bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quittant tout, nous partîmes: quitteretpartirà la lumière des changements de relation locative
Authors: AURNAGUE MICHEL 
Published: March 2011

RÉSUMÉCe travail propose une comparaison des emplois spatiaux dequitteretpartirs'appuyant sur l'exploitation d'exemples de la base Frantext entre 1880 et 1970. Après avoir exposé les principales oppositions quantitatives et qualitatives émergeant de ce recensement, nous proposons une analyse departirqui tente de déterminer la/les relation(s) locative(s) élémentaire(s) sous-tendant son contenu sémantique. Cette analyse sert de point de départ à l'étude dequitter, verbe dont l'examen montre qu'il peut asserter puis nier un éventail beaucoup plus large de relations spatiales. L'article se termine par une discussion faisant apparaître que la nature des sites (entités de référence ou localisatrices) auxquels font appel les deux verbes est largement conditionnée par les relations locatives présentes dans leur sémantisme et que seulpartirdénote des déplacements au sens strict.
A cost comparison of more and less nutritious food choices in US supermarkets
Authors: Katz David L , Doughty Kim , Njike Valentine , Treu Judith A , Reynolds Jesse , Walker Jennifer , Smith Erica , Katz Catherine 
Published: March 2011

AbstractObjectiveThe present study directly compared prices of more and less nutritious foods within given categories in US supermarkets.DesignFoods selected from six supermarkets in Jackson County were categorized using the five criteria of the Nutrition Detectives™ (ND) programme and an item-to-item cost comparison was made using posted prices. The nutritional quality of foods was distinguished using the clues of the ND nutrition education programme for elementary-school children and validated using the Overall Nutritional Quality Index.SettingSupermarkets in Jackson County, MO, USA.SubjectsNot applicable.ResultsThe average price of the item for more nutritious foods did not differ significantly from that of less nutritious foods overall ($US 2·89 (sd$US 0·74)v.$US 2·85 (sd$0·68),P= 0·76). More nutritious breads cost more than less nutritious breads ($US 3·36 (sd$ US 0·28)v.$US 2·56 (sd$US 0·80,P= 0·03), whereas more nutritious cereals ($US 2·46 (sd$US 0·69)v.$US 3·50 (sd$US 0·30),P< 0·01) and cookies ($US 2·76 (sd$US 0·50)v.$US 3·40 (sd$US0·28),P< 0·01) cost less.ConclusionsOur findings indicate that it is possible to choose more nutritious foods within many common categories without spending more money and suggest that making small improvements in dietary choices does not invariably cost more.
Family meals and body weight in US adults
Authors: Sobal Jeffery , Hanson Karla 
Published: March 2011

AbstractObjectiveFamily meals are an important ritual in contemporary societies and many studies have reported associations of family meals with several biopsychosocial outcomes among children and adolescents. However, few representative analyses of family meals have been conducted in samples of adults, and adults may differ from young people in predictors and outcomes of family meal consumption. We examined the prevalence and predictors of adult family meals and body weight outcomes.DesignThe cross-sectional 2009 Cornell National Social Survey (CNSS) included questions about the frequency of family meals, body weight as BMI and sociodemographic characteristics.SettingThe CNSS telephone survey used random digit dialling to sample individuals.SubjectsWe analysed data from 882 adults living with family members in a nationally representative US sample.ResultsPrevalence of family meals among these adults revealed that 53 % reported eating family meals seven or more times per week. Predictive results revealed that adults who more frequently ate family meals were more likely to be married and less likely to be employed full-time, year-round. Outcome results revealed that the overall frequency of family meals among adults was not significantly associated with any measure of body weight. However, interaction term analysis suggested an inverse association between frequency of family meals and BMI for adults with children in the household, and no association among adults without children.ConclusionsThese findings suggest that family meals among adults are commonplace, associated with marital and work roles, and marginally associated with body weight only in households with children.
Antibody-Mediated Self-Limiting Self-Assembly for Quantitative Analysis of Nanoparticle Surfaces by Atomic Force Microscopy
Authors: Geronimo Carly Lay A. , MacCuspie Robert I. 
Published: March 2011

AbstractQuantification of very low density molecular coatings on large (60 nm) gold nanoparticles (AuNPs) is demonstrated via the use of antibody-mediated self-limiting self-assembly of small and large AuNPs into raspberry-like structures subsequently imaged by atomic force microscopy (AFM). AFM imaging is proposed as an automated, lower-cost, higher-throughput alternative to immunostaining and imaging by transmission electron microscopy. Synthesis of large AuNPs, containing one of three ligand molecules in one of three stoichiometries (1, 2, or 10 ligands per AuNP), and small probe AuNPs with one of three antibody molecules in a one antibody per AuNP ratio, enabled a range of predicted self-limiting self-assembled structures. A model predicting the probability of observing a given small to large AuNP ratio based on a topography measurement such as AFM is described, in which random orientational deposition is assumed and which accounts for the stochastic synthesis method of the library AuNPs with varied ligand ratios. Experimental data were found to agree very well with the predictive models when using an established AFM sample preparation method that avoids drying-induced aggregation.
Hardware efficient receiver for low-cost ultra-high rate 60 GHz wireless communications
Authors: Ulusoy Ahmet Çağrı , Liu Gang , Trasser Andreas , Schumacher Hermann 
Published: March 2011

This paper presents a hardware efficient receiver architecture, to be used in low-cost, ultra-high rate 60 GHz wireless communication systems. The receiver utilizes a simple, feed-forward carrier recovery concept, performing phase and frequency synchronization in the analog domain. This enables 1-bit baseband processing without a need of ultra-high speed and high precision analog-to-digital conversion, offering a strong simplification of the system architecture and comparatively low power consumption. In a first prototype implementation, the receiver is realized in a low-cost SiGe technology as two separate ICs: the 60 GHz/5 GHz downconverter, and the intermediate frequency synchronous demodulator. The simple synchronous reception concept is experimentally validated for up to 3.5 Gbit/s data rate, which constituted the limit of the existing experimental setup. Furthermore, the downconverter demonstrates that low-cost technologies (fop/fmax ~ 0.75) can be used to realize short-range data links at 60 GHz, with low-noise amplifiers in a more performant technology as needed.
Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale
Authors: Caruso Tancredi , Chan Yuki , Lacap Donnabella C , Lau Maggie C Y , McKay Christopher P , Pointing Stephen B 
Published: March 2011

Abstract
Extreme arid regions in the worlds' major deserts are typified by quartz pavement terrain. Cryptic hypolithic communities colonize the ventral surface of quartz rocks and this habitat is characterized by a relative lack of environmental and trophic complexity. Combined with readily identifiable major environmental stressors this provides a tractable model system for determining the relative role of stochastic and deterministic drivers in community assembly. Through analyzing an original, worldwide data set of 16S rRNA-gene defined bacterial communities from the most extreme deserts on the Earth, we show that functional assemblages within the communities were subject to different assembly influences. Null models applied to the photosynthetic assemblage revealed that stochastic processes exerted most effect on the assemblage, although the level of community dissimilarity varied between continents in a manner not always consistent with neutral models. The heterotrophic assemblages displayed signatures of niche processes across four continents, whereas in other cases they conformed to neutral predictions. Importantly, for continents where neutrality was either rejected or accepted, assembly drivers differed between the two functional groups. This study demonstrates that multi-trophic microbial systems may not be fully described by a single set of niche or neutral assembly rules and that stochasticity is likely a major determinant of such systems, with significant variation in the influence of these determinants on a global scale.
Connectedness of PPI network neighborhoods identifies regulatory hub proteins
Authors: Fox Andrew D. , Hescott Benjamin J. , Blumer Anselm C. , Slonim Donna K. 
Published: March 2011

Abstract
Motivation: With the growing availability of high-throughput protein–protein interaction (PPI) data, it has become possible to consider how a protein's local or global network characteristics predict its function.
Results: We introduce a graph-theoretic approach that identifies key regulatory proteins in an organism by analyzing proteins' local PPI network structure. We apply the method to the yeast genome and describe several properties of the resulting set of regulatory hubs. Finally, we demonstrate how the identified hubs and putative target gene sets can be used to identify causative, functional regulators of differential gene expression linked to human disease.
Availability: Code is available at http://bcb.cs.tufts.edu/hubcomps.
Contact: fox.andrew.d@gmail.com; slonim@cs.tufts.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
MemLoci: predicting subcellular localization of membrane proteins in eukaryotes
Authors: Pierleoni Andrea , Martelli Pier Luigi , Casadio Rita 
Published: March 2011

Abstract
Motivation: Subcellular localization is a key feature in the process of functional annotation of both globular and membrane proteins. In the absence of experimental data, protein localization is inferred on the basis of annotation transfer upon sequence similarity search. However, predictive tools are necessary when the localization of homologs is not known. This is so particularly for membrane proteins. Furthermore, most of the available predictors of subcellular localization are specifically trained on globular proteins and poorly perform on membrane proteins.
Results: Here we develop MemLoci, a new support vector machine-based tool that discriminates three membrane protein localizations: plasma, internal and organelle membrane. When tested on an independent set, MemLoci outperforms existing methods, reaching an overall accuracy of 70% on predicting the location in the three membrane types, with a generalized correlation coefficient as high as 0.50.
Availability: The MemLoci server is freely available on the web at: http://mu2py.biocomp.unibo.it/memloci. Datasets described in the article can be downloaded at the same site.
Contact: casadio@biocomp.unibo.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Diabetes Blockade of Sevoflurane Postconditioning Is Not Restored by Insulin in the Rat Heart
Authors: Drenger Benjamin , Ostrovsky Israel A. , Barak Michal , Nechemia-Arbely Yael , Ziv Ehud , Axelrod Jonathan H. 
Published: March 2011

Background
The possibility of restoring sevoflurane postconditioning (sevo-postC) cardioprotection in diabetic animals is uncertain. We hypothesized that attenuation of myocardial injury by sevo-postC might be hindered by inhibition of signal transducer and activator of transcription (STAT) 3-regulated activity of phosphatidylinositol 3-kinase (PI3K) in diabetic animals. To determine whether postC cardioprotection can be restored by normoglycemia, we treated rats with insulin.

Methods
Diabetic or nondiabetic rats were randomly subjected to 30-min ischemia/reperfusion, with ischemic postC or sevo-postC, with and without mitochondrial adenosine triphosphate-dependent potassium channel blocker 5-hydroxy decanoate sodium and PI3K antagonist wortmannin. The infarct area, phosphorylated STAT3, and apoptosis were examined. Studies were repeated after insulin treatment.

Results
Ischemic postC and sevo-postC significantly reduced infarct size by 50% in the nondiabetic rats (P < 0.002), a phenomenon completely reversed by 5-hydroxy decanoate sodium and wortmannin. Diabetes mellitus blocked the protective effect of postC, and insulin treatment to achieve normoglycemia did not restore cardioprotection. Phosphorylated STAT3 nuclear retention was significantly increased after ischemia-reperfusion and was further enhanced in response to ischemic postC (P < 0.05) but was significantly reduced in diabetic rats (by 43%; P < 0.01).

Conclusions
The effective reduction in infarct size and apoptosis in the nondiabetic rat heart by postC was completely abrogated in diabetic rats. This inhibition is not relieved by insulin-induced normoglycemia. The PI3K pathway and mitochondrial adenosine triphosphate-dependent potassium channel activation are involved in the mechanism of postC. In diabetic rats, STAT3 activation was strongly reduced, as was postC cardioprotection, suggesting that the inability of insulin to restore postC may be attributed to diabetes-induced STAT3-mediated inhibition of PI3K signaling.
Preparation of Live Testis Squashes inDrosophila
Authors: Bonaccorsi Silvia , Giansanti Maria G. , Cenci Giovanni , Gatti Maurizio 
Published: March 2011

INTRODUCTIONThe easiest and fastest method for the analysis of spermatocyte growth and male meiosis is the examination of living testis squashes in aqueous solutions. These preparations allow unambiguous recognition of most cell types ofDrosophilaspermatogenesis, as well as most phases of male meiosis. Living testes squashes can be carried out successfully using a variety of aqueous solutions. This protocol describes a standard method for preparing live testes squashes and the various aqueous solutions that can be used.
Labeling Neuronal Membrane Receptors with Quantum Dots
Authors: Lévi Sabine , Dahan Maxime , Triller Antoine 
Published: March 2011

INTRODUCTIONThis protocol describes a highly sensitive approach for tracking the motion of membrane molecules over extended time periods with single-molecule resolution. This technique uses nanometer-sized quantum dots (QDs) linked to the extracellular part of the proteins to be followed. Single-fluorophore epifluorescence imaging then reveals the membrane diffusion of the particle of interest. Two methods are presented for labeling neurons with the primary antibody of choice along with a secondary anti-Fab antibody that is either biotinylated or directly coupled to the desired QD. The behavior of QD-labeled molecules can then be followed within the cell using epifluorescence imaging.
Microinjecting Cells Using a Pulsed-Flow Microinjection System
Authors: Dean David A. , Gasiorowski Joshua Z. 
Published: March 2011

INTRODUCTIONThe efficient delivery of exogenous DNA to cells for expression and function studies is an essential technique of modern cell biology, and direct delivery of genetic material by microinjection remains a reliable means of transfection. A pulsed-flow microinjection system, such as the Eppendorf InjectMan and FemtoJet systems, permits a high level of control over the microinjection parameters, ensuring reproducibility. The system is also easy to use, is rapid, and is less likely to damage cells than the constant-flow method.
Microinjecting Cells Using a Constant-Flow Microinjection System
Authors: Dean David A. , Gasiorowski Joshua Z. 
Published: March 2011

INTRODUCTIONThe efficient delivery of exogenous DNA to cells for expression and function studies is an essential technique of modern cell biology, and direct delivery of genetic material by microinjection remains a reliable means of transfection. In the system described here a constant flow of sample is delivered from the tip of the pipette, and the amount of sample injected into the cell is determined by how long the pipette remains in the cell. The system can be assembled at relatively low cost using commercially available components: Typically, a pressure regulator that can be adjusted for two pressures (back pressure and injection pressure), a capillary holder, and coarse and fine micromanipulators. A constant-flow system, by design, injects less reproducible cell volumes than does a pulsed-flow system. However, with practice, this difference can be made negligible.
MRI in Developmental Biology and the Construction of Developmental Atlases
Authors: Ruffins Seth W. , Jacobs Russell E. 
Published: March 2011

INTRODUCTIONMicroscopic magnetic resonance imaging (μMRI) is a noninvasive, nonoptical imaging modality that allows the entire volume of opaque specimens to be imaged. Because μMRI is not a destructive method, biologists are afforded anatomically unperturbed imagery of embryonic development and the ability to observe morphogenetic movements deep within optically inaccessible embryos. Compared with optical methods, μMRI data acquisition is slow, and image resolution is very low. This might suggest that μMRI is not viable for developmental studies. In this article, we discuss when μMRI is an appropriate imaging modality and how it has contributed to a richer understanding of embryonic development by allowing direct observation of dynamic processes in optically inaccessible regions of unperturbed embryos. We close the article with a discussion of μMRI for the construction of digital anatomical developmental atlases and how such atlases can be used.
Nonviral Gene Delivery
Authors: Dean David A. , Gasiorowski Joshua Z. 
Published: March 2011

INTRODUCTIONModern cell biology increasingly relies on molecular tools to facilitate the study of cellular processes. With the advent of recombinant DNA technology, reverse transcription–polymerase chain reaction (RT-PCR) to amplify almost any gene, and fluorescent proteins that can be fused to any desired target protein, the number and scope of functional studies designed to determine the roles of proteins within cells have exploded. Creating the appropriate fusion protein plasmid is a key step, but the DNA must also be delivered to the cell for expression and function studies. There are several common approaches for delivering DNA, including liposome- and polymer-mediated transfection, electroporation, and direct DNA delivery by microinjection. This article provides an overview of several of these nonviral gene delivery methods, with an emphasis on direct injection of plasmids into cells.
Integration of the life of field seismic data with the reservoir model at the Valhall Field‡
Authors: van Gestel Jean‐Paul , Best Kevin D. , Barkved Olav I. , Kommedal Jan H. 
Published: March 2011

ABSTRACTThe frequent time‐lapse observations from the life of field seismic system across the Valhall field provide a wealth of information. The responses from the production and injection wells can be observed through time‐shift and amplitude changes. These observations can be compared to modelled synthetic seismic responses from a reservoir simulation model of the Valhall Field. The observed differences between the observations and the modelling are used to update and improve the history match of the reservoir model. The uncertainty of the resulting model is reduced and a more confident prediction of future reservoir performance is provided.A workflow is presented to convert the reservoir model to a synthetic seismic response and compare the results to the observed time‐lapse responses for any time range and area of interest. Correlation based match quality factors are calculated to quantify the visual differences. This match quality factor allows us to quantitatively compare alternative reservoir models to help identify the parameters that best match the seismic observations.Three different case studies are shown where this workflow has helped to reduce the uncertainty range associated with specific reservoir parameters. By updating various reservoir model parameters we have been able to improve the match to the observations and thereby improve the overall reservoir model predictability. The examples show positive results in a range of different reservoir modelling issues, which indicates the flexibility of this workflow and the ability to have an impact in most reservoir modelling challenges.
Wave equation least square imaging using the local angular Hessian for amplitude correction
Authors: Ren Haoran , Wu Ru‐Shan , Wang Huazhong 
Published: March 2011

ABSTRACTLocal angular Hessian can be used to improve wave equation least square migration images. By decomposing the original Hessian operator into the local wavenumber domain or the local angle domain, the least square migration image is obtained as the solution of a linearized least‐squares inversion in the frequency and local angle domains. The local angular Hessian contains information about the acquisition geometry and the propagation effects based on the given velocity model. The inversion scheme based on the local angular Hessian avoids huge computation on the exact inverse Hessian matrix. To reduce the instability in the inversion, damping factors are introduced into the deconvolution filter in the local wavenumber domain and the local angle domain. The algorithms are tested using the SEG/EAGE salt2D model and the Sigsbee2A model. Results show improved image quality and amplitudes.
Maintaining northern peatland ecosystems in a changing climate: effects of soil moisture, drainage and drain blocking on craneflies
Authors: CARROLL MATTHEW J. , DENNIS PETER , PEARCE‐HIGGINS JAMES W. , THOMAS CHRIS D. 
Published: March 2011

AbstractThe capacity of peatlands in the northern hemisphere to provide carbon storage, maintain water quality and support northern biodiversity is threatened by a combination of climate change and inappropriate land management. Historical drainage and increasing temperatures threaten the maintenance of the high water tables required for effective peatland functioning, and there is an urgent need to develop appropriate adaptation strategies. Here we use a large‐scale replicated experimental design to test the effects of artificial drainage and drain blocking upon soil moisture and cranefly (Diptera: Tipulidae) abundance. Craneflies constitute a key component of peatland biological communities; they are important herbivores and a major prey item for breeding birds. However, they are also susceptible to drought, so are at risk from future climate change. We found that cranefly abundance increased with soil moisture, in a wedge‐shaped relationship; high soil moisture is a necessary condition for high cranefly abundance. Blocking drains increased both soil moisture (by 0.06 m3 m−3 in 2009 and 0.23 m3 m−3 in 2010) and cranefly abundance (1.3‐fold in 2009, 4.5‐fold in 2010), but the strength and significance of the effects varied between years. The benefits of restoring ecosystem moisture levels are likely to be greatest during dry years and at dry sites. This study provides some of the first evidence that adaptation management can potentially reduce some of the negative effects of climate change on vulnerable peatland systems. Management to maintain or increase soil moisture in peatlands can therefore be expected to increase populations of craneflies and their avian predators (which are of conservation and economic interest), but also increase the resilience of the ecosystem to future warming and increasingly frequent droughts, and improve carbon storage and water quality.