bluuebunny/crossref_metadata_2025_split huggingface dataset:
What does it take to resolve relationships and to identify species with molecular markers? An example from the epiphytic Rhipsalideae (Cactaceae)
Authors: Korotkova Nadja , Borsch Thomas , Quandt Dietmar , Taylor Nigel P. , Müller Kai F. , Barthlott Wilhelm 
Published: September 2011

• Premise of the study: The Cactaceae are a major New World plant family and popular in horticulture. Still, taxonomic units and species limits have been difficult to define, and molecular phylogenetic studies so far have yielded largely unresolved trees, so relationships within Cactaceae remain insufficiently understood. This study focuses on the predominantly epiphytic tribe Rhipsalideae and evaluates the utility of a spectrum of plastid genomic regions.• Methods: We present a phylogenetic study including 52 of the 53 Rhipsalideae species and all the infraspecific taxa. Seven regions (trnK intron, matK, rbcL, rps3‐rpl16, rpl16 intron, psbA‐trnH, trnQ‐rps16), ca. 5600 nucleotides (nt) were sequenced per sample. The regions used were evaluated for their phylogenetic performance and performance in DNA‐based species recognition based on operational taxonomic units (OTUs) defined beforehand.• Key results: The Rhipsalideae are monophyletic and contain five clades that correspond to the genera Rhipsalis, Lepismium, Schlumbergera, Hatiora, and Rhipsalidopsis. The species‐level tree was well resolved and supported; the rpl16 and trnK introns yielded the best phylogenetic signal. Although the psbA‐trnH and trnQ‐rps16 spacers were the most successful individual regions for OTU identification, their success rate did not significantly exceed 70%. The highest OTU identification rate of 97% was found using the combination of psbA‐trnH, rps3‐rpl16, trnK intron, and trnQ‐rps16 as a minimum possible marker length (ca. 1660 nt).• Conclusions: The phylogenetic performance of a marker is not determined by the level of sequence variability, and species discrimination power does not necessarily correlate with phylogenetic utility.
Failure of Pre-Emptive Treatment of Cytomegalovirus Infections and Antiviral Resistance in Stem Cell Transplant Recipients
Authors: van der Beek Martha T , Marijt Erik WAF , Vossen Ann CTM , van der Blij-de Brouwer Caroline S , Wolterbeek Ron , Halkes Constantijn JM , Claas Eric CJ , Kroes Aloys CM 
Published: September 2011

Background Treatment of cytomegalovirus (CMV) infections after stem cell transplantation (SCT) does not always lead to a rapid viral response. The causes of treatment failure may be either viral resistance or immunological failure to control viral replication. This study investigated the response to pre-emptive treatment in CMV infections in order to define risk factors for treatment failure, including the role of antiviral resistance. Methods Adult recipients of allogeneic T-cell depleted SCT were studied retrospectively ( n=92). CMV infections were treated with (val)ganciclovir according to a CMV DNA-load-based pre-emptive strategy. Treatment failure was defined as a CMV DNA load of 1,000 copies/ml or more after at least 2 weeks of treatment. Resistance was analysed by nucleotide sequence analysis of the UL97 and UL54 genes in the first CMV DNA-positive sample and in samples during treatment failure. Results Treatment failure occurred in 26 of the 47 pre-emptively treated patients (55%) and in 39 of 86 (45%) treatment episodes. The risk of treatment failure was increased during first treatment episodes ( P=0.01) and during the use of immunosuppressive medication ( P=0.02). Antiviral resistance was found in only 1 patient (4%) with treatment failure. Conclusions A slow response to pre-emptive antiviral treatment occurred frequently in CMV infections in SCT recipients. Antiviral resistance was observed but played a minor role in treatment failure.
Bilan organisationnel des compétences individuelles en fonction de leur criticité
Authors: Cesar Marianne 
Published: September 2011

Afin de dépasser les limites d’une conception réductrice de la gestion des compétences axée sur l’évaluation d’une somme d’apprentissages individuels, le développement des capacités adaptatives d’une organisation a été abordé sous l’angle d’un processus d’apprentissage organisationnel. La construction d’un modèle cyclique de la dynamique d’apprentissage organisationnel a servi de cadre à l’opérationnalisation de la première de ses quatre phases, portant sur la répartition des compétences détenues par une organisation. Afin de décrire le risque de perte de compétences et de localiser les compétences détenues par rapport aux entités structurelles de l’organisation et aux activités qu’elle met en œuvre, la notion de compétence critique a été définie au regard de cinq facteurs de criticité (nombre de détenteurs, fréquence de mise en œuvre des compétences, autonomie des détenteurs, formalisation des compétences et âge des détenteurs). L’étude de ces facteurs réalisée dans une entreprise de tuyauterie industrielle a permis de distinguer des services caractérisés par un risque massif de perte de compétences et des services caractérisés par des difficultés à développer les compétences détenues, mais aussi des services « mixtes » caractérisés par ces deux types de risques. Ces résultats mettent en évidence la nécessité de décentraliser la fonction ressources humaines grâce à l’implication des chefs de service dans la gestion des compétences, mais également l’importance de redéfinir les modalités d’évaluation des compétences au regard du niveau individuel, collectif ou organisationnel de réalisation des apprentissages.
Réviser un texte procédural en manipulant un dispositif : implications sur l'élaboration de différents niveaux de représentation et sur la qualité du texte produit
Authors: Ganier Franck , Pétillon Sabine 
Published: September 2011

Cet article a pour objectif de montrer l’importance que revêtent la présence d’un dispositif et sa manipulation lors de la révision de documents procéduraux. Une expérience a été conçue pour vérifier que la présence ou l’absence du dispositif à manipuler pouvait avoir une influence sur l’élaboration de différents niveaux de représentation (littérale, sémantique et référentielle ; Dixon, Harrison & Taylor, 1993). Les résultats montrent qu’en l’absence du dispositif à manipuler, les rédacteurs chargés de réviser sa notice se focalisent surtout sur l’élaboration de représentations littérales – mais aussi sémantiques – du texte. En revanche, en présence du dispositif, les rédacteurs se focalisent plutôt sur l’élaboration de représentations pragmatiques (ou référentielles) et sémantiques. En l’absence du dispositif, les révisions touchent plus particulièrement les aspects de surface (par exemple, l’orthographe) et sémantiques du texte, alors qu’en sa présence, elles concernent plutôt les aspects pragmatiques (mais aussi sémantiques) du texte, au détriment des aspects de surface (Diehl, 2004). Complémentairement à cette expérience, trois notices ont été évaluées comparativement : celle fournie par le fabricant, une notice révisée en l’absence du dispositif et une notice révisée en présence du dispositif. Les résultats montrent que la notice révisée en présence du dispositif est choisie préférentiellement aux deux autres, la notice du fabricant étant le plus souvent classée en dernière position. L’ensemble de l’étude donne lieu à des préconisations pour la révision des documents procéduraux.
Visual and IOP Outcomes After PRK in Pigment Dispersion Syndrome
Authors: Bower Kraig S. , Sia Rose K. , Ryan Denise S. , Mines Michael J. , Stutzman Richard D. , Kuzmowych Chrystyna P. , Eaddy Jennifer B. , Coe Charles D. , Wroblewski Keith J. 
Published: September 2011

PURPOSE:
To report the results of photorefractive keratectomy (PRK) in patients with pigment dispersion syndrome.

METHODS:
The pre- and postoperative records of patients with pigment dispersion syndrome who underwent PRK between January 2002 and March 2009 were reviewed. Data for analysis included gender, age, ablation depth, surgical complications, manifest refraction spherical equivalent, uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), intraocular pressure (IOP), central corneal thickness (CCT), cup-to-disc (c/d) ratio, and postoperative complications.

RESULTS:

Thirty-seven eyes of 19 patients (17 men and 2 women) with a mean age of 37.5±6.9 years were included for review. At final follow-up, mean 404.1±119.5 days postoperative, UDVA was 20/15 or better in 67.6%, 20/20 or better in 91.9%, and 20/25 or better in 100% of eyes; 94.6% of eyes were within 0.50 diopters (D) and 100% were within 1.00 D of emmetropia. Corrected distance visual acuity was unchanged from preoperative in 73% and improved by one line in 27% of eyes. No eye lost 1 or more lines of CDVA. When corrected for change in CCT and curvature, mean postoperative IOP was elevated from baseline (16.7±3.8 mmHg) at 1 month (18.1±4.9 mmHg,
P
=.044) but unchanged at any other time postoperatively. Two (11%) of 19 patients were steroid responders, requiring a single topical agent until completing the course of steroids. No significant change was noted in mean c/d ratio from baseline (0.35±0.12) to final postoperative (0.35±0.13,
P
=.99).

CONCLUSIONS:
Although PRK in patients with pigment dispersion syndrome resulted in excellent UDVA, retention of CDVA, and low incidence of adverse effects 1 to 2 years after surgery, long-term safety and efficacy outcomes of PRK in this cohort remain speculative.
Analysis of the Relationship Between Drusen Size and Drusen Area in Eyes With Age-Related Macular Degeneration
Authors: Friberg Thomas R. , Bilonick Richard A. , Brennen Peter M. 
Published: September 2011

BACKGROUND AND OBJECTIVE:
To examine the relationship between drusen counts and drusen area in eyes with age-related macular degeneration, and to correlate drusen areas between fellow eyes.

PATIENTS AND METHODS:
Digital images from 378 patients (756 eyes) were analyzed using a validated drusen detection algorithm. Total drusen area and the number of drusen of various sizes (small: < 62 microns, intermediate: 63–124 microns, large: 125–249 microns, etc) were recorded for the central 1,000- and 3,000-micron diameter macular regions. Correlations were assessed using structural equation models.

RESULTS:
For the 1,000-micron region, the number of intermediate drusen was more highly correlated to total drusen area than the number of large drusen (R = 0.91 vs 0.82); this difference was statistically significant. The correlation coefficients for drusen area between fellow eyes was 0.73.

CONCLUSION:
The number of large drusen does not correlate better with total drusen area than drusen of other sizes. The number of large drusen is not necessarily a good surrogate for total drusen area.
Numerical Study of a 3D Two-Phase PEM Fuel Cell Model Via a Novel Automated Finite Element/Finite Volume Program Generator
Authors: Sun Pengtao , Zhou Su , Hu Qiya , Liang Guoping 
Published: September 2011

AbstractNumerical methods of a 3D multiphysics, two-phase transport model of proton exchange membrane fuel cell (PEMFC) is studied in this paper. Due to the coexistence of multiphase regions, the standard finite element/finite volume method may fail to obtain a convergent nonlinear iteration for a two-phase transport model of PEMFC [49,50]. By introducing Kirchhoff transformation technique and a combined finite element-upwind finite volume approach, we efficiently achieve a fast convergence and reasonable solutions for this multiphase, multiphysics PEMFC model. Numerical implementation is done by using a novel automated finite element/finite volume program generator (FEPG). By virtue of a high-level algorithm description language (script), component programming and human intelligence technologies, FEPG can quickly generate finite element/finite volume source code for PEMFC simulation. Thus, one can focus on the efficient algorithm research without being distracted by the tedious computer programming on finite element/finite volume methods. Numerical success confirms that FEPG is an efficient tool for both algorithm research and software development of a 3D, multiphysics PEMFC model with multicomponent and multiphase mechanism.
An Adaptive Moving Mesh Method for Two-Dimensional Relativistic Hydrodynamics
Authors: He Peng , Tang Huazhong 
Published: September 2011

AbstractThis paper extends the adaptive moving mesh method developed by Tang and Tang [36] to two-dimensional (2D) relativistic hydrodynamic (RHD) equations. The algorithm consists of two “independent” parts: the time evolution of the RHD equations and the (static) mesh iteration redistribution. In the first part, the RHD equations are discretized by using a high resolution finite volume scheme on the fixed but nonuniform meshes without the full characteristic decomposition of the governing equations. The second part is an iterative procedure. In each iteration, the mesh points are first redistributed, and then the cell averages of the conservative variables are remapped onto the new mesh in a conservative way. Several numerical examples are given to demonstrate the accuracy and effectiveness of the proposed method.
Degenerate Anisotropic Elliptic Problems and Magnetized Plasma Simulations
Authors: Brull Stéphane , Degond Pierre , Deluzet Fabrice 
Published: September 2011

AbstractThis paper is devoted to the numerical approximation of a degenerate anisotropic elliptic problem. The numerical method is designed for arbitrary space-dependent anisotropy directions and does not require any specially adapted coordinate system. It is also designed to be equally accurate in the strongly and the mildly anisotropic cases. The method is applied to the Euler-Lorentz system, in the drift-fluid limit. This system provides a model for magnetized plasmas.
Diffusion of Electronic Health Records and electronic communication in Norway
Authors: Grimsmo A. , Faxvaag A. , Heimly V. 
Published: September 2011

SummaryObjective: To assess the diffusion of Electronic Health Record (EHR) systems over time in Norwegian health care.Methods: This study was based on a retrospective cross-sectional questionnaire survey. Questionnaires for three groups of responders were based on two validated questionnaires from prior studies, which were further customized through workshops. The questionnaires were sent to a random sample of 180 municipalities and 150 general practices in all 26 hospitals in Norway.Results: The diffusion curves for EHR systems from 1980 to 2008 were established and analyzed. The most striking finding was the length of time from the availability of the first adequate EHR systems until full coverage was achieved in general practice and in hospitals. Diffusion of EHRs into nursing homes and maternal and child health centers started ten years later, and the diffusion for these centers has also been slow. In general practice the diffusion seems to follow the classical s-curve of diffusion. Costs and the increasing complexity of EHR systems were regarded by respondents as the most important challenges and concerns for the future. Resistance among health personnel was seen only as a small problem.Conclusion: National strategic processes account for the slow diffusion and complexity of EHR systems in the health sector.
Empirical Look at the Factors Affecting Perception of Business Ethics in Turkey
Authors: Akman Vedat 
Published: September 2011

This study aims to explore the influence of gender, age, education, profession and sector choices towards factors affecting business ethics in Turkey. Self-administered questionnaire with scale of 1-5 was used to measure attitudes towards business ethics (1= "strongly agree" to 5="strongly disagree") with reasonable good score on Cronbach's realibility test. With Cronbach alpha of .692 and KMO (Kaiser-Meyer-Olkin Meaure of Sampling Adequecy) .746 (which sould be greater than .5 for a satisfactor analysis) we proceeded to our analysis successfully. Choice job, sector, age and gender were significant determinants to factors affecting perception of business ethics but education level was not a significant determinant.
Relation of dry eye to disease activity in juvenile rheumatoid arthritis
Authors: El-Shazly Amany Abdel-Fattah , Mohamed Ahmed Abdullah 
Published: September 2011

Purpose To study the frequency and severity of dry eye in patients with juvenile rheumatoid arthritis (JRA) and its relation to disease activity. Patients and Methods Evaluation for dry eye was done in 40 patients with juvenile rheumatoid arthritis referred for ocular assessment in the Ophthalmology Clinics, Faculty of Medicine, Ain Shams University. They were 28 girls and 12 boys with age range of 7–12 years. Medical history, clinical examination, and full ophthalmologic evaluation were performed for each patient. The dry eye tests included tear film break-up time, Schirmer-1 test, and corneal fluorescein staining. Dry eye severity grading was used. Twenty healthy, age- and sex-matched children were assessed for dry eye as a control group. Results Thirty patients (75%) showed findings consistent with the diagnosis of dry eye. Twenty patients (50%) showed first-degree dryness, 8 (20%) showed second-degree, and 2 (5%) showed third-degree. The score of dry eye severity was significantly lower in remission compared to disease activity. Multiregression analysis showed the only factor affecting dry eye parameters was the duration of illness. Conclusions Dry eye is a common incident in children with JRA and should be screened for in all patients with this disease. Severity of eye dryness is highly correlated with the disease activity.
Prevalence and risk factors for diabetic retinopathy: an Iranian eye study
Authors: Heydari Behrouz , Yaghoubi Gholamhossein , Yaghoubi Mohammad Ali , Miri Mohammad Reza 
Published: September 2011

Purpose The aim of this study was to determine the prevalence of diabetic retinopathy among diabetic patients in Iran and its association with some predisposing factors. Methods All diabetic patients who attended the diabetes clinic underwent ocular examination, including slit-lamp biomicroscopy. The blood pressure and blood biochemical parameters were then measured. Results The prevalence of diabetic retinopathy among 1022 diabetic participants was 23.6% (241 cases). This study showed that there is a statistically significant relation between diabetic retinopathy and mean blood pressure, fasting blood sugar, blood urea nitrogen, and level of HbA1c. There was no difference in lipid profile between patients with and without retinopathy. The duration of diabetes was a predicting factor for retinopathy as well as presence of renal and cardiovascular diseases and fasting glucose >126 as independent variables. Conclusions The duration of diabetes was the most important risk factor for progression of retinopathy.
A Status Update of Modified Oligonucleotides for Chemotherapeutics Applications
Authors: Sanghvi Yogesh S. 
Published: September 2011

AbstractThis unit presents an update of recent developments and clinical progress in chemically modified oliogonucleotides useful for therapeutic applications. During the last decade, the number of therapeutic oligonucleotides in clinical trials has nearly tripled. This is primarily due to advances in the synthesis protocols, better understanding of the biology, improved delivery, and better formulation technologies. Currently, over 100 clinical trials with oligonucleotide‐based drugs are ongoing in the United States for potential treatment of a variety of life‐threatening diseases. Among various oligonucleotides, antisense technology has been at the forefront, with one product on the market. Antisense technologies represent about half of the active clinical trials. Similarly, siRNA, aptamers, spiegelmers microRNA, shRNA, IMO, and CpG have been other active classes of oligonucleotides that are also undergoing clinical trials. This review attempts to summarize the current status of synthesis, chemical modifications, purification, and analysis in light of the rapid progress with multitude of oligonucleotides pursued as therapeutic modality. Curr. Protoc. Nucleic Acid Chem. 46:4.1.1‐4.1.22. © 2011 by John Wiley & Sons, Inc.
Preparation of Photoresponsive DNA Tethering Ortho‐Methylated Azobenzene as a Supra‐Photoswitch
Authors: Asanuma Hiroyuki , Nishioka Hidenori , Ishikawa Teruchika , Liang Xingguo 
Published: September 2011

AbstractThis unit describes synthetic procedures of photoresponsive DNA via a phosphoramidite monomer composed of D‐threoninol as a scaffold and 4‐carboxy‐2′,6′‐dimethylazobenzene or 4‐carboxy‐2′‐methylazobenzene that works as a photoswitch more efficiently than previous nonmodified azobenzene (4‐phenylazobenzoic acid). With these newly modified‐azobenzenes, photoregulatory efficiency of DNA hybridization can be greatly improved. Furthermore, thermal stability of cis‐azobenzene of 4‐carboxy‐2′,6′‐dimethylazobenzene remarkably increases compared with the previous non‐modified azobenzene. Curr. Protoc. Nucleic Acid Chem. 46:4.45.1‐4.45.18. © 2011 by John Wiley & Sons, Inc.
Use of Chromophoric Ligands to Visually Screen Co‐Crystals of Putative Protein‐Nucleic Acid Complexes
Authors: Jiang Xiaohua , Egli Martin 
Published: September 2011

AbstractDistinguishing between crystals of protein‐nucleic acid complexes and those containing protein alone is a common problem in structural studies of protein‐nucleic acid interactions. Currently, there are several methods available for detecting nucleic acid in crystals, including gel electrophoresis, SYBR Gold fluorescence dye staining, and methyl violet staining. However, they require either that the crystals be sacrificed or access to a fluorescence microscope. In this protocol, we describe an approach that allows direct visualization of either the presence or absence of oligonucleotides in crystals grown from solutions containing both protein and nucleic acid—labeling with the Cy5 dye. In addition to offering the advantage of being able to distinguish between crystals of complex and protein alone with the naked eye or a light microscope, crystals of covalently Cy5‐labeled DNA can be directly used for X‐ray diffraction data collection. Curr. Protoc. Nucleic Acid Chem. 46:7.15.1‐7.15.8. © 2011 by John Wiley & Sons, Inc.
Gene Identification in Prokaryotic Genomes, Phages, Metagenomes, and EST Sequences with GeneMarkS Suite
Authors: Borodovsky Mark , Lomsadze Alex 
Published: September 2011

AbstractThis unit describes how to use several gene‐finding programs from the GeneMark line developed for finding protein‐coding ORFs in genomic DNA of prokaryotic species, in genomic DNA of eukaryotic species with intronless genes, in genomes of viruses and phages, and in prokaryotic metagenomic sequences, as well as in EST sequences with spliced‐out introns. These bioinformatics tools were demonstrated to have state‐of‐the‐art accuracy and have been frequently used for gene annotation in novel nucleotide sequences. An additional advantage of these sequence‐analysis tools is that the problem of algorithm parameterization is solved automatically, with parameters estimated by iterative self‐training (unsupervised training). Curr. Protoc. Bioinform. 35:4.5.1‐4.5.17. © 2011 by John Wiley & Sons, Inc.
Eukaryotic Gene Prediction Using GeneMark.hmm‐E and GeneMark‐ES
Authors: Borodovsky Mark , Lomsadze Alex 
Published: September 2011

AbstractThis unit describes how to use the gene‐finding programs GeneMark.hmm‐E and GeneMark‐ES for finding protein‐coding genes in the genomic DNA of eukaryotic organisms. These bioinformatics tools have been demonstrated to have state‐of‐the‐art accuracy for many fungal, plant, and animal genomes, and have frequently been used for gene annotation in novel genomic sequences. An additional advantage of GeneMark‐ES is that the problem of algorithm parameterization is solved automatically, with parameters estimated by iterative self‐training (unsupervised training). Curr. Protoc. Bioinform. 35:4.6.1‐4.6.10. © 2011 by John Wiley & Sons, Inc.