bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Entrainment and Bypass at Screened Irrigation Canals on Juvenile Steelhead
Authors: Simpson William G. , Ostrand Kenneth G. 
Published: May 2012

AbstractExpensive bypass screens have been installed throughout the western United States to prevent the entrainment of valuable anadromous salmonids into irrigation canals. However, few studies have quantified the annual extent and variability of entrainment and bypass success for anadromous salmonids emigrating through screened irrigation diversion networks in a basinwide context. By monitoring the movement of hatchery steelhead Oncorhynchus mykiss surrogates marked with passive integrated transponder tags through three irrigation canals, we estimated canal entrainment, bypass success, and survival for threatened juvenile steelhead emigrating from the Umatilla River in northeast Oregon. Annual entrainment of steelhead was positively related to the days of canal operation and negatively related to mean seasonal river flow. The relationship between flow and entrainment differed by canal; as a result, steelhead entrainment was not always greatest at canals with the largest water diversion rates. Binary models (steelhead entrainment or no entrainment) that best described daily entrainment depicted the influence of annual differences in river flows on canal entrainment and indicated that this relationship can change under different values of thermal experience (sum of daily mean temperatures). Most of the entrained hatchery steelhead (range = 97–100%) were returned to the river by screened bypasses, even when large percentages of the steelhead population were entrained. Based on similarities in movement, hatchery steelhead were good surrogates for the entrainment of naturally reared steelhead. We estimated that the three fish screens in the Umatilla River basin prevented losses of up to 25% of the steelhead population to irrigation canals over 5 years. Interannual variability in fish entrainment should be considered when monitoring irrigation canals, and managers should not necessarily limit entrainment monitoring or screening projects to canals that divert the most water.
Prey Density and Nonvisual Feeding by Larval Striped Bass
Authors: Duston J. , Astatkie T. 
Published: May 2012

AbstractLarvae of striped bass Morone saxatilis from the Shubenacadie River, Nova Scotia, exhibited a good nonvisual feeding mechanism that may be valuable for survival in their turbid estuarine nursery habitat. Their capture of brine shrimp Artemia salina nauplii during 60‐min feeding trials in darkness was significantly affected by the interaction between prey density and larval age. Mean capture rate among larvae that were offered 50, 200, and 800 prey/L at 9 d posthatch (dph) was 3, 7, and 15 prey·larva−1·h−1, respectively, and increased progressively with age to 26, 92, and 220 prey·larva−1·h−1 at 22 dph. By comparison, prey capture rate in the light (20 lx) among 8–13‐dph larvae that were offered 50 prey/L was about fourfold higher than the capture rate for nonvisual feeding; however, at 800 prey/L, capture rates in lighted conditions and in darkness were similar. Among larvae with noninflated swim bladders, prey capture in the dark was severely inhibited.
THE BENEFITS OF MIGRATION
Authors: Damelang Andreas , Haas Anette 
Published: May 2012

ABSTRACT
Assuming that migration and integration have lasting effects on economic and social processes, this paper analyses if a diverse cultural environment has a positive impact on labour market success. We expect that culturally diverse labour markets provide new opportunities through an open and tolerant climate, thus contributing to overall economic growth. We test this assumption by analysing the successful transition from education to work depending on the regional distribution and ethnic mix of the foreign population in Germany (cultural diversity). To account for variation within Germany, cultural diversity is observed at small administrative units. We analyse a cohort of young adults at the time of the successful completion of their apprenticeship in Germany and follow them through the beginning of their career. The concentration on a homogenous group regarding occupational certificates enables us to focus on the effects of the local and social environment as well as individual characteristics such as their national background on finding a job (or not). We apply an instrumental variable design to disentangle the effects of cultural diversity and share of foreigners. The results show that both young foreigners and Germans face significantly lower barriers for employment entry in culturally more diverse German regions.
A New Metric of Antibiotic Class Resistance in Gram-Negative Bacilli Isolated from Hospitalized Children
Authors: Patel Sameer J. , O'Toole Dana , Larson Elaine 
Published: May 2012

Objective.The purpose of this study was to describe patterns of infection or colonization with antibiotic-resistant gram-negative bacilli (GNB) in hospitalized children utilizing an electronic health record.Setting.Tertiary care facility.Participants.Pediatric patients 18 years of age or younger hospitalized from January 1, 2006, to December 31, 2008.Methods.Children were identified who had (1) at least 1 positive culture for a multidrug-resistant (MDR) GNB, defined as a GNB with resistance to 3 or more antibiotic classes; or (2) additive drug resistance, defined as isolation of more than 1 GNB that collectively as a group demonstrated resistance to 3 or more antibiotic classes over the study period. Differences in clinical characteristics between the 2 groups were ascertained, including history of admissions and transfers, comorbid conditions, receipt of procedures, and antibiotic exposure.Results.Of 56,235 pediatric patients, 46 children were infected or colonized with an MDR GNB, of which 16 were resistant to 3 classes and 30 were resistant to 4 classes. Another 39 patients had positive cultures for GNB that exhibited additive drug resistance. Patients with additive drug resistance were more likely than patients with MDR GNB to have had previous admissions to a long-term facility (8 vs 2; P = .04) and had more mean admissions (7 vs 3; P <.01) and more mean antibiotic-days (P < .01 to P = .02). Six patients with additive drug resistance later had a positive culture with an MDR GNB.Conclusions.An electronic health record can be used to track antibiotic class resistance in GNB isolated from hospitalized children over multiple cultures and hospitalizations.
Preoperative Skin Antiseptic Preparations for Preventing Surgical Site Infections: A Systematic Review
Authors: Kamel Chris , McGahan Lynda , Polisena Julie , Mierzwinski-Urban Monika , Embil John M. 
Published: May 2012

Objective.To evaluate the clinical effectiveness of preoperative skin antiseptic preparations and application techniques for the prevention of surgical site infections (SSIs).Design.Systematic review of the literature using Medline, EMBASE, and other databases, for the period January 2001 to June 2011.Methods.Comparative studies (including randomized and nonrandomized trials) of preoperative skin antisepsis preparations and application techniques were included. Two researchers reviewed each study and extracted data using standardized tables developed before the study. Studies were reviewed for their methodological quality and clinical findings.Results.Twenty studies (n = 9,520 patients) were included in the review. The results indicated that presurgical antiseptic showering is effective for reducing skin flora and may reduce SSI rates. Given the heterogeneity of the studies and the results, conclusions about which antiseptic is more effective at reducing SSIs cannot be drawn.Conclusions.The evidence suggests that preoperative antiseptic showers reduce bacterial colonization and may be effective at preventing SSIs. The antiseptic application method is inconsequential, and data are lacking to suggest which antiseptic solution is the most effective. Disinfectant products are often mixed with alcohol or water, which makes it difficult to form overall conclusions regarding an active ingredient. Large, well-conducted randomized controlled trials with consistent protocols comparing agents in the same bases are needed to provide unequivocal evidence on the effectiveness of one antiseptic preparation over another for the prevention of SSIs.
Integration of perovskite PZT thin films on diamond substrate without buffer layer
Authors: Chandran Maneesh , Tiwari Brajesh , Kumaran C R , Samji Sunil K , Bhattacharya S S , Rao M S Ramachandra 
Published: May 2012

Abstract
Integration of lead zirconate titanate (PZT) thin film on diamond substrate offers a great deal of potential for the application of multifunctional devices under extreme conditions. However, fabrication of perovskite PZT thin films on diamond substrate without a buffer layer has not been realized to date. We report for the first time on the successful deposition of PZT thin film directly on a diamond substrate without any buffer layer using the pulsed-laser deposition technique. The perovskite phase was realized only under specific growth conditions. X-ray diffraction and Raman studies confirmed the perovskite phase. The ferroelectric behaviour of the deposited PZT thin film was confirmed using piezo response microscope phase image and ferroelectric hysteresis loop.
Magnetization reversal analysis of a thin B2-type ordered Co50Fe50 film by magnetooptic Kerr effect
Authors: Kuschel T , Hamrle J , Pištora J , Saito K , Bosu S , Sakuraba Y , Takanashi K , Wollschläger J 
Published: May 2012

Abstract
The magnetic structure of a thin B2 ordered Co50Fe50 film is determined by vectorial magnetometry using magnetooptic Kerr effect including different polarizations of the incident light and varied directions of the external magnetic field. Both the magnetic reversal process and the magnetic remanence reveal two in-plane magnetic easy axes of different strengths which are not orthogonal. Atypical magnetization curves including multidomain states in magnetic remanence with some magnetic moments providing antiparallel alignment to the direction of the previously applied external field (if projected to the direction of the external field) confirm the appearance of different strong magnetic easy axes. This magnetic structure can be explained by a cubic magnetic anisotropy (CMA) induced by the crystalline film structure superimposed by an additional uniaxial magnetic anisotropy (UMA) which is not parallel to one of the magnetic easy axes of the CMA. The results are compared with the regular magnetic behaviour of a thin A2 ordered Co50Fe50 film with UMA parallel to one of the magnetic easy axes of the CMA.
Investigations on a nano-scale periodical waveguide structure taking surface plasmon polaritons into consideration
Authors: Liu Weihao , Zhong Renbin , Zhou Jun , Zhang Yaxin , Hu Min , Liu Shenggang 
Published: May 2012

Abstract
Detailed theoretical analysis and computer simulations on the electromagnetic characteristics of a nano-scale periodical waveguide structure, taking surface plasmon polaritons (SPPs) into consideration, are carried out in this paper. The results show that SPPs will significantly influence the electromagnetic characteristics of the structure. When the operation frequency is in a certain band—the ‘radial confinement band’, neither radial surface plasmon waves nor guided waves, which both will lead to radial energy loss, can be excited in the structure. And the electromagnetic waves are completely confined within the longitudinal waveguide and propagate along it with little attenuation. The radial energy loss is then significantly reduced. These results are of great significance not only for increasing the efficiency of the radiation sources based on the nano-scale periodical waveguide structure but also for the development of high-efficiency waveguides and wide-band filters in the infrared and visible light regimes.
Measurement of the densities of Cu and Ag vapours in a low-voltage switch using the hook method
Authors: Lins Günter 
Published: May 2012

Abstract
In a research model of a low-voltage circuit breaker with fixed contacts and windows for optical access, arcs powered by either a high-current transformer or a capacitor bank were initiated by the explosion of tungsten wires. Air at atmospheric pressure was the switching medium. The number densities of neutral silver and copper vapours from contacts and arc runners were measured simultaneously by the hook method using a Mach–Zehnder interferometer combined with a 1 m spectrograph and a gated intensified CCD camera. When an arc current was flowing, a substantial fraction of the metal vapour was ionized, and thus not amenable to a density measurement with the technique chosen. To nevertheless obtain approximate density values, the arc current was forced to zero within 8 to 10 µs at a preset time and measurements were carried out 100 µs after extinction of the arc. At that time the metal vapour was expected to have recombined to a large extent but not yet diffused to the walls in significant amounts. Depending on the current amplitude reached within the arc duration the arc remained anchored to the silver contacts or commutated to the copper arc runners. At a maximum current amplitude of 650 A Ag vapour densities of the order of 1022 m−3 were observed near the anode outweighing the Cu vapour density by a factor of 20. When at 1600 A the arc commutated to the arc runners a Cu vapour density of 8 × 1021 m−3 was reached while the Ag density remained limited to 2 × 1021 m−3.
On the choice of electromagnetic model for short high-intensity arcs, applied to welding
Authors: Choquet Isabelle , Shirvan Alireza Javidi , Nilsson Håkan 
Published: May 2012

Abstract
We have considered four different approaches for modelling the electromagnetic fields of high-intensity electric arcs: (i) three-dimensional, (ii) two-dimensional axi-symmetric, (iii) the electric potential formulation and (iv) the magnetic field formulation. The underlying assumptions and the differences between these models are described in detail. Models (i) to (iii) reduce to the same limit for an axi-symmetric configuration with negligible radial current density, contrary to model (iv). Models (i) to (iii) were retained and implemented in the open source CFD software OpenFOAM. The simulation results were first validated against the analytic solution of an infinite electric rod. Perfect agreement was obtained for all the models tested. The electromagnetic models (i) to (iii) were then coupled with thermal fluid mechanics, and applied to axi-symmetric gas tungsten arc welding test cases with short arc (2, 3 and 5 mm) and truncated conical electrode tip. Models (i) and (ii) lead to the same simulation results, but not model (iii). Model (iii) is suited in the specific limit of long axi-symmetric arc with negligible electrode tip effect, i.e. negligible radial current density. For short axi-symmetric arc with significant electrode tip effect, the more general axi-symmetric formulation of model (ii) should instead be used.
Modulation of the operational characteristics of amorphous In–Ga–Zn–O thin-film transistors by In2O3 nanoparticles
Authors: Lee Min-Jung , Lee Tae Il , Park Jee Ho , Kim Jung Han , Chae Gee Sung , Jun Myung Chul , Hwang Yong Kee , Baik Hong Koo , Lee Woong , Myoung Jae-Min 
Published: May 2012

Abstract
The structure of thin-film transistors (TFTs) based on amorphous In–Ga–Zn–O (a-IGZO) was modified by spin coating a suspension of In2O3 nanoparticles on a SiO2/p++ Si layered wafer surface prior to the deposition of IGZO layer by room-temperature sputtering. The number of particles per unit area (surface density) of the In2O3 nanoparticles could be controlled by applying multiple spin coatings of the nanoparticle suspension. During the deposition of IGZO, the In2O3 nanoparticles initially located on the substrate surface migrated to the top of the IGZO layer indicating that they were not embedded within the IGZO layer, but they supplied In to the IGZO layer to increase the In concentration in the channel layer. As a result, the channel characteristics of the a-IGZO TFT were modulated so that the device showed an enhanced performance as compared with the reference device prepared without the nanoparticle treatment. Such an improved device performance is attributed to the nano-scale changes in the structure of (InO)
n
ordering assisted by increased In concentration in the amorphous channel layer.
Diffusion of Ag ions under random potential barriers in silver-containing chalcogenide glasses
Authors: Stehlik S , Shimakawa K , Wagner T , Frumar M 
Published: May 2012

Abstract
We show that a random walk model of diffused ions interprets well the experimentally deduced Nyquist plots in ionic chalcogenide glasses. Fitting of the model to the experimental data in the Nyquist plots of Ag–As–S(Se) glasses taken as case examples yields important physical parameters such as number of mobile Ag+ ions, hopping relaxation time and diffusion coefficient. It was found that the number of freely moving Ag+ ions is almost independent of Ag content in Ag
x
(As0.33S(Se)0.67)100−x
glasses, while the maximum hopping relaxation time is highly dependent on Ag concentration.
Towards the use of protein A-tagged gold nanoparticles for signal amplification of electrochemical immunosensors in virus detection
Authors: Huy Tran Quang , Tuan Mai Anh , Thuy Nguyen Thanh , Chung Pham Van , Hong Hanh Nguyen Thi 
Published: May 2012

Abstract
In this paper we represent a study on the potential use of protein A-tagged gold nanoparticles applied for signal amplification of electrochemical immunosensors. Gold nanoparticles (GNPs) were synthesized by the chemical reduction of tetrachloroauric (III) acid trihydrate using sodium ascorbate, and then tagged with protein A (PrA) via ultracentrifugation. UV-Vis spectroscopy and transmission electron microscopy were used to verify the characteristics of formed GNPs/PrA complex. The analyzed results indicate that GNPs were found spherically, homogeneously, and with an average diameter of about 10 nm. Immunoelectron microscopy was then used to investigate the bioactivity of the GNPs/PrA complex in solution by the effective binding of GNPs to viral particles. Scanning electron and fluorescence microscopies were also used to investigate the distribution and the bioactivity of the GNPs/PrA complex on the surface of the interdigitated sensor. Consequently, this study provided some assumptions of the potential application of protein A-tagged gold nanoparticles for signal amplification of electrochemical immunosensors in virus detection from clinical samples.
Utilizing RNA-Seq data for de novo coexpression network inference
Authors: Iancu Ovidiu D. , Kawane Sunita , Bottomly Daniel , Searles Robert , Hitzemann Robert , McWeeney Shannon 
Published: May 2012

Abstract
Motivation: RNA-Seq experiments have shown great potential for transcriptome profiling. While sequencing increases the level of biological detail, integrative data analysis is also important. One avenue is the construction of coexpression networks. Because the capacity of RNA-Seq data for network construction has not been previously evaluated, we constructed a coexpression network using striatal samples, derived its network properties and compared it with microarray-based networks.
Results: The RNA-Seq coexpression network displayed scale-free, hierarchical network structure. We detected transcripts groups (modules) with correlated profiles; modules overlap distinct ontology categories. Neuroanatomical data from the Allen Brain Atlas reveal several modules with spatial colocalization. The network was compared with microarray-derived networks; correlations from RNA-Seq data were higher, likely because greater sensitivity and dynamic range. Higher correlations result in higher network connectivity, heterogeneity and centrality. For transcripts present across platforms, network structure appeared largely preserved. From this study, we present the first RNA-Seq data de novo network inference.
Contact: iancuo@ohsu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
FindGeo: a tool for determining metal coordination geometry
Authors: Andreini Claudia , Cavallaro Gabriele , Lorenzini Serena 
Published: May 2012

Abstract
Summary: Metals are essential for the structure and function of many proteins and nucleic acids. The geometrical arrangement of the atoms that coordinate a metal in a biological macromolecule is an important determinant of the specificity and role of that metal. At present, however, this information can be retrieved only from the literature, which sometimes contains an improper or incorrect description of the geometry, and often lacks it altogether. Thus, we developed FindGeo to quickly and easily determine the coordination geometry of selected, or all, metals in a given structure. FindGeo works by superimposing the metal-coordinating atoms in the input structure to a library of templates with alternative ideal geometries, which are ranked by RMSD to identify the best geometry assignment.
Availability: FindGeo is freely available as a web service and as a stand-alone program at http://metalweb.cerm.unifi.it/tools/findgeo/.
Contact: andreini@cerm.unifi.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Ka-me: a Voronoi image analyzer
Authors: Khiripet Noppadon , Khantuwan Wongarnet , Jungck John R. 
Published: May 2012

Abstract
Summary: Ka-me is a Voronoi image analyzer that allows users to analyze any image with a convex polygonal tessellation or any spatial point distribution by fitting Voronoi polygons and their dual, Delaunay triangulations, to the pattern. The analytical tools include a variety of graph theoretic and geometric tools that summarize the distribution of the numbers of edges per face, areas, perimeters, angles of Delaunay triangle edges (anglograms), Gabriel graphs, nearest neighbor graphs, minimal spanning trees, Ulam trees, Pitteway tests, circumcircles and convexhulls, as well as spatial statistics (Clark–Evans Nearest Neighborhood and Variance to Mean Ratio) and export functions for standard relationships (Lewis's Law, Desch's Law and Aboav–Weaire Law).
Availability: Ka-me: a Voronoi image analyzer is available as an executable with documentation and sample applications from the BioQUEST Library (http://bioquest.org/downloads/kame_1.0.rar).
Contact: noppadon.khiripet@nectec.or.th
graph2tab, a library to convert experimental workflow graphs into tabular formats
Authors: Brandizi Marco , Kurbatova Natalja , Sarkans Ugis , Rocca-Serra Philippe 
Published: May 2012

Abstract
Motivations: Spreadsheet-like tabular formats are ever more popular in the biomedical field as a mean for experimental reporting. The problem of converting the graph of an experimental workflow into a table-based representation occurs in many such formats and is not easy to solve.
Results: We describe graph2tab, a library that implements methods to realise such a conversion in a size-optimised way. Our solution is generic and can be adapted to specific cases of data exporters or data converters that need to be implemented.
Availability and Implementation: The library source code and documentation are available at http://github.com/ISA-tools/graph2tab.
Contact: brandizi@ebi.ac.uk.
Supplementary Information: A supplementary document describes the theoretical and technical details about the library implementation.