bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finite element assembly strategies on multi‐core and many‐core architectures
Authors: Markall G. R. , Slemmer A. , Ham D. A. , Kelly P. H. J. , Cantwell C. D. , Sherwin S. J. 
Published: January 2012

SUMMARYWe demonstrate that radically differing implementations of finite element methods (FEMs) are needed on multi‐core (CPU) and many‐core (GPU) architectures, if their respective performance potential is to be realised. Our numerical investigations using a finite element advection–diffusion solver show that increased performance on each architecture can only be achieved by committing to specific and diverse algorithmic choices that cut across the high‐level structure of the implementation. Making these commitments to achieve high performance for a single architecture leads to a loss of performance portability. Data structures that include redundant data but enable coalesced memory accesses are faster on many‐core architectures, whereas redundancy‐free data structures that are accessed indirectly are faster on multi‐core architectures. The Addto algorithm for global assembly is optimal on multi‐core architectures, whereas the Local Matrix Approach is optimal on many‐core architectures despite requiring more computation than the Addto algorithm. These results demonstrate the value in making the correct choice of algorithm and data structure when implementing FEMs, spectral element methods and low‐order discontinuous Galerkin methods on modern high‐performance architectures. Copyright © 2012 John Wiley & Sons, Ltd.
Toenail trace element status and risk of Barrett's oesophagus and oesophageal adenocarcinoma: Results from the FINBAR study
Authors: O'Rorke Michael A. , Cantwell Marie M. , Abnet Christian C. , Brockman and John D. , Murray Liam J. ,   on behalf of the FINBAR Study Group
Published: January 2012

AbstractTrace elements have been cited as both inhibitory and causative agents of cancer but importantly exposure to them is potentially modifiable. Our study aimed to examine toenail trace element status and risk of Barrett's oesophagus (BO) and oesophageal adenocarcinoma (OAC). Toenail clippings from each hallux were obtained from 638 participants of the FINBAR (Factors Influencing the Barrett's Adenocarcinoma Relationship) study comprising 221 healthy controls, 98 reflux oesophagitis, 182 BO and 137 OAC cases. The concentrations of eight toenail trace elements were determined using instrumental neutron activation analysis. Using multivariable adjusted logistic regression analysis, odds ratios (OR) and 95% confidence intervals (CIs) were calculated within tertiles of trace element concentrations. A twofold increased risk of BO was observed, but not OAC, among individuals in the highest tertile of toenail zinc status OR 2.21 (95% CI, 1.11–4.40). A higher toenail selenium status was not associated with risk of OAC OR 0.94 (95% CI, 0.44–2.04) or BO OR 0.89 (95% CI, 0.37–2.12). A borderline significant increased risk of BO was detected with a higher toenail cobalt concentration, OR 1.97 (95% CI, 1.01–3.85). No association was found between toenail levels of chromium, cerium, mercury and OAC or BO risk. This is the first case–control study to investigate a variety of trace elements in relation to OAC and BO risk. Despite antioxidant and proapoptotic properties, no associations were found with selenium. Higher concentrations of toenail zinc and cobalt were associated with an increased BO risk, but not OAC. These findings need confirmation in prospective analysis.
Intake of red meat and heterocyclic amines, metabolic pathway genes and bladder cancer risk
Authors: Lin Jie , Forman Michele R. , Wang Jianming , Grossman H. Barton , Chen Meng , Dinney Colin P. , Hawk Ernest T. , Wu Xifeng 
Published: January 2012

AbstractWe analyzed the association between meat intake, heterocyclic amines (HCAs) and bladder cancer (BC) risk in a large case‐control study comprised of 884 BC cases and 878 healthy controls, recruited from 1999 to 2009. Epidemiologic and dietary data were collected via an in‐person interview. Compared to the lowest quartile of red meat intake, the odds ratios (ORs) for the second, third and fourth quartiles were 1.17 (95% CI: 0.87–1.58), 1.47 (95% CI: 1.09–1.99) and 1.95 (95% CI: 1.41–2.68), respectively, (p‐for trend <0.001). In a subset of participants with intakes of HCAs available, compared with those with the lowest quartile of intake, the ORs for the second, third and fourth quartiles were 1.47 (95% CI: 0.60–3.64), 2.58 (95% CI: 1.09–6.11) and 3.32 (95% CI: 1.37–8.01), respectively, (p for trend <0.001). In cumulative analysis of SNPs in the pathway, compared with subjects carrying 0–4 unfavorable genotypes, subjects carrying 5 and 6 or more unfavorable genotypes were at 1.60‐fold (95% CI: 1.20–2.12) and 2.37‐fold (95% CI: 1.82–3.10) increased risk, respectively. Moreover, subjects carrying six or more unfavorable genotypes and whose red meat intake was in the highest quartile were at 5.09‐fold increased risk (95% CI: 2.89–8.96; p < 0.001). These results strongly support that high red meat intake, high intake of HCAs and carrying high number of unfavorable genotypes in the HCA metabolic pathways are associated with increased risk of BC in the study population.
Tumor–platelet interaction in solid tumors
Authors: Buergy Daniel , Wenz Frederik , Groden Christoph , Brockmann Marc A. 
Published: January 2012

AbstractElevated platelet counts in patients diagnosed with malignant tumors were first described more than 100 years ago. Today it is well known that in many types of solid tumors, thrombocytosis at the time of diagnosis is associated with shorter survival. From this well‐documented clinical correlation between platelet count and prognosis of solid tumors, the following questions arise: (i) Are the increased platelet counts the reason for shortened survival as platelet‐secreted cytokines might boost tumor growth and angiogenesis? (ii) Do platelets affect tumor metastasis thereby shortening survival time? or (iii) Are increased platelet counts simply an epiphenomenon of tumor growth with larger tumors resulting in higher platelet counts and shorter survival times? We address these three questions within our review of the current literature to provide a comprehensive overview of the current concepts in tumor–platelet interaction.
Diagnostic value of fecal tumor M2‐pyruvate kinase for CRC screening: A systematic review and meta‐analysis
Authors: Li Rui , Liu Jianjun , Xue Huiping , Huang Gang 
Published: January 2012

AbstractThe measurement of fecal tumor M2‐pyruvate kinase (PKM2), overexpressed in tumor cells, has been proposed as a novel tool for detecting colorectal cancer (CRC). However, the sensitivity and specificity of this test varied among studies. The aim of this meta‐analysis was to determine the diagnostic accuracy of fecal PKM2 for CRC and to evaluate its utility in the CRC screening. It was compared to guaiac fecal occult blood test (gFOBT) or immunological fecal occult blood test (iFOBT). Through comprehensive literature search, 10 studies met the inclusion criteria and were included. Summary estimates for sensitivity and specificity were calculated by using the bivariate random effect model. The hierarchical summary receiver operating characteristic curve was also undertaken. The overall sensitivity and specificity of fecal PKM2 for detecting CRC were 79% (95% CI = 75–83%) and 81% (95% CI = 73–87%), respectively. The summary positive predictive value and negative predictive value were 74% (95% CI = 56–87%) and 86% (95% CI = 79–91%), respectively. The pooled diagnostic odds ratio was 16 (95% CI = 10–26). In head‐to‐head comparison, the diagnostic odds ratio of PKM2 and gFOBT for CRC were 10.167 (95% CI = 5.992–17.250) and 6.557 (95% CI = 3.467–12.403), respectively. The diagnostic odds ratio of PKM2 and iFOBT for CRC were 9.542 (95% CI = 5.893–15.452) and 67.248 (95% CI = 16.194–279.26), respectively. The fecal PKM2 test was a diagnostic tool with moderate sensitivity and specificity for detecting CRC. Its diagnostic efficiency was similar to that of gFOBT. Because of its relatively low specificity and positive predict value, fecal PKM2 was not recommended used alone as a screening tool for CRC.
Fourier transform infrared microspectroscopy identifies protein propionylation in histone deacetylase inhibitor treated glioma cells
Authors: Singh Bhawana , Boopathy Sivaraman , Somasundaram Kumaravel , Umapathy Siva 
Published: January 2012

AbstractHistone deacetylase inhibitors (HDIs) have attracted considerable attention as potential drug molecules in tumour biology. In order to optimise chemotherapy, it is important to understand the mechanisms of regulation of histone deacetylase (HDAC) enzymes and modifications brought by various HDIs. In the present study, we have employed Fourier transform infrared microspectroscopy (FT‐IRMS) to evaluate modifications in cellular macromolecules subsequent to treatment with various HDIs. In addition to CH3 (methyl) stretching bands at 2872 and 2960 cm–1, which arises due to acetylation, we also found major changes in bands at 2851 and 2922 cm–1, which originates from stretching vibrations of CH2 (methylene) groups, in valproic acid treated cells. We further demonstrate that the changes in CH2 stretching are concentration‐dependent and also induced by several other HDIs. Recently, HDIs have been shown to induce propionylation besides acetylation [1]. Since propionylation involves CH2 groups, we hypothesized that CH2 vibrational frequency changes seen in HDI treated cells could arise due to propionylation. As verification, pre‐treatment of cells with propionyl CoA synthetase inhibitor resulted in loss of CH2 vibrational changes in histones, purified from valproic acid treated cells. This was further proved by western blot using propionyl‐lysine specific antibody. Thus we demonstrate for the first time that propionylation could be monitored by studying CH2 stretching using IR spectroscopy and further provide a platform for monitoring HDI induced multiple changes in cells. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Analysis of cholesterol oxidation products by Fast gas chromatography/mass spectrometry
Authors: Cardenia Vladimiro , Rodriguez‐Estrada Maria T. , Baldacci Elena , Savioli Stefano , Lercker Giovanni 
Published: January 2012

AbstractThe aim of the present study was to set‐up a Fast gas chromatography/mass spectrometry method for the analysis of cholesterol oxidation products (COPs). A silylated mixture of seven oxysterol standards was injected into a Fast GC/MS system. A capillary GC column (10 m×0.1 mm internal diameter×0.1 μm film thickness) coated with 95% dimethyl‐ and 5% diphenyl‐polysiloxane, was used. The method gave a fast (total analysis time=3.5 min) and satisfactory resolution (R>1.2) of the COPs standards, with a good repeatability and sensitivity, similar to those of conventional GC/MS; recoveries were tested on mice liver. Fast GC/MS method suitability for COPs analysis in food was also tested on an oxidized sardine fillet, which had been previously saponified and purified by NH2 solid‐phase extraction (SPE); a good repeatability and sensitivity was also obtained. The analytical performance of the Fast GC/MS method for the determination of COPs, together with the consequent significant reduction of the analysis time and consumables, demonstrates that Fast GC/MS represents a valid alternative to conventional GC/MS and evinces the great potential of such an analytical technique, which could be applied for both food and biological samples.
Radical formation during phenol oxidation in aqueous media
Authors: Shendrik A. N. , Odaryuk I. D. , Kanibolotska L. V. , Kalinichenko E. A. , Tsyapalo A. S. , Beznos V. V. , Kanibolotsky A. L. 
Published: January 2012

AbstractKinetics of oxygen consumption, reaction product formation, and chemiluminescence during polyphenol oxidation by molecular oxygen in alkaline aqueous media with additions of l‐ascorbic acid (AscH2) and homocysteine (HCys) has been investigated. In these processes, AscH2 and HCys have been shown to act as typical radical‐reaction inhibitors that can be used for determinations of the radical formation rates. The rates of radical formation during oxidation of hydroquinone (p‐QH2), chlorohydroquinone (Cl‐QH2), 2,5‐dichlorohydroquinone (2,5Cl‐QH2), catechol (PK), 4‐methylcatechol (4CH3‐PK), pyrogallol (PG), gallic acid (GK) have been estimated. © 2012 Wiley Periodicals, Inc. Int J Chem Kinet 44: 414–422, 2012
Synthesis and Characterization of Poly(acrylic acid) Brushes: “Grafting‐Onto” Route
Authors: Sudre Guillaume , Siband Elodie , Hourdet Dominique , Creton Costantino , Cousin Fabrice , Tran Yvette 
Published: January 2012

AbstractA guideline for the synthesis of poly(acrylic acid) brushes on planar silica surfaces by the “grafting‐onto” approach is described. It is demonstrated that some thermal precautions must be taken to obtain extended brushes. It is also shown that neutron reflectivity is well suited for the characterization of each step of the synthesis, while it is (unfortunately) rarely used for that purpose. The steps are the following: first, the substrates are covered with a self‐assembled monolayer of epoxy‐terminated molecules; then, the poly(tert‐butyl acrylate) brushes are built using preformed and end‐functionalized chains; finally, the deprotection of the ester group is performed using a pyrolysis reaction to convert the poly(tert‐butyl acrylate) brushes into poly(acrylic acid) brushes.
Synthesis and Polymerization of Fused‐Ring Thienodipyrrole Monomers
Authors: Nguyen Hien Q. , Rainbolt Elizabeth A. , Sista Prakash , Stefan Mihaela C. 
Published: January 2012

AbstractThe synthesis and polymerization of fused‐ring 1,7‐didodecyl‐1,7‐dihydrothieno[3,2‐b:4,5‐b′]dipyrrole monomer are reported. The FeCl3‐mediated oxidative polymerization and Stille coupling polymerization of the thienodipyrrole monomer were employed to generate homopolymers and an alternating copolymer with thiophene. The synthesized polymers have molecular weights ranging from 1600 to 6500 g mol−1 and display the absorption maxima at ≈355 nm.
The influence of maternal–fetal attachment and health practices on neonatal outcomes in low‐income, urban women
Authors: Alhusen Jeanne L. , Gross Deborah , Hayat Matthew J. , (Nancy) Woods Anne B. , Sharps Phyllis W. 
Published: January 2012

AbstractMaternal–fetal attachment (MFA) has been associated with health practices during pregnancy, but less is known about this relationship in low‐income women, and no identified studies have examined this relationship to neonatal outcomes. This longitudinal descriptive study was conducted to examine the relationships among MFA, health practices during pregnancy, and neonatal outcomes in a sample of low‐income, predominantly African‐American women and their neonates. MFA was associated with health practices during pregnancy and adverse neonatal outcomes. Health practices during pregnancy mediated the relationships of MFA and adverse neonatal outcomes. The results support the importance of examining MFA in our efforts to better understand the etiology of health disparities in neonatal outcomes. © 2012 Wiley Periodicals, Inc. Res Nurs Health 35:112–120, 2012
The interplay of HER2/HER3/PI3K and EGFR/HER2/PLC‐γ1 signalling in breast cancer cell migration and dissemination
Authors: Balz Lydia M , Bartkowiak Kai , Andreas Antje , Pantel Klaus , Niggemann Bernd , Zänker Kurt S , Brandt Burkhard H , Dittmar Thomas 
Published: January 2012

AbstractHER2 signalling by heterodimerisation with EGFR and HER3 in breast cancer is associated with worst outcome of the afflicted patients, which is attributed not only to the aggressiveness of such tumours but also to therapy resistance. Thus, in the present study we investigated the role of EGFR, HER2 and HER3 lateral signalling in cell migration by applying the MDA‐MB‐468‐HER2 (MDA‐HER2) breast cancer cell line, representing a valid model system. Knockdown of HER3 expression by siRNA resulted in decreased phosphorylated AKT (pAKT) levels, abrogated epidermal growth factor (EGF)‐mediated PLC‐γ1 activation and a diminished EGF‐induced migratory activity, depicting the interplay of EGF receptor (EGFR)/HER2/PLC‐γ1 and HER2/HER3/PI3K signalling in mediating the migration of EGFR/HER2/HER3‐expressing breast cancer cells. Since therapy failure usually arises from metastatic cells, we further investigated whether HER3 signalling was active in established breast cancer disseminated tumour cell (DTC) lines as well as in primary DTCs derived from breast cancer patients. EGF treatment of DTC lines resulted solely in increased pAKT S473 levels, whereas in MDA‐HER2 cells both pAKT S473 and pAKT T308 levels were increased upon EGF stimulation. Moreover, despite active HER3 molecules, as indicated by pTyr1222 staining, about 90% of analysed breast cancer patient DTCs exhibited very low or even no detectable pAKT S473 levels, suggesting that these cells might have fallen into dormancy. In summary, our data indicate the important role in EGFR, HER2 and HER3 lateral signalling in breast cancer cell migration. Moreover, our data further show that primary tumour cells and DTCs can vary in their HER activation status, which is important to know in the context of cancer therapy. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Design for validation of acute myocardial infarction cases in Mini‐Sentinel
Authors: Cutrona Sarah L. , Toh Sengwee , Iyer Aarthi , Foy Sarah , Cavagnaro Elizabeth , Forrow Susan , Racoosin Judith A. , Goldberg Robert , Gurwitz Jerry H. 
Published: January 2012

ABSTRACTPurposeTo describe the acute myocardial infarction (AMI) validation project, a test case for health outcome validation within the US Food and Drug Administration–funded Mini‐Sentinel pilot program.MethodsThe project consisted of four parts: (i) case identification—developing an algorithm based on the International Classification of Diseases, Ninth Revision, to identify hospitalized AMI patients within the Mini‐Sentinel Distributed Database; (ii) chart retrieval—establishing procedures that ensured patient privacy (collection and transfer of minimum necessary amount of information, and redaction of direct identifiers to validate potential cases of AMI); (iii) abstraction and adjudication—trained nurse abstractors gathered key data using a standardized form with cardiologist adjudication; and (iv) calculation of the positive predictive value of the constructed algorithm.ResultsKey decision points included (i) breadth of the AMI algorithm, (ii) centralized versus distributed abstraction, and (iii) approaches to maintaining patient privacy and to obtaining charts for public health purposes. We used an algorithm limited to International Classification of Diseases, Ninth Revision, codes 410.x0‐410.x1. Centralized data abstraction was performed because of the modest number of charts requested (<155). The project's public health status accelerated chart retrieval in most instances.ConclusionsWe have established a process to validate AMI within Mini‐Sentinel, which may be used for other health outcomes. Challenges include the following: (i) ensuring that only minimum necessary data are transmitted by Data Partners for centralized chart review, (ii) establishing procedures to maintain data privacy while still allowing for timely access to medical charts, and (iii) securing access to charts for public health uses that do not require approval from an institutional review board while maintaining patient privacy. Copyright © 2012 John Wiley & Sons, Ltd.
A systematic review of validated methods for identifying lymphoma using administrative data
Authors: Herman Ronald A. , Gilchrist Bradley , Link Brian K. , Carnahan Ryan 
Published: January 2012

ABSTRACTPurposeTo systematically review published studies for algorithms that identified lymphoma as a health outcome of interest in administrative or claims data and examined the validity of the algorithm to identify lymphoma cases.MethodsA systematic literature search was executed using PubMed and the Iowa Drug Information Service database. Two investigators reviewed search results to identify studies using administrative or claims databases from the USA or Canada that both reported and validated an algorithm to identify lymphoma.ResultsThe search identified 713 unique citations with 402 eliminated by an initial screen of the article abstract. The remaining 311 resulted in one study that identified and validated an algorithm. Ten other studies reported algorithms but were not validated. The validated study reported four possible algorithms that had a specificity (> 99%), but the algorithm using two diagnostic codes recorded within 2 months had the best positive predictive value (PPV = 62.83%) and a sensitivity (79.81%). The most comprehensive algorithm required multiple diagnostic codes 2 months apart or diagnostic, and procedure codes on the same day had the greatest sensitivity (88.31%) and a PPV = 56.69%. The algorithm that required only a single diagnostic or procedure code had the worst PPV (34.72%).ConclusionThe International Classification of Disease, Ninth Revision diagnostic, clinical procedure, and complication codes for lymphoma can identify incident hematologic malignancies and solid tumors with high specificity but with relatively low to moderate sensitivity and PPVs. When diagnostic and procedure codes were required on the same visit or multiple codes between visits, then PPV was increased. Relying on a single registry to confirm true positive cases is also not sufficient. Copyright © 2012 John Wiley & Sons, Ltd.
A systematic review of validated methods for identifying transfusion‐related sepsis using administrative and claims data
Authors: Carnahan Ryan M. , Herman Ronald A. , Moores Kevin G. 
Published: January 2012

ABSTRACTPurposeTo systematically review algorithms to identify transfusion‐related sepsis or septicemia in administrative data, with a focus on studies that have examined the validity of the algorithms.MethodsA literature search was conducted using PubMed, the database of the Iowa Drug Information Service (IDIS/Web), and Embase. A Google Scholar search was conducted because of difficulty identifying relevant studies. Reviews were conducted by two investigators to identify studies using data sources from the USA or Canada, because these data sources were most likely to reflect the coding practices of Mini‐Sentinel data sources.ResultsNo studies that were identified that used administrative data to identify sepsis or septicemia related to transfusion of blood products. Thus, four studies that studied the validity of algorithms to identify sepsis and two that studied algorithms to identify allogeneic blood transfusion are described in this review. Two studies found acceptable positive predictive values of 80% and 89% for algorithms to identify sepsis in hospitalized patients. One study reported a negative predictive value of 80% in hospitalized patients, and another, a sensitivity of 75%. One study of veterans receiving surgery reported much worse performance characteristics. Two studies reported near‐perfect specificity of codes for allogeneic red blood cell transfusion, but sensitivity ranged from 21% to 83%.ConclusionsThere is no information to assess the validity of algorithms to identify transfusion‐related sepsis or septicemia. Codes to identify sepsis performed well in most studies. Algorithms to identify transfusions need further research that includes a broader range of transfusion types. Copyright © 2012 John Wiley & Sons, Ltd.