bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study
Authors: Ferná;ndez Elmer A. , Girotti María R. , del Olmo Juan A. López , Llera Andrea S. , Podhajcer Osvaldo L. , Cantet Rodolfo J. C. , Balzarini Mónica 
Published: September 2008

Abstract
Motivation: Difference in-gel electrophoresis (DIGE)-based protein expression analysis allows assessing the relative expression of proteins in two biological samples differently labeled (Cy5, Cy3 CyDyes). In the same gel, a reference sample is also used (Cy2 CyDye) for spot matching during image analysis and volume normalization. The standard statistical techniques to identify differentially expressed (DE) proteins are the calculation of fold-changes and the comparison of treatment means by the t-test. The analyses rarely accounts for other experimental effects, such as CyDye and gel effects, which could be important sources of noise while detecting treatment effects.
Results: We propose to identify DIGE DE proteins using a two-stage linear mixed model. The proposal consists of splitting the overall model for the measured intensity into two interconnected models. First, we fit a normalization model that accounts for the general experimental effects, such as gel and CyDye effects as well as for the features of the associated random term distributions. Second, we fit a model that uses the residuals from the first step to account for differences between treatments in protein-by-protein basis. The modeling strategy was evaluated using data from a melanoma cell study. We found that a heteroskedastic model in the first stage, which also account for CyDye and gel effects, best normalized the data, while allowing for an efficient estimation of the treatment effects. The Cy2 reference channel was used as a covariate in the normalization model to avoid skewness of the residual distribution. Its inclusion improved the detection of DE proteins in the second stage.
Contact: elmer.fernandez@ucc.edu.ar
Supplementary information: R and SAS codes to analyze DIGE data with the proposed approach are available at http://www.uccor.edu.ar/modelo.php?param=3.8.5.15.2
Faecal microbiota profile of Crohn’s disease determined by terminal restriction fragment length polymorphism analysis
Authors: ANDOH A. , TSUJIKAWA T. , SASAKI M. , MITSUYAMA K. , SUZUKI Y. , MATSUI T. , MATSUMOTO T. , BENNO Y. , FUJIYAMA Y. 
Published: September 2008

SummaryBackground  Terminal restriction fragment length polymorphism (T‐RFLP) analyses are powerful tools to assess the diversity of complex microbiota. T‐RFLPs permit rapid comparisons of microbiota from many samples.Aim  To perform T‐RFLP analyses of faecal microbiota in Crohn’s disease (CD) patients to investigate potential alterations in faecal microbial communities and furthermore to analyse the effects of elemental diet on faecal microbiota profiles.Methods  Thirty‐four patients with CD and 30 healthy individuals were enrolled in the study. DNA was extracted from stool samples and 16S rRNA genes were amplified by PCR. PCR products were digested with BslI restriction enzymes and T‐RF lengths were determined.Results  Faecal microbial communities were classified into seven clusters. Almost all healthy individuals (28/30) were included in cluster I, II and III, but the majority of CD patients (25/34) could be divided into another four clusters (cluster IV–VII). Prediction of bacteria based on the BslI‐digested T‐RFLP database showed a significant decrease in Clostridium cluster IV, Clostridium cluster XI and subcluster XIVa in CD patients. In contrast, Bacteroides significantly increased in CD patients. Significant increases in Enterobacteriales were also observed in CD patients. Furthermore, elemental diets modulated faecal bacterial communities in CD patients.Conclusions  Terminal restriction fragment length polymorphism analyses showed that the diversity of faecal microbiota in patients with CD differed from that of healthy individuals. Furthermore, elemental diets modulated faecal microbiota composition, and this effect may be involved in mechanisms of clinical effects of elemental diet.
Nursing emotion work and interprofessional collaboration in general internal medicine wards: a qualitative study
Authors: Miller Karen‐Lee , Reeves Scott , Zwarenstein Merrick , Beales Jennifer D. , Kenaszchuk Chris , Conn Lesley Gotlib 
Published: September 2008

AbstractTitle.  Nursing emotion work and interprofessional collaboration in general internal medicine wards: a qualitative study Aim.  This paper is a report of a study to examine nursing emotion work and interprofessional collaboration in order to understand and improve collaborative nursing practice.Background.  Nursing standards identify collaborative practice as necessary for quality patient care yet many nurses are often reluctant to participate in interprofessional teams. Strategies intended to improve participation often fail which suggests that the factors underpinning nurses’ disinclination towards interprofessional collaboration have yet to be understood. The concept of emotion work has not been applied to nursing interprofessionalism, and holds the potential to improve collaborative practice. Nursing emotion work is defined as the management of the emotions of self and others in order to improve patient care.Methods.  Qualitative data were collected in 2006 using non‐participant observation, shadowing and semi‐structured interviews with nursing, medical and allied professionals in the general internal medicine wards of three hospitals in urban Canada.Findings.  Nurses’ collaborations with other professionals are influenced by emotion work considerations. The establishment and maintenance of a nursing esprit de corps, corridor conflicts with physicians, and the failure of the interdisciplinary team to acknowledge the importance of nursing’s core caring values are important factors underpinning nurses’ interprofessional disengagement.Conclusion.  Longstanding emotion work issues must be addressed before nurses will engage collaboratively. We suggest improving nursing collaboration through the refining of holistic nursing information, and reflections on practice by all interprofessional team members.
Making robust decisions for conservation with restricted money and knowledge
Authors: McDonald‐Madden Eve , Baxter Peter W.J. , Possingham Hugh P. 
Published: September 2008

Summary

In conservation decision‐making, we operate within the confines of limited funding. Furthermore, we often assume particular relationships between management impact and our investment in management. The structure of these relationships, however, is rarely known with certainty – there is model uncertainty. We investigate how these two fundamentally limiting factors in conservation management, money and knowledge, impact optimal decision‐making.
We use information‐gap decision theory to find strategies for maximizing the number of extant subpopulations of a threatened species that are most immune to failure due to model uncertainty. We thus find a robust framework for exploring optimal decision‐making.
The performance of every strategy decreases as model uncertainty increases.
The strategy most robust to model uncertainty depends not only on what performance is perceived to be acceptable but also on available funding and the time horizon over which extinction is considered.
Synthesis and applications. We investigate the impact of model uncertainty on robust decision‐making in conservation and how this is affected by available conservation funding. We show that subpopulation triage can be a natural consequence of robust decision‐making. We highlight the need for managers to consider triage not as merely giving up, but as a tool for ensuring species persistence in light of the urgency of most conservation requirements, uncertainty and the poor state of conservation funding. We illustrate this theory by a specific application to allocation of funding to reduce poaching impact on the Sumatran tiger Panthera tigris sumatrae in Kerinci Seblat National Park.
The nodule inception‐like protein 7 modulates nitrate sensing and metabolism in Arabidopsis
Authors: Castaings Loren , Camargo Antonio , Pocholle Delphine , Gaudon Virginie , Texier Yves , Boutet‐Mercey Stéphanie , Taconnat Ludivine , Renou Jean‐Pierre , Daniel‐Vedele Françoise , Fernandez Emilio , Meyer Christian , Krapp Anne 
Published: September 2008

SummaryNitrate is an essential nutrient, and is involved in many adaptive responses of plants, such as localized proliferation of roots, flowering or stomatal movements. How such nitrate‐specific mechanisms are regulated at the molecular level is poorly understood. Although the Arabidopsis ANR1 transcription factor appears to control stimulation of lateral root elongation in response to nitrate, no regulators of nitrate assimilation have so far been identified in higher plants. Legume‐specific symbiotic nitrogen fixation is under the control of the putative transcription factor, NIN, in Lotus japonicus. Recently, the algal homologue NIT2 was found to regulate nitrate assimilation. Here we report that Arabidopsis thaliana NIN‐like protein 7 (NLP7) knockout mutants constitutively show several features of nitrogen‐starved plants, and that they are tolerant to drought stress. We show that nlp7 mutants are impaired in transduction of the nitrate signal, and that the NLP7 expression pattern is consistent with a function of NLP7 in the sensing of nitrogen. Translational fusions with GFP showed a nuclear localization for the NLP7 putative transcription factor. We propose NLP7 as an important element of the nitrate signal transduction pathway and as a new regulatory protein specific for nitrogen assimilation in non‐nodulating plants.
Contribution of salicylic acid glucosyltransferase, OsSGT1, to chemically induced disease resistance in rice plants
Authors: Umemura Kenji , Satou Junji , Iwata Michiaki , Uozumi Nobuyuki , Koga Jinichiro , Kawano Tomonori , Koshiba Tomokazu , Anzai Hiroyuki , Mitomi Masaaki 
Published: September 2008

SummarySystemic acquired resistance (SAR), a natural disease response in plants, can be induced chemically. Salicylic acid (SA) acts as a key endogenous signaling molecule that mediates SAR in dicotyledonous plants. However, the role of SA in monocotyledonous plants has yet to be elucidated. In this study, the mode of action of the agrochemical protectant chemical probenazole was assessed by microarray‐based determination of gene expression. Cloning and characterization of the most highly activated probenazole‐responsive gene revealed that it encodes UDP‐glucose:SA glucosyltransferase (OsSGT1), which catalyzes the conversion of free SA into SA O‐β‐glucoside (SAG). We found that SAG accumulated in rice leaf tissue following treatment with probenazole or 2,6‐dichloroisonicotinic acid. A putative OsSGT1 gene from the rice cultivar Akitakomachi was cloned and the gene product expressed in Escherichia coli was characterized, and the results suggested that probenazole‐responsive OsSGT1 is involved in the production of SAG. Furthermore, RNAi‐mediated silencing of the OsSGT1 gene significantly reduced the probenazole‐dependent development of resistance against blast disease, further supporting the suggestion that OsSGT1 is a key mediator of development of chemically induced disease resistance. The OsSGT1 gene may contribute to the SA signaling mechanism by inducing up‐regulation of SAG in rice plants.
The GhACS1 gene encodes an acyl‐CoA synthetase which is essential for normal microsporogenesis in early anther development of cotton
Authors: Wang Xiu‐Lan , Li Xue‐Bao 
Published: September 2008

SummaryMicrosporogenesis, associated with the functional expression of many genes, is a highly programmed and regulated process in flowering plants. To elucidate the roles of genes during anther development, two anther‐specific cDNAs (designated GhACS1 and GhACS2) encoding acyl‐CoA synthetases (ACSs) were isolated from a cotton (Gossypium hirsutum) flower cDNA library. Subsequently, the corresponding GhACS1 gene was isolated from a cotton genomic DNA library. Real‐time quantitative RT‐PCR and northern blot analyses revealed that GhACS1 transcripts were predominantly accumulated in the developing anthers of cotton. The specificity of GhACS1 expression in primary sporogenous cells (PSCs), pollen mother cells (PMCs), microspores, and tapetal cells was demonstrated by in situ hybridization as well as histochemical assay of GUS expression controlled under the GhACS1 promoter. High levels of GhACS1 activity are crucial for fatty acid metabolism in PSCs, PMCs, microspores and particularly tapetal cells. Reduction of ACS enzymatic activity by suppressing GhACS1 expression severely affected the tapetal cells and consequently blocked normal microsporogenesis in early anther development. Aberrant and defective microspores were generated in the transgenic anthers. As a result, the transgenic plants failed to produce functional pollen grains and were male‐sterile, suggesting that the GhACS1 gene is required for normal microsporogenesis in early anther development of cotton.
Cryptostomid Bryozoans From The Sassito Formation, Upper Ordovician Cool‐Water Carbonates of the Argentinean Precordillera
Authors: ERNST ANDREJ , CARRERA MARCELO 
Published: September 2008

Abstract:  Two new bryozoan species are described from the Upper Ordovician Sassito Formation of the Argentinean Precordillera: Moyerella spinata sp. nov. and Phylloporina sassitoensis sp. nov. The bryozoans are found in cool‐water carbonates. The Silurian genus Moyerella is reported the first time in the Ordovician, showing palaeobiogeographic connections with Estonia and Siberia.
SYSTEMATIC REVISION OF PSEUDOBEACONIA BORDAS, 1944, AND MENDOCINICHTHYS WHITLEY, 1953 (ACTINOPTERYGII: ‘PERLEIDIFORMES’) FROM THE TRIASSIC OF ARGENTINA
Authors: LÓPEZ‐ARBARELLO ADRIANA , ZAVATTIERI ANA M. 
Published: September 2008

Abstract:  The ‘perleidiform’Mendocinichthys and Pseudobeaconia from the Potrerillos and Santa Clara Abajo formations (Upper Triassic; Argentina) are reviewed. Mendocinichthys has been known from a review of this species that is not based on the type material, but on referred specimens in the American Museum of Natural History. However, those specimens are found here to represent a new species of Pseudobeaconia, P. celestae sp. nov. Consequently, Mendocinichthys is restricted here to the type material and, within it, to the only specimen that clearly represents a distinct taxon and is thus designated lectotype. We further performed a cladistic analysis and propose a new family, Pseudobeaconiidae for these two South American Triassic genera, which is mainly characterized by the presence of an incomplete dorsal ridge of spine‐like scales between the skull and the dorsal fin, and scales with straight posterior border, an elevated central region and marginal concentric ridges of ganoine. The cladistic analysis further indicates the existence of some lineages endemic to certain areas of Gondwana and Europe. Pseudobeaconia celestae sp. nov. represents the first record of Pseudobeaconia in the Cacheuta sub‐basin of the Cuyana Basin. The genus was previously known from the Santa Clara sub‐basin of the Cuyana Basin only, and the new record confirms the previous hypothesis of correlation between the sedimentary infilling of these sub‐basins.
Party Competition and Government Formation in Multilevel Settings: Evidence from Germany
Authors: Debus Marc 
Published: September 2008

AbstractGoverning in multilevel settings has become a prominent research field in comparative political science. This article asks if German state parties adopt similar ideological positions and coalition strategies to the parties on the federal stage. The results of a content analysis of state and federal election manifestos show that German political parties on the state level indeed adopt different programmatic positions to the federal parties'. Government formation on the state level, however, is not only influenced by the state parties' programmatic viewpoints, but also by the predominant patterns of coalition politics at the federal level.
The Swedish Conservative Party and the Welfare State: Institutional Change and Adapting Preferences
Authors: Lindbom Anders 
Published: September 2008

AbstractAfter the 2006 elections, a bourgeois government came to power in Sweden. This article argues that the popularity of the ‘universal’ Swedish welfare state has led the dominant ‘neoliberal’ party (Moderaterna) to adapt its policies; the party has accepted that the modern welfare state is irreplaceable. In the short run the party can only hope to achieve incremental changes, but at the same time the party wants to change society (lower taxes) in the long run. The differences between the allegedly neoliberal 1980s and 2006 should not conceal that the mechanism of welfare popularity remains largely the same. The party's policy proposals tend to suggest only incremental changes in both periods.
Teaching and Assessing Procedural Skills Using Simulation: Metrics and Methodology
Authors: Lammers Richard L. , Davenport Moira , Korley Frederick , Griswold‐Theodorson Sharon , Fitch Michael T. , Narang Aneesh T. , Evans Leigh V. , Gross Amy , Rodriguez Elliot , Dodge Kelly L. , Hamann Cara J. , Robey III Walter C. 
Published: September 2008

AbstractSimulation allows educators to develop learner‐focused training and outcomes‐based assessments. However, the effectiveness and validity of simulation‐based training in emergency medicine (EM) requires further investigation. Teaching and testing technical skills require methods and assessment instruments that are somewhat different than those used for cognitive or team skills. Drawing from work published by other medical disciplines as well as educational, behavioral, and human factors research, the authors developed six research themes: measurement of procedural skills; development of performance standards; assessment and validation of training methods, simulator models, and assessment tools; optimization of training methods; transfer of skills learned on simulator models to patients; and prevention of skill decay over time. The article reviews relevant and established educational research methodologies and identifies gaps in our knowledge of how physicians learn procedures. The authors present questions requiring further research that, once answered, will advance understanding of simulation‐based procedural training and assessment in EM.
On the anomalous silicate emission features of active galactic nuclei: a possible interpretation based on porous dust
Authors: Li M. P. , Shi Q. J. , Li Aigen 
Published: September 2008

Abstract
The recent Spitzer detections of the 9.7 μm Si–O silicate emission in type 1 active galactic nuclei (AGN) provide support for the AGN unification scheme. The properties of the silicate dust are of key importance to understand the physical, chemical and evolutionary properties of the obscuring dusty torus around the AGN. Compared to that of the Galactic interstellar medium (ISM), the 10 μm silicate emission profile of type 1 AGN is broadened and has a clear shift of peak position to longer wavelengths. In literature, this is generally interpreted as an indication of the deviations of the silicate composition, size and degree of crystallization of the AGN from that of the Galactic ISM. In this Letter, we show that the observed peak shift and profile broadening of the 9.7 μm silicate emission feature can be explained in terms of porous composite dust consisting of ordinary interstellar amorphous silicate, amorphous carbon and vacuum. Porous dust is naturally expected in the dense circumnuclear region around the AGN, as a consequence of grain coagulation.
Adverse impact of industrial animal agriculture on the health and welfare of farmed animals
Authors: D'SILVA Joyce 
Published: September 2008

AbstractIndustrial animal agriculture is grounded in the concept of maximizing productivity and profit. Selective breeding for maximum productivity in one characteristic of the animal (e.g. milk yield in cows, or breast meat in broiler chickens) has resulted in genotypes and phenotypes that may predispose the animals to poor health and welfare. The conditions in which these individuals are kept may also frustrate many inherited behaviors that they are strongly motivated to perform. In order to curb the resulting harmful aberrant behaviors, such as feather‐pecking in chickens, we sometimes resort to mutilating the animals. In many places chickens are routinely de‐beaked by means of a hot metal guillotine. Compassion in World Farming (an international organization that promotes the humane treatment of farm animals) believes that it is unethical to treat sentient beings in such ways. We have a duty to respect farm animals' sentience by providing them with housing conditions that take their needs and wants into account, and by reverting to the use of dual‐purpose, slower‐growing breeds that have the potential for good welfare. Alternatives to current farming practices are available, and we owe it to the animals, and to our consciences, to pursue them.
Adiabatic limit of the eta invariant over cofinite quotients of PSL(2, ℝ)
Authors: Loya Paul , Moroianu Sergiu , Park Jinsung 
Published: September 2008

AbstractThe eta invariant of the Dirac operator over a non-compact cofinite quotient of PSL(2,ℝ) is defined through a regularized trace following Melrose. It reduces to the standard definition in terms of eigenvalues in the case of a totally non-trivial spin structure. When the S1-fibers are rescaled, the metric becomes of non-exact fibered-cusp type near the ends. We completely describe the continuous spectrum of the Dirac operator with respect to the rescaled metric and its dependence on the spin structure, and show that the adiabatic limit of the eta invariant is essentially the volume of the base hyperbolic Riemann surface with cusps, extending some of the results of Seade and Steer.
Chebyshev’s bias in function fields
Authors: Cha Byungchul 
Published: September 2008

AbstractWe study a function field analog of Chebyshev’s bias. Our results, as well as their proofs, are similar to those of Rubinstein and Sarnak in the case of the rational number field. Following Rubinstein and Sarnak, we introduce the grand simplicity hypothesis (GSH), a certain hypothesis on the inverse zeros of Dirichlet L-series of a polynomial ring over a finite field. Under this hypothesis, we investigate how primes, that is, irreducible monic polynomials in a polynomial ring over a finite field, are distributed in a given set of residue classes modulo a fixed monic polynomial. In particular, we prove under the GSH that, like the number field case, primes are biased toward quadratic nonresidues. Unlike the number field case, the GSH can be proved to hold in some cases and can be violated in some other cases. Also, under the GSH, we give the necessary and sufficient conditions for which primes are unbiased and describe certain central limit behaviors as the degree of modulus under consideration tends to infinity, all of which have been established in the number field case by Rubinstein and Sarnak.
Quasi-elementary contractions of Fano manifolds
Authors: Casagrande Cinzia 
Published: September 2008

AbstractLet X be a smooth complex Fano variety. We study ‘quasi-elementary’ contractions of fiber type of X, which are a natural generalization of elementary contractions of fiber type. If f:X→Y is such a contraction, then the Picard numbers satisfy ρX≤ρY+ρF, where F is a general fiber of f. We show that, if dim Y ≤3 and ρY≥4, then Y is smooth and Fano; if moreover ρY≥6, then X is a product. This yields sharp bounds on ρX when dim X=4 and X has a quasi-elementary contraction of fiber type, and other applications in higher dimensions.