bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acephate, methamidophos and monocrotophos residues in a laboratory‐scale oil refining process
Authors: Yeoh Chee Beng , Chong Chiew Let 
Published: March 2009

AbstractAcephate, methamidophos and monocrotophos are insecticides used in oil palm plantations for the control of bagworms and leaf‐eating caterpillars. The main purpose of this study was to determine whether the physical refining process at laboratory scale, which simulated the manufacturing process, could remove the residues of these three insecticides in crude palm oil, in the unlikely event that crude palm oil were contaminated with these organophosphorus insecticides. A series of crude palm oil samples spiked with low (0.1 µg/g) and high (1.0 µg/g) levels of these insecticides were subjected to a laboratory‐scale physical oil refining process. Oil samples drawn at various stages of the refining process, namely, degumming, bleaching and deodorization, were analyzed using an in‐house analytical method. The results obtained from these experiments suggest that the physical refining process is capable of effectively removing residual insecticides from crude palm oil. The final product of crude palm oil refining, the refined, bleached and deodorized palm oil, was found to have no detectable levels of acephate, methamidophos and monocrotophos.
Genomic instability in giant cell tumor of bone. A study of 52 cases using DNA ploidy, relocalization FISH, and array‐CGH analysis
Authors: Moskovszky Linda , Szuhai Károly , Krenács Tibor , Hogendoorn Pancras C. W. , Szendrői Miklós , Benassi Maria Serena , Kopper László , Füle Tibor , Sápi Zoltán 
Published: March 2009

AbstractGenetic instability in relation to clinical behavior was studied in 52 cases of giant cell tumor of bone (GCTB). Ploidy was determined in the mononuclear cell population by using native cell smears and image cytometry. A relocalization technique allowed fluorescent in situ hybridization (FISH) analysis of CD68‐negative neoplastic cells for numerical changes of chromosomes X, 3, 4, 6, 11, and telomeric association on 11p. Genome‐wide alterations were tested using array comparative genomic hybridization (array‐CGH) on magnetically separated CD68‐negative tumor cells. CTNNB1, TP53, and BCL2 protein expression was also analyzed in formol‐paraffin sections to see if their pathways are involved in the development of chromosomal instability. CD68‐positive histiocytes showed no significant numerical chromosome and telomeric alterations. Based on ploidy values and clinical outcome, we could distinguish five groups as follows: diploid nonrecurrent (n = 20), tetraploid nonrecurrent (n = 6), diploid recurrent (n = 5), tetraploid and/or aneuploid recurrent (n = 14), and malignant cases (n = 7). Random individual‐cell aneusomy was significantly (P < 0.001) more frequent in the recurrent groups (36.01 ± 11.94%) than in the benign nonrecurrent cases (10.65 ± 3.66%). The diploid recurrent group showed significantly (P < 0.001) increased balanced aneusomy compared with the diploid nonrecurrent group and the tetraploid nonrecurrent group represented eusomic polysomy. Array‐CGH and FISH showed clonal aberrations almost exclusively in the malignant group. None of the protein markers tested showed significant correlation with elevated aneuploidy/polysomy (P = 0.56). Our results show that ploidy determination combined with FISH analysis may help predicting recurrence potential of GCTB and suggest that chromosomal abnormalities superimposed on telomeric associations could be responsible for an aggressive clinical course. © 2009 Wiley‐Liss,Inc.
Pathway analysis by adaptive combination of P‐values
Authors: Yu Kai , Li Qizhai , Bergen Andrew W. , Pfeiffer Ruth M. , Rosenberg Philip S. , Caporaso Neil , Kraft Peter , Chatterjee Nilanjan 
Published: March 2009

AbstractIt is increasingly recognized that pathway analyses—a joint test of association between the outcome and a group of single nucleotide polymorphisms (SNPs) within a biological pathway—could potentially complement single‐SNP analysis and provide additional insights for the genetic architecture of complex diseases. Building upon existing P‐value combining methods, we propose a class of highly flexible pathway analysis approaches based on an adaptive rank truncated product statistic that can effectively combine evidence of associations over different SNPs and genes within a pathway. The statistical significance of the pathway‐level test statistics is evaluated using a highly efficient permutation algorithm that remains computationally feasible irrespective of the size of the pathway and complexity of the underlying test statistics for summarizing SNP‐ and gene‐level associations. We demonstrate through simulation studies that a gene‐based analysis that treats the underlying genes, as opposed to the underlying SNPs, as the basic units for hypothesis testing, is a very robust and powerful approach to pathway‐based association testing. We also illustrate the advantage of the proposed methods using a study of the association between the nicotinic receptor pathway and cigarette smoking behaviors. Genet. Epidemiol. 33:700–709, 2009. Published 2009 Wiley‐Liss, Inc.
Reliability and validity of revised Turkish version of Mini Mental State Examination (rMMSE‐T) in community‐dwelling educated and uneducated elderly
Authors: Keskinoglu Pembe , Ucku Reyhan , Yener Görsev , Yaka Erdem , Kurt Pınar , Tunca Zeliha 
Published: March 2009

AbstractObjectiveTo evaluate the reliability and validity of the revised Turkish version of Mini Mental State Examination (rMMSE‐T) in educated and uneducated community‐dwelling elderly, to re‐organize the present Turkish version of MMSE and to determine cut‐off point of the revised test.MethodsThis cross‐sectional and analytical study involved totally 490 elderly subjects selected by cluster sampling method. Receiver operating characteristic (ROC) analysis, kappa analysis and Cronbach's α coefficients were used for statistical analysis.ResultsAreas under ROC curve in educated and uneducated elderly were found as 0.953 and 0.907. Cut‐off point of 22/23 of rMMSE‐T in educated elderly had the highest sensitivity (90.9), specificity (97.0) and positive likelihood ratio (30.3), whereas cut‐off point of 18/19 of the test in uneducated elderly had the highest sensitivity (82.7), specificity (92.3) and positive likelihood ratio (10.7). The Cronbach's α values of the rMMSE‐T for educated and uneducated elderly were higher than 0.7 (sign of good internal consistency of the test). A significant correlations between intrarater and interrater test–retest in educated elderly subjects were observed (0.966 (p = 0.000); 0.855 (p = 0.000), respectively), and also in uneducated elderly (0.988 (p = 0.000); 0.934 (p = 0.000), respectively). Kappa value of the test in educated and uneducated elderly showed a perfect agreement interraters (1.000) and a substantial agreement in intraraters (1.000, 0.784; 0.826, 0.656, respectively).ConclusionrMMSE‐T had a high reliability and validity. It will be more appropriate to use the revised test and the new cut‐off point for the diagnosis and screening of dementia among community‐dwelling Turkish elderly population. Copyright © 2009 John Wiley & Sons, Ltd.
How long should a trial of escitalopram treatment be in patients with major depressive disorder, generalised anxiety disorder or social anxiety disorder? An exploration of the randomised controlled trial database
Authors: Baldwin David S. , Stein Dan J. , Dolberg Ornah T. , Bandelow Borwin 
Published: March 2009

AbstractObjectiveTo extend the knowledge of course of improvement in patients with major depressive disorder (MDD), social anxiety disorder (SAD) or generalised anxiety disorder (GAD) participating in randomised placebo‐controlled trials (RCTs) and to infer the optimal duration of initial escitalopram treatment in clinical practice, after which intervention might be reasonable in case of non‐response.Methods
Post hoc analysis of pooled clinical trial database for escitalopram in MDD (14 studies), GAD (4 studies) and SAD (2 studies). ‘Onset’ of action was defined as a 20% or more decrease from baseline score in disorder‐specific psychopathological rating scales: ‘response’ as a 50% or more decrease from baseline score.ResultsIn MDD, the probability of responding at week 8 if no onset was apparent at week 2 was 43%; in patients with an onset of effect the probability was nearly 80%. Similar patterns were observed in GAD and SAD. The chance of responding beyond week 4 in MDD, GAD and SAD was 20% or less if no effect had occurred by week 2.ConclusionsThe pattern of response in these RCTs suggests that in patients with MDD, GAD or SAD in wider clinical practice, a period of at least 4 weeks is worthwhile before considering further intervention. Copyright © 2009 John Wiley & Sons, Ltd.
Transient or steady‐state? Using vertical temperature profiles to quantify groundwater–surface water exchange
Authors: Anibas Christian , Fleckenstein Jan H. , Volze Nina , Buis Kerst , Verhoeven Ronny , Meire Patrick , Batelaan Okke 
Published: March 2009

AbstractHeat is recognized as a natural tracer to identify the exchange of water between the groundwater and surface water compartment. One‐dimensional (1D) heat transport models have the ability to obtain quantitative estimates of vertical fluxes through the sediment matrix. Input to these models can come from temperatures observed in the surface water and in the bed material of rivers and lakes. The upper thermal boundary condition at the groundwater–surface water interface is affected by seasonal and diurnal temperature variations. We hypothesize that effects of these transient influences are negligible at certain times of the year, such that the vertical temperature distribution can be approximated to be at steady state. Temperature time series observed over a year in the surface water and at several depths below a river in Belgium and in sediments of an acid mine lake in Eastern Germany were simulated with a heat balance model implemented in FEMME and the water and energy model VS2DH to obtain seepage fluxes. Temperature variations throughout the year at all depths could be adequately reproduced with the transient models. Vertical temperature profiles at several measuring times during the year were also fitted with an analytical, steady‐state solution for 1D heat transport and the obtained fluxes compared to the results from transient simulations. Fluxes obtained from the much simpler steady‐state solution were compared well with the flux rates from transient simulations for moments between mid and late summer, as well as during the winter. During transitional seasons (fall and spring), the fluxes from the steady‐state solution deviated significantly from the transient estimates with a tendency to underestimate at the beginning and to overestimate towards the end of those seasons. We conclude that fitting a simple analytical solution for 1D vertical heat transport to temperature data observed at particular well‐selected times of the year can provide an inexpensive, simple method to obtain accurate point estimates of groundwater–surface water exchange in rivers and lakes. Copyright © 2009 John Wiley & Sons, Ltd.
Implications of noise and resolution on mechanical properties of trabecular bone estimated by image‐based finite‐element analysis
Authors: Rajapakse Chamith S. , Magland Jeremy , Zhang X. Henry , Liu X. Sherry , Wehrli Suzanne L. , Guo X. Edward , Wehrli Felix W. 
Published: March 2009

AbstractRecent advances in micro‐magnetic resonance imaging (µMRI) now allow noninvasive assessment of mechanical properties of trabecular bone (TB) in vivo by micro finite‐element analysis. The first aim of this work was to address the implications of limited resolution and signal‐to‐noise ratio on elastic properties of TB derived under conditions of in vivo imaging via simulation at various resolutions and noise levels on the basis of models derived from µCT images at 21 µm isotropic voxel size from cores of cadaveric human TB (n = 13) from three anatomic sites. The second aim was to compare how elastic constants derived from actual MR images at 9.4 Tesla at 50 µm isotropic voxel size compare with those from high‐resolution µCT. Elastic moduli computed from simulated in vivo µMR images were highly correlated with those obtained from µCT (R2 = 0.99) and the data were relatively immune to noise. Correlations of similar strength were obtained between estimated moduli from µCT and acquired high‐field MR images. Systematic errors manifesting in significant deviations of the slopes from unity are caused by higher apparent bone‐volume fraction of the MR images but can potentially be corrected with appropriate histogram‐standardization techniques. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27:1263–1271, 2009
Hip resurfacing increases bone strains associated with short‐term femoral neck fracture
Authors: Long Jason P. , Santner Thomas J. , Bartel Donald L. 
Published: March 2009

AbstractShort‐term femoral neck fracture is a primary complication associated with contemporary hip resurfacing. Some fractures are associated with neck notching, while others occur in the absence of notching. These unexplained fractures may be due to large magnitude strains near the implant rim, which could cause bone damage accumulation and eventual neck fracture. We used statistically augmented finite element analysis to identify design and environmental variables that increase bone strains near the implant rim after resurfacing, and lead to strain magnitudes sufficient for rapid damage accumulation. After resurfacing, the compressive strains in the inferior, peripheral neck increased by approximately 25%, particularly when the implant shell was bonded. While the tensile strains in the peripheral neck were low in magnitude in the immediate postoperative models, they increased substantially following compressive damage accumulation. Low bone modulus, within the range of normal bone, and high head load contributed the most to large magnitude strains. Therefore, in some cases, hip resurfacing may cause a region of compressive bone damage to develop rapidly, which in turn leads to large tensile strains and potential neck fracture. Our study suggests that indications for surgery should account for bone material quality, and that rehabilitation protocols should avoid high‐load activities. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27:1319–1325, 2009
Vibrational spectroscopy of a compound with a CS7 ring
Authors: Parker Stewart F. , Refson Keith , Tavender Susan M. , Albers Peter , Hannebauer Bernd , Janik Matthias , Müller Arndt , Martens Jürgen , Watzke Martin , Shankland Kenneth , Leech Charlotte , Offermanns Heribert 
Published: March 2009

AbstractThe product of the Asinger reaction between elemental sulfur, n‐butylamine and acetophenone is 8‐(n‐butylaminophenylmethyliden)‐1,2,3,4,5,6,7‐heptathiocane which contains a CS7 ring. A combination of infrared, Raman and inelastic neutron scattering spectroscopies with periodic density functional theory calculations is used to provide a complete assignment of the vibrational spectra of this unusual species. The similarity between the Raman spectra of the compound and that of elemental sulfur is particularly striking. Copyright © 2009 John Wiley & Sons, Ltd.
Raman spectroscopic study of the antimonate mineral brandholzite Mg[Sb2(OH)12]·6H2O
Authors: Frost Ray L. , Čejka Jiří , Sejkora Jiří , Ozdín Daniel , Bahfenne Silmarilly , Keeffe Eloise C. 
Published: March 2009

AbstractRaman spectra of brandholzite Mg[Sb2(OH)12]·6H2O were studied, complemented with infrared spectra, and related to the structure of the mineral. An intense Raman sharp band at 618 cm−1 is attributed to the SbO symmetric stretching mode. The low‐intensity band at 730 cm−1 is ascribed to the SbO antisymmetric stretching vibration. Low‐intensity Raman bands were found at 503, 526 and 578 cm−1. Corresponding infrared bands were observed at 527, 600, 637, 693, 741 and 788 cm−1. Four Raman bands observed at 1043, 1092, 1160 and 1189 cm−1 and eight infrared bands at 963, 1027, 1055, 1075, 1108, 1128, 1156 and 1196 cm−1 are assigned to δ SbOH deformation modes. A complex pattern resulting from the overlapping band of the water and hydroxyl units is observed. Raman bands are observed at 3240, 3383, 3466, 3483 and 3552 cm−1; infrared bands at 3248, 3434 and 3565 cm−1. The Raman bands at 3240 and 3383 cm−1 and the infrared band at 3248 cm−1 are assigned to water‐stretching vibrations. The two higher wavenumber Raman bands observed at 3466 and 3552 cm−1 and two infrared bands at 3434 and 3565 cm−1 are assigned to the stretching vibrations of the hydroxyl units. Observed Raman and infrared bands in the OH stretching region are associated with O‐H···O hydrogen bonds and their lengths 2.72, 2.79, 2.86, 2.88 and 3.0 Å (Raman) and 2.73, 2.83 and 3.07 Å (infrared). Copyright © 2009 John Wiley & Sons, Ltd.
To b or not to b: The ongoing saga of peptide b ions
Authors: Harrison Alex G. 
Published: March 2009

AbstractModern soft ionization techniques readily produce protonated or multiply protonated peptides. Collision‐induced dissociation (CID) of these protonated species is often used as a method to obtain sequence information. In many cases fragmentation occurs at amide bonds. When the charge resides on the C‐terminal fragment so‐called y ions are produced which are known to be protonated amino acids or truncated peptides. When the charge resides on the N‐terminal fragment so‐called b ions are produced. Often the sequence of y and b ions are essential for peptide sequencing. The b ions have many possible structures, a knowledge of which is useful in this sequencing. The structures of b ions are reviewed in the following with particular emphasis on the variation of structure with the number of amino acid residues in the b ion and the effect of peptide side chain on b ion structure. The recent discovery of full cyclization of larger b ions results in challenges in peptide sequencing. This aspect is discussed in detail. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 28:640–654, 2009
Malnutrition and neutropenia in children treated for Burkitt lymphoma in Malawi
Authors: Israëls Trijn , van de Wetering Marianne D. , Hesseling Peter , van Geloven Nan , Caron Huib N. , Molyneux Elizabeth M. 
Published: March 2009

AbstractBackgroundInfection in neutropenic children is a major cause of morbidity and mortality in children treated for cancer. In developing countries, children with cancer are often malnourished at diagnosis. In Blantyre, Malawi, children with Burkitt lymphoma are treated with a local protocol with limited toxicity. The aim of this study was to evaluate the incidence and outcome of febrile neutropenia during this treatment and the association with malnutrition at diagnosis.MethodsWe documented nutritional status, febrile and/or neutropenic episodes, antibiotic therapy and short term outcome of all children with Burkitt lymphoma treated according to the local protocol and admitted from January 2007 to March 2008.ResultsFifty eight (69%) of 84 patients were acutely malnourished at diagnosis with an arm muscle area (AMA) below the 5th percentile. Malnutrition at diagnosis was associated with a significantly higher rate of profound neutropenia. This association remained significant (OR 12; 95% C.I. 1.5 ‐ infinitely; P = 0.012) after control for clinical stage of disease, bone marrow involvement and HIV infection which are possible confounders. All patients with profound neutropenia, prolonged neutropenia and treatment related deaths were malnourished at diagnosis. Four (4.9%) of 81 patients died of treatment related causes; three of them due to a Gram negative septicaemia.ConclusionAcute malnutrition at diagnosis is associated with significantly more treatment related profound neutropenia. The intensity of chemotherapeutic regimens has to be adapted to the level of available supportive care and patients' nutritional status and tolerance to avoid unacceptable morbidity and mortality. This local treatment protocol for Burkitt lymphoma has a treatment related mortality of 5% in patients in Malawi. Pediatr Blood Cancer 2009;53:47–52. © 2009 Wiley‐Liss, Inc.
Proteomic analysis of a filamentous fungal endophyte using EST datasets
Authors: Bassett Shalome A. , Bond Judy J. , Kwan Fiona Y. S. , McCulloch Alan F. , Haynes Paul A. , Johnson Richard D. , Bryan Gregory T. , Jordan T. William 
Published: March 2009

AbstractProteomic analysis of many species of fungi, particularly filamentous fungi, is difficult due to the lack of publicly available genome sequence data and the problems associated with cross‐species comparisons. Furthermore, the detection of fungal proteins in biological systems where there are a greater number of proteins present from other eukaryote species provides additional challenges. We present an EST‐based approach for identifying proteins from a fungal endophyte of temperate grasses and demonstrate that this method is well suited for fungi with minimal sequence data.
Unbiased proteomic screen for binding proteins to modified lysines on histone H3
Authors: Chan Doug W. , Wang Yi , Wu Meng , Wong Jiemin , Qin Jun , Zhao Yingming 
Published: March 2009

AbstractWe report a sensitive peptide pull‐down approach in combination with protein identification by LC‐MS/MS and qualitative abundance measurements by spectrum counting to identify proteins binding to histone H3 tail containing dimethyl lysine 4 (H3K4me2), dimethyl lysine 9 (H3K9me2), or acetyl lysine 9 (H3K9ac). Our study identified 86 nuclear proteins that associate with the histone H3 tail peptides examined, including seven known direct binders and 16 putative direct binders with conserved PHD finger, bromodomain, and WD40 domains. The reliability of our proteomic screen is supported by the fact that more than one‐third of the proteins identified were previously described to associate with histone H3 tail directly or indirectly. To our knowledge, the results presented here are the most comprehensive analysis of H3K4me2, H3K9me2, and H3K9ac associated proteins and will provide a useful resource for researchers studying the mechanisms of histone code effector proteins.
Growth and long‐term lung function in cystic fibrosis: A longitudinal study of patients diagnosed by neonatal screening
Authors: Assael Baroukh Maurice , Casazza Giovanni , Iansa Patrizia , Volpi Sonia , Milani Silvano 
Published: March 2009

AbstractObjectiveSo far there is no long‐term analysis relating the achievement of growth milestones (such as prepubertal and pubertal take‐off and peak velocity) to the course of respiratory function from childhood to adulthood in cystic fibrosis. This study was designed to evaluate linear growth and severity of lung disease, find a correlation between growth and disease severity throughout childhood.PatientsOne hundred sixty‐three patients from one center were selected according to: diagnosis by neonatal screening, complete follow‐up available (four height measurements/year) until the age of 20, respiratory tests available from the age of 5–6 years until adulthood, lung transplantation, or death. Disease was classified as mild or severe according to FEV1 (group 1 and group 2). A third group of patients (group 3) consisted of those who died or underwent lung transplantation before the age of 18.MethodsIndividual growth profiles were fitted with a seven‐constant nonlinear growth function. A multivariate linear model was fitted, with gender and severity of disease as covariates, and age, height, and height velocity at growth milestones as dependent variables. Data were compared with those of the normal Italian population.ResultsLung disease severity correlates with delayed prepubertal and pubertal growth milestones. Peak height velocities were significantly reduced in relation to the severity of the disease.ConclusionsPatients with severe forms of cystic fibrosis exhibit reduced growth velocity values at an early age, before a clear decline in pulmonary function. Pediatr Pulmonol. 2009; 44:209–215. © 2009 Wiley‐Liss, Inc.