bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observations of Irminger Sea Anticyclonic Eddies
Authors: Fan Xue , Send Uwe , Testor Pierre , Karstensen Johannes , Lherminier Pascale 
Published: January 2013

Abstract
Mesoscale anticyclonic eddies in the Irminger Sea are observed using a mooring and a glider. Between 2002 and 2009, the mooring observed 53 anticyclones. Using a kinematic model, objective estimates of eddy length scales and velocity structure are made for 16 eddies. Anticyclones had a mean core diameter of 12 km, and their mean peak observed azimuthal speed was 0.1 m s−1. They had core salinities and potential temperatures of 34.91–34.98 and 4.48°–5.34°C, respectively, making them warm and salty features. These properties represent a typical salinity anomaly of 0.03 and a temperature anomaly of 0.28°C from noneddy values. All eddies had small (≪1) Rossby numbers. In 2006, the glider observed two anticyclones having diameters of about 20 km and peak azimuthal speeds of about 0.3 m s−1. Similar salinity anomalies were detected throughout the Irminger Sea by floats profiling in anticyclones. Two formation regions for the eddies are identified: one to the west of the Reykjanes Ridge and the other off the East Greenland Irminger Current near Cape Farewell close to the mooring. Observations indicate that eddies formed in the former region are larger than eddies observed at the mooring. A clear increase in eddy salinity is observed between 2002 and 2009. The observed breakup of these eddies in winter implies that they are a source of salt for the central gyre. The anticyclones are similar to those found in both the Labrador Sea and Norwegian Sea, making them a ubiquitous feature of the subpolar North Atlantic basins.
Subharmonic Energy Transfer from the Semidiurnal Internal Tide to Near-Diurnal Motions over Kaena Ridge, Hawaii
Authors: Sun Oliver M. , Pinkel Robert 
Published: January 2013

Abstract
Nonlinear energy transfers from the semidiurnal internal tide to high-mode, near-diurnal motions are documented near Kaena Ridge, Hawaii, an energetic generation site for the baroclinic tide. Data were collected aboard the Research Floating Instrument Platform (FLIP) over a 35-day period during the fall of 2002, as part of the Hawaii Ocean Mixing Experiment (HOME) Nearfield program.
Energy transfer terms for a PSI resonant interaction at midlatitude are identified and compared to those for near-inertial PSI close to the M2 critical latitude. Bispectral techniques are used to demonstrate significant energy transfers in the Nearfield, between the low-mode M2 internal tide and subharmonic waves with frequencies near M2/2 and vertical wavelengths of O(120 m). A novel prefilter is used to test the PSI wavenumber resonance condition, which requires the subharmonic waves to propagate in opposite vertical directions. Depth–time maps of the interactions, formed by directly estimating the energy transfer terms, show that energy is transferred predominantly from the tide to subharmonic waves, but numerous reverse energy transfers are also found. A net forward energy transfer rate of 2 × 10−9 W kg−1 is found below 400 m.
The suggestion is that the HOME observations of energy transfer from the tide to subharmonic waves represent a first step in the open-ocean energy cascade. Observed PSI transfer rates could account for a small but significant fraction of the turbulent dissipation of the tide within 60 km of Kaena Ridge. Further extrapolation suggests that integrated PSI energy transfers equatorward of the M2 critical latitude may be comparable to PSI energy transfers previously observed near 28.8°N.
Parameterizing Surface and Internal Tide Scattering and Breaking on Supercritical Topography: The One- and Two-Ridge Cases
Authors: Klymak Jody M. , Buijsman Maarten , Legg Sonya , Pinkel Robert 
Published: January 2013

Abstract
A parameterization is presented for turbulence dissipation due to internal tides generated at and impinging upon topography steep enough to be “supercritical” with respect to the tide. The parameterization requires knowledge of the topography, stratification, and the remote forcing—either barotropic or baroclinic. Internal modes that are arrested at the crest of the topography are assumed to dissipate, and faster modes assumed to propagate away. The energy flux into each mode is predicted using a knife-edge topography that allows linear numerical solutions. The parameterization is tested using high-resolution two-dimensional numerical models of barotropic and internal tides impinging on an isolated ridge, and for the generation problem on a two-ridge system. The recipe is seen to work well compared to numerical simulations of isolated ridges, so long as the ridge has a slope steeper than twice the critical steepness. For less steeply sloped ridges, near-critical generation becomes more dominant. For the two-ridge case, the recipe works well when compared to numerical model runs with very thin ridges. However, as the ridges are widened, even by a small amount, the recipe does poorly in an unspecified manner because the linear response at high modes becomes compromised as it interacts with the slopes.
Safely cared for or empowered in mental health care? Yes, please
Authors: Rise Marit B , Westerlund Heidi , Bjørgen Dagfinn , Steinsbekk Aslak 
Published: January 2013

Background: High-quality health services include both safe care as well as involving service users in treatment and decision-making. Material: The aim was to explore how mental health service users perceive the relationship between safe care on the one hand and increased influence and decision-making on the other. This was a qualitative study of 15 User Interviewing User evaluation reports, including 417 service users. Discussion: Safe and predictable care was essential in poor illness phases, while increased influence and independence were more important in better phases. Conclusions: High-quality services are flexible enough to adjust to users’ varying symptoms and needs.
Accessibility and facilities for the disabled in public and university library buildings in Iran
Authors: Bodaghi Nahid Bayat , Zainab A.N. 
Published: January 2013

The study examines the views of architect experts and physically disabled users on the accessibility status of 14 public and university library buildings in Iran. The respondents rated on the availability of items listed in a checklist grouped under five categories: parking, ramps, interior layout, exclusive space and public space for the disabled. The checklist was based on the American Disability Act and International Federation of Library Associations and Institutions checklist for libraries for the disabled. The results indicate that the point of view of both disabled users and architects on all criteria is similar except for the ratings on the ramp and the interior layout for the disabled in library buildings. Based on the architects’ responses, 53.8 percent of libraries did not provide ramps and 63.0 percent had no exclusive space for the disabled. Disabled users who rated higher on library accessibility were frequent visitors to the library. The provision of access and equipment met minimum compliant standards on the standard checklist, but there is room for improvements.
‘Best practice’ in developing and evaluating palliative and end-of-life care services: A meta-synthesis of research methods for the MORECare project
Authors: Evans Catherine J , Harding Richard , Higginson Irene J ,   on behalf of MORECare
Published: January 2013

Background: Improved and cost-effective palliative and end-of-life care is an international policy imperative. Developments are impeded by a weak and often inconsistent evidence base. Aim: To examine the main methodological challenges and limitations to developing and evaluating palliative and end-of-life care services and requirements to further this field of research. Design: A meta-synthesis to systematically appraise the evidence from systematic reviews on the research methods used in studies evaluating the effectiveness of palliative care services for patients with advanced illness and/or carers meeting inclusion and quality criteria. We extracted data from the reviews on the methodological issues reported on the included studies into Excel spreadsheets and generated textual descriptions coded and analysed in NVivo. Data sources: Six electronic databases, reference chaining and expert advice. Results: In total, 27 systematic reviews were included on the effectiveness of palliative care services for patients with cancer ( n = 6), advanced illness ( n = 10) or mixed populations ( n = 11) across care settings. Main methodological challenges were implementation as a continuum, active precise recruitment, addressing randomisation and economic evaluation beyond cost savings. Conclusions: The complexity of delivering and evaluating palliative and end-of-life care services requires the accumulation of knowledge from multiple sources to understand the active components of an intervention to deliver patient benefit and examine the evaluation methods to detect change and reveal processes prior to a definitive trial. The implementation of evidence into practice should form a continuum throughout the evaluation stages to reveal understanding on the process of intervention delivery, the context and the intended outcome(s).
Unilateral Hallux Valgus
Authors: Young Ki Won , Park Young Uk , Kim Jin Su , Jegal Hyuk , Lee Kyung Tai 
Published: January 2013

Background: This study was undertaken to determine whether unilateral hallux valgus progresses unilaterally and to evaluate the demographics, etiologies, and radiographic findings associated with symptomatic unilateral hallux valgus deformities. Methods: Patients treated for hallux valgus between January 2004 and December 2008 were identified, and of these, 33 patients with unilateral deformities were enrolled. Progression of deformities in normal feet were evaluated at last follow-up visit, and the clinical information and radiographic measurements of those with a deformed normal foot or an unchanged normal foot were compared. Results: Thirty-three patients (3.4%) had a unilateral hallux valgus deformity on preoperative radiographs. The mean length of follow up was 4.7 years (range, 2.4-11). Twenty-four cases had no deformity of the normal foot at last follow-up (the unchanged group), but 15 cases had developed hallux valgus deformity (the deformed group). No significant intergroup differences were found in terms of metatarsus adductus angle ( P = .412), Meary angle ( P = .771), talocalcaneal angle ( P = 1.000), or calcaneal pitch angle ( P = .267). However, members of the deformed group were significantly younger at disease onset ( P = .045), exhibited a curved first metatarsal head ( P = .046), and had a larger initial hallux valgus angle ( P < .001). Conclusions: The frequency of bilateral symptomatic hallux valgus was found to be over 97.3%, and significant differences were found between the deformed and unchanged groups in terms of age of onset, metatarsal head shape, and hallux valgus angle. Level of Evidence: Level III, case-control study.
Peridural Anesthesia or Ultrasound-Guided Continuous 3-in-1 Block
Authors: Luger Thomas J. , Kammerlander Christian , Benz Maureen , Luger Markus F. , Garoscio Ivo 
Published: January 2013

Purpose: The aim of our study was to investigate the clinical relevance of preoperative acute pain management and cardiovascular stability by ultrasound-guided continuous 3-in-1 nerve block in very elderly patients with hip fracture when compared to epidural anesthesia (PDA). Methods: To study the analgesic effect, we enrolled 37 very elderly patients with hip fractures, of whom 3 patients with dementia had to be excluded. Thus, 34 patients were randomized to 1 of the 3 groups: group A (ultrasound-guided continuous 3-in-1 block, bupivacaine; n = 10, dropout rate: 0), group B (PDA, bupivacaine; n = 14, dropout rate: 8), and group C (systemic pain therapy, piritramide/paracetamol; n = 10, dropout rate: 0). Pain intensity was assessed preoperatively and up to 24 hours postoperatively using a visual analog scale, verbal rating scale, analgesic consumption, scale of well-being, and cardiocirculatory parameters (eg, serum troponin T). Results: Our data show that in the preoperative period both regional anesthesia (RA) procedures (analgesia responders after 1 hour: 86.7% and 100%; P = .001) were superior to systemic analgesia (analgesia responders: 46.7%), and the rescue medication requirement in the 2 RA groups was significantly lower ( P = .02). Serum troponin T level increased only in the systemic analgesia group ( P = .04). In the emergency department, the disadvantage of PDA in geriatric patients with hip fracture was the fact that procedures were more complex, resulting in a high dropout rate (57.1%). The use of PDA has to be critically discussed for ethical concerns. Conclusion: In the specific situation of acute hospital admission, the ultrasound-guided continuous 3-in-1 block appears to be indicated as a stress-free means of providing adequate preoperative pain relief in very elderly patients with hip fracture. However, these findings should be corroborated by studies involving larger numbers of patients.
Hyperdiploidy with 58-66 chromosomes in childhood B-acute lymphoblastic leukemia is highly curable: 58951 CLG-EORTC results
Authors: Dastugue Nicole , Suciu Stefan , Plat Geneviève , Speleman Frank , Cavé Hélène , Girard Sandrine , Bakkus Marleen , Pagès Marie Pierre , Yakouben Karima , Nelken Brigitte , Uyttebroeck Anne , Gervais Carine , Lutz Patrick , Teixeira Manuel R. , Heimann Pierre , Ferster Alice , Rohrlich Pierre , Collonge Marie Agnès , Munzer Martine , Luquet Isabelle , Boutard Patrick , Sirvent Nicolas , Karrasch Matthias , Bertrand Yves , Benoit Yves 
Published: January 2013

Key Points
Patients with 58-66 chromosomes have 99% event-free survival and 100% overall survival in the 58951 EORTC-CLG study. The higher the ploidy, the better the prognosis in the 58951 EORTC-CLG study.
Hyers-Ulam stability of functional equations in matrix normed spaces
Authors: Lee Jung Rye , Shin Dong Yun , Park Choonkil 
Published: January 2013

Abstract
In this paper, we prove the Hyers-Ulam stability of the Cauchy additive functional equation and the quadratic functional equation in matrix normed spaces.

MSC:47L25, 39B82, 46L07, 39B52.
Mojo Hand, a TALEN design tool for genome editing applications
Authors: Neff Kevin L , Argue David P , Ma Alvin C , Lee Han B , Clark Karl J , Ekker Stephen C 
Published: January 2013

Abstract

Background
Recent studies of transcription activator-like (TAL) effector domains fused to nucleases (TALENs) demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecting appropriate genetic features, finding pairs of binding sites based on a consensus sequence, and, in some cases, identifying endogenous restriction sites for downstream molecular genetic applications.

Results
We present the web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (http://www.talendesign.org). We describe the algorithm and its implementation. The features of Mojo Hand include (1) automatic download of genomic data from the National Center for Biotechnology Information, (2) analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3) selection of restriction-enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4) output files designed for subsequent TALEN construction using the Golden Gate assembly method.

Conclusions
Mojo Hand enables the rapid identification of TAL binding sites for use in TALEN design. The assembly of TALEN constructs, is also simplified by using the TAL-site prediction program in conjunction with a spreadsheet management aid of reagent concentrations and TALEN formulation. Mojo Hand enables scientists to more rapidly deploy TALENs for genome editing applications.
CySBGN: A Cytoscape plug-in to integrate SBGN maps
Authors: Gonçalves Emanuel , Iersel Martijn van , Saez-Rodriguez Julio 
Published: January 2013

Abstract

Background
A standard graphical notation is essential to facilitate exchange of network representations of biological processes. Towards this end, the Systems Biology Graphical Notation (SBGN) has been proposed, and it is already supported by a number of tools. However, support for SBGN in Cytoscape, one of the most widely used platforms in biology to visualise and analyse networks, is limited, and in particular it is not possible to import SBGN diagrams.

Results
We have developed CySBGN, a Cytoscape plug-in that extends the use of Cytoscape visualisation and analysis features to SBGN maps. CySBGN adds support for Cytoscape users to visualize any of the three complementary SBGN languages: Process Description, Entity Relationship, and Activity Flow. The interoperability with other tools (CySBML plug-in and Systems Biology Format Converter) was also established allowing an automated generation of SBGN diagrams based on previously imported SBML models. The plug-in was tested using a suite of 53 different test cases that covers almost all possible entities, shapes, and connections. A rendering comparison with other tools that support SBGN was performed. To illustrate the interoperability with other Cytoscape functionalities, we present two analysis examples, shortest path calculation, and motif identification in a metabolic network.

Conclusions
CySBGN imports, modifies and analyzes SBGN diagrams in Cytoscape, and thus allows the application of the large palette of tools and plug-ins in this platform to networks and pathways in SBGN format.
JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
Authors: Seitzer Phillip , Huynh Tu Anh , Facciotti Marc T 
Published: January 2013

Abstract

Background
Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species. Existing tools to investigate genomic contexts, however, lack features for dynamically comparing and exploring genomic regions from multiple species. As DNA sequencing technologies improve and the number of whole sequenced microbial genomes increases, a user-friendly genome context comparison platform designed for use by a broad range of users promises to satisfy a growing need in the biological community.

Results
Here we present JContextExplorer: a tool that organizes genomic contexts into branching diagrams. We implement several alternative context-comparison and tree rendering algorithms, and allow for easy transitioning between different clustering algorithms. To facilitate genomic context analysis, our tool implements GUI features, such as text search filtering, point-and-click interrogation of individual contexts, and genomic visualization via a multi-genome browser. We demonstrate a use case of our tool by attempting to resolve annotation ambiguities between two highly homologous yet functionally distinct genes in a set of 22 alpha and gamma proteobacteria.

Conclusions
JContextExplorer should enable a broad range of users to analyze and explore genomic contexts. The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.
Random generalized linear model: a highly accurate and interpretable ensemble predictor
Authors: Song Lin , Langfelder Peter , Horvath Steve 
Published: January 2013

AbstractBackgroundEnsemble predictors such as the random forest are known to have superior accuracy but their black-box predictions are difficult to interpret. In contrast, a generalized linear model (GLM) is very interpretable especially when forward feature selection is used to construct the model. However, forward feature selection tends to overfit the data and leads to low predictive accuracy. Therefore, it remains an important research goal to combine the advantages of ensemble predictors (high accuracy) with the advantages of forward regression modeling (interpretability). To address this goal several articles have explored GLM based ensemble predictors. Since limited evaluations suggested that these ensemble predictors were less accurate than alternative predictors, they have found little attention in the literature.ResultsComprehensive evaluations involving hundreds of genomic data sets, the UCI machine learning benchmark data, and simulations are used to give GLM based ensemble predictors a new and careful look. A novel bootstrap aggregated (bagged) GLM predictor that incorporates several elements of randomness and instability (random subspace method, optional interaction terms, forward variable selection) often outperforms a host of alternative prediction methods including random forests and penalized regression models (ridge regression, elastic net, lasso). This random generalized linear model (RGLM) predictor provides variable importance measures that can be used to define a “thinned” ensemble predictor (involving few features) that retains excellent predictive accuracy.ConclusionRGLM is a state of the art predictor that shares the advantages of a random forest (excellent predictive accuracy, feature importance measures, out-of-bag estimates of accuracy) with those of a forward selected generalized linear model (interpretability). These methods are implemented in the freely available R software packagerandomGLM.
Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an RNA virus
Authors: Cabanillas Laura , Arribas María , Lázaro Ester 
Published: January 2013

Abstract

Background
When beneficial mutations present in different genomes spread simultaneously in an asexual population, their fixation can be delayed due to competition among them. This interference among mutations is mainly determined by the rate of beneficial mutations, which in turn depends on the population size, the total error rate, and the degree of adaptation of the population. RNA viruses, with their large population sizes and high error rates, are good candidates to present a great extent of interference. To test this hypothesis, in the current study we have investigated whether competition among beneficial mutations was responsible for the prolonged presence of polymorphisms in the mutant spectrum of an RNA virus, the bacteriophage Qβ, evolved during a large number of generations in the presence of the mutagenic nucleoside analogue 5-azacytidine.

Results
The analysis of the mutant spectra of bacteriophage Qβ populations evolved at artificially increased error rate shows a large number of polymorphic mutations, some of them with demonstrated selective value. Polymorphisms distributed into several evolutionary lines that can compete among them, making it difficult the emergence of a defined consensus sequence. The presence of accompanying deleterious mutations, the high degree of recurrence of the polymorphic mutations, and the occurrence of epistatic interactions generate a highly complex interference dynamics.

Conclusions
Interference among beneficial mutations in bacteriophage Qβ evolved at increased error rate permits the coexistence of multiple adaptive pathways that can provide selective advantages by different molecular mechanisms. In this way, interference can be seen as a positive factor that allows the exploration of the different local maxima that exist in rugged fitness landscapes.