bluuebunny/crossref_metadata_2025_split huggingface dataset:
The hp‐multigrid method applied to hp‐adaptive refinement of triangular grids
Authors: Mitchell William F. 
Published: March 2010

AbstractRecently the hp version of the finite element method, in which adaptivity occurs in both the size, h, of the elements and in the order, p, of the approximating piecewise polynomials, has received increasing attention. It is desirable to combine this optimal order discretization method with an optimal order algebraic solution method like multigrid. An intriguing notion is to use the values of p as the levels of a multilevel method. In this paper we present such a method, known as hp‐multigrid, for high‐order finite elements and hp‐adaptive grids. We present a survey of the development of p‐multigrid and hp‐multigrid, define an hp‐multigrid algorithm based on the p‐hierarchical basis for the p levels and h‐hierarchical basis for an h‐multigrid solution of the p=1 ‘coarse grid’ equations, and present numerical convergence results using hp‐adaptive grids. The numerical results suggest that the method has a convergence rate of \documentclass{article}\usepackage{amssymb}\usepackage{amsbsy}\usepackage[mathscr]{euscript}\footskip=0pc\pagestyle{empty}\begin{document}$\frac{1}{2}$\end{document} for Poisson's equation. Published in 2010 by John Wiley & Sons, Ltd.
Operator‐based interpolation for bootstrap algebraic multigrid
Authors: Manteuffel T. , McCormick S. , Park M. , Ruge J. 
Published: March 2010

AbstractBootstrap algebraic multigrid (BAMG) is a multigrid‐based solver for matrix equations of the form Ax=b. Its aim is to automatically determine the interpolation weights used in algebraic multigrid (AMG) by locally fitting a set of test vectors that have been relaxed as solutions to the corresponding homogeneous equation, Ax=0, and are then possibly improved later using a multilevel eigensolver. This paper introduces a flexible variant of BAMG that determines the interpolation weights indirectly by ‘collapsing’ the unwanted connections in ‘operator interpolation’. Compared to BAMG, this indirect BAMG approach (iBAMG) is more in the spirit of classical AMG, which collapses unwanted connections in operator interpolation based on the (restrictive) assumption that smooth error is locally constant. This paper studies the numerical performance of iBAMG and establishes an equivalence, under certain assumptions, between it and a slightly modified (standard) BAMG scheme. To focus on camparing BAMG and iBAMG and exposing their behavior as the problem size grows, the numerical experiments concentrate on Poisson‐like scalar problems. Copyright © 2010 John Wiley & Sons, Ltd.
Q‐FISH analysis of telomere and chromosome instability in the oesophagus with and without squamous cell carcinoma in situ
Authors: Takubo Kaiyo , Fujita Masahiro , Izumiyama Naotaka , Nakamura Ken‐ichi , Ishikawa Naoshi , Poon Steven S , Fujiwara Mutsunori , Sawabe Motoji , Matsuura Masaaki , Grabsch Heike , Arai Tomio , Aida Junko 
Published: March 2010

AbstractChromosomal and genomic instability due to telomere dysfunction is known to play an important role in carcinogenesis. To study telomere dysfunction in the surrounding background epithelium of squamous cell carcinoma in situ (CIS) of the oesophagus, we measured telomere lengths of basal and parabasal cells of epithelia with and without CIS using quantitative fluorescence in situ hybridization (Q‐FISH) and our original software, Tissue Telo. Additionally, we assessed histological inflammation and the anaphase bridge index. In non‐cancerous epithelium, telomeres in basal cells were significantly longer than those in parabasal cells, whereas CIS showed a homogeneous telomere pattern in the basal and parabasal cells. Telomeres in basal and parabasal cells were significantly shorter in the background with CIS than in epithelium from age‐matched normal controls. Significant negative correlation was observed between the normalized telomere : centromere ratio (reflected telomere length) and the anaphase bridge index in non‐cancerous epithelia from both normal controls and the CIS background with no histological inflammation. These findings indicate that tissue stem cells may be located among basal cells, and that telomere length distribution in component cell types differs between CIS and non‐cancerous epithelium. We have demonstrated conclusively that oesophageal CIS arises from epithelium with short telomeres and chromosomal instability in the absence of histological inflammation. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
On the nature of some biradicaloid and antiaromatic Vis/NIR‐chromophores
Authors: Fabian Jürgen , Peichert Rasmus 
Published: March 2010

AbstractDyes derived from the biradicalic oxyallyl and cyclopentadienylium were calculated by time‐dependent density functional theory (TDDFT) and the characteristics of the prominent low‐energy transitions revealed by graphical means. According to theoretical and experimental studies, 4‐aminophenyl‐substituted dyes absorb intensely at long wavelengths up to the near infrared. If the amino groups are removed the absorption wavelengths are changed little. As found in the previous studies on the squaraine and croconaine oxyallyl dyes, the substituents play only a minor role in the spectral excitation. Charge‐transfer‐type excitations do not occur between the donor aryl substituents and the central oxyallyl or cyclopentadienylium acceptor group. This behaviour is exceptional since donor–acceptor compounds tend to produce charge‐transfer‐ or polymethine‐type electronic transitions. The hitherto rarely used electron density difference (EDD) maps clearly unveiled the spectral excitation features. The spectral excitation of the title compounds is predominantly localized at the oxyallyl and cyclopentadienylium groups, respectively. Characteristics of simple chromophoric compounds and of conventional CT‐ and polymethine dyes are given for comparison. The biradicaloid character of these dyes is supported by the calculated low singlet–triplet splitting energies. Spin properties were characterized in terms of expectation values of the S2‐operator and antiaromatic properties in terms of nucleus‐independent chemical shifts (NICS). According to the ΔES/T and <S2> criteria compounds with the acyclic oxyallyl fragment are more biradicaloid. The parent compounds oxyallyl, thioxyallyl and cyclopentadienylium, display extremely large <S2> values. These compounds are triplets in the ground state. The absorption wavelengths of selected biradicaloid species were also calculated by the multi‐reference SORCI method. Copyright © 2010 John Wiley & Sons, Ltd.
Knowledge of genomic testing among early‐stage breast cancer patients
Authors: Richman Alice R. , Tzeng Janice P. , Carey Lisa A. , Retèl Valesca P. , Brewer Noel T. 
Published: March 2010

AbstractBackground: Genomic recurrence risk test results now inform clinical decisions about adjuvant treatment for women with early‐stage breast cancer. We sought to understand patients' knowledge of these tests and correlates of their knowledge.Methods: Participants in this cross‐sectional study were 78 women, treated for early‐stage, estrogen receptor‐positive breast cancer with 0–3 positive lymph nodes, whose medical records indicated they received Oncotype DX testing earlier. We mailed a questionnaire that assessed knowledge of genomic recurrence risk testing (13 item scale, alpha=0.83) and reviewed medical charts of consenting patients.Results: Knowledge about genomic recurrence risk testing was low (mean knowledge score=67%, SD=0.23). Low knowledge scores were more commonly due to responses of ‘don't know’ than incorrect answers. Most women (91%) clearly understood that test results can aid decisions about chemotherapy, and few (22%) understood that the test's estimate of the chance of metastasis assumes the patient is receiving hormone therapy. Higher knowledge about genomic recurrence risk testing was associated with higher education, reading ability, and numeracy. Knowledge was higher among women who recalled receiving both verbal and printed information about the test and among women who had active roles in deciding about their treatments. Higher knowledge was also associated with having fewer concerns about genomic testing.Discussion: Among early‐stage breast cancer patients who received Oncotype DX, we found low knowledge about many aspects of genomic recurrence risk testing. Research is needed to understand testing information provided to patients and best practices for patient education. Copyright © 2010 John Wiley & Sons, Ltd.
Psychological distress and quality of life of partners of individuals with familial adenomatous polyposis
Authors: Douma Kirsten F. L. , Bleiker Eveline M. A. , Vasen Hans F. A. , Gundy Chad M. , Gerritsma Miranda A. , Aaronson Neil K. 
Published: March 2010

AbstractObjective: Familial adenomatous polyposis (FAP) is a genetic condition characterized by the development of multiple adenomas in the colorectum that could lead to colorectal cancer. Our aim was to assess levels and predictors of psychological distress and quality of life (QOL) among partners of FAP‐patients.Methods: A nationwide, cross‐sectional survey using validated self‐report questionnaires assessing psychological distress and QOL.Results: One hundred and twenty‐nine partners completed the questionnaire (84% response rate), 30% of whom reported moderate‐to‐severe levels of distress. The partners' distress was associated significantly with the patients' distress, having children, and feelings of guilt. Fifty‐seven percent of the partners with moderate‐to‐severe distress levels had received professional psychosocial support. Partners did not differ significantly from the general population in QOL. However, 9–21% reported that FAP had affected their work, leisure time activities, and relationships.Conclusions: Clinicians should be particularly alert for heightened distress levels in partners of patients who are themselves distressed, and among those with children. Copyright © 2010 John Wiley & Sons, Ltd.
Effects of organic‐farming‐compatible insecticides on four aphid natural enemy species
Authors: Jansen Jean P , Defrance Thibaut , Warnier Anne M 
Published: March 2010

AbstractBACKGROUND: The toxicities of pyrethrins + rapeseed oil, pyrethrins + piperonyl butoxide (PBO), potassium salts of fatty acids and linseed oil were assessed in the laboratory on the parasitic wasp Aphidius rhopalosiphi (Destefani‐Perez), the ladybird Adalia bipunctata (L.), the rove beetle Aleochara bilineata (Gyll.) and the carabid beetle Bembidion lampros (Herbst.). The methods selected were residual contact toxicity tests on inert and natural substrates.RESULTS: Both the pyrethrin products led to 100% mortality in the adult parasitic wasps and ladybird larvae on glass plates and plants. The pyrethrins + PBO formulation was toxic for B. lampros on sand and natural soil, but the pyrethrins + rapeseed oil formulation was harmless for this species. Insecticidal soaps were harmless for all these beneficial species. None of the tested products significantly affected the parasitism of the onion fly pupae by A. bilineata.CONCLUSION: The results indicated the potentially high toxicity of natural pyrethrins for beneficial arthropods. Although this toxicity needs to be confirmed in field conditions, the toxicity levels obtained in the laboratory were similar to or higher than those of several synthetic insecticides known to be toxic in the field. Insecticidal soaps could be considered as an alternative for aphid control in organic farming in terms of selectivity. Copyright © 2010 Society of Chemical Industry
Bone Marrow-Derived Mesenchymal Stem Cells Prevent the Loss of Niemann-Pick Type C Mouse Purkinje Neurons by Correcting Sphingolipid Metabolism and Increasing Sphingosine-1-phosphate
Authors: Lee Hyun , Lee Jong Kil , Min Woo-Kie , Bae Jae-Hoon , He Xingxuan , Schuchman Edward H. , Bae Jae-sung , Jin Hee Kyung 
Published: March 2010

Abstract
Niemann-Pick type C (NP-C) disease exhibits neuronal sphingolipid storage and cerebellar Purkinje neuron (PN) loss. Although it is clear that PNs are compromised in this disorder, it remains to be defined how neuronal lipid storage causes the PN loss. Our previous studies have shown that bone marrow-derived mesenchymal stem cells (BM-MSCs) transplantation prevent PN loss in NP-C mice. The aim of the present study was therefore to examine the neuroprotective mechanism of BM-MSCs on PNs. We found that NP-C PNs exhibit abnormal sphingolipid metabolism and defective lysosomal calcium store compared to wild-type mice PNs. BM-MSCs promote the survival of NP-C PNs by correction of the altered calcium homeostasis, restoration of the sphingolipid imbalance, as evidenced by increased sphingosine-1-phosphate levels and decreased sphingosine, and ultimately, inhibition of apoptosis pathways. These effects suggest that BM-MSCs modulate sphingolipid metabolism of endogenous NP-C PNs, resulting in their survival and improved clinical outcome in mice.
Butyrate Greatly Enhances Derivation of Human Induced Pluripotent Stem Cells by Promoting Epigenetic Remodeling and the Expression of Pluripotency-Associated Genes
Authors: Mali Prashant , Chou Bin-Kuan , Yen Jonathan , Ye Zhaohui , Zou Jizhong , Dowey Sarah , Brodsky Robert A. , Ohm Joyce E. , Yu Wayne , Baylin Stephen B. , Yusa Kosuke , Bradley Allan , Meyers David J. , Mukherjee Chandrani , Cole Philip A. , Cheng Linzhao 
Published: March 2010

Abstract
We report here that butyrate, a naturally occurring fatty acid commonly used as a nutritional supplement and differentiation agent, greatly enhances the efficiency of induced pluripotent stem (iPS) cell derivation from human adult or fetal fibroblasts. After transient butyrate treatment, the iPS cell derivation efficiency is enhanced by 15- to 51-fold using either retroviral or piggyBac transposon vectors expressing 4 to 5 reprogramming genes. Butyrate stimulation is more remarkable (&gt;100- to 200-fold) on reprogramming in the absence of either KLF4 or MYC transgene. Butyrate treatment did not negatively affect properties of iPS cell lines established by either 3 or 4 retroviral vectors or a single piggyBac DNA transposon vector. These characterized iPS cell lines, including those derived from an adult patient with sickle cell disease by either the piggyBac or retroviral vectors, show normal karyotypes and pluripotency. To gain insights into the underlying mechanisms of butyrate stimulation, we conducted genome-wide gene expression and promoter DNA methylation microarrays and other epigenetic analyses on established iPS cells and cells from intermediate stages of the reprogramming process. By days 6 to 12 during reprogramming, butyrate treatment enhanced histone H3 acetylation, promoter DNA demethylation, and the expression of endogenous pluripotency-associated genes, including DPPA2, whose overexpression partially substitutes for butyrate stimulation. Thus, butyrate as a cell permeable small molecule provides a simple tool to further investigate molecular mechanisms of cellular reprogramming. Moreover, butyrate stimulation provides an efficient method for reprogramming various human adult somatic cells, including cells from patients that are more refractory to reprogramming.
The Senescence-Related Mitochondrial/Oxidative Stress Pathway is Repressed in Human Induced Pluripotent Stem Cells
Authors: Prigione Alessandro , Fauler Beatrix , Lurz Rudi , Lehrach Hans , Adjaye James 
Published: March 2010

Abstract
The ability of stem cells to propagate indefinitely is believed to occur via the fine modulation of pathways commonly involved in cellular senescence, including the telomerase, the p53, and the mitochondrial/oxidative stress pathways. Induced pluripotent stem cells (iPSCs) are a novel stem cell population obtained from somatic cells through forced expression of a set of genes normally expressed in embryonic stem cells (ESCs). These reprogrammed cells acquire self-renewal properties and appear almost undistinguishable from ESCs in terms of morphology, gene expression, and differentiation potential. Accordingly, iPSCs exhibit alterations of the senescence-related telomerase and p53 signaling pathways. However, although treatments with antioxidants have been recently shown to enhance cellular reprogramming, detailed information regarding the state of the mitochondrial/oxidative stress pathway in iPSCs is still lacking. Mitochondria undergo specific changes during organismal development and aging. Thus, addressing whether somatic mitochondria within iPSCs acquire ESC-like features or retain the phenotype of the parental cell is an unanswered but relevant question. Herein, we demonstrate that somatic mitochondria within human iPSCs revert to an immature ESC-like state with respect to organelle morphology and distribution, expression of nuclear factors involved in mitochondrial biogenesis, content of mitochondrial DNA, intracellular ATP level, oxidative damage, and lactate generation. Upon differentiation, mitochondria within iPSCs and ESCs exhibited analogous maturation and anaerobic-to-aerobic metabolic modifications. Overall, the data highlight that human iPSCs and ESCs, although not identical, share similar mitochondrial properties and suggest that cellular reprogramming can modulate the mitochondrial/oxidative stress pathway, thus inducing a rejuvenated state capable of escaping cellular senescence.
Model‐based quality assurance of protocol documentation: tools and methodology
Authors: Grieskamp Wolfgang , Kicillof Nicolas , Stobie Keith , Braberman Victor 
Published: March 2010

AbstractMicrosoft is producing interoperability documentation for Windows client–server and server–server protocols. The Protocol Engineering Team in the Windows organization is responsible for verifying the documentation to ensure that it is of the highest quality. Various test‐driven methods are being applied including, when appropriate, a model‐based approach. This paper describes core aspects of the quality assurance process and tools that were put in place, and specifically focuses on model‐based testing (MBT). Experience so far confirms that MBT works and that it scales, provided it is accompanied by sound tool support and clear methodological guidance. Copyright © 2010 John Wiley & Sons, Ltd.
Class cover catch digraphs
Authors: Marchette David 
Published: March 2010

AbstractThe class cover problem is one of finding a small number of sets covering (containing) points from one class without covering any points from a second class. The class cover catch digraph provides a solution to the class cover problem, which can be extended to a nonparametric classifier, similar in flavor to a reduced nearest neighbor classifier. This article describes the class cover catch digraph and its application to classification. Copyright © 2010 John Wiley & Sons, Inc.This article is categorized under:

Data: Types and Structure > Graph and Network Data
Nanoparticle detection of respiratory infection
Authors: Halfpenny Kristin C. , Wright David W. 
Published: March 2010

AbstractRespiratory viruses are a constant concern for all demographics. Examples include established viruses such as respiratory syncytial virus (RSV), the leading cause of respiratory infection in infants and young children, and emerging viruses such as severe acute respiratory syndrome (SARS), which reached near pandemic levels in 2003, or H1N1 (swine) influenza. Despite this prevalence, traditional methods of virus detection are typically labor intensive and require several days to successfully confirm infection. Recently, however, nanoparticle‐based detection strategies have been employed in an effort to develop detection assays that are both sensitive and expedient. Each of these platforms capitalizes on the unique properties of nanoparticles for the detection of respiratory viruses. In this article, several nanoparticle‐based scaffolds are discussed.Gold nanoparticles (AuNPs) have been functionalized with virus specific antibodies or oligonucleotides. In each of these constructs, AuNPs act as both an easily conjugated scaffolding system for biological molecules and a powerful fluorescence quencher. AuNPs have also been immobilized and used as electrochemical transducers. They efficiently serve as a conducting interface of electrocatalyic activity making them a powerful tool in this application. Quantum dots (QDs) posses unique fluorescence properties that have also been explored for their application to virus detection when combined with direct antibody conjugation or streptavidin‐biotin binding systems. QDs have an advantage over many traditional fluorophores because their fluorescence properties can be finely tuned and they are resistant to photobleaching. The development of these nanoparticle‐based detection strategies holds the potential to be a powerful method to quickly and easily confirm respiratory virus infection. WIREs Nanomed Nanobiotechnol 2010 2 277–290This article is categorized under:

Diagnostic Tools > In Vitro Nanoparticle-Based Sensing
Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease
Opening myrmecochory's black box: what happens inside the ant nest?
Authors: Servigne Pablo , Detrain Claire 
Published: March 2010

AbstractIn the process of seed dispersal by ants (myrmecochory), foragers bring diaspores back to their nest, then eat the elaiosome and usually reject viable seeds outside the nest. Here, we investigate what happens inside the nest, a barely known stage of the myrmecochory process, for two seed species (Viola odorata, Chelidonium majus) dispersed either by the insectivorous ant Myrmica rubra or by the aphid‐tending ant Lasius niger. Globally, elaiosome detachment decreased ants’ interest towards seeds and increased their probability of rejecting them. However, we found marked differences in seed management by ants inside the nest. The dynamics of elaiosome detachment were ant‐ and plant‐specific whereas the dynamic of seed rejection were mainly ant‐specific. Seeds remained for a shorter period of time inside the nest of the carnivorous ant Myrmica rubra than in Lasius niger nest. Thus, elaiosome detachment and seed rejection were two competing dynamics whose relative efficiency leads to variable outcomes in terms of types of dispersed items and of nutrient benefit to the ants. This is why some seeds remained inside the nest even without an elaiosome, and conversely, some seeds were rejected with an elaiosome still attached. Fresh seeds may be deposited directly in contact with the larvae. However, the dynamics of larvae‐seeds contacts were also highly variable among species. This study illustrates the complexity and variability of the ecological network of ant–seed interactions.