bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gastrointestinal Models: Intestinal Transit, Gastric Emptying, and Ulcerogenic Activity in the Rat
Authors: Guillaume Philippe , Provost Daniel , Lacroix Pierre 
Published: October 2008

AbstractThe protocols described in this unit are designed to assess the effects of substances on intestinal transit and gastric emptying and to evaluate their ulcerogenic potential on the stomach and duodenum of the rat. Examples of results obtained with atropine or morphine (intestinal transit), loperamide (gastric emptying), or indomethacin (ulcerogenic activity) used as reference substances are provided for illustrative purposes. Atropine and morphine clearly reduce intestinal transit. Atropine, morphine, and loperamide clearly reduce gastric emptying. Indomethacin shows a marked ulcerogenic potential. Curr. Protoc. Pharmacol. 42:5.3.1‐5.3.12. © 2008 by John Wiley & Sons, Inc.
Chemical Synthesis of Oligoribonucleotides with 2′‐O‐(2‐Cyanoethoxymethyl)‐Protected Phosphoramidites
Authors: Ohgi Tadaaki , Kitagawa Hidetoshi , Yano Junichi 
Published: October 2008

AbstractAn RNA synthetic method with 2‐cyanoethoxymethyl (CEM) as the 2′‐hydroxyl protecting group allows the synthesis of long oligoribonucleotides from CEM‐amidites with an efficiency and final purity comparable to that obtained in DNA synthesis. The CEM‐amidites give a high coupling efficiency, because the CEM group minimizes steric hindrance in the coupling reaction. The CEM group shows satisfactory stability under solid‐phase synthetic conditions, avoids the generation of asymmetric centers, and is easily cleaved to give the final product. This unit describes the synthesis of the four CEM‐amidites, the preparation of reagents, the solid‐phase synthesis of oligoribonucleotides on an automated DNA synthesizer, and their deprotection. Curr. Protoc. Nucleic Acid Chem. 34:2.15.1‐2.15.19. © 2008 by John Wiley & Sons, Inc.
RNA Intramolecular Dynamics by Single‐Molecule FRET
Authors: Hengesbach Martin , Kobitski Andrei , Voigts‐Hoffmann Felix , Frauer Carina , Nienhaus G. Ulrich , Helm Mark 
Published: October 2008

AbstractInvestigation of single RNA molecules using fluorescence resonance energy transfer (FRET) is a powerful approach to investigate dynamic and thermodynamic aspects of the folding process of a given RNA. Its application requires interdisciplinary work from the fields of chemistry, biochemistry, and physics. The present work gives detailed instructions on the synthesis of RNA molecules labeled with two fluorescent dyes interacting by FRET, as well as on their investigation by single‐molecule fluorescence spectroscopy. Curr. Protoc. Nucleic Acid Chem. 34:11.12.1‐11.12.22. © 2008 by John Wiley & Sons, Inc.
Synthesis of Fluoroneplanocin A
Authors: Jeong Lak Shin , Tosh Dilip K. , Choi Won Jun , Pal Shantana 
Published: October 2008

AbstractFluoroneplanocin 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

AbstractMatrix 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

AbstractThe 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

AbstractThe 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

AbstractThis 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

AbstractCytoscape 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

AbstractThe 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

AbstractVascular 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

AbstractHuman 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

AbstractNeural 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

Abstract
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

Abstract
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.
Phase 2/3 Trials
Authors: Liu Qing 
Published: October 2008

Abstract
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

Abstract

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

Abstract
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

AbstractRandomized 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

AbstractThis 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

Abstract
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

Abstract
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

Abstract
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

AbstractThe 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.