indicating an immunomodulatory effect of phosphatidylcholine. Copyright © 2008 John Wiley & Sons, Ltd.