bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of glycoproteins associated with different histological subtypes of ovarian tumors using quantitative glycoproteomics
Authors: Tian Yuan , Yao Zhihao , Roden Richard B. S. , Zhang Hui 
Published: November 2011

AbstractOvarian cancer is the most lethal gynecologic malignancy in adult women. The origin of epithelial ovarian tumors is both morphologically and biologically heterogeneous, and different subtypes of ovarian tumors have different clinical outcomes. In spite of the heterogeneous nature of ovarian carcinoma, the current biomarkers and treatments for this disease are not subtype‐specific. To discover the molecular basis of the ovarian tumor subtypes, we analyzed extracellular glycoproteins of seven common subtypes and normal ovary tissues using quantitative glycoproteomic analysis. Glycoproteins for different ovarian tumor subtypes were identified by liquid chromatography‐tandem mass spectrometry and quantitated by spectral counting and then verified by iTRAQ labeling and Western blotting. Glycoproteins uniquely expressed in different subtypes of ovarian tumors or commonly expressed in most subtypes were identified. Using Western blots, we verified that mesothelin was overexpressed in serous carcinoma and transitional‐cell carcinoma, CEA5 and CEA6 were overexpressed only in mucinous carcinoma, while versican and periostin were overexpressed in most subtypes of ovarian tumors. This study presents the first proteomic characterization of different ovarian tumor subtypes. The identified glycoproteins for histological subtypes of ovarian tumors will facilitate the understanding of the molecular basis, diagnosis of ovarian tumor subtypes, and predictions for treatment responses to therapeutic agents.
An empirical phase diagram approach to investigate conformational stability of “second‐generation” functional mutants of acidic fibroblast growth factor‐1
Authors: Alsenaidy Mohammad A. , Wang Tingting , Kim Jae Hyun , Joshi Sangeeta B. , Lee Jihun , Blaber Michael , Volkin David B. , Middaugh C. Russell 
Published: November 2011

AbstractAcidic fibroblast growth factor‐1 (FGF‐1) is an angiogenic protein which requires binding to a polyanion such as heparin for its mitogenic activity and physicochemical stability. To evaluate the extent to which this heparin dependence on solution stability could be reduced or eliminated, the structural integrity and conformational stability of 10 selected FGF‐1 mutants were examined as a function of solution pH and temperature by a series of spectroscopic methods including circular dichroism, intrinsic and extrinsic fluorescence spectroscopy and static light scattering. The biophysical data were summarized in the form of colored empirical phase diagrams (EPDs). FGF‐1 mutants were identified with stability profiles in the absence of heparin comparable to that of wild‐type FGF‐1 in the presence of heparin while still retaining their biological activity. In addition, a revised version of the EPD methodology was found to provide an information rich, high throughput approach to compare the effects of mutations on the overall conformational stability of proteins in terms of their response to environmental stresses such as pH and temperature.
From Observations to Forecasts – Part 14: Communicating forecasts
Authors: Eden Philip 
Published: November 2011

AbstractThis excellent series has given readers an informative and wide‐ranging view of the history and present status of observational techniques and of forecasting. This contribution is rather different. It is, perhaps, polemical rather than factual: a heartfelt lament that the communication of forecasts to paying customers – and, in the case of public service forecasts and warnings, to the general public – has been badly neglected but is nevertheless a very important aspect of forecasting. My hope is that these words will provoke a healthy debate from which we might all learn something. Copyright © 2011 Royal Meteorological Society
Towards application driven security dashboards in future middleware
Authors: Joosen Wouter , Lagaisse Bert , Truyen Eddy , Handekyn Koen 
Published: November 2011

Abstract
Contemporary middleware must facilitate the customization of a built-in services framework, such that non-functional requirements emerging from the engineering process are met. This must be achieved by facilitating adaptation and selection of appropriate services without carrying the load, footprint, and overhead of a bloated system.
We illustrate the concept and approach with an example in the domain of security engineering of a large scale, internet based application in the domain of online document processing. In addition, we sketch why such an approach cannot only yield the desired variants of middleware security services, but also application-driven security dashboards, i.e. the tools to monitor and manage the actual security environment. The resulting research findings plead for a research agenda that revisits reflection and that enables model-driven software techniques to be used in the just-in-time generation of co-existing middleware variants.
The role of parenting and goal selection in positive youth development: A person‐centered approach☆
Authors: Napolitano Christopher M. , Bowers Edmond P. , Gestsdottir Steinunn , Depping Miriam , von Eye Alexander , Chase Paul , Lerner Jacqueline V. 
Published: November 2011

ABSTRACTUsing a person‐centered approach, we examined the relations between goal selection, various indicators of parenting, and positive development among 510 Grades 9 to 11 participants (68% female) in the 4‐H Study of Positive Youth Development (PYD), a longitudinal study involving U.S. adolescents. Goal selection was operationalized by the “Selection” (S) subscale of the Selection, Optimization, and Compensation intentional self‐regulation measure. Using Configural Frequency Analysis, we assessed the association between Selection, parenting (warmth, monitoring, and school involvement), and PYD. Results indicated that, while having the combination of consistently high Selection and above‐median levels of the parenting variables was the most common path to PYD, having consistently low levels of Selection across grades was also related to positive development at Grade 11, regardless of parenting factors. We interpret these findings based in relation to the PYD and the identity development literatures and discuss implications for applied programs.
Potential flaws of interdecadal changes over eastern China around the early 1990s in the National Centers for Environmental Prediction‐National Center for Atmospheric Research reanalyses
Authors: Liu Ge , Zhao Ping , Wu Renguang , Chen Junming 
Published: November 2011

This study compares interdecadal changes in tropospheric temperature and geopotential height over eastern China in four reanalyses and upper air radiosonde (UAR) observations. It is found that the tropospheric temperature and geopotential height over eastern China during the period 1992–2000 were systematically lower in the National Centers for Environmental Prediction (NCEP)‐National Center for Atmospheric Research (NCAR) reanalysis‐1 and the NCEP‐Department of Energy reanalysis‐2 compared to the UAR observations. Accordingly, the tropospheric temperature and geopotential height over eastern China in the NCEP reanalyses showed a pronounced interdecadal decrease around 1992, while this decrease was not significant in the UAR observations, the 40 year European Centre for Medium‐Range Weather Forecasts (ERA‐40) reanalysis, and the 25 year Japanese Meteorological Agency (JRA‐25) reanalysis. The overestimated interdecadal change in the NCEP reanalyses may lead to an inconsistent variation between tropospheric and surface climates. When summer surface air temperature increases (decreases) over southern China, summer tropospheric temperature over eastern China generally increases (decreases) in the ERA‐40, JRA‐25, and UAR data sets, which is physically supported by the NCAR Community Climate System Model version 3. However, this link between the troposphere and surface is not observed in the two NCEP reanalyses. The interdecadal bias in tropospheric temperature after 1992 in the NCEP reanalyses is possibly related to an operational change in the bias correction tables since 1992.
The electrochemistry of quinizarin revealed through its mediated reduction of oxygen
Authors: Batchelor-McAuley Christopher , Dimov Ivan B. , Aldous Leigh , Compton Richard G. 
Published: November 2011

After 35 years the hunt for improved anthracycline antibiotics is unabated but has yet to achieve the levels of clinical success desired. Electrochemical techniques provide a large amount of kinetic and thermodynamic information, but the use of such procedures is hindered by issues of sensitivity and selectivity. This work demonstrates how by harnessing the mechanism of catalytic reduction of oxygen by the quinone functionality present within the anthracycline structure it is possible to study the reactive moiety in nanomolar concentration. This methodology allows electrochemical investigation of the intercalation of quinizarin into DNA and, in particular, the quinone oxidation and degradation mechanism. The reversible reduction of the quinizarin, which in the presence of oxygen leads to the formation of reactive oxygen species, is found to occur at -0.535 V (vs. SCE) pH 6.84 and the irreversible oxidation leading to the molecules degradation occurs at +0.386 V (vs. SCE) pH 6.84.
PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs
Authors: Lischer H. E. L. , Excoffier L. 
Published: November 2011

Abstract
Summary: The analysis of genetic data often requires a combination of several approaches using different and sometimes incompatible programs. In order to facilitate data exchange and file conversions between population genetics programs, we introduce PGDSpider, a Java program that can read 27 different file formats and export data into 29, partially overlapping, other file formats. The PGDSpider package includes both an intuitive graphical user interface and a command-line version allowing its integration in complex data analysis pipelines.
Availability: PGDSpider is freely available under the BSD 3-Clause license on http://cmpg.unibe.ch/software/PGDSpider/
Contact: heidi.lischer@iee.unibe.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Staggered overdose pattern and delay to hospital presentation are associated with adverse outcomes following paracetamol‐induced hepatotoxicity
Authors: Craig Darren G. N. , Bates Caroline M. , Davidson Janice S. , Martin Kirsty G. , Hayes Peter C. , Simpson Kenneth J. 
Published: November 2011

WHAT IS ALREADY KNOWN ON THIS SUBJECT• Paracetamol hepatotoxicity is the commonest cause of acute liver failure (ALF) in the UK.• Relatively little is known regarding the impact of staggered overdose pattern or delayed hospital presentation upon subsequent mortality or need for emergency liver transplantation.WHAT THIS STUDY ADDS• Staggered paracetamol overdoses, frequently taken to relieve pain, are strongly associated with reduced survival compared with single time point overdose.• Staggered paracetamol overdoses should be treated as high risk for the development of multiorgan failure, and should be considered for N‐acetyl cysteine treatment irrespective of admission serum paracetamol concentrations.• The King's College poor prognostic criteria may have reduced sensitivity in staggered overdose patients.AIMS Paracetamol (acetaminophen) poisoning remains the major cause of severe acute hepatotoxicity in the UK. In this large single centre cohort study we examined the clinical impact of staggered overdoses and delayed presentation following paracetamol overdose.RESULTS Between 1992 and 2008, 663 patients were admitted with paracetamol‐induced severe liver injury, of whom 161 (24.3%) had taken a staggered overdose. Staggered overdose patients were significantly older and more likely to abuse alcohol than single time point overdose patients. Relief of pain (58.2%) was the commonest rationale for repeated supratherapeutic ingestion. Despite lower total ingested paracetamol doses and lower admission serum alanine aminotransferase concentrations, staggered overdose patients were more likely to be encephalopathic on admission, require renal replacement therapy or mechanical ventilation and had higher mortality rates compared with single time point overdoses (37.3% vs. 27.8%, P= 0.025), although this overdose pattern did not independently predict death. The King's College poor prognostic criteria had reduced sensitivity (77.6, 95% CI 70.8, 81.5) for this pattern of overdose. Of the 396/450 (88.0%) single time point overdoses in whom accurate timings could be obtained, 178 (44.9%) presented to medical services >24 h following overdose. Delayed presentation beyond 24 h post overdose was independently associated with death/liver transplantation (OR 2.25, 95% CI 1.23, 4.12, P= 0.009).CONCLUSIONS Both delayed presentation and staggered overdose pattern are associated with adverse outcomes following paracetamol overdose. These patients are at increased risk of developing multi‐organ failure and should be considered for early transfer to specialist liver centres.
The tumour suppressor FOXO3 is a key regulator of mantle cell lymphoma proliferation and survival
Authors: Obrador‐Hevia Antònia , Serra‐Sitjar Margalida , Rodríguez José , Villalonga Priam , de Mattos Silvia Fernández 
Published: November 2011

SummaryThe FOXO3 (Forkhead/winged helix box class O 3) transcription factor is a crucial regulator of haematopoietic cell fate that controls proliferation and apoptosis, among other processes. Despite the central role of FOXO3 as a tumour suppressor and phosphatidylinositol 3‐kinase (PI3K)/AKT effector, little is known about its involvement in mantle cell lymphoma (MCL) biology. This study investigated the expression and activity of FOXO3 in MCL cell lines and in primary cultures. We analysed the expression of key FOXO regulators and targets, and studied the effect of modulators of FOXO function on cell viability and apoptosis. FOXO3 was constitutively inactivated in MCL cell lines, and showed cytoplasmic localization in patient‐derived cells. PI3K and AKT, but not mammalian target of rapamycin (mTOR), inhibitors induced FOXO3 nuclear translocation and activation in correlation with their impact on MCL proliferation and survival. Moreover, FOXO3‐defective cells were resistant to PI3K/AKT inhibitors. Reactivation of FOXO function with a nuclear export inhibitor had a profound effect on cell viability, consistent with FOXO3 nuclear accumulation. Interestingly, inhibition of FOXO3 nuclear export enhanced the effect of doxorubicin. Taken together, our results confirm that FOXO3 is a relevant regulator of proliferation and apoptosis in MCL, and suggest that reactivation of FOXO3 function might be a useful therapeutic strategy in MCL patients.
Integrating behaviour with life history: boldness of the field cricket, Gryllus integer, during ontogeny
Authors: Niemelä Petri T. , Vainikka Anssi , Hedrick Ann V. , Kortet Raine 
Published: November 2011

Summary1. According to a recent hypothesis, personality traits should form integrative pace‐of‐life syndromes with life‐history traits. Potential life‐history traits that explain personality variation are immune defence and growth rate.2. We studied whether boldness, measured as hiding behaviour, is repeatable during ontogeny in the field cricket, Gryllus integer, and if it relates to the efficiency of immune function (i.e. the capacity to encapsulate a nylon implant), growth rate, developmental time and size as an adult.3. Hiding behaviour was rank‐order repeatable, and in general, juveniles were bolder than adults. Individuals that were cautious at early juvenile stages had higher encapsulation responses late in life compared with bold individuals. Most clearly, fast‐growing individuals matured early and invested little in immune defence compared with their slower‐growing conspecifics, i.e. showed patterns of a ‘grow fast, die young’ life‐history strategy.4. Our results may arise from a trade‐off between immunity‐dependent survival and bold behaviour. Trade‐offs between investment in survival and behaviour could account for the maintenance of variation in personality traits by favouring certain combinations of behavioural and life‐history strategies (i.e. pace‐of‐life‐syndromes).
Geographic adaptation in plant–soil mutualisms: tests using Acacia spp. and rhizobial bacteria
Authors: Barrett Luke G. , Broadhurst Linda M. , Thrall Peter H. 
Published: November 2011

Summary1. Variation in the effectiveness of mutualistic associations is well characterized in plant–soil symbiont interactions, yet there are little empirical data providing insight into how such variation evolves and persists in natural settings.2. Heterogeneity in the strength and direction of co‐evolutionary selection among spatially discrete demes is predicted to be important for the maintenance of genetic variation in species interactions. Here, we experimentally test the potential for local adaptation to generate phenotypic divergence among wild host–symbiont populations using two leguminous host species that differ in their specificity for rhizobial partners.3. Molecular characterization of host populations and associated rhizobial communities revealed significant among‐population genetic differentiation. Reciprocal cross‐inoculation experiments testing for variation in the fitness of nine populations of Acacia salicina and A. stenophylla in response to inoculation with rhizobia revealed variation in host response to the mutualism (both host species), and the benefit conferred by different rhizobial populations (A. salicina only). However, there was no indication that host population‐by‐rhizobial population interactions influence the outcomes of mutualism for the host.4. We further examined potential correlations between (i) plant response to inoculation and (ii) rhizobial effectiveness, with variation in soil fertility at the sites from which plant and rhizobial samples originated. Data from the cross‐inoculation experiments revealed no correlations between soil chemistry, water availability and either host or rhizobial performance. However, analysis of results from an extensive whole‐soil inoculation trial including nearly 60 A. salicina and A. stenophylla sites showed a significant negative correlation between levels of soil nitrogen and plant response to inoculation.5. Overall, these findings suggest that selection for local adaptation may play little role in maintaining phenotypic variation in these interactions. We hypothesize that mutualistic interactions occurring among communities of hosts and symbionts do not favour co‐evolutionary divergence among populations.
Flavour of natural and roasted Turkish hazelnut varieties (Corylus avellana L.) by descriptive sensory analysis, electronic nose and chemometrics
Authors: Alasalvar Cesarettin , Pelvan Ebru , Bahar Banu , Korel Figen , Ölmez Hülya 
Published: November 2011

SummaryA total of eighteen natural and roasted hazelnut varieties (amongst which only Tombul variety is classified as prime quality), grown in the Giresun province of Turkey, were compared for their differences in descriptive sensory analysis (DSA), electronic nose (e‐nose) data and chemometrics. Differences in some descriptive of DSA between natural and roasted hazelnuts as well as within the varieties were observed. Although Tombul hazelnut was selected as one of the best varieties in terms of flavour attributes and received the highest intensities in general, no significant differences (P > 0.05) existed among hazelnut varieties except in certain flavour attributes (‘after taste’ and ‘nutty’). DSA and e‐nose data of natural and roasted hazelnuts were also evaluated for discrimination using principal component analysis (PCA) and cluster analysis. Results of PCA using e‐nose data showed that extracted principal components explained 99.7% and 99.8% of the total variance of the data for natural and roasted hazelnut varieties, respectively. Both DSA and e‐nose can be used for discrimination of natural and roasted hazelnuts.
Starch–methylcellulose–whey protein film properties
Authors: Yoo SeungRan , Krochta John M. 
Published: November 2011

SummaryFour % (wt/wt) aqueous solutions were prepared at corn starch:methylcellulose:whey protein isolate (CS:MC:WPI) ratios of 2:2:2, 1:2:3, 2:1:3, 2:2:0, 1:2:0 and 2:1:0. Glycerol (gly) was used as a plasticiser at CS–MC–WPI:gly ratios of 2:1, 2.5:1 and 3:1. CS–MC–WPI blend films were stronger than CS–WPI films and had lower oxygen permeability (OP) than MC–WPI films. The highest tensile strength (TS) of blend films was 8.01 ± 3.41 MPa, at CS:MC:WPI ratio of 2:2:0 and CS–MC–WPI:gly ratio of 3:1. Lowest OP value was 45.05 ± 7.24 cm3 μm m−2 per day kPa−1, at CS:MC:WPI ratio of 2:2:2 and CS–MC–WPI:gly ratio of 3:1. OP values were predictable based on relative amounts of components. However, TS and elastic modulus properties of the CS–MC–WPI blend films did not reflect the relative amounts of the components. All of CS–MC–WPI films were translucent indicating some degree of immiscibility among the CS, MC and WPI. These results indicate the influence of complex molecular interactions among the components.
Adsorption behaviour of some anthocyanins by wheat gluten and its fractions in acidic conditions
Authors: Mazzaracchio Palmira , Kindt Maddalena , Pifferi Pier G. , Tozzi Silvia , Barbiroli Giancarlo 
Published: November 2011

SummarySome anthocyanins, both commercial delphinidin‐3‐O‐β‐d‐glucoside chloride and cyanidin‐3‐O‐β‐d‐rutinoside chloride (Dp3glu and Cy3rut) and extracted from plants, were adsorbed by gluten or its fractions to carry out a study that can be considered a premise to estimate the potential effect on bioavailability of anthocyanin adsorption. This process was studied by means of adsorption kinetics and isotherms. Among the parameters determining adsorption, the temperature and the pH value were evaluated. The data show that gluten and its fraction have a great adsorption capacity (about 1.0 mg g−1 of gluten). The results indicate that the structure of the anthocyanins plays an important role in their adsorption by gluten or its fractions; in fact, the adsorption kinetics show that Dp3glu is more adsorbed than Cy3rut. The isotherms of anthocyanin adsorption by gluten indicate the presence of a strong interaction between the two types of molecules. This could be an important finding to obtain functionalised‐based gluten products.