bluuebunny/crossref_metadata_2025_split huggingface dataset:
The increased expression of periostin during early stages of prostate cancer and advanced stages of cancer stroma
Authors: Tsunoda Toshiyuki , Furusato Bungo , Takashima Yasuo , Ravulapalli Suma , Dobi Albert , Srivastava Shiv , McLeod David G. , Sesterhenn Isabell A. , Ornstein David K. , Shirasawa Senji 
Published: May 2009

AbstractBACKGROUNDThree‐dimensional culture (3DC) is a relevant in vitro model used to study prostate development and carcinogenesis. Recent studies have indicated that 3DC‐associated genes would be more sensitive as prognostic markers for cancer; however, no 3DC‐associated genes in prostate cancer (CaP) have thus far been elucidated.METHODSCandidate 3DC‐associated genes in non‐malignant prostatic epithelial cells, RWPE‐1 and TA2, were selected, based on a comparison of microarray gene expression data between cells grown in two‐dimensional culture (2DC) and in 3DC. To extract CaP‐associated genes among the 3DC‐associated genes, gene expression levels from the microdissected tissue samples were compared between 20 well‐differentiated or 20 poorly differentiated CaP, as well as matched normal prostate epithelium. The expression levels of CaP‐associated genes in 3DC were validated by quantitative RT‐PCR using TA2 cells in 2DC and 3DC. Protein expression of periostin (POSTN), which is one of the 3DC CaP‐associated genes, was further evaluated in the clinical samples by immunohistochemistry.RESULTSSeveral genes including POSTN were identified as CaP‐associated genes using a 3DC system. Immunohistochemical analyses revealed that POSTN expression was increased in the early stages of CaP (Gleason score 6–7), but not in the advanced stages of CaP. Furthermore, the positive ratio observed for the expression of POSTN in tumor‐associated stroma was significantly correlated with the degree of malignancy.CONCLUSIONSPOSTN, one of the 3DC‐associated genes, may serve as a potential biomarker for predicting the pathological grade and prognosis of CaP. Prostate 69: 1398–1403, 2009. © 2009 Wiley‐Liss, Inc.
Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X‐ray studies
Authors: Sharma Alok , Sekar K. , Vijayan M. 
Published: May 2009

AbstractMolecular dynamics simulations have been carried out on all the jacalin–carbohydrate complexes of known structure, models of unliganded molecules derived from the complexes and also models of relevant complexes where X‐ray structures are not available. Results of the simulations and the available crystal structures involving jacalin permit delineation of the relatively rigid and flexible regions of the molecule and the dynamical variability of the hydrogen bonds involved in stabilizing the structure. Local flexibility appears to be related to solvent accessibility. Hydrogen bonds involving side chains and water bridges involving buried water molecules appear to be important in the stabilization of loop structures. The lectin–carbohydrate interactions observed in crystal structures, the average parameters pertaining to them derived from simulations, energetic contribution of the stacking residue estimated from quantum mechanical calculations, and the scatter of the locations of carbohydrate and carbohydrate‐binding residues are consistent with the known thermodynamic parameters of jacalin–carbohydrate interactions. The simulations, along with X‐ray results, provide a fuller picture of carbohydrate binding by jacalin than provided by crystallographic analysis alone. The simulations confirm that in the unliganded structures water molecules tend to occupy the positions occupied by carbohydrate oxygens in the lectin–carbohydrate complexes. Population distributions in simulations of the free lectin, the ligands, and the complexes indicate a combination of conformational selection and induced fit. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Prediction of global and local quality of CASP8 models by MULTICOM series
Authors: Cheng Jianlin , Wang Zheng , Tegge Allison N. , Eickholt Jesse 
Published: May 2009

AbstractEvaluating the quality of protein structure models is important for selecting and using models. Here, we describe the MULTICOM series of model quality predictors which contains three predictors tested in the CASP8 experiments. We evaluated these predictors on 120 CASP8 targets. The average correlations between predicted and real GDT‐TS scores of the two semi‐clustering methods (MULTICOM and MULTICOM‐CLUSTER) and the one single‐model ab initio method (MULTICOM‐CMFR) are 0.90, 0.89, and 0.74, respectively; and their average difference (or GDT‐TS loss) between the global GDT‐TS scores of the top‐ranked models and the best models are 0.05, 0.06, and 0.07, respectively. The average correlation between predicted and real local quality scores of the semi‐clustering methods is above 0.64. Our results show that the novel semi‐clustering approach that compares a model with top ranked reference models can improve initial quality scores generated by the ab initio method and a simple meta approach. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Attraction and antennal response of the common wasp, Vespula vulgaris (L.), to selected synthetic chemicals in New Zealand beech forests
Authors: El‐Sayed Ashraf M , Manning Lee‐Anne , Unelius C Rikard , Park Kye Chung , Stringer Lloyd D , White Nicola , Bunn Barry , Twidle Andrew , Suckling David M 
Published: May 2009

AbstractBACKGROUND: The common wasp, Vespula vulgaris (L.), and the German wasp, Vespula germanica (F.), are significant problems in New Zealand beech forests (Nothofagus spp.), adversely affecting native birds and invertebrate biodiversity. This work was undertaken to develop synthetic attractants for these species to enable more efficient monitoring and management.RESULTS: Seven known wasp attractants (acetic acid, butyl butyrate, isobutanol, heptyl butyrate, octyl butyrate and 2,4‐hexadienyl butyrate) were field tested, and only heptyl butyrate and octyl butyrate attracted significantly higher numbers of wasps than a non‐baited trap. Accordingly, a series of straight‐chain esters from methyl to decyl butyrate were prepared and field tested for attraction of social wasps. Peak biological activity occurred with hexyl butyrate, heptyl butyrate, octyl butyrate and nonyl butyrate. Polyethylene bags emitting approximately 18.4–22.6 mg day−1 of heptyl butyrate were more attractive than polyethylene bags emitting approximately 14.7–16.8 mg day−1 of heptyl butyrate in the field. Electroantennogram (EAG) studies indicated that queens and workers of V. vulgaris had olfactory receptor neurons responding to various aliphatic butyrates.CONCLUSION: These results are the first to be reported on the EAG response and the attraction of social wasps to synthetic chemicals in New Zealand beech forests and will enable monitoring of social wasp activity in beech forests. Copyright © 2009 Society of Chemical Industry
Evidence for 2,4‐D mineralisation in Mediterranean soils: impact of moisture content and temperature
Authors: Bouseba Bachir , Zertal Abdennour , Beguet Jérémie , Rouard Nadine , Devers Marion , Martin Christophe , Martin‐Laurent Fabrice 
Published: May 2009

AbstractBACKGROUND: The 2,4‐D degradation ability of the microbiota of three arable Mediterranean soils was estimated. The impact of soil moisture and temperature on 2,4‐D degradation was investigated.RESULTS: The microbiota of the three soils regularly exposed to 2,4‐D were able rapidly to mineralise this herbicide. The half‐life of 2,4‐D ranged from 8 to 30 days, and maximum mineralisation of 14C‐2,4‐D ranged from 57 to 71%. Extractable 14C‐2,4‐D and 14C‐bound residues accounted for less than 1 and 15% respectively of the 14C‐2,4‐D initially added. The highest amounts of 14C‐2,4‐D bound residues were recorded in the soil with the lowest 2,4‐D‐mineralising ability. Although all three soils were able to mineralise 2,4‐D, multivariate analysis revealed that performance of this degrading microbial activity was dependent on clay content and magnesium oxide. Soil temperature affected the global structure of soil microbial community, but it had only a moderate effect on 2,4‐D‐mineralising ability. 2,4‐D‐mineralising ability was positively correlated with soil moisture content. Negligible 2,4‐D mineralisation occurred in all three soils when incubated at 10 or 15% soil moisture content, i.e. within the range naturally occurring under the Mediterranean climate of Algeria.CONCLUSION: This study shows that, although soil microbiota can adapt to rapid mineralisation of 2,4‐D, this microbial activity is strongly dependent on climatic parameters. It suggests that only limited pesticide biodegradation occurs under Mediterranean climate, and that arable Mediterranean soils are therefore fragile and likely to accumulate pesticide residues. Copyright © 2009 Society of Chemical Industry
Cycloate, an inhibitor of fatty acid elongase, modulates the metabolism of very‐long‐side‐chain alkylresorcinols in rye seedlings
Authors: Magnucka Elzbieta G , Suzuki Yoshikatsu , Pietr Stanislaw J , Kozubek Arkadiusz , Zarnowski Robert 
Published: May 2009

AbstractBACKGROUND: Cycloate inhibits the biosynthesis of very‐long‐chain fatty acids, the essential constituents of plant waxes and suberin. Fatty acids also serve as precursors of aliphatic carbon chains in resorcinolic lipids, which play a fundamental role in the plant defence system against fungal pathogens. In this study, the effect of cycloate on the biosynthesis of 5‐n‐alkylresorcinols in rye seedlings (Secale cereale L.) grown under various light and thermal conditions was examined.RESULTS: The content of alkylresorcinols biosynthesised in rye was generally increased by the herbicide in both green and etiolated plants. The presence of cycloate also affected patterns of alkylresorcinol homologues in plants grown at 15 and 22 °C; very‐long‐side‐chain compounds were less abundant, whereas both short‐chain saturated and unsaturated homologues were generally accumulated. No cycloate‐related effects caused by homologue pattern modifications were observed at elevated temperature.CONCLUSION: This study extends present understanding of the mode of action of thiocarbamate herbicides. Cycloate markedly affected the biosynthesis of very‐long‐side‐chain resorcinolic lipids in rye seedlings, confirming the existence of parallels in both fatty acid and alkylresorcinol biosynthetic pathways. The observed cycloate‐driven accumulation of 5‐n‐alkylresorcinols may improve the resistance of cereals to infections caused by microbial pathogens. Copyright © 2009 Society of Chemical Industry
Fertility, mobility and labour‐force participation: a study of synchronicity
Authors: Clark William A. V. , Withers Suzanne Davies 
Published: May 2009

AbstractDelayed childbearing is common in a workforce that is now dominated by dual‐income households, and survey results report increasing concerns about how to manage family formation and labour‐force participation. In the past, mobility research tended to focus on the mobility event and looked at fertility as a ‘triggering’ event that stimulates mobility and migration. In contrast this research focuses on the fertility event and explores the relationship between fertility events and both mobility and labour‐force outcomes. Using the Panel Study of Income Dynamics, we undertake an analysis of ‘windows’ around fertility events and look for mobility activity, and for a smaller subsample, labour‐force events. Then we also examine ‘windows’ around mobility events to test competing explanations for fertility behaviour and mobility behaviour. The research moves beyond parental status and the links to mobility and labour‐force participation to the actual synchronicity of these behaviours. While it is no surprise that women do drop out of the labour force to have children, many fewer actually leave the labour force than expected and they re‐enter at significantly high rates. The results for mobility are even more mixed, and while there is some evidence of increased mobility with fertility, it is much weaker than suggested by other research. Overall, this research reaffirms an emerging view of mobility and migration behaviour as much more complex than earlier research presented. Copyright © 2009 John Wiley & Sons, Ltd.
Oxygen vacancy induced ferromagnetism in rutile TiO2–x
Authors: Han Guang‐bing , Hu Shu‐jun , Yan Shi‐shen , Mei Liang‐mo 
Published: May 2009

AbstractFirst‐principles LDA + U calculations have been performed to study the effects of oxygen vacancies (VO) on the electronic structure and magnetism in undoped rutile TiO2–x . Instead of treated as an adjustive parameter, the value of U was determined by constrained‐density‐functional calculations. The calculated electronic structure reveals that the valence electrons released by VO would occupy mainly the neighboring Ti:3d orbital which then becomes spin‐polarized due to intra‐atomic exchange interaction, thereby giving rise to the half‐metallic ferromagnetism. The magnetization induced by VO in rutile TiO2–x is almost proportional to the VO concentration (x) for x > 0.0625, and becomes 0 for x ≤ 0.0417. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of three different doses of a fruit extract of Terminalia chebula on metabolic components of metabolic syndrome, in a rat model
Authors: Singh Inderjeet , Singh Pawan Kumar , Bhansali Shobhit , Shafiq Nusrat , Malhotra Samir , Pandhi Promila , Pal Singh Amrit 
Published: May 2009

AbstractThere is documented evidence of the use of Terminalia chebula for various ailments in the Ayurvedic literature. The extract has been shown to possess glucose lowering activity and to improve insulin sensitivity in animal models of type 2 diabetes mellitus. The present study was carried out to study the dose response relationship of this extract in a rat model of metabolic syndrome. Six groups of rats were fed a high fructose diet (HFD) for a period of 20 days to induce metabolic syndrome. Three doses of fruit extract of T. chebula 50, 100 and 200 mg/kg were administered orally and pioglitazone 2.7 mg/kg was used as a positive control. Blood samples were collected at days 0, 20 and 40 from the tail vein. Systolic blood pressure (SBP) was measured using the tail cuff method and an oral glucose tolerance test (OGTT) was done on the day of blood collection. Administration of HFD for 20 days significantly increased fasting blood glucose (FBG), SBP and the area under the curve of OGTT. On day 40 the FBG in the 50, 100 and 200 mg/kg group was 97.33 ± 5.82 (NS), 86.83 ± 5.08 (p = 0.038) and 85.67 ± 6.74 (p = 0.15), respectively. These results show that the fruit extract of T. chebula exerts a significant and dose‐dependent glucose lowering effect in the rat model of metabolic syndrome. Copyright © 2009 John Wiley & Sons, Ltd.
Classification of Src Kinase Inhibitors Based on Support Vector Machine
Authors: Zhu Jinxiu , Lu Wencong , Liu Liang , Gu Tianhong , Niu Bing 
Published: May 2009

AbstractIn this work, the support vector machine (SVM), an effective machine learning method, was employed to make a distinction within a class of Src kinase inhibitors. The minimum redundancy maximum relevance (mRMR) feature selection method was used to remove redundant variables, then sequential forward selection (SFS) and sequential backward selection (SBS) methods were used to extract informative features. It had been demonstrated that sequential forward selection (SFS) and sequential backward selection (SBS) methods were useful tools for variable selection. As a special cross‐validation method, leave one out cross validation (LOOCV) method was used to test the generalization and reliability of the model obtained. By using the SVM, the support vector classification (SVC) model was obtained, with a classification accuracy of 94%. And the prediction accuracy of activities of the Src kinase inhibitors is 92.4% in LOOCV method. The results show that SVM method could be employed to SAR modeling with much improved quality and predictability.
Basic inferences of scientific reasoning, argumentation, and discovery
Authors: Lawson Anton E. 
Published: May 2009

AbstractHelping students better understand how scientists reason and argue to draw scientific conclusions has long been viewed as a critical component of scientific literacy, thus remains a central goal of science instruction. However, differences of opinion persist regarding the nature of scientific reasoning, argumentation, and discovery. Accordingly, the primary goal of this paper is to employ the inferences of abduction, retroduction, deduction, and induction to introduce a pattern of scientific reasoning, argumentation, and discovery that is postulated to be universal, thus can serve as an instructional framework to improve student reasoning and argumentative skills. The paper first analyzes three varied and presumably representative case histories in terms of the four inferences (i.e., Galileo's discovery of Jupiter's moons, Rosemary and Peter Grants' research on Darwin's finches, and Marshall Nirenberg's Nobel Prize–winning research on genetic coding). Each case history reveals a pattern of reasoning and argumentation used during explanation testing that can be summarized in anIf/then/Thereforeform. The paper then summarizes additional cases also exemplary of the form. Implications of the resulting theory are discussed in terms of improving the quality of research and classroom instruction. © 2009 Wiley Periodicals, Inc.Sci Ed94:336–364, 2010
Benefits of global software development: exploring the unexplored
Authors: Ó Conchúir Eoin , Holmström Olsson Helena , Ågerfalk Pär J. , Fitzgerald Brian 
Published: May 2009

AbstractOrganizations are increasingly moving to the global software development (GSD) model because of significant benefits that can accrue. However, GSD is fraught with challenges arising from geographical, temporal and socio‐cultural distances. The emphasis in the literature to date has typically been on how to overcome the challenges associated with GSD. While a number of GSD benefits have been widely referred to in the literature, there are also a number of less obvious benefits that can be inferred as potentially accruing from GSD. In this article, we identify the various benefits of GSD, labeling them as ‘referred’ and ‘inferred’, respectively. We provide a categorization in terms of (a) organizational, (b) team and (c) process/task. While the ‘referred’ benefits most often apply at the organizational level (e.g. cost savings, access to large multi‐skilled workforces, reduced time to market and proximity to customer), the ‘inferred’ benefits apply to a greater extent at team and process/task level (e.g. task modularization, team autonomy, improved documentation and clearly defined processes). In the decision of whether or not to globalize software development activities, a categorization including both ‘referred’ and ‘inferred’ benefits will be helpful in providing a synthesis of all potential benefits associated with GSD. Copyright © 2009 John Wiley & Sons, Ltd.
Tissue‐specific in vivo inhibition of cholinesterases by the organophosphate fenthion in Oreochromis niloticus
Authors: Üner Nevin , Sevgiler Yusuf , Piner Petek 
Published: May 2009

AbstractThis study was designed to elucidate the effect of the organophosphate fenthion exposure on cholinesterase‐specific activities in brain, liver, and kidney tissues of juvenile Oreochromis niloticus, and to define the best indicator tissue to fenthion exposure. The 96‐h LC50 value was determined as 2.27 mg/L and fish were exposed to 20% of this concentration for 24‐, 48‐, and 96‐h. Recovery periods in similar durations were provided to evaluate the ChE activities. AChE and BChE activities were determined spectrophotometrically. The activities of these enzymes were significantly inhibited in all the tissues tested, liver was the most and kidney was the least affected tissues. The inhibition percentages of AChE and BChE were at similar levels in the liver while BChE was more affected in kidney. BChE was not detected in the brain. A significant positive correlation in ChE inhibitions was found among tissues, and the effect of fenthion on ChE activities was tissue specific. In general enzymes activities were not significantly recovered in 96‐h recovery period; however, an elevation in AChE inhibition was observed in brain. Based on the data of this study, the liver may be suggested as the best indicator tissue especially for phosphorothioate exposure. © 2009 Wiley Periodicals, Inc. Environ Toxicol 25: 391–399, 2010.
Reducing the cost of detection of congenital heart disease in fetuses of women with pregestational diabetes mellitus
Authors: Bernard L. S. , Ramos G. A. , Fines V. , Hull A. D. 
Published: May 2009

AbstractObjectiveTo provide a cost minimization analysis to support a paradigm shift in the use of comprehensive ultrasound and echocardiography in the prenatal diagnosis of congenital heart disease (CHD) in fetuses of women with diabetes mellitus (DM).MethodsIn this retrospective cohort study, the diabetic clinic service database of the University of California San Diego was searched from January 2001 to June 2004 for pregnant women with Type I or II DM and HbA1c >6.3%. Subjects underwent comprehensive ultrasound examination (with four‐chamber views and outflow tracts) and fetal echocardiography according to a standard protocol. Newborns were examined for cardiac defects and underwent postnatal echocardiography as indicated. The cost of screening was evaluated.ResultsOf 115 neonates and two terminations of pregnancy there were 20 (17%) cases of CHD. Six of these CHD were major and all six were detected prenatally by both ultrasound and echocardiography. Three additional clinically insignificant cases of CHD were identified by fetal echocardiography. Eleven cases of CHD were identified by postnatal echocardiography only, all of which were clinically insignificant lesions. The prenatal detection rate of major CHD was 100% (6/6) for both ultrasound and echocardiography. The sensitivites of ultrasound (30% (95% CI, 13–54%)) and echocardiography (45% (95% CI, 24–68%)) were similar (P = 0.32). A cost minimization analysis was done using the published Medicaid (California) system's relative value unit and conversion factors. Accordingly, our current protocol costs $6503.43 per case of major CHD detected. If echocardiography had been performed only as indicated and postnatal echocardiography had been performed on all neonates, the cost would have been $7056.83 per case of major CHD detected. Alternatively, combined targeted ultrasound with indicated prenatal and postnatal echocardiography would have been associated with a cost of $4996.05 per case of major CHD detected.ConclusionDetection of major CHD was excellent with both comprehensive prenatal ultrasound and echocardiography. Echocardiography added little to the prenatal diagnosis of CHD if the comprehensive ultrasound examination was normal. The highest cost–benefit ratio and most efficacious protocol for screening based on our data would be comprehensive ultrasound with prenatal and postnatal echocardiography only as indicated. Further prospective studies are warranted. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.