bluuebunny/crossref_metadata_2025_split huggingface dataset:
Missing data in the exposure of interest and marginal structural models: A simulation study based on the Framingham Heart Study
Authors: Shortreed Susan M. , Forbes Andrew B. 
Published: December 2009

AbstractMissing data are common in longitudinal studies and can occur in the exposure interest. There has been little work assessing the impact of missing data in marginal structural models (MSMs), which are used to estimate the effect of an exposure history on an outcome when time‐dependent confounding is present. We design a series of simulations based on the Framingham Heart Study data set to investigate the impact of missing data in the primary exposure of interest in a complex, realistic setting. We use a standard application of MSMs to estimate the causal odds ratio of a specific activity history on outcome. We report and discuss the results of four missing data methods, under seven possible missing data structures, including scenarios in which an unmeasured variable predicts missing information.In all missing data structures, we found that a complete case analysis, where all subjects with missing exposure data are removed from the analysis, provided the least bias. An analysis that censored individuals at the first occasion of missing exposure and includes a censorship model as well as a propensity model when creating the inverse probability weights also performed well. The presence of an unmeasured predictor of missing data only slightly increased bias, except in the situation such that the exposure had a large impact on missing data and the unmeasured variable had a large impact on missing data and outcome. A discussion of the results is provided using causal diagrams, showing the usefulness of drawing such diagrams before conducting an analysis. Copyright © 2009 John Wiley & Sons, Ltd.
Water‐Dispersible, Multifunctional, Magnetic, Luminescent Silica‐Encapsulated Composite Nanotubes
Authors: Zhou Hongjun , Chen Jingyi , Sutter Eli , Feygenson Mikhail , Aronson M. C. , Wong Stanislaus S. 
Published: December 2009

AbstractA multifunctional one‐dimensional nanostructure incorporating both CdSe quantum dots (QDs) and Fe3O4 nanoparticles (NPs) within a SiO2‐nanotube matrix is successfully synthesized based on the self‐assembly of preformed functional NPs, allowing for control over the size and amount of NPs contained within the composite nanostructures. This specific nanostructure is distinctive because both the favorable photoluminescent and magnetic properties of QD and NP building blocks are incorporated and retained within the final silica‐based composite, thus rendering it susceptible to both magnetic guidance and optical tracking. Moreover, the resulting hydrophilic nanocomposites are found to easily enter into the interiors of HeLa cells without damage, thereby highlighting their capability not only as fluorescent probes but also as possible drug‐delivery vehicles of interest in nanobiotechnology.
Ultrathin Alumina Membranes for Surface Nanopatterning in Fabricating Quantum‐Sized Nanodots
Authors: Wu Minghong , Wen Liaoyong , Lei Yong , Ostendorp Stefan , Chen Kai , Wilde Gerhard 
Published: December 2009

AbstractUsing ultrathin alumina membranes (UTAMs) as evaporation or etching masks large‐scale ordered arrays of surface nanostructures can be synthesized on substrates. However, it is a challenge for this technique to synthesize quantum‐sized surface structures. Here an innovative approach to prepare UTAMs with regularly arrayed pores in the quantum size range is reported. This new approach is based on a well‐controlled pore‐opening process and a modulated anodization process. Using UTAMs with quantum‐sized pores for the surface patterning process, ordered arrays of quantum dots are synthesized on silicon substrates. This is the first time in realizing large‐scale regularly arrayed surface structures in the quantum size range using the UTAM technique, which is an important breakthrough in the field of surface nanopatterning.
Formal methods applied to high‐performance computing software design: a case study of MPI one‐sided communication‐based locking
Authors: Pervez Salman , Gopalakrishnan Ganesh , Kirby Robert M. , Thakur Rajeev , Gropp William 
Published: December 2009

AbstractThere is a growing need to address the complexity of verifying the numerous concurrent protocols employed in the high‐performance computing software. Today's approaches for verification consist of testing detailed implementations of these protocols. Unfortunately, this approach can seldom show the absence of bugs, and often results in serious bugs escaping into the deployed software. An approach calledModel Checkinghas been demonstrated to be eminently helpful in debugging these protocols early in the software life cycle by offering the ability to represent and exhaustively analyze simplified formal protocol models. The effectiveness of model checking has yet to be adequately demonstrated in high‐performance computing. This paper presents a case study of a concurrent protocol that was thought to be sufficiently well tested, but proved to contain two very non‐obvious deadlocks in them. These bugs were automatically detected through model checking. The protocol models in which these bugs were detected were also easy to create. Recent work in our group demonstrates that even this tedium of model creation can be eliminated by employing dynamic source‐code‐level analysis methods. Our case study comes from the important domain of Message Passing Interface (MPI)‐based programming, which is universally employed for simulating and predicting anything from the structural integrity of combustion chambers to the path of hurricanes. We argue that model checking must be taught as well as used widely within HPC, given this and similar success stories. Copyright © 2009 John Wiley & Sons, Ltd.
Inflammatory Myofibroblastic Tumor of the Liver: A Cohort Study
Authors: Tang Liang , Lai Eric C. H. , Cong Wen‐ming , Li Ai‐jun , Fu Si‐yuan , Pan Ze‐ya , Zhou Wei‐ping , Lau Wan Yee , Wu Meng‐Chao 
Published: December 2009

AbstractBackgroundInflammatory myofibroblastic tumor (IMT) is a rare condition. The aim of the present study was to evaluate the clinical characteristics and surgical outcomes for IMT of the liver in our large cohort of patients.MethodsFrom January 2001 to December 2007, all patients with a pathological diagnosis of IMT of the liver who underwent partial hepatectomy were retrospectively analyzed.ResultsDuring the study period, 64 patients underwent partial hepatectomy for IMT of the liver in our tertiary referral center. The commonest clinical presentation was abdominal pain (53%), followed by fever (41%); 15.6% of patients were asymptomatic. Preoperative diagnosis of IMT was suspected in only five patients (8%). The indications for surgery included suspicion of malignancy (60.9%), uncertain diagnosis (40.6%), symptomatic disease (26.6%), and spontaneous rupture (3.1%). The postoperative complication rate was low (17.2%). There was no hospital mortality. After a median follow‐up of 30 months, no patient developed recurrence.ConclusionsAlthough there are various treatment options for IMT of the liver, surgical resection for good risk patients is preferred.
Intraoperative Near‐Infrared Fluorescent Cholangiography (NIRFC) in Mouse Models of Bile Duct Injury
Authors: Figueiredo Jose‐Luiz , Siegel Cory , Nahrendorf Matthias , Weissleder Ralph 
Published: December 2009

AbstractBackgroundAccidental injury to the common bile duct is a rare but serious complication of laparoscopic cholecystectomy. Accurate visualization of the biliary ducts may prevent injury or allow its early detection. Conventional X‐ray cholangiography is often used and can mitigate the severity of injury when correctly interpreted. However, it may be useful to have an imaging method that could provide real‐time extrahepatic bile duct visualization without changing the field of view from the laparoscope. The purpose of the present study was to test a new near‐infrared (NIR) fluorescent agent that is rapidly excreted via the biliary route in preclinical models to evaluate intraoperative real‐time near infrared fluorescent cholangiography (NIRFC).MethodsTo investigate probe function and excretion, a lipophilic near‐infrared fluorescent agent with hepatobiliary excretion was injected intravenously into one group of C57/BL6 control mice and four groups of C57/BL6 mice under the following experimentally induced conditions: (1) chronic biliary obstruction, (2) acute biliary obstruction (3) bile duct perforation, and (4) choledocholithiasis, respectively. The biliary system was imaged intravitally for 1 h with near‐infrared fluorescence (NIRF) with an intraoperative small animal imaging system (excitation 649 nm, emission 675 nm).ResultsThe extrahepatic ducts and extraluminal bile were clearly visible due to the robust fluorescence of the excreted fluorochrome. Twenty‐five minutes after intravenous injection, the target‐to‐background ratio peaked at 6.40 ± 0.83 but signal was clearly visible for ~60 min. The agent facilitated rapid identification of biliary obstruction and bile duct perforation. Implanted beads simulating choledocholithiasis were promptly identifiable within the common bile duct lumen.ConclusionsNear‐infrared fluorescent agents with hepatobiliary excretion may be used intraoperatively to visualize extrahepatic biliary anatomy and physiology. Used in conjunction with laparoscopic imaging technologies, the use of this technique should enhance hepatobiliary surgery.
High-starch diets induce precocious adipogenic gene network up-regulation in longissimus lumborum of early-weaned Angus cattle
Authors: Graugnard Daniel E. , Berger Larry L. , Faulkner Dan B. , Loor Juan J. 
Published: December 2009

Adipocyte differentiation is probably controlled by transcriptional and post-transcriptional regulation. Longissimus lumborum from Angus steers (aged 155 d; seven animals per diet) fed high-starch or low-starch diets for 112 d (growing phase) followed by a common high-starch diet for an additional 112 d (finishing phase) was biopsied at 0, 56, 112 and 224 d for transcript profiling via quantitative PCR of twenty genes associated with adipogenesis and energy metabolism. At 56 d steers fed high starch had greater expression of PPARγ as well as the lipogenic enzymes ATP citrate lyase (ACLY), glucose-6-phosphate dehydrogenase (G6PD), fatty acid synthase (FASN), fatty acid binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD), glycerol-3-phosphate acyltransferase, mitochondrial (GPAM), and diacylglycerol O-acyltransferase homologue 2 (DGAT2), and the adipokine adiponectin (ADIPOQ). Expression of insulin-induced gene 1 (INSIG1) was also greater with high starch at 56 d. Steers fed low starch experienced a marked increase in FASN, FABP4, SCD, DGAT2 and thyroid hormone-responsive (SPOT14 homologue, rat) (THRSP) between 56 and 112 d of feeding. A greater expression of the transcription factors sterol regulatory element-binding transcription factor 1 (SREBF1) and MLX interacting protein-like (MLXIPL) was observed at 224 d in steers fed high starch, suggesting a nutritional imprinting effect. Carryover effects of low starch feeding were discerned by greater expression at 224 d of THRSP, FABP4, SCD and DGAT2. These steers also had greater PPARγ at 224 d. Despite these responses, low starch led to greater expression at 224 d of nuclear receptor subfamily 2, group F, member 2 (NR2F2), a known repressor of rodent adipocyte differentiation through its negative effects on PPARγ, ADIPOQ and FABP4. Results suggested that early exposure to high starch induced precocious intramuscular adipocyte proliferation and metabolic imprinting of lipogenic transcription regulators. Low starch might have blunted the PPARγ-driven adipogenic response through up-regulation of NR2F2 but the endogenous ligand for this nuclear receptor remains unknown.
Predicting in vivo starch digestibility coefficients in newly weaned piglets from in vitro assessment of diets using multivariate analysis
Authors: Doucet Frederic J. , White Gavin A. , Wulfert Florian , Hill Sandra E. , Wiseman Julian 
Published: December 2009

The study was based on correlating a dataset of in vivo mean starch digestibility coefficients obtained in the immediate post-weaning phase of piglets with a range of dietary in vitro variables. The paper presents a model that predicts (R2 0·71) in vivo average starch digestibility coefficients in the 0·5 small-intestinal region of newly weaned piglets fed cereal-based diets using seven in vitro variables describing starch properties that are fundamentally associated with the quality of feed materials, i.e. hydration, structure and amylolytic digestion. The variables were: Rapid Visco Analyser (RVA; measures the viscosity of materials when sheared under defined hydration and temperature regimens); RVA end viscosity; RVA (gelatinisation) peak viscosity; ΔH (gelatinisation enthalpy that provides an estimate of helical order or degree of crystallinity in starch); water solubility index (WSI; that denotes the amount of soluble polysaccharides released from starch granules to the aqueous phase); grain endogenous amylase (concentration of endogenous α-amylase in cereals, assessed by pasting cereal flours in 25 g of AgNO3, an amylase inhibitor v. water using RVA).
Physiological concentrations of dietary polyphenols regulate vascular endothelial cell expression of genes important in cardiovascular health
Authors: Nicholson Sonja K. , Tucker Gregory A. , Brameld John M. 
Published: December 2009

Previous cell culture-based studies have shown potential health beneficial effects on gene expression of dietary polyphenols, including those found in red wine and green tea. However, these studies have tended to use higher concentrations (2–100 μm) than those observed in blood (0·1–1 μm) after consuming polyphenol-rich foods or beverages. The present study investigated effects of physiological concentrations of different classes of dietary polyphenol on the expression of genes important in cardiovascular health (endothelial NO synthase (eNOS), endothelin-1 (ET-1) and vascular endothelial growth factor (VEGF)) by cultured vascular endothelial cells (human umbilical vein endothelial cells) in the absence or presence of H2O2. Resveratrol and quercetin (0·1–1 μm) increased eNOS and VEGF mRNA expression particularly in the absence of H2O2 (50 μm) and decreased H2O2-induced ET-1 mRNA expression (P < 0·001 for polyphenol × H2O2 interactions). Similarly, resveratrol and quercetin decreased endothelin secretion into the media, blocking the stimulatory effect of 50 μm-H2O2 (P < 0·001 for polyphenol × H2O2 interaction). Of the nine other polyphenols tested, only epigallocatechin gallate had similar effects on both the eNOS and ET-1 mRNA expression, but to a lesser extent than resveratrol at an equimolar concentration (0·1 μm). The observed effects on gene expression would be expected to result in vasodilation and thereby reduced blood pressure. Since only three of the eleven polyphenols tested had biological activity, it is unclear whether particular structures are important or whether the effects might relate to the relatively high antioxidant capacities of the three active polyphenols.
III Report on Bolivia, 1827
Authors: Pentland Joseph Barclay , Fifer J. Valerie 
Published: December 2009

Maps 170Introduction 173Text 182Chapter III A Review of the Present State of the Mines, and of their Former Produce 182Chapter IV A Review of the Commercial Relations, Foreign and Domestic 213Chapter V A Short View of the Present Political State of Bolivia, Embracing the History of the Country Since its Independence, its Government, Laws and Institutions 240Appendices 264
II Documents concerning the Negotiation of the Anglo-French Treaty of March 1550
Authors: Potter D.L. 
Published: December 2009

IntroductionI The treaty of Boulogne and the documents 59II The sources 65III Notes on the main negotiators 70IV Note on presentation and acknowledgements 71Main series of documents 74AppendicesI Documents related to Anglo-French negotiations included in the 1550 register 163II The start of the negotiations, November 1549 170III French negotiations with the Irish princes, 1549–50 172IV List of extant correspondence of the English commissioners and related materials in English archives 176MapsI Fortifications around Boulogne, 1549 73II The English position in Scotland, 1547–50 1301
II William Latymer's Chronickille of Anne Bulleyne
Authors: Dowling Maria 
Published: December 2009

Acknowledgements 25Abbreviations 26IntroductionThe text 27The author 27Latymer's purpose in writing the ‘Cronickille’ 29Latymer's veracity 33Other early biographies and notices of Anne Boleyn 37The value of Latymer's account 43Editorial Procedure 45Text 46I am grateful to the Keeper of Western Manuscripts, the Bodleian Library, Oxford for permission to publish the text offered here, Bodleian MS Don. C. 42, fos 21–33. I wish to thank Mr J.A.S. Green, the County Archivist of Berkshire, for information about Trumble MS and the staff of the following institutions for their assistance and cooperation: the Bodleian Library, Oxford; the British Library, Dr Williams's Library, Institute of Historical Research and Public Record Office, London; and the Bibliotheque Albert I, Brussels. Professor E.W. Ives has given valuable advice and constructive criticism, and Mr L.R. Gardiner offered much useful discussion of the nature of Tudor biography. I would like to thank Ms Catharine Davies and Ms Joy Shakespeare both for references and for suggestions. Thanks are due to Mr Stephen Baskerville, Miss Joan Henderson and Ms Susan Wabuda for enthusiastic discussion and kind encouragement.
IV The Undergraduate Account Book of John and Richard Newdigate, 1618–1621
Authors: Larminie Vivienne 
Published: December 2009

Introduction 151The Oxford and Temple Account 154The Newdigates and the education of the gentleman 156Editorial Practice 160Part I: Oxford 161Part II: Inner Temple 217The Oxford and Temple Bookis one of a series of account books kept for and by the Newdigates of Arbury Hall, between Coventry and Nuneaton in Warwickshire, from 1608 to 1642, and now surviving among the family papers deposited at Warwickshire Record Office. All the accounts detail receipts from rents and farming, interest and borrowing, and expenditure on estate, household and personal items, but that kept between 1618 and 1621, printed here, also records the expenses of two brothers at university and the inns of court, of two family marriages and related settlements and of wardship and suing for livery of estates.
POST-RACISM?
Authors: Pettigrew Thomas F. 
Published: December 2009

AbstractDoes President Obama's momentous election victory signify a new, post-racism era in America? Many observers, such as a New York Times science editor, think so. But, unfortunately, this claim is premature for a host of reasons. [1] It took “a perfect storm” of interlocking factors to elect Obama. [2] Many bigots actually voted for Obama. [3] Two logical fallacies underlie this too-optimistic view. [4] Racist attitudes and actions repeatedly occurred throughout the campaign. [5] White Southern and older voters both demonstrated that rank racism remains. [6] Increased turn-out of young and minority voters was crucial. The paper closes by considering what changes in American race relations may take place during the Obama presidency.
THINKING ABOUT ROBERT PUTNAM'S ANALYSIS OF DIVERSITY
Authors: Kilson Martin 
Published: December 2009

AbstractThe article evaluates Robert Putnam's discussion of two differing concepts of the role of the diversity perspective toward inter-ethnic/inter-racial relationships in American society since the 1960s—namely, the “contact theory” and the “conflict theory.” The former was initially formulated by Harvard social psychologist Gordon Allport in The Nature of Prejudice (1954). Putnam's analysis—published in the comparative politics journal Scandinavian Political Studies (Vol. 30, No. 2, 2007)—favors the “conflict theory,” which holds that diversity sharpens “us-against-them” inter-ethnic/inter-racial interactions. Putnam's view opposes diversity-influenced public policies. By contrast, “contact theory” holds that diversity erodes “us-against-them” interactions and thus eventually democratizes such interactions, and thereby American society generally. “Contact theory” influenced the NAACP-led civil-rights movement's quest for desegregation public policies during the 1950s, 1960s, and onward.
CRIME, URBAN POVERTY, AND SOCIAL SCIENCE
Authors: Bobo Lawrence D. 
Published: December 2009

Todd R. Clear,Imprisoning Communities: How Mass Incarceration Makes Disadvantaged Neighborhoods Worse. New York: Oxford University Press, 2007. 255 pages, ISBN: 978-0-19-538720-9. Paper, $21.95.Sudhir Venkatesh,Gang Leader for a Day: A Rogue Sociologist Takes to the Streets. New York: Penguin Press, 2008. 303 pages, ISBN: 978-1-59420-150-9. Cloth, $25.95.In recent years, sociologists have conducted enormously important research on the intersection of urban poverty, crime, and the racial divide. Quantitative stratification sociologist Bruce Western provides a meticulous tracing of the emergence of mass incarceration, tracking its steady development and identifying how and why—both economically and politically—this trend has fallen so heavily on low-income Black communities (Western 2006). Quantitative stratification sociologist Devah Pager carries out remarkably innovative and compelling field experiments showing the terrible toll incarceration takes on the employment prospects and, therefore, the greater life chances of former felons, particularly those who are Black (Pager 2007). And the combined efforts of quantitative criminologist Chris Uggen and quantitative political sociologist Jeff Manza reveal the extraordinary distortion of our local and national politics that results from the practice of felon disfranchisement (Manza and Uggen, 2006).
A CONVERSATION WITH CLAUDE M. STEELE
Authors: Gates Henry Louis , Steele Claude M. 
Published: December 2009

Henry Louis Gates, Jr.: Claude, what exactly is “stereotype threat”? And why does it matter for the intellectual performance of Black youth at school?Claude M. Steele: Stereotype threat is a very simple experience that everybody has, I believe, a couple times a day. It refers to being in a situation or doing something for which a negative stereotype about one of your identities—your age, your race, your gender—is relevant to you. You know then that you could be seen and treated in terms of that stereotype. And if you care about what you're doing, the prospect of being judged and treated this way can be upsetting, distracting, and can interfere with your functioning in the situation.
The moral intellectualism of Plato’s Socrates
Authors: Balaban Oded 
Published: December 2009

Commentators do not take Socrates’ theses in the Hippias Minor seriously. They believe it is an aporetic dialogue and even that Socrates does not mean what he says. Hence they are unable to understand the presuppositions behind Socrates’ two interconnected theses: that those who do wrong and lie voluntarily are better than those who do wrong unintentionally, and that no one does wrong and lies voluntarily. Arguing that liars are better than the unenlightened, Socrates concludes that there are no liars. Instead, there are only those who know and those who don’t. The unenlightened cannot lie, and alien volitions, desires, or emotions are unlikely to mislead and deceive those who know, i. e., the wise. Why, then, is a thinker like Socrates ready to defy the experience and moral convictions of his contemporaries and even our own to such an extent?