bluuebunny/crossref_metadata_2025_split huggingface dataset:
The integrated DM approach within the Scottish National Health System
Authors: Halsey Graham 
Published: November 2014

Background: Scotland has historically had one of the highest rates of poor health and corresponding work related absence in the developed world. To address this challenge, the Scottish government formed a specialised unit in 2006, the Scottish Centre for Healthy Working Lives (SCHWL). Functioning as an extension of the government funded National Health System (NHS), SCHWL's principle goal was to engage employers and enable them to protect and improve the health of their employees.Hypothesis: The establishment of disability management services within the National Health Service would create a primary link between medical/health services and employers/employees, resulting in improved timeframes for return to work and reduced absence rates.Methods: The SCHWL established three pilot projects to deliver Vocational Rehabilitation Services across Scotland. This included the provision of disability management services to enable workers to return to or remain in work, with the intention of creating a necessary bridge between the health care system and employers/employees. SCHWL determined that specialised training of health professional staff working within the NHS would be a critical requirement for success. In 2009, SCHWL engaged KMG Health Partners to begin delivery of the NIDMAR education programme to a cross section of staff working within the NHS. KMG has now trained over 50 health professionals who have achieved their Certified Disability Management Professional (CDMP) designation and who work with the NHS across Scotland. Principle Findings: The CDMP's function as a critical link between the traditional health services accessed at the initial stages of an employee's injury or illness. Their primary role facilitates and supports return to work from the initial onset of medical/health treatment.Conclusion: The innovative approach implemented by SCHWL has achieved measurable improvements in the communication process between NHS treating health professionals and employers, employer engagement in the return to work process, and reduced employee timeframes for return to work.
An introduced pentastomid parasite (Raillietiella frenata) infects native cane toads (Rhinella marina) in Panama
Authors: KELEHEAR CRYSTAL , SALTONSTALL KRISTIN , TORCHIN MARK E. 
Published: November 2014

SUMMARYThe pentastomid parasite, Raillietiella frenata, is native to Asia where it infects the Asian House gecko, Hemidactylus frenatus. This gecko has been widely introduced and recently R. frenata was found in introduced populations of cane toads (Rhinella marina) in Australia, indicating a host-switch from introduced geckos to toads. Here we report non-native adult R. frenata infecting the lungs of native cane toads in Panama. Eight of 64 toads were infected (median = 2·5, range = 1–80 pentastomids/toad) and pentastomid prevalence was positively associated with the number of buildings at a site, though further sampling is needed to confirm this pattern. We postulate that this pattern is likely due to a host shift of this parasite from an urban-associated introduced gecko. This is the first record of this parasite infecting cane toads in their native range, and the first instance of this parasite occurring in Central America.
ECONOMIC EVALUATION OF NEBULIZED MAGNESIUM SULPHATE IN ACUTE SEVERE ASTHMA IN CHILDREN
Authors: Petrou Stavros , Boland Angela , Khan Kamran , Powell Colin , Kolamunnage-Dona Ruwanthi , Lowe John , Doull Iolo , Hood Kerry , Williamson Paula 
Published: November 2014

Objectives: The aim of this study was to estimate the cost-effectiveness of nebulized magnesium sulphate (MgSO4) in acute asthma in children from the perspective of the UK National Health Service and personal social services.Methods: An economic evaluation was conducted based on evidence from a randomized placebo controlled multi-center trial of nebulized MgSO4 in severe acute asthma in children. Participants comprised 508 children aged 2–16 years presenting to an emergency department or a children's assessment unit with severe acute asthma across thirty hospitals in the United Kingdom. Children were randomly allocated to receive nebulized salbutamol and ipratropium bromide mixed with either 2.5 ml of isotonic MgSO4 or 2.5 ml of isotonic saline on three occasions at 20-min intervals. Cost-effectiveness outcomes were constructed around the Yung Asthma Severity Score (ASS) after 60 min of treatment; whilst cost-utility outcomes were constructed around the quality-adjusted life-year (QALY) metric. The nonparametric bootstrap method was used to present cost-effectiveness acceptability curves at alternative cost-effectiveness thresholds for either: (i) a unit reduction in ASS; or (ii) an additional QALY.Results: MgSO4 had a 75.1 percent probability of being cost-effective at a GBP 1,000 (EUR 1,148) per unit decrement in ASS threshold, an 88.0 percent probability of being more effective (in terms of reducing the ASS) and a 36.6 percent probability of being less costly. MgSO4 also had a 67.6 percent probability of being cost-effective at a GBP 20,000 (EUR 22,957) per QALY gained threshold, an 8.5 percent probability of being more effective (in terms of generating increased QALYs) and a 69.1 percent probability of being less costly. Sensitivity analyses showed that the results of the economic evaluation were particularly sensitive to the methods used for QALY estimation.Conclusions: The probability of cost-effectiveness of nebulized isotonic MgSO4, given as an adjuvant to standard treatment of severe acute asthma in children, is less than 70 percent across accepted cost-effectiveness thresholds for an additional QALY.
±10.5 V 16‐channel programmable pulse generator using high‐voltage BCD CMOS process
Authors: Wang Chua‐Chin , Wang Deng‐Shian , Sung Tzu‐Chiao , Wu Yi‐Hong , Shmilovitz Doron 
Published: November 2014

A ±10.5 V programmable pulse generator (PPG) fabricated by high‐voltage (HV) BCD CMOS technology is demonstrated, where a charge pump composed of five cascaded voltage doublers is included to boost the voltage from 2.5 V to be higher than 10 V. A cross‐voltage‐domain operational amplifier is proposed to carry out voltage level conversion and amplification. HV analogue switches are also proposed to change the direction of output currents. The proposed 16‐channel PPG is realised on silicon, where the die area is 5.43 mm2. Physical measurements justify that the maximum output current is 525 μA, and the largest voltage of the pulses is ±10.5 V.
Digital predistortion technique based on non‐uniform MP model and interpolated LUT for linearising PAs with memory effects
Authors: Feng Xiaowen , Feuvrie Bruno , Descamps Anne‐Sophie , Wang Yide 
Published: November 2014

A new digital predistortion technique based on a direct learning architecture is proposed for linearising power amplifiers (PAs) with nonlinear memory effects. It is based on the non‐uniform memory polynomial (MP) model and with a quadratically interpolated LUT. There are mainly two innovations. First, compared with the conventional MP model, the non‐uniform MP model achieves the same modelling accuracy with less coefficients. Secondly, compared with the linearly interpolated LUT, the quadratically interpolated LUT has higher accuracy, which is adopted to realise a part of the mathematical computations in the predistortion. The proposed solution is validated on a real PA ZFL‐2500. It reduces the number of the model's coefficients and achieves a spectrum regrowth suppression of about 15 dB with a table size of only 8.
Hardware‐assisted estimation of entropy norm for high‐speed network traffic
Authors: Lai Yu‐Kuen , Wellem Theophilus , You Hui‐Ping 
Published: November 2014

The computation of the entropy of a high‐speed data stream in a one‐pass fashion is crucial to many network security applications. Motivated by the work of Lall et al., this study examines the design trade‐off of processing speed and accuracy for estimating the entropy norm. The proposed scheme leverages the Count Sketch with constant memory access on counter update and point query operations. With a bounded relative error and a constant memory access cycle, the design can process incoming traffic with a throughput of 30 Gbit/s.
5 × 5 scattered temperature sensor front‐end based on single‐doide with non‐trimmed ±0.7°C 3σ relative inaccuracy
Authors: Vosooghi Bozorgmehr , Lu Li , Li Changzhi 
Published: November 2014

A bipolar junction transistor (BJT)‐based scattered relative temperature sensor front‐end with a 5 × 5 remote sensor node array in 180 nm CMOS process is presented. To eliminate diode mismatches and reduce the sensor node area, a single‐diode approach that accurately switches different amounts of currents into a single PNP BJT is employed. Dynamic element matching (DEM) is applied to the current mirrors so that the current ratio is precisely controlled. The 5 × 5 sensor nodes with a unit size of only 15 × 10 µm2 are distributed across the chip. Experimental results show that the minimum supply voltage (analogue) is 1 V over a temperature range of 0–125°C. The measured 3σ relative inaccuracy was <±0.7°C without trimming across the 0–125°C temperature range while drawing a current of < 22 µA. Furthermore, the multi‐location thermal monitoring function has been demonstrated experimentally and a 4°C/mm on‐chip temperature gradient was detected.
Quantifying the Uncertainty of a Juvenile Chinook Salmon Race Identification Method for a Mixed-Race Stock
Authors: Harvey Brett N. , Jacobson David P. , Banks Michael A. 
Published: November 2014

AbstractExpected daily FL ranges (length at date) of juvenile Chinook Salmon Oncorhynchus tshawytscha have been used throughout California's Central Valley to identify federally listed winter-run and spring-run juveniles in a mixed four-race stock. Accurate race identification is critical both to species recovery and to management of the water supply for 25 million people and a multibillion-dollar agricultural industry. We used genetic race assignment of 11,609 juveniles sampled over 6 years to characterize the accuracy of the length-at-date approach, specifically by testing two of its central assumptions: (1) juvenile FL distributions do not overlap between races on a daily basis; and (2) the growth rates that are used to project FL at date are accurate. We found that 49% of FLs for genetically identified juveniles occurred outside the expected length-at-date ranges for their respective races, and we observed a high degree of overlap in FL ranges among the four races. In addition, empirical growth rates were well below those from which length-at-date criteria were derived. Given the high degree of FL overlap between races, we conclude that modification of the length-at-date method will not substantially reduce identification error. Thus, we recommend that genetic assignment be used at least as a supplemental approach to improve Central Valley Chinook Salmon race identification, research, and management.
Received January 7, 2014; accepted July 22, 2014
Optimizing Hospital Infection Control: The Role of Mathematical Modeling
Authors: Doan Tan N. , Kong David C. M. , Kirkpatrick Carl M. J. , McBryde Emma S. 
Published: November 2014

Multidrug-resistant bacteria are major causes of nosocomial infections and are associated with considerable morbidity, mortality, and healthcare costs. Preventive strategies have therefore become increasingly important. Mathematical modeling has been widely used to understand the transmission dynamics of nosocomial infections and the quantitative effects of infection control measures. This review will explore the principles of mathematical modeling used in nosocomial infections and discuss the effectiveness of infection control measures investigated using mathematical modeling.Infect Control Hosp Epidemiol 2014;35(12):1521–1530
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
Authors: Suzek Baris E. , Wang Yuqi , Huang Hongzhan , McGarvey Peter B. , Wu Cathy H. ,   the UniProt Consortium
Published: November 2014

Abstract
Motivation: UniRef databases provide full-scale clustering of UniProtKB sequences and are utilized for a broad range of applications, particularly similarity-based functional annotation. Non-redundancy and intra-cluster homogeneity in UniRef were recently improved by adding a sequence length overlap threshold. Our hypothesis is that these improvements would enhance the speed and sensitivity of similarity searches and improve the consistency of annotation within clusters.
Results: Intra-cluster molecular function consistency was examined by analysis of Gene Ontology terms. Results show that UniRef clusters bring together proteins of identical molecular function in more than 97% of the clusters, implying that clusters are useful for annotation and can also be used to detect annotation inconsistencies. To examine coverage in similarity results, BLASTP searches against UniRef50 followed by expansion of the hit lists with cluster members demonstrated advantages compared with searches against UniProtKB sequences; the searches are concise (∼7 times shorter hit list before expansion), faster (∼6 times) and more sensitive in detection of remote similarities (&gt;96% recall at e-value &lt;0.0001). Our results support the use of UniRef clusters as a comprehensive and scalable alternative to native sequence databases for similarity searches and reinforces its reliability for use in functional annotation.
Availability and implementation: Web access and file download from UniProt website at http://www.uniprot.org/uniref and ftp://ftp.uniprot.org/pub/databases/uniprot/uniref. BLAST searches against UniRef are available at http://www.uniprot.org/blast/
Contact: huang@dbi.udel.edu
M3D: a kernel-based test for spatially correlated changes in methylation profiles
Authors: Mayo Tom R. , Schweikert Gabriele , Sanguinetti Guido 
Published: November 2014

AbstractMotivation: DNA methylation is an intensely studied epigenetic mark implicated in many biological processes of direct clinical relevance. Although sequencing-based technologies are increasingly allowing high-resolution measurements of DNA methylation, statistical modelling of such data is still challenging. In particular, statistical identification of differentially methylated regions across different conditions poses unresolved challenges in accounting for spatial correlations within the statistical testing procedure.Results: We propose a non-parametric, kernel-based method, M3D, to detect higher order changes in methylation profiles, such as shape, across pre-defined regions. The test statistic explicitly accounts for differences in coverage levels between samples, thus handling in a principled way a major confounder in the analysis of methylation data. Empirical tests on real and simulated datasets show an increased power compared to established methods, as well as considerable robustness with respect to coverage and replication levels.Availability and implementation: R/Bioconductor package M3D.Contact: G.Sanguinetti@ed.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips
Authors: Marcus Shoshana , Lee Hayan , Schatz Michael C. 
Published: November 2014

Abstract
Motivation: Genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach that analyzes multiple individuals together. A compressed de Bruijn graph is a sophisticated data structure for representing the genomes of entire populations. It robustly encodes shared segments, simple single-nucleotide polymorphisms and complex structural variations far beyond what can be represented in a collection of linear sequences alone.
Results: We explore deep topological relationships between suffix trees and compressed de Bruijn graphs and introduce an algorithm, splitMEM, that directly constructs the compressed de Bruijn graph in time and space linear to the total number of genomes for a given maximum genome size. We introduce suffix skips to traverse several suffix links simultaneously and use them to efficiently decompose maximal exact matches into graph nodes. We demonstrate the utility of splitMEM by analyzing the nine-strain pan-genome of Bacillus anthracis and up to 62 strains of Escherichia coli , revealing their core-genome properties.
Availability and implementation: Source code and documentation available open-source http://splitmem.sourceforge.net .
Contact: mschatz@cshl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images
Authors: Handfield Louis-François , Strome Bob , Chong Yolanda T. , Moses Alan M. 
Published: November 2014

AbstractMotivation: Quantifying variability in protein expression is a major goal of systems biology and cell-to-cell variability in subcellular localization pattern has not been systematically quantified.Results: We define a local measure to quantify cell-to-cell variability in high-throughput microscope images and show that it allows comparable measures of variability for proteins with diverse subcellular localizations. We systematically estimate cell-to-cell variability in the yeast GFP collection and identify examples of proteins that show cell-to-cell variability in their subcellular localization.Conclusions: Automated image analysis methods can be used to quantify cell-to-cell variability in microscope images.Contact: alan.moses@utoronto.caAvailability and Implementation: Software and data are available at http://www.moseslab.csb.utoronto.ca/louis-f/Supplementary information: Supplementary data are available at Bioinformatics online.
High-speed photospheric material flow observed at the polarity inversion line of a δ-type sunspot producing an X5.4 flare on 2012 March 7
Authors: Shimizu Toshifumi , Lites Bruce W. , Bamba Yumi 
Published: November 2014

Abstract
Solar flares abruptly release the free energy stored as a non-potential magnetic field in the corona and may be accompanied by eruptions of the coronal plasma. Formation of a non-potential magnetic field and the mechanisms for triggering the onset of flares are still poorly understood. In particular, photospheric dynamics observed near those polarity inversion lines that are sites of major flare production have not been well observed with high spatial resolution spectro-polarimetry. This paper reports on a remarkable high-speed material flow observed along the polarity inversion line located between flare ribbons at the main energy release side of an X5.4 flare on 2012 March 7. Observations were carried out by the spectro-polarimeter of the Solar Optical Telescope on board Hinode. The high-speed material flow was observed in the horizontally oriented magnetic field formed nearly parallel to the polarity inversion line. This flow persisted from at least six hours before the onset of the flare, and continued for at least several hours after the onset of the flare. Observations suggest that the observed material flow represents neither the emergence nor convergence of the magnetic flux. Rather, it may be considered to be material flow working both to increase the magnetic shear along the polarity inversion line and to develop magnetic structures favorable for the onset of the eruptive flare.
Molecular Structure and Organization of Starch Granules from Developing Wheat Endosperm
Authors: Waduge Renuka N. , Kalinga Danusha N. , Bertoft Eric , Seetharaman Koushik 
Published: November 2014

ABSTRACTWheat starches isolated from seeds harvested between 7 and 49 days after anthesis (DAA) were fractionated into large (>8 μm) and small (<8 μm) granules and studied for starch structure and architecture. Starch granules at 7 DAA possessed unimodal size distribution, whereas it was bimodal at later maturity stages. The apparent amylose fraction of starch granules at early maturity (7 and 14 DAA) consisted of intermediate‐type materials, whereas starch at later maturity stages (28 and 49 DAA) contained branched amylose. Wide‐angle X‐ray scattering (WAXS) revealed a well‐developed polymorphic structure already at 7 DAA. Although the presence of a small proportion of B‐type crystallites mixed with A‐type crystallites was observed in the X‐ray diffractogram of starches at early maturation (7 and 14 DAA), it was masked by the A‐type crystallites at later maturity stages. However, the large granules had a higher proportion of B‐type crystallites and lower relative crystallinity (RC) than their small‐granule counterpart. The iodine absorption properties of the starch granules demonstrated different levels of mobility of the starch polymers at different stages of maturity and the mobility of more glucan polymers in the large granule population compared with the small granules at the same maturity stage. Iodine did not change the characteristic A‐type crystalline pattern of starch, but it increased RC. Changes in peak width at half height based on WAXS data further suggested the possible interaction of iodine with amylopectin intercluster chain segments and branch chains in formation of inclusion complexes.
Soaking Conditions During Brown Rice Parboiling Impact the Level of Breakage‐Susceptible Rice Kernels
Authors: Buggenhout Joke , Brijs Kristof , Delcour Jan A. 
Published: November 2014

ABSTRACTIf properly executed, parboiling, a hydrothermal treatment consisting of soaking, steaming, and drying of rice, substantially reduces its milling breakage susceptibility. Here, brown rice was soaked at 40, 55, or 65°C for different times (150 s to 240 min) and subsequently parboiled under standardized steaming and drying conditions. The moisture absorption during initial soaking induced fissures in more than 90% of the rice grains, which disappeared with further soaking. The fissuring incidence in the soaked rice samples was related to that of the parboiled rice samples. The extent of starch gelatinization during steaming increased with the moisture content of the soaked grains. In addition, as a result of starch gelatinization, the level of white bellies (i.e., parboiled grains with translucent outer layers and an opaque center) decreased from over 90% to less than 3%. Rice grains need to absorb sufficient moisture during soaking to minimize the level of breakage‐susceptible white bellies and fissured rice grains in the parboiled end product.