bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defending legitimate epidemiologic research: combating Lysenko pseudoscience
Authors: Enstrom James E 
Published: October 2007

AbstractThis analysis presents a detailed defense of my epidemiologic research in the May 17, 2003British Medical Journalthat found no significant relationship between environmental tobacco smoke (ETS) and tobacco-related mortality. In order to defend the honesty and scientific integrity of my research, I have identified and addressed in a detailed manner several unethical and erroneous attacks on this research. Specifically, I have demonstrated that this research is not "fatally flawed," that I have not made "inappropriate use" of the underlying database, and that my findings agree with other United States results on this relationship. My research suggests, contrary to popular claims, that there is not a causal relationship between ETS and mortality in the U.S. responsible for 50,000 excess annual deaths, but rather there is a weak and inconsistent relationship. The popular claims tend to damage the credibility of epidemiology.In addition, I address the omission of my research from the 2006 Surgeon General's Report on Involuntary Smoking and the inclusion of it in a massive U.S. Department of Justice racketeering lawsuit. I refute erroneous statements made by powerful U.S. epidemiologists and activists about me and my research and I defend the funding used to conduct this research. Finally, I compare many aspect of ETS epidemiology in the U.S. with pseudoscience in the Soviet Union during the period of Trofim Denisovich Lysenko. Overall, this paper is intended to defend legitimate research against illegitimate criticism by those who have attempted to suppress and discredit it because it does not support their ideological and political agendas. Hopefully, this defense will help other scientists defend their legitimate research and combat "Lysenko pseudoscience."
Role of reaction kinetics and mass transport in glucose sensing with nanopillar array electrodes
Authors: Anandan Venkataramani , Yang Xiaoling , Kim Euihyeon , Rao Yeswanth L , Zhang Guigen 
Published: October 2007

Abstract
The use of nanopillar array electrodes (NAEs) for biosensor applications was explored using a combined experimental and simulation approach to characterize the role of reaction kinetics and mass transport in glucose detection with NAEs. Thin gold electrodes with arrays of vertically standing gold nanopillars were fabricated and their amperometric current responses were measured under bare and functionalized conditions. Results show that the sensing performances of both the bare and functionalized NAEs were affected not only by the presence and variation of the nanoscale structures on the electrodes but also by the reaction kinetics and mass transport of the analyte species involved. These results will shed new light for enhancing the performance of nanostructure based biosensors.
Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris
Authors: He Yong-Qiang , Zhang Liang , Jiang Bo-Le , Zhang Zheng-Chun , Xu Rong-Qi , Tang Dong-Jie , Qin Jing , Jiang Wei , Zhang Xia , Liao Jie , Cao Jin-Ru , Zhang Sui-Sheng , Wei Mei-Liang , Liang Xiao-Xia , Lu Guang-Tao , Feng Jia-Xun , Chen Baoshan , Cheng Jing , Tang Ji-Liang 
Published: October 2007

Abstract
Background
Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood.

Results
We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated the genetic diversity and host specificity of Xcc by array-based comparative genome hybridization analyses of 18 virulent strains. The results demonstrate that a genetic core comprising 3,405 of the 4,186 coding sequences (CDSs) spotted on the array are conserved and a flexible gene pool with 730 CDSs is absent/highly divergent (AHD). The results also revealed that 258 of the 304 proved/presumed pathogenicity genes are conserved and 46 are AHD. The conserved pathogenicity genes include mainly the genes involved in type I, II and III secretion systems, the quorum sensing system, extracellular enzymes and polysaccharide production, as well as many other proved pathogenicity genes, while the AHD CDSs contain the genes encoding type IV secretion system (T4SS) and type III-effectors. A Xcc T4SS-deletion mutant displayed the same virulence as wild type. Furthermore, three avirulence genes (avrXccC, avrXccE1 and avrBs1) were identified. avrXccC and avrXccE1 conferred avirulence on the hosts mustard cultivar Guangtou and Chinese cabbage cultivar Zhongbai-83, respectively, and avrBs1 conferred hypersensitive response on the nonhost pepper ECW10R.

Conclusion
About 80% of the Xcc CDSs, including 258 proved/presumed pathogenicity genes, is conserved in different strains. Xcc T4SS is not involved in pathogenicity. An efficient strategy to identify avr genes determining host specificity from the AHD genes was developed.
Systemic inflammation and end organ damage following trauma involves functional TLR4 signaling in both bone marrow-derived cells and parenchymal cells
Authors: Mollen Kevin P , Levy Ryan M , Prince Jose M , Hoffman Rosemary A , Scott Melanie J , Kaczorowski David J , Vallabhaneni Raghuveer , Vodovotz Yoram , Billiar Timothy R 
Published: October 2007

AbstractEndogenous damage-associated molecular pattern (DAMP) molecules are released from cells during traumatic injury, allowing them to interact with pattern recognition receptors such as the toll-like receptors (TLRs) on other cells and subsequently, to stimulate inflammatory signaling. TLR4, in particular, plays a key role in systemic and remote organ responses to hemorrhagic shock (HS) and peripheral tissue injury in the form of bilateral femur fracture. TLR4 chimeric mice were generated to investigate the cell lineage in which functional TLR4 is needed to initiate the injury response to trauma. Chimeric mice were generated by adoptive bone marrow (BM) transfer, whereby donor marrow was given to an irradiated host using reciprocal combinations of TLR4 wild-type (WT; C3H/HeOuJ) and TLR4 mutant (Mu; C3H/HeJ) mice. After a period of engraftment, chimeric mice were then subjected to HS or bilateral femur fracture. Control groups, including TLR4-WT mice receiving WT BM and TLR4-Mu mice receiving Mu BM, responded to injury in a similar pattern to unaltered HeOuJ and HeJ mice, and protection was afforded to those mice lacking functional TLR4. In contrast, TLR4-WT mice receiving Mu BM and TLR4-Mu mice receiving WT BM demonstrated intermediate inflammatory and cellular damage profiles. These data demonstrate that functional TLR4 is required in BM-derived cells and parenchymal cells for an optimal inflammatory response to trauma.
A Quantitative Trait Locus on Chromosome 13q Affects Fasting Glucose Levels in Hispanic Children
Authors: Cai Guowen , Cole Shelley A. , Butte Nancy F. , Voruganti V. Saroja , Comuzzie Anthony G. 
Published: October 2007

Abstract
Objective: The prevalence of childhood obesity has increased dramatically in the United States. Early presentation of type 2 diabetes has been observed in children and adolescents, especially in the Hispanic population. The genetic contribution of glucose homeostasis related to childhood obesity is poorly understood. The objective of this study was to localize quantitative trait loci influencing fasting serum glucose levels in Hispanic children participating in the Viva La Familia Study.
Design: Subjects were 1030 children ascertained through an overweight child from 319 Hispanic families. Fasting serum glucose levels were measured enzymatically, and genetic linkage analyses were conducted using SOLAR software.
Results: Fasting glucose was heritable, with a heritability of 0.62 ± 0.08 (P &lt; 0.01). Genome-wide scan mapped fasting serum glucose to markers D13S158–D13S173 on chromosome 13q (LOD score of 4.6). A strong positional candidate gene is insulin receptor substrate 2, regulator of glucose homeostasis and a candidate gene for obesity. This region was reported previously to be linked to obesity- and diabetes-related phenotypes.
Conclusions: A quantitative trait locus on chromosome 13q contributes to the variation in fasting serum glucose levels in Hispanic children at high risk for obesity.
RyR1-specific requirement for depolarization-induced Ca2+ sparks in urinary bladder smooth muscle
Authors: Fritz Nicolas , Morel Jean-Luc , Jeyakumar Loice H. , Fleischer Sidney , Allen Paul D. , Mironneau Jean , Macrez Nathalie 
Published: October 2007

Ryanodine receptor subtype 1 (RyR1) has been primarily characterized in skeletal muscle but several studies have revealed its expression in smooth muscle. Here, we used Ryr1-null mice to investigate the role of this isoform in Ca2+ signaling in urinary bladder smooth muscle. We show that RyR1 is required for depolarization-induced Ca2+ sparks, whereas RyR2 and RyR3 are sufficient for spontaneous or caffeine-induced Ca2+ sparks. Immunostaining revealed specific subcellular localization of RyR1 in the superficial sarcoplasmic reticulum; by contrast, RyR2 and RyR3 are mainly expressed in the deep sarcoplasmic reticulum. Paradoxically, lack of depolarization-induced Ca2+ sparks in Ryr1–/– myocytes was accompanied by an increased number of cells displaying spontaneous or depolarization-induced Ca2+ waves. Investigation of protein expression showed that FK506-binding protein (FKBP) 12 and FKBP12.6 (both of which are RyR-associated proteins) are downregulated in Ryr1–/– myocytes, whereas expression of RyR2 and RyR3 are unchanged. Moreover, treatment with rapamycin, which uncouples FKBPs from RyR, led to an increase of RyR-dependent Ca2+ signaling in wild-type urinary bladder myocytes but not in Ryr1–/– myocytes.
In conclusion, although decreased amounts of FKBP increase Ca2+ signals in Ryr1–/– urinary bladder myocytes the depolarization-induced Ca2+ sparks are specifically lost, demonstrating that RyR1 is required for depolarization-induced Ca2+ sparks and suggesting that the intracellular localization of RyR1 fine-tunes Ca2+ signals in smooth muscle.
Diagnostic usefulness of a third-generation anti-cyclic citrulline antibody test in patients with recent-onset polyarthritis
Authors: Luis Caro-Oleas José , Fernández-Suárez Antonio , Reneses Cesteros Sonsoles , Porrino Carmen , Núñez-Roldán Antonio , Wichmann Schlipf Ingeborg 
Published: October 2007

AbstractClin Chem Lab Med 2007;45:1396–401.
Isobutyryl-CoA dehydrogenase deficiency with a novel ACAD8 gene mutation detected by tandem mass spectrometry newborn screening
Authors: Yoo Eun-Hyung , Cho Hyun-Jung , Ki Chang-Seok , Lee Soo-Youn 
Published: October 2007

AbstractIsobutyryl-CoA dehydrogenase (IBD) is an enzyme involved in the catabolism of the branched-chain amino acid valine. IBD deficiency is a very rare metabolic disorder, whereby only a few cases have been reported thus far. Recently, we observed a Korean newborn boy with elevated concentration of CClin Chem Lab Med 2007;45:1495–7.
Post-Apartheid Challenges: Household Access and Use of Health Care in South Africa
Authors: Gilson Lucy , McIntyre Di 
Published: October 2007

This is the final part of the special section, edited by Professors Margaret Whitehead and Göran Dahlgren, on the equity impacts of different health care systems, which includes studies conducted within the framework of the Affordability Ladder Program. Since 1994 the South African government has placed equity at the heart of its health policy goals. However, there has as yet been surprisingly little assessment of the success of policies in reducing inequity. This article provides insights on these issues by applying the Affordability Ladder conceptual framework in synthesizing evidence drawn from a series of household surveys and studies undertaken between 1992 and 2003. These data suggest that, despite policy efforts, inequities in access and utilization between socioeconomic groups remain. Underlying challenges include worsening community perceptions of the quality of publicly provided care and the influence of insurance status on utilization patterns. Further and more detailed evaluation of household-level policy impacts requires both improvements in the quality of South African survey data, particularly in enhancing consistency in survey design over time, and more detailed, focused studies.
Computational Fracture Mechanics
Authors: Ingraffea Anthony R. 
Published: October 2007

Abstract
An overview of computational fracture mechanics (CFM) is presented in the framework of a taxonomy of methods of representation of cracks in computational models. This taxonomy has two main branches: geometrical and nongeometrical approaches to representation. Within each branch, there are numerous methods, each of which is described by way of example applications, and evaluated for its relative advantages and disadvantages with respect to computational difficulty and ability to support fundamental physics and mechanics of cracking processes.
The purpose of this chapter is to survey examples of historical and state‐of‐the‐art techniques of CFM for its role in determining crack driving forces, and in predicting material resistance to cracking. It is intended for the student of CFM trying to make sense of its vast literature and myriad methods. It is hoped that the chapter will provide a basis for deciding which of these methods would be better suited for providing support for improved physics or mechanics, or at least improved efficiency, whether research or practice oriented, the student is addressing.
Computational Geomechanics Including Consolidation
Authors: Carter John P. , Small John C. 
Published: October 2007

Abstract
A review is presented of the role of computational mechanics in geotechnical engineering. Discussions of the conventional deterministic techniques used for numerical modeling in geomechanics and a brief discussion of the stochastic techniques for dealing with the uncertainties encountered in geotechnical practice are included. Considerable emphasis is given to the methods commonly used for the solution of boundary and initial value problems. Significantly, the chapter also includes a discussion of the limitations of the various numerical modeling techniques. Constitutive modeling of soil and rock mass behavior and material interfaces is an essential component of this type of computing, and so a review of recent developments and capabilities of constitutive models for geomaterials is also included. Problems involving the interaction of the ground with other engineering structures are also addressed. Some of the concepts described in the paper are illustrated with examples taken from research and practice. Emphasis has been placed on the mechanical behavior of soil, but it is noted that many of the models and techniques described also have application in rock mechanics and rock engineering.
Multiscale and Stabilized Methods
Authors: Hughes Thomas J. R. , Scovazzi Guglielmo , Franca Leopoldo P. 
Published: October 2007

AbstractThis article presents an introduction to multiscale and stabilized methods, which represent unified approaches to modeling and numerical solution of fluid dynamic phenomena. Finite element applications are emphasized but the ideas are general and apply to other numerical methods as well. (They have been used in the development of finite difference, finite volume, and spectral methods, in addition to finite‐element methods.) The analytical ideas are first illustrated for time‐harmonic wave‐propagation problems in unbounded fluid domains governed by the Helmholtz equation. This leads to the well‐known Dirichlet‐to‐Neumann formulation. A general treatment of the variational multiscale method in the context of an abstract Dirichlet problem is then presented, which is applicable to advective–diffusive processes and other processes of physical interest. It is shown how the exact theory represents a paradigm for subgrid‐scale models and a posteriori error estimation. Hierarchicalp‐methods and bubble function methods are examined in order to understand and ultimately approximate the ‘fine‐scale Green's function’ that appears in the theory. Relationships among so‐called residual‐free bubbles, element Green's functions, and stabilized methods are exhibited. These ideas are then generalized to a class of nonsymmetric, linear evolution operators formulated in space–time. The variational multiscale method also provides guidelines and inspiration for the development of stabilized methods (e.g. SUPG, GLS, etc.) that have attracted considerable interest and have been extensively utilized in engineering and the physical sciences. An overview of stabilized methods for advective–diffusive equations is presented. A variational multiscale treatment of incompressible viscous flows, including turbulence is also described. This represents an alternative formulation of large eddy simulation (LES), which provides a simplified theoretical framework of LES with potential for improved modeling.
Residual Distribution Schemes: Foundations and Analysis
Authors: Deconinck Herman , Ricchiuto Mario 
Published: October 2007

AbstractIn this article, we introduce and analyze the class of numerical schemes known as residual distribution or fluctuation splitting schemes. The root of this family of discretizations is found mainly in works aiming at generalizing the finite volume techniques to a genuinely multidimensional upwinding context, as in, for example (Hall, Morton, Ni, Roe). However, the final result is a numerical method sharing a lot with other techniques, such as finite element schemes (Carette, Deconinck, Paillere and Roe, 1995).Our aim is to look at fluctuation splitting/residual distribution methods from a generic theoretical point of view. We discuss in a general way the basic principles and the criteria used in the design of the schemes: positivity, k‐exacteness, energy stability, well‐balancedness. We also show similarities with known, more classical, discretization techniques, as well as the main distinguishing features that make residual distribution methods a valid alternative to these classical schemes.Finally, we present some numerical applications and comparisons. Throughout the text, we give an extensive overview of the existing literature, and finally conclude the chapter by reviewing most of the ongoing research on the topic.
Explicit Finite Element Methods for Large Deformation Problems in Solid Mechanics
Authors: Benson David J. 
Published: October 2007

AbstractExplicit finite methods are often the best choice for solving large deformation, high strain rate problems in solids mechanics. They are simple to implement, robust, efficient, and scale well on massively parallel computers. Their commercial applications include simulations of automobile crashes to the more prosaic drop testing of cell phones. This chapter presents an introduction of explicit finite element methods with an emphasis on the topics that distinguish the explicit formulation from the more traditional implicit one, including stable time step size estimation, energy conservation, shock viscosities, zero energy modes, and stress rotations.
Regulation of the Cell Cycle, Cell Cycle Checkpoints, and Cancer
Authors: Delia Domenico , Buscemi Giacomo 
Published: October 2007

Abstract
DNA damage response (DDR) pathways are triggered to ensure proper repair of DNA lesions and preserve genome integrity. Key intracellular transducers of the DNA damage are ataxia‐telangiectasia mutated kinase (ATM) and ataxia‐telangiectasia and Rad3‐related kinase (ATR). These nuclear proteins, through dynamic interaction with chromatin‐bound sensory components and phosphorylation at T/SQ residues of a multitude of substrates, including the checkpoint kinases Chk1 and Chk2, activate a network of pathways important for DNA repair, multiple cell cycle–phase arrest, transcription, and apoptosis. Interestingly, the DDR machinery is a key mediator of telomere‐dependent and telomere‐independent forms of cellular senescence, and provides a barrier to aberrant DNA replication induced by oncogenic stimuli. These findings and the constitutive activation of the DDR in human precancerous lesions, underscore the role of the DDR as a tumour suppressor constraining transformation by driving incipient tumour cells into apoptosis or senescence. Since genetic abnormalities of the DDR hypersensitize to genotoxic anticancer agents, this pathway represents a relevant target to increase tumour cell kill and possibly overcome drug resistance. The promising results with a number of chemical inhibitors of ATM, Chk1 and Chk2 are paving the way for new chemoradiation strategies that exploit the DDR machinery.
Tobacco Use and Cancer
Authors: Hecht Stephen S. 
Published: October 2007

AbstractAlthough considerable advances have been achieved in tobacco control, the use of tobacco products continues to be an immense problem worldwide. There are about 1200 million smokers in the world and hundreds of millions of smokeless tobacco users. The link between tobacco use and cancer is unguestionable, with cigarette smoking causing about 30% of all cancer mortality in developed countries. Experimental studies have firmly established the cancer causing properties of tobacco products in laboratory animals. Carcinogens in tobacco products have been identified and their mechanisms of action are well understood. Biomarkers related to these carcinogens have been developed and widely applied. Collectively, the currently available data provide a strong framework for further mechanistic understanding leading to continued progress in tobacco control and prevention of tobacco‐induced cancer.
Multidisciplinary Team Management of Lung Cancer
Authors: Giaccone Giuseppe , Smit Egbert , Senan Suresh , Paul Rick 
Published: October 2007

Abstract
Lung cancer should preferably be managed within the context of a multidisciplinary team, especially for early lung cancer cases and cases where combined modality approaches are required. The treatment of limited‐disease small cell lung cancer (SCLC), resectable non‐small cell lung cancer (NSCLC), and stage III NSCLC all require a multidisciplinary approach. Chemotherapy represents the standard therapy for SCLC and a large proportion of NSCLCs, given either as the sole treatment modality for palliation or as part of a combined modality programme for less advanced cases.
Multidisciplinary Team Management of Gynaecological Cancers
Authors: Harrison Michelle L. , Ind Thomas , Blake Peter , Gore Martin E. 
Published: October 2007

Abstract
Gynaecological malignancies represent a highly specialized area of oncology and should be managed within the context of a multidisciplinary team (MDT). This model is becoming standard not only in gynaecology but also with all cancer types. In this chapter we discuss the benefits of this approach in terms of delivery of care, compliance with best practice, patient outcomes, and requirements for the establishment and running of an MDT.
An overview of the management for newly diagnosed gynaecological malignancies, including ovarian, fallopian tube, peritoneal, endometrial, cervical, vulval, and vaginal cancers is provided. Preoperative imaging is crucial for surgical and radiotherapy planning, in particular, magnetic resonance imaging (MRI), which is now an integral part of assessment. The role of surgery, radiotherapy, and chemotherapy is reviewed with an emphasis on the controversial issues and recent advances in each of the tumour types.