bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Numerical Modeling Study of the Upwelling Source Waters along the Oregon Coast during 2005
Authors: Rivas David , Samelson R. M. 
Published: September 2010

Abstract
Regional ocean circulation along the Oregon coast is studied numerically for forcing fields derived from year 2005 and climatological-mean conditions. The primary object is to study directly the Lagrangian pathways by which fluid arrives in the Oregon upwelling zone. Roughly half of the upwelling fluid is found to arrive in the regional domain from alongshelf source points, primarily north but also south of the Oregon upwelling zone, while the other half ultimately arrives from points offshore and west of the zone. For both the year 2005 and the climatological simulations, different regimes of dominant alongshelf source waters are found, with Cape Blanco being a dividing point for northern versus southern sources, and with the water parcels coming primarily from depths below 100 m. For the offshore sources, most upwelling fluid originates from depths between 150 and 250 m during 2005, but from within the upper 150 m for the climatological simulations. In both cases there are specific regions along the shelf of enhanced vertical motion, which appear to be associated with topographic features such as submarine banks and canyons. A perhaps surprising result is the apparently small role played by the poleward undercurrent as a direct, immediate source of upwelling fluid; on the seasonal time scale considered here, most trajectories are found to move southward over the slope and shelf, with weaker northward motion only farther offshore, in the deep interior. In 2005 the water parcels cover distances longer than in the climatology, and the meridional exchange along their paths is more vigorous. These differences are likely associated in part with the presence of mesoscale vortical structures seaward of the shelf, which are largely absent in the climatological simulation, perhaps because their formation may depend on the large-amplitude, short-time-scale wind variations and reversals that occur in the year 2005 wind field but not in the multiyear mean climatological wind field.
Assessing the Performance of an Ensemble Forecast System in Predicting the Magnitude and the Spectrum of Analysis and Forecast Uncertainties
Authors: Satterfield Elizabeth , Szunyogh Istvan 
Published: September 2010

The ability of an ensemble to capture the magnitude and spectrum of uncertainty in a local linear space spanned by the ensemble perturbations is assessed. Numerical experiments are carried out with a reduced resolution 2004 version of the model component of the National Centers for Environmental Prediction (NCEP) Global Forecast System (GFS). The local ensemble transform Kalman filter (LETKF) data assimilation system is used to assimilate observations in three steps, gradually adding more realistic features to the observing network. In the first experiment, randomly placed, noisy, simulated vertical soundings, which provide 10% coverage of horizontal model grid points, are assimilated. Next, the impact of an inhomogeneous observing system is introduced by assimilating simulated observations in the locations of real observations of the atmosphere. Finally, observations of the real atmosphere are assimilated.The most important findings of this study are the following: predicting the magnitude of the forecast uncertainty and the relative importance of the different patterns of uncertainty is, in general, a more difficult task than predicting the patterns of uncertainty; the ensemble, which is tuned to provide near-optimal performance at analysis time, underestimates not only the total magnitude of the uncertainty, but also the magnitude of the uncertainty that projects onto the space spanned by the ensemble perturbations; and finally, a strong predictive linear relationship is found between the local ensemble spread and the upper bound of the local forecast uncertainty.
The distinctive lexicon and consensual conception of e-Government: an exploratory perspective
Authors: Guangwei Hu  , Wenwen Pan  , Jie Wang  
Published: September 2010

Presently, the field of e-Government still lacks a coherent identity. For its future development, it would be useful to identify a distinctive lexicon and widely shared conception to help scholars understand its essence. In this study, exploratory work was conducted using a large-scale survey of e-Government articles from 1993 to 2008. A total of 752 abstracts from the world’s leading databases (i.e. Science Citation Index Expanded (SCIE), Social Sciences Citation Index (SSCI), Arts & Humanities Citation Index (A&HCI) and Conference Proceedings Citation Index-Science (CPCI-S)) were retrieved, and 528 were analyzed using Computer-Aided Text Analysis (CATA) software. Based on the content analysis, a widely shared conception of the field held by its members was determined and a methodology to obtain a consensual definition of an academic field was designed. Points for practitioners By determining and presenting a widely shared conception of e-Government, this study aims to provide scholars, particularly the young, with a deeper understanding of the scope and meaning of the field. This consensual conception may serve either as a screen or as a magnet for future practitioners and academics. The methodology may be applied to several academic fields, including administration science, library science, management science, computer science, and others.
In what we trust? A multi-level study into trust in parliament as an evaluation of state characteristics
Authors: van der Meer Tom 
Published: September 2010

A basic level of trust in the political system is considered to be the cornerstone of modern-day democracy. Consequently, scholars and politicians have been concerned with low or declining levels of trust in political institutions. This article focuses on trust in parliament. Many theories have been offered to explain cross-national differences or longitudinal changes in trust, but they have not been subject to systematic empirical tests. This article aims to fill that theoretical and empirical gap. I conceptualize trust in parliament as citizens’ rather rational evaluations of the state—citizen relationship along four dimensions: competence, intrinsic care, accountability, and reliability. Next, I relate state characteristics to each of these four aspects, and hypothesize how they might affect political trust. These hypotheses are tested simultaneously by multi-level analysis on stapled data from the European Social Survey 2002—06. The tests show that three factors explain very well the cross-national differences in trust: corruption, the electoral system, and former regime type. Somewhat surprisingly, economic performance is not related to trust in parliament. Although the analyses do not explain changes in trust across time very well, they at least dismiss some of the existing explanations. Points for practitioners This article describes to what extent levels of trust in parliament differ across countries and change across time, and tests several explanations for comparatively low or longitudinally declining levels of trust. It offers practitioners a theoretical approach to make sense of trust issues by distinguishing four trust aspects. Moreover, it shows that objective state characteristics are crucial in explaining cross-national differences. Widespread perceptions of corruption are most harmful to trust in parliament, while democratic rule and a proportional electoral system are beneficial. Equally important, actual economic performance is unrelated to trust. Institutional designs that emphasize care and integrity appear to be more beneficial than ones that emphasize competence and performance.
Has the Whitehall Model survived?
Authors: Page Edward 
Published: September 2010

The expression ‘Whitehall Model’ has a certain heuristic value for describing four key features of the British civil service, namely political neutrality, generalism, life-long career paths and a strong policy advisory role. This model has been challenged by politicization, changes in career management and recruitment as well as increasing competition from other sources of policy advice. The UK civil service’s role in relation to ministers seems to have become increasingly defined in managerial terms and decreasingly as policy advisers, not least because a range of other individuals and bodies (advisers, consultants, think tanks, party research departments) now share this role. While it appears to be enjoying a diminishing policy role, the senior civil service has not, at least so far, managed to occupy the high ground in its managerial role. The biggest change in the model is a collapse of confidence in the civil service, not only among citizens, but also among politicians and civil servants themselves. Points for practitioners In many of its features, the Whitehall Model, describing the UK civil service and its political role, has been remarkably resilient in the face of major changes to the UK politico-administrative system. Top civil servants have traditionally avoided becoming involved in managing the detailed development of policy. With the decline in the political power of the civil service as the most noticeable of the changes in the Whitehall Model, greater attention to this policy development role might help improve the quality of decision-making.
Managing emergent and complex change: the case of Dutch agencification
Authors: Kickert Walter J.M. 
Published: September 2010

An analysis is made of agencification reform in the Netherlands from the viewpoint of the management of the complex change process. We will present a processual analysis of the complex change process of agencification reform by means of organization science insights on ‘emergent change’ and administrative science insights on ‘complex networks’. The analysis of the process of change events shows that it is not an example of centrally planned and controlled change. The reform is rather an example of ‘emergent and complex change’. The reform is a complex system of different intertwined change processes with many different decentralized actors, which is ‘managed’ by different central ‘change agents’. The ‘change managers’ themselves form a complex system as well. Points for practitioners One of the important reform trends in Dutch central administration is the ‘agencification’ of executive government organizations, that is, the increase of managerial autonomy of executive parts of ministerial departments. In this article we analyse how this two-decades-long reform process was ‘managed’ by various central actors like Parliament, the National Audit Office, the Ministry of Finance, the Ministry of Home Affairs, various internal and external advisory committees and supervisory committees. It turned out that the reform can hardly be described as a centrally planned and controlled process. Initiatives for reform, in fact, popped up locally within the various ministries and agencies. The reform process was more a continuous accumulation of local initiatives for agencification. The various central actors tried to exercise some coordinating or supervisory influence, but that was rather indirect, reactive and limited.
Child nutrition policies and recommendations
Authors: Juby Cindy , Meyer Erika Elizabeth 
Published: September 2010

• Summary: Child malnutrition often invokes images of children with thin extremities and pot bellies. Rarely, do we relate malnutrition to obesity; however, in the United States, poor children are especially vulnerable to obesity related malnutrition. Policies that increase the cost of nutrient-dense fruits and vegetables make it more difficult for poor families to purchase nutritious foods, thereby, increasing their risk of malnutrition. At the same time, cheaper foods tend to be more calorie-dense and to provide fewer nutrients. • Findings: This article discusses current policies that contribute to malnutrition and obesity in children from poor families and examines current changes within the political system regarding this topic. • Applications: Recommendations are provided for social workers whose clientele include children and families in poverty.
Moderators and mediators in social work research: Toward a more ecologically valid evidence base for practice
Authors: Magill Molly 
Published: September 2010

• Summary: Evidence-based practice involves the consistent and critical consumption of the social work research literature. As methodologies advance, primers to guide such efforts are often needed. In the present work, common statistical methods for testing moderation and mediation are identified, summarized, and corresponding examples, drawn from the substance abuse, domestic violence, and mental health literature, are provided. • Findings: Analyses of these third variable effects can provide an optimal fit for the complexity involved in the provision of evidence-based social work services. While a moderator may identify the trait or state requirement for a causal relationship to occur, a mediator is concerned with the transmission of that relationship. In social work practice, these are questions of ‘under what conditions and for whom?’ and of the ‘how?’ of behavior change. • Implications: Implications include a need for greater attention to these methods among practitioners and evaluation researchers. With knowledge gained through the present review, social workers can benefit from a more ecologically valid evidence base for practice.
Ligation of complement receptor 1 increases erythrocyte membrane deformability
Authors: Glodek Aleksandra M. , Mirchev Rossen , Golan David E. , Khoory Joseph A. , Burns Jennie M. , Shevkoplyas Sergey S. , Nicholson-Weller Anne , Ghiran Ionita C. 
Published: September 2010

AbstractMicrobes as well as immune complexes and other continuously generated inflammatory particles are efficiently removed from the human circulation by red blood cells (RBCs) through a process called immune-adherence clearance. During this process, RBCs use complement receptor 1 (CR1, CD35) to bind circulating complement-opsonized particles and transfer them to resident macrophages in the liver and spleen for removal. We here show that ligation of RBC CR1 by antibody and complement-opsonized particles induces a transient Ca++ influx that is proportional to the RBC CR1 levels and is inhibited by T1E3 pAb, a specific inhibitor of TRPC1 channels. The CR1-elicited RBC Ca++ influx is accompanied by an increase in RBC membrane deformability that positively correlates with the number of preexisting CR1 molecules on RBC membranes. Biochemically, ligation of RBC CR1 causes a significant increase in phosphorylation levels of β-spectrin that is inhibited by preincubation of RBCs with DMAT, a specific casein kinase II inhibitor. We hypothesize that the CR1-dependent increase in membrane deformability could be relevant for facilitating the transfer of CR1-bound particles from the RBCs to the hepatic and splenic phagocytes.
Transfer of influenza vaccine–primed costimulated autologous T cells after stem cell transplantation for multiple myeloma leads to reconstitution of influenza immunity: results of a randomized clinical trial
Authors: Stadtmauer Edward A. , Vogl Dan T. , Luning Prak Eline , Boyer Jean , Aqui Nicole A. , Rapoport Aaron P. , McDonald Kenyetta R. , Hou Xiaoling , Murphy Heather , Bhagat Rita , Mangan Patricia A. , Chew Anne , Veloso Elizabeth A. , Levine Bruce L. , Vonderheide Robert H. , Jawad Abbas F. , June Carl H. , Sullivan Kathleen E. 
Published: September 2010

AbstractSevere immune deficiency follows autologous stem cell transplantation for multiple myeloma and is associated with significant infectious morbidity. This study was designed to evaluate the utility of a pretransplantation vaccine and infusion of a primed autologous T-cell product in stimulating specific immunity to influenza. Twenty-one patients with multiple myeloma were enrolled from 2007 to 2009. Patients were randomly assigned to receive an influenza-primed autologous T-cell product or a nonspecifically primed autologous T-cell product. The study endpoint was the development of hemagglutination inhibition titers to the strain-specific serotypes in the influenza vaccine. Enzyme-linked immunospot assays were performed to confirm the development of influenza-specific B-cell and T-cell immunity. Patients who received the influenza-primed autologous T-cell product were significantly more likely to seroconvert in response to the influenza vaccine (P = .001). Seroconversion was accompanied by a significant B-cell response. No differences were observed in the global quantitative recovery of T-cell and B-cell subsets or in global T-cell and B-cell function. The provision of a primed autologous T-cell product significantly improved subsequent influenza vaccine responses. This trial was registered at www.clinicaltrials.gov as #NCT00499577.
Phosphorylation of threonine 154 in p40phox is an important physiological signal for activation of the neutrophil NADPH oxidase
Authors: Chessa Tamara A. M. , Anderson Karen E. , Hu Yanhua , Xu Qingbo , Rausch Oliver , Stephens Len R. , Hawkins Phillip T. 
Published: September 2010

AbstractThe neutrophil nicotinamide adenine dinucleotide phosphate-oxidase is a multisubunit enzyme (comprising gp91phox, p22phox, p67phox, p40phox, p47phox, and Rac) that plays a vital role in microbial killing. The recent discovery of a chronic granulomatous disease patient who expresses a mutant p40phox subunit, together with the development of mouse models of p40phox function, indicate phosphatidylinositol 3-phosphate binding to the PX domain of p40phox is an important signal for oxidase activation. However, the presence of other conserved residues and domains in p40phox suggest further regulatory roles for this protein. To test this, we introduced wild-type and mutated versions of p40phox into fully differentiated mouse neutrophils by retroviral transduction of p40phox−/− bone marrow progenitors and repopulation of the bone marrow compartment in radiation chimaeras. Phosphorylation of p40phox on threonine 154, but not serine 315, was required for full oxidase activation in response to formylated bacterial peptide fMLP, serum-opsonized S aureus, and immunoglobulin-opsonized sheep red blood cells. A functional SH3 domain was not required for oxidase activation, and deletion of the entire domain resulted in enhanced oxidase responses. Phosphorylation of threonine 154 in response to S aureus was mediated by protein kinase Cδ and was required for full translocation of p47phox to phagosomes. These results define an important new element in the physiological activation of the oxidase.
Improving performance of mammalian microRNA target prediction
Authors: Liu Hui , Yue Dong , Chen Yidong , Gao Shou-Jiang , Huang Yufei 
Published: September 2010

Abstract

Background
MicroRNAs (miRNAs) are single-stranded non-coding RNAs known to regulate a wide range of cellular processes by silencing the gene expression at the protein and/or mRNA levels. Computational prediction of miRNA targets is essential for elucidating the detailed functions of miRNA. However, the prediction specificity and sensitivity of the existing algorithms are still poor to generate meaningful, workable hypotheses for subsequent experimental testing. Constructing a richer and more reliable training data set and developing an algorithm that properly exploits this data set would be the key to improve the performance current prediction algorithms.

Results
A comprehensive training data set is constructed for mammalian miRNAs with its positive targets obtained from the most up-to-date miRNA target depository called miRecords and its negative targets derived from 20 microarray data. A new algorithm SVMicrO is developed, which assumes a 2-stage structure including a site support vector machine (SVM) followed by a UTR-SVM. SVMicrO makes prediction based on 21 optimal site features and 18 optimal UTR features, selected by training from a comprehensive collection of 113 site and 30 UTR features. Comprehensive evaluation of SVMicrO performance has been carried out on the training data, proteomics data, and immunoprecipitation (IP) pull-down data. Comparisons with some popular algorithms demonstrate consistent improvements in prediction specificity, sensitivity and precision in all tested cases. All the related materials including source code and genome-wide prediction of human targets are available at http://compgenomics.utsa.edu/svmicro.html.

Conclusions
A 2-stage SVM based new miRNA target prediction algorithm called SVMicrO is developed. SVMicrO is shown to be able to achieve robust performance. It holds the promise to achieve continuing improvement whenever better training data that contain additional verified or high confidence positive targets and properly selected negative targets are available.
Conservation, duplication, and loss of the Tor signaling pathway in the fungal kingdom
Authors: Shertz Cecelia A , Bastidas Robert J , Li Wenjun , Heitman Joseph , Cardenas Maria E 
Published: September 2010

Abstract

Background
The nutrient-sensing Tor pathway governs cell growth and is conserved in nearly all eukaryotic organisms from unicellular yeasts to multicellular organisms, including humans. Tor is the target of the immunosuppressive drug rapamycin, which in complex with the prolyl isomerase FKBP12 inhibits Tor functions. Rapamycin is a gold standard drug for organ transplant recipients that was approved by the FDA in 1999 and is finding additional clinical indications as a chemotherapeutic and antiproliferative agent. Capitalizing on the plethora of recently sequenced genomes we have conducted comparative genomic studies to annotate the Tor pathway throughout the fungal kingdom and related unicellular opisthokonts, including Monosiga brevicollis, Salpingoeca rosetta, and Capsaspora owczarzaki.

Results
Interestingly, the Tor signaling cascade is absent in three microsporidian species with available genome sequences, the only known instance of a eukaryotic group lacking this conserved pathway. The microsporidia are obligate intracellular pathogens with highly reduced genomes, and we hypothesize that they lost the Tor pathway as they adapted and streamlined their genomes for intracellular growth in a nutrient-rich environment. Two TOR paralogs are present in several fungal species as a result of either a whole genome duplication or independent gene/segmental duplication events. One such event was identified in the amphibian pathogen Batrachochytrium dendrobatidis, a chytrid responsible for worldwide global amphibian declines and extinctions.

Conclusions
The repeated independent duplications of the TOR gene in the fungal kingdom might reflect selective pressure acting upon this kinase that populates two proteinaceous complexes with different cellular roles. These comparative genomic analyses illustrate the evolutionary trajectory of a central nutrient-sensing cascade that enables diverse eukaryotic organisms to respond to their natural environments.