bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abolition of Respiratory-Motion Artifact in Computed Tomography Coronary Angiography with Ultrafast Examinations: A Comparison between 64-row and 320-row Multidetector Scanners
Authors: Torres Felipe S. , Crean Andrew M. , Nguyen Elsie T. , Menezes Ravi , Doyle Deirdre , Ayyappan Anoop P. , Abadi Sobhi , Paul Narinder 
Published: October 2009

Purpose To compare the incidence of respiratory artifact in computed tomography (CT) coronary angiography performed with 64-row and 320-row multidetector scanners and to assess its effect on coronary evaluability. Methods A retrospective review of consecutive coronary angiograms performed on a 64-row multidetector CT from March to April 2007 (group 1: 115 patients, 63 men; mean age [standard deviation] 59.6 ± 12.8 years) and on a 320-row multidetector CT from March to April 2008 (group 2: 169 patients, 89 men; mean [SD] age 57.9 ± 11.6 years). Two cardiac radiologists assessed the occurrence of respiratory artifact and coronary evaluability in studies with respiratory artifacts. Unevaluable coronary segments because of motion at the same anatomical level of the respiratory artifact were considered unevaluable because of this artifact. The association between the occurrence of respiratory artifact and patient biometrics, medication, and scan parameters was examined. Results Respiratory artifacts were detected in 9 of the 115 patients from group 1 (7.8%) and in none of the 169 patients from group 2 ( P < .001). Group 1 had longer scan times (median, 9.3 seconds; range, 7.5−14.4 seconds) compared with group 2 (median, 1.5 seconds; range, 1.1−3.5 seconds; P < .001). In group 1, 4 patients (3.5%) showed unevaluable coronary segments because of respiratory artifacts, and the CT coronary angiography was repeated in 1 patient (0.9%). Conclusions Respiratory artifacts are important in CT coronary angiography performed with 64-row multidetector scanners and impair the diagnostic utility of the examination in up to 3.5% of the studies. These artifacts can be virtually eliminated with a faster scan time provided by 320-row multidetector CT.
Honorary Coauthorship: Does it Matter?
Authors: O'Brien Jeremy , Baerlocher Mark Otto , Newton Marshall , Gautam Tina , Noble Jason 
Published: October 2009

Objective To examine the perception of honorary coauthorship among medical academics and to determine whether a potential effect of honorary coauthorship exists on patient care. Methods Corresponding authors of every fourth primary research paper published in JAMA, Journal of the American Medical Association (2001−2003), Canadian Medical Association Journal (2001−2003), British Medical Journal (1998−2000), and Lancet (1998−2000) were surveyed electronically. Questions were focused on each author's personal experience and perception of honorary coauthorship. Results Sixty-five percent of corresponding authors responded (127/195). Fifty-five percent of respondents had published more than 50 peer-reviewed journal articles, and 52% had been listed with an honorary coauthor at some point in their career. Eighteen percent of respondents had been required at some point to list authors who had provided data via a commercial relationship. A majority of authors believed that there were potential negative effects of honorary coauthorship for both the authors themselves (73%) and for their coauthors (83%). These negative effects included personal liability for honorary authors (29%) and dilution of relative contribution for their coauthors (54%). Sixty-two percent of respondents said that honorary coauthorship may have a negative effect on patient care; however, only 2% had been involved in a case in which this phenomenon had actually occurred. Conclusion Honorary coauthorship remains prevalent in the medical literature, even among highly published authors, and has the potential to negatively affect patient care. Respondents believed that a number of possible negative consequences of this phenomenon exist for honorary authors, their coauthors, and patients. Efforts to understand the true influence of honorary authorship on patient care may help further curb this practice in the literature.
Psychometric properties of Chronic Pain Acceptance Questionnaires: A systematic review
Authors: Reneman Michiel F. , Dijkstra Arie , Geertzen Jan H.B. , Dijkstra Pieter U. 
Published: October 2009

AbstractBackground: Theoretically, acceptance of chronic pain (CP) is an important determinant in the functional status and well‐being of patients with CP. Several questionnaires that aim to measure acceptance of CP have been developed. An overview of the psychometric properties of these questionnaires is unavailable.Methods: A systematic review of the literature of the psychometric properties of questionnaires that aim to measure acceptance of CP was performed. Psychometric properties including content construct and criterion validity, internal consistency. agreement, reliability, responsiveness, floor/ceiling effects and interpretability, were assessed using a standardized protocol. All studies were assessed by two observers independent from each other.Results: A total of 23 studies including 4 questionnaires or subscales were identified. The questionnaires/subscales included were the Chronic Pain Acceptance Questionnaire (CPAQ), Illness Cognitions Questionnaire (ICQ), Pain Solutions Questionnaire (PASOL) and Acceptance of Illness Scale (AIS) adapted to pain. When applying the criteria of the protocol, results indicate that none of the questionnaires are currently able to meet all 9 criteria for psychometric quality. Individual questionnaires met between 0 and 3 of the criteria.Conclusions: If strict psychometric quality criteria are applied, none of the questionnaires are currently able to meet all nine criteria for psychometric quality, but overlooking the cumulative results over all the studies conducted, especially for the CPAQ, it can be concluded that information on several important characteristics has been reported and a fairly clear picture emerges about the psychometric properties of the CPAQ.
Epidural analgesia and labor
Authors: O'Sullivan Geraldine 
Published: October 2009

AbstractWhilst women vary in their needs and desire for analgesia in labor it must be acknowledged that neuraxial analgesia is the only technique that can completely relieve the pain of labor. However the technique is not without its own inherent complications, both for the mother and for the process of labor and delivery. In this article the techniques for establishing and maintaining neuraxial analgesia in labor are discussed and the advantages and disadvantages of neuraxial analgesia in labor are explored.
Everything you always wanted to know about SEM (structural equations modeling) but were afraid to ask
Authors: Iacobucci Dawn 
Published: October 2009

AbstractThis article is intended to serve as a primer for structural equations models for the behavioral researcher. The technique is not mysterious—it is a natural extension of factor analysis and regression. The measurement part of a structural equations model is essentially a confirmatory factor analysis, and the structural part of the model is like a regression but vastly more flexible in the types of theoretical models that may be tested. The models and notation are introduced and the syntax is provided to replicate the analyses in the paper. Part II of this article will appear in the next issue of the Journal of Consumer Psychology, and it covers advanced issues, including fit indices, sample size, moderators, longitudinal data, mediation, and so forth.
A Bayesian approach to the alignment of mass spectra
Authors: Kong Xiaoxiao , Reilly Cavan 
Published: October 2009

AbstractMotivation: The need to align spectra to correct for mass-to-charge experimental variation is a problem that arises in mass spectrometry (MS). Most of the MS-based proteomic data analysis methods involve a two-step approach, identify peaks first and then do the alignment and statistical inference on these identified peaks only. However, the peak identification step relies on prior information on the proteins of interest or a peak detection model, which are subject to error. Also numerous additional features such as peak shape and peak width are lost in simple peak detection, and these are informative for correcting mass variation in the alignment step.Results: Here, we present a novel Bayesian approach to align the complete spectra. The approach is based on a parametric model which assumes that the spectrum and alignment function are Gaussian processes, but the alignment function is monotone. We show how to use the expectation–maximization algorithm to find the posterior mode of the set of alignment functions and the mean spectrum for a patient population. After alignment, we conduct tests while controlling for error attributable to multiple comparisons on the level of the peaks identified from the absolute mean spectra difference of two patient populations.Contact: cavanr@biostat.umn.edu
Inferring relative proportions of DNA variants from sequencing electropherograms
Authors: Carr I. M. , Robinson J. I. , Dimitriou R. , Markham A. F. , Morgan A. W. , Bonthron D. T. 
Published: October 2009

Abstract
Motivation: Determination of the relative copy number of single-nucleotide sequence variants (SNVs) within a DNA sample is a frequent experimental goal. Various methods can be applied to this problem, although hybridization-based approaches tend to suffer from high-setup cost and poor adaptability, while others (such as pyrosequencing) may not be accessible to all laboratories. The potential to extract relative copy number information from standard dye-terminator electropherograms has been little explored, yet this technology is cheap and widely accessible. Since several biologically important loci have paralogous copies that interfere with genotyping, and which may also display copy number variation (CNV), there are many situations in which determination of the relative copy number of SNVs is desirable.
Results: We have developed a desktop application, QSVanalyzer, which allows high-throughput quantification of the proportions of DNA sequences containing SNVs. In reconstruction experiments, QSVanalyzer accurately estimated the known relative proportions of SNVs. By analyzing a large panel of genomic DNA samples, we demonstrate the ability of the software to analyze not only common biallelic SNVs, but also SNVs within a locus at which gene conversion between four genomic paralogs operates, and within another that is subject to CNV.
Availability and Implementation: QSVanalyzer is freely available at http://dna.leeds.ac.uk/qsv/. It requires the Microsoft .NET framework version 2.0, which can be installed on all Microsoft operating systems from Windows 98 onwards.
Contact: msjimc@leeds.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Cod, haddock, saithe, herring, and capelin in the Barents Sea and adjacent waters: a review of the biological value of the area
Authors: Olsen Erik , Aanes Sondre , Mehl Sigbjørn , Holst Jens Christian , Aglen Asgeir , Gjøsæter Harald 
Published: October 2009

Abstract
Olsen, E., Aanes, S., Mehl, S., Holst, J. C., Aglen, A., and Gjøsæter, H. 2010. Cod, haddock, saithe, herring, and capelin in the Barents Sea and adjacent waters: a review of the biological value of the area. – ICES Journal of Marine Science, 67: 87–101. Cod, haddock, saithe, herring, and capelin are the most important fish species in the Barents Sea and adjacent waters. Ecosystem-based management requires species-specific knowledge of the biological value and vulnerability throughout their life history and distributional range. For each of the five species and four annual quarters, the spawning (egg) areas, nursery areas for larvae and juveniles, and feeding grounds for adults are described and mapped. Areas of eggs (spawning) and larvae were the most important because these are the life stages when fish are most vulnerable to anthropogenic impact. The greatest overlap of spawning areas was from Røstbanken in the south to the Varanger Peninsula in the northeast, and overlap of larval distribution was more extensive.
What controls the spatial distribution of the North Sea plaice spawning population? Confronting ecological hypotheses through a model selection framework
Authors: Loots Christophe , Vaz Sandrine , Planque Benjamin , Koubbi Philippe 
Published: October 2009

Abstract
Loots, C., Vaz, S., Planque, B., and Koubbi, P. 2010. What controls the spatial distribution of the North Sea plaice spawning population? Confronting ecological hypotheses through a model selection framework. – ICES Journal of Marine Science, 67: 244–257. The spatial dynamics of spawning fish are crucial because they influence the survival rates of eggs and larvae and ultimately impact the reproductive success of populations. The factors that control these dynamics are complex and potentially many, and they interact. A model-selection-based approach was developed to confront various hypotheses of control of the spatial distribution of spawning population of North Sea plaice (Pleuronectes platessa). For each hypothesis or combination thereof, statistical models were constructed. These were then ranked and selected based on their ability to adjust and predict observed spatial distributions. The North Sea plaice population seems to have developed strong attachment to specific spawning sites, where geographic location and population memory are important controlling factors. Temporal changes in spatial distribution patterns appear to be influenced primarily by population size and demography. Variations in hydrographic conditions such as temperature and salinity do not appear to control interannual fluctuations in spatial distribution. This means that, for reproduction, applying conventional habitat models may falsely attribute major controlling effects to environmental conditions. It is concluded that a multiple-hypothesis approach is essential to understanding and predicting the present and future distribution of the North Sea plaice population during its spawning season.
The Impact of Water Deficiency on Leaf Cuticle Lipids of Arabidopsis
Authors: Kosma Dylan K. , Bourdenx Brice , Bernard Amélie , Parsons Eugene P. , Lü Shiyou , Joubès Jérôme , Jenks Matthew A. 
Published: October 2009

AbstractArabidopsis (Arabidopsis thaliana) plants subjected to water deficit, sodium chloride (NaCl), or abscisic acid treatments were shown to exhibit a significant increase in the amount of leaf cuticular lipids. These stress treatments led to increases in cuticular wax amount per unit area of 32% to 80%, due primarily to 29% to 98% increases in wax alkanes. Of these treatments, only water deficit increased the total cutin monomer amount (by 65%), whereas both water deficit and NaCl altered the proportional amounts of cutin monomers. Abscisic acid had little effect on cutin composition. Water deficit, but not NaCl, increased leaf cuticle thickness (by 49%). Electron micrographs revealed that both water-deprived and NaCl-treated plants had elevated osmium accumulation in their cuticles. The abundance of cuticle-associated gene transcripts in leaves was altered by all treatments, including those performed in both pot-grown and in vitro conditions. Notably, the abundance of the ECERIFERUM1 gene transcript, predicted to function in alkane synthesis, was highly induced by all treatments, results consistent with the elevated alkane amounts observed in all treatments. Further, this induction of cuticle lipids was associated with reduced cuticle permeability and may be important for plant acclimation to subsequent water-limited conditions. Taken together, these results show that Arabidopsis provides an excellent model system to study the role of the cuticle in plant response to drought and related stresses, and its associated genetic and cellular regulation.
Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology
Authors: Joung Je-Gun , Corbett Anthony M. , Fellman Shanna Moore , Tieman Denise M. , Klee Harry J. , Giovannoni James J. , Fei Zhangjun 
Published: October 2009

AbstractThe information and resources generated from diverse “omics” technologies provide opportunities for producing novel biological knowledge. It is essential to integrate various kinds of biological information and large-scale omics data sets through systematic analysis in order to describe and understand complex biological phenomena. For this purpose, we have developed a Web-based system, Plant MetGenMAP, which can comprehensively integrate and analyze large-scale gene expression and metabolite profile data sets along with diverse biological information. Using this system, significantly altered biochemical pathways and biological processes under given conditions can be retrieved rapidly and efficiently, and transcriptional events and/or metabolic changes in a pathway can be easily visualized. In addition, the system provides a unique function that can identify candidate promoter motifs associated with the regulation of specific biochemical pathways. We demonstrate the functions and application of the system using data sets from Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectively. The results obtained by Plant MetGenMAP can aid in a better understanding of the mechanisms that underlie interesting biological phenomena and provide novel insights into the biochemical changes associated with them at the gene and metabolite levels. Plant MetGenMAP is freely available at http://bioinfo.bti.cornell.edu/tool/MetGenMAP.
Phenotypic Plasticity of Adventitious Rooting in Arabidopsis Is Controlled by Complex Regulation of AUXIN RESPONSE FACTOR Transcripts and MicroRNA Abundance
Authors: Gutierrez Laurent , Bussell John D. , Păcurar Daniel I. , Schwambach Josèli , Păcurar Monica , Bellini Catherine 
Published: October 2009

Abstract
The development of shoot-borne roots, or adventitious roots, is indispensable for mass propagation of elite genotypes. It is a complex genetic trait with a high phenotypic plasticity due to multiple endogenous and environmental regulatory factors. We demonstrate here that a subtle balance of activator and repressor AUXIN RESPONSE FACTOR (ARF) transcripts controls adventitious root initiation. Moreover, microRNA activity appears to be required for fine-tuning of this process. Thus, ARF17, a target of miR160, is a negative regulator, and ARF6 and ARF8, targets of miR167, are positive regulators of adventitious rooting. The three ARFs display overlapping expression domains, interact genetically, and regulate each other's expression at both transcriptional and posttranscriptional levels by modulating miR160 and miR167 availability. This complex regulatory network includes an unexpected feedback regulation of microRNA homeostasis by direct and nondirect target transcription factors. These results provide evidence of microRNA control of phenotypic variability and are a significant step forward in understanding the molecular mechanisms regulating adventitious rooting.
MOSAIC FLORAL ORGANS1, anAGL6-Like MADS Box Gene, Regulates Floral Organ Identity and Meristem Fate in Rice
Authors: Ohmori Shinnosuke , Kimizu Mayumi , Sugita Maiko , Miyao Akio , Hirochika Hirohiko , Uchida Eiji , Nagato Yasuo , Yoshida Hitoshi 
Published: October 2009

AbstractFloral organ identity and meristem determinacy in plants are controlled by combinations of activities mediated by MADS box genes. AGAMOUS-LIKE6 (AGL6)-like genes are MADS box genes expressed in floral tissues, but their biological functions are mostly unknown. Here, we describe an AGL6-like gene in rice (Oryza sativa), MOSAIC FLORAL ORGANS1 (MFO1/MADS6), that regulates floral organ identity and floral meristem determinacy. In the flower of mfo1 mutants, the identities of palea and lodicule are disturbed, and mosaic organs were observed. Furthermore, the determinacy of the floral meristem was lost, and extra carpels or spikelets developed in mfo1 florets. The expression patterns of floral MADS box genes were disturbed in the mutant florets. Suppression of another rice AGL6-like gene, MADS17, caused no morphological abnormalities in the wild-type background, but it enhanced the phenotype in the mfo1 background, indicating that MADS17 has a minor but redundant function with that of MFO1. Whereas single mutants in either MFO1 or the SEPALLATA-like gene LHS1 showed moderate phenotypes, the mfo1 lhs1 double mutant showed a severe phenotype, including the loss of spikelet meristem determinacy. We propose that rice AGL6-like genes help to control floral organ identity and the establishment and determinacy of the floral meristem redundantly with LHS1.
Endogenous, Tissue-Specific Short Interfering RNAs Silence the Chalcone Synthase Gene Family inGlycine maxSeed Coats
Authors: Tuteja Jigyasa H. , Zabala Gracia , Varala Kranthi , Hudson Matthew , Vodkin Lila O. 
Published: October 2009

AbstractTwo dominant alleles of the I locus in Glycine max silence nine chalcone synthase (CHS) genes to inhibit function of the flavonoid pathway in the seed coat. We describe here the intricacies of this naturally occurring silencing mechanism based on results from small RNA gel blots and high-throughput sequencing of small RNA populations. The two dominant alleles of the I locus encompass a 27-kb region containing two perfectly repeated and inverted clusters of three chalcone synthase genes (CHS1, CHS3, and CHS4). This structure silences the expression of all CHS genes, including CHS7 and CHS8, located on other chromosomes. The CHS short interfering RNAs (siRNAs) sequenced support a mechanism by which RNAs transcribed from the CHS inverted repeat form aberrant double-stranded RNAs that become substrates for dicer-like ribonuclease. The resulting primary siRNAs become guides that target the mRNAs of the nonlinked, highly expressed CHS7 and CHS8 genes, followed by subsequent amplification of CHS7 and CHS8 secondary siRNAs by RNA-dependent RNA polymerase. Most remarkably, this silencing mechanism occurs only in one tissue, the seed coat, as shown by the lack of CHS siRNAs in cotyledons and vegetative tissues. Thus, production of the trigger double-stranded RNA that initiates the process occurs in a specific tissue and represents an example of naturally occurring inhibition of a metabolic pathway by siRNAs in one tissue while allowing expression of the pathway and synthesis of valuable secondary metabolites in all other organs/tissues of the plant.
If SWORD is the answer, what is the question?
Authors: Lewis Stuart , Hayes Leonie , Newton‐Wade Vanessa , Corfield Antony , Davis Richard , Donohue Tim , Wilson Scott 
Published: October 2009

PurposeThe purpose of this paper is to describe the repository deposit protocol, Simple Web‐service Offering Repository Deposit (SWORD), its development iteration, and some of its potential use cases. In addition, seven case studies of institutional use of SWORD are provided.Design/methodology/approachThe paper describes the recent development cycle of the SWORD standard, with issues being identified and overcome with a subsequent version. Use cases and case studies of the new standard in action are included to demonstrate the wide range of practical uses of the SWORD standard.FindingsSWORD has many potential use cases and has quickly become the de facto standard for depositing items into repositories. By making use of a widely‐supported interoperable standard, tools can be created that start to overcome some of the problems of gathering content for deposit into institutional repositories. They can do this by changing the submission process from a “one‐size‐fits‐all” solution, as provided by the repository's own user interface, to customised solutions for different users.Originality/valueMany of the case studies described in this paper are new and unpublished, and describe methods of creating novel interoperable tools for depositing items into repositories. The description of SWORD version 1.3 and its development give an insight into the processes involved with the development of a new standard.