bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review of the reliability and validity of OPCRIT in relation to its use for the routine clinical assessment of mental health patients
Authors: Brittain Philip J. , Stahl Daniel , Rucker James , Kawadler Jamie , Schumann Gunter 
Published: May 2013

AbstractThe OPCRIT program is a symptom checklist with accompanying algorithms producing operationally defined diagnoses. We undertook a review of studies which had used OPCRIT and had reported statistics concerning its reliability and validity, producing summary measures from 44 studies. The first main measure of interest was inter‐rater reliability where mean kappa values indicated that agreement between raters was “substantial” with a marginal improvement at the diagnostic (0.76) versus individual item (0.69) level. The second main measure of interest was convergent validity – the agreement between OPCRIT and clinical diagnoses. Most studies reported these figures as concordance rates suggesting mean agreement, unadjusted for chance, of 69%. Very few studies used the chance‐adjusted kappa statistic but where this was used agreement was “fair” (0.39). Agreement between OPCRIT and other research diagnoses was “moderate” (0.60). We also considered differences between the way OPCRIT has traditionally been used in research settings and the naturalistic manner in which it will be employed in the hospital ward. This review provides a summary of the reliability and validity of OPCRIT, which will be considered during the preparation for its use in the routine characterization of mental health patients in clinical settings. Copyright © 2013 John Wiley & Sons, Ltd.
3He pO2 mapping is limited by delayed‐ventilation and diffusion in chronic obstructive pulmonary disease
Authors: Marshall Helen , Parra‐Robles Juan , Deppe Martin H. , Lipson David A. , Lawson Rod , Wild Jim M. 
Published: May 2013

PurposeLung pO2 mapping with 3He MRI assumes that the sources of signal decay with time during a breath‐hold are radiofrequency depolarization and oxygen‐dependent T1 relaxation, but the method is sensitive to other sources of spatio‐temporal signal change such as diffusion. The purpose of this work was to assess the use of 3He pO2 mapping in patients with chronic obstructive pulmonary disease.MethodsTen patients with moderate to severe chronic obstructive pulmonary disease were scanned with a 3D single breath‐hold pO2 mapping sequence.ResultsImages showed signal increasing over time in some lung regions due to delayed ventilation during breath‐hold. Regions of physically unrealistic negative pO2 values were seen in all patients, and regional mean pO2 values of −0.3 bar were measured in the two patients most affected by delayed ventilation (where mean time to signal onset was 3–4 s).ConclusionsMovement of gas within the lungs during breath‐hold causes regional changes in signal over time that are not related to oxygen concentration, leading to erroneous pO2 measurements using the linear oxygen‐dependent signal decay model. These spatio‐temporal sources of signal change cannot be reliably separated at present, making pO2 mapping using this methodology unreliable in chronic obstructive pulmonary disease patients with significant bullous emphysema or delayed ventilation. Magn Reson Med 71:1172–1178, 2014. © 2013 Wiley Periodicals, Inc.
APT‐weighted and NOE‐weighted image contrasts in glioma with different RF saturation powers based on magnetization transfer ratio asymmetry analyses
Authors: Zhou Jinyuan , Hong Xiaohua , Zhao Xuna , Gao Jia‐Hong , Yuan Jing 
Published: May 2013

PurposeTo investigate the saturation‐power dependence of amide proton transfer (APT)‐weighted and nuclear Overhauser enhancement‐weighted image contrasts in a rat glioma model at 4.7 T.MethodsThe 9L tumor‐bearing rats (n = 8) and fresh chicken eggs (n = 4) were scanned on a 4.7‐T animal magnetic resonance imaging scanner. Z‐spectra over an offset range of ±6 ppm were acquired with different saturation powers, followed by the magnetization transfer‐ratio asymmetry analyses around the water resonance.ResultsThe nuclear Overhauser enhancement signal upfield from the water resonance (−2.5 to −5 ppm) was clearly visible at lower saturation powers (e.g., 0.6 µT) and was larger in the contralateral normal brain tissue than in the tumor. Conversely, the APT effect downfield from the water resonance was maximized at relatively higher saturation powers (e.g., 2.1 µT) and was larger in the tumor than in the contralateral normal brain tissue. The nuclear Overhauser enhancement decreased the APT‐weighted image signal, based on the magnetization transfer‐ratio asymmetry analysis, but increased the APT‐weighted image contrast between the tumor and contralateral normal brain tissue.ConclusionThe APT and nuclear Overhauser enhancement image signals in tumor are maximized at different saturation powers. The saturation power of roughly 2 μT is ideal for APT‐weighted imaging at clinical B0 field strengths. Magn Reson Med 70:320–327, 2013. © 2013 Wiley Periodicals, Inc.
Simulation of drilling‐induced compaction bands using discrete element method
Authors: Rahmati H. , Nouri A. , Chan D. , Vaziri H. 
Published: May 2013

SummaryRock failure is observed around boreholes often with certain types of failure zones, which are called breakouts. Laboratory‐scale drilling tests in some high‐porosity quartz‐rich sandstone have shown breakouts in the form of narrow localized compacted zones in the minimum horizontal stress direction. They are called fracture‐like breakouts. Such compaction bands may affect hydrocarbon extraction by forming barriers that inhibit fluid flow and may also be a source of sand production.This paper presents the results of numerical simulations of borehole breakouts using 3D discrete element method to investigate the mechanism of the fracture‐like breakouts and to identify the role of far‐field stresses on the breakout dimensions. The numerical tool was first verified against analytical solutions. It was then utilized to investigate the failure mechanism and breakout geometry for drilled cubic rock samples of Castlegate sandstone subjected to different pre‐existing far‐field stresses.Results show that failure occurs in the zones of the highest concentration of tangential stress around the borehole. It is concluded that fracture‐like breakout develops as a result of a nondilatant failure mechanism consisting of localized grain debonding and repacking and grain crushing that lead to the formation of a compaction band in the minimum horizontal stress direction. In addition, it is found that the length of fracture‐like breakouts depends on both the mean stress and stress anisotropy. However, the width of the breakout is not significantly changed by the far‐field stresses. Copyright © 2013 John Wiley & Sons, Ltd.
Identification of recurrent FGFR3 fusion genes in lung cancer through kinome‐centred RNA sequencing
Authors: Majewski Ian J , Mittempergher Lorenza , Davidson Nadia M , Bosma Astrid , Willems Stefan M , Horlings Hugo M , de Rink Iris , Greger Liliana , Hooijer Gerrit KJ , Peters Dennis , Nederlof Petra M , Hofland Ingrid , de Jong Jeroen , Wesseling Jelle , Kluin Roelof JC , Brugman Wim , Kerkhoven Ron , Nieboer Frank , Roepman Paul , Broeks Annegien , Muley Thomas R , Jassem Jacek , Niklinski Jacek , van Zandwijk Nico , Brazma Alvis , Oshlack Alicia , van den Heuvel Michel , Bernards René 
Published: May 2013

AbstractOncogenic fusion genes that involve kinases have proven to be effective targets for therapy in a wide range of cancers. Unfortunately, the diagnostic approaches required to identify these events are struggling to keep pace with the diverse array of genetic alterations that occur in cancer. Diagnostic screening in solid tumours is particularly challenging, as many fusion genes occur with a low frequency. To overcome these limitations, we developed a capture enrichment strategy to enable high‐throughput transcript sequencing of the human kinome. This approach provides a global overview of kinase fusion events, irrespective of the identity of the fusion partner. To demonstrate the utility of this system, we profiled 100 non‐small cell lung cancers and identified numerous genetic alterations impacting fibroblast growth factor receptor 3 (FGFR3) in lung squamous cell carcinoma and a novel ALK fusion partner in lung adenocarcinoma. © 2013 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Spatial variation in herbicide leaching from a marine clay soil via subsurface drains
Authors: Ulén Barbro M , Larsbo Mats , Kreuger Jenny K , Svanbäck Annika 
Published: May 2013

AbstractBackgroundSubsurface transport via tile drains can significantly contribute to pesticide contamination of surface waters. The spatial variation in subsurface leaching of normally applied herbicides was examined together with phosphorus losses in 24 experimental plots with water sampled flow‐proportionally. The study site was a flat, tile‐drained area with 60% marine clay in the topsoil in southeast Sweden. The objectives were to quantify the leaching of frequently used herbicides from a tile drained cracking clay soil and to evaluate the variation in leaching within the experimental area and relate this to topsoil management practices (tillage method and structure liming).ResultsIn summer 2009, 0.14, 0.22 and 1.62%, respectively, of simultaneously applied amounts of MCPA, fluroxypyr and clopyralid were leached by heavy rain five days after spraying. In summer 2011, on average 0.70% of applied bentazone was leached by short bursts of intensive rain 12 days after application. Peak flow concentrations for 50% of the treated area for MCPA and 33% for bentazone exceeded the Swedish no‐effect guideline values for aquatic ecosystems. Approximately 0.08% of the glyphosate applied was leached in dissolved form in the winters of 2008/2009 and 2010/2011. Based on measurements of glyphosate in particulate form, total glyphosate losses were twice as high (0.16%) in the second winter. The spatial inter‐plot variation was large (72–115%) for all five herbicides studied, despite small variations (25%) in water discharge.ConclusionsThe study shows the importance of local scale soil transport properties for herbicide leaching in cracking clay soils. © 2013 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
A flexible QoS architecture for DVB‐RCS2
Authors: Fairhurst Gorry , Secchi Raffaello , Yun Ana 
Published: May 2013

SUMMARYThis paper presents a QoS, architecture for the Higher Layers Satellite in the second generation Digital Video Broadcasting with Return Channel via Satellite standard. It describes the flexibility offered by integrating link and network functions to support internet protocol‐based differentiated QoS. The operation of key mechanisms is outlined and analysed to show how these may be combined to realise differentiated services by defining mappings between per‐hop behaviours, to queues in the traffic plane and return channel satellite terminal request classes in the control plane. Simulation is used to show that an appropriate mapping can be used to can tune the offered service to different traffic classes and that an appropriate assignment can significantly improve the satellite bandwidth efficiency and/or the performance/QoS supplied to a traffic class. Copyright © 2013 John Wiley & Sons, Ltd.
Urban transport and CO2 emissions: some evidence from Chinese cities
Authors: Darido Georges , Torres‐Montoya Mariana , Mehndiratta Shomik 
Published: May 2013

The work presented below was conducted as part of the World Bank's economic and sector work titled ‘Urban Transport and Climate Change’. It is first a compendium of data—most of it collected as part of the ‘China–GEF–World Bank Urban Transport Partnership Program’—and also provides a preliminary analysis of urban transport characteristics, energy use, and greenhouse gas (GHG) emissions for a diverse set of cities in China. This working paper is not in itself intended to be a strategy for urban transport and climate change in China. It is the view of the authors that this research could be an input toward the development of such a strategy in China and more broadly. Although transport in general, and urban transport in particular, is acknowledged to be an important and growing source of GHG emissions, work still needs to be done to develop robust and standardized datasets and frameworks to support a decision‐making process. The paper is intended as a background document to support ongoing discussions about a climate change strategy and to establish a dataset to be made available as a platform for future studies and further refinement. It is hoped that others will take advantage of the dataset created for this study and use it as a basis for projections, comparative analysis, and to test their own hypothesis. Reviewers of this paper have also raised many specific possibilities and interesting ideas for further work, which are summarized in the conclusions. The authors would particularly like to thank AusAID (the Australian Government's overseas aid program), ESMAP (Energy Sector Management Assistance Program), and GEF (Global Environment Facility) who provided partial financing for this work. The authors would also like to acknowledge the management of the World Bank's Sustainable Development units in East Asia & Pacific Region and Latin American & the Caribbean Region for their support.This article is categorized under:

Energy Efficiency > Systems and Infrastructure
Energy Infrastructure > Systems and Infrastructure
Energy and Climate > Systems and Infrastructure
Understanding pancreatic cancer genomes
Authors: Cowley Mark J. , Chang David K. , Pajic Marina , Johns Amber L. , Waddell Nicola , Grimmond Sean M. , Biankin Andrew V. 
Published: May 2013

AbstractPancreatic cancer is the fourth leading cause of cancer death in our society, with a mortality that virtually parallels its incidence, a median survival of <12 months even with maximal therapy, and a 5‐year survival rate of <5 %. The diversity of clinical outcomes and the molecular heterogeneity of histopathologically similar cancer types, incomplete knowledge of the genomic aberrations that drive carcinogenesis and the lack of therapeutics that specifically target most known genomic aberrations necessitates large‐scale detailed analysis of cancer genomes to identify novel potential therapeutic strategies. As part of the International Cancer Genome Consortium (ICGC), the Australian Pancreatic Cancer Genome Initiative (APGI) used exomic sequencing and copy number analysis to define genomic aberrations that characterize a large, clinically focused, prospectively accrued cohort of patients with pancreatic cancer. The cohort consisted of early (clinical stages I and II) non‐pre‐treated patients with pancreatic ductal adenocarcinoma who underwent operative resection with curative intent. We devised approaches to adjust for low epithelial content in primary tumours and to define the genomic landscape of pancreatic cancer to identify novel candidate driver genes and mechanisms. We aim to develop stratified, molecular phenotype‐guided therapeutic strategies using existing therapeutics that are either rescued, repurposed, in development, or are known to be effective in an undefined subgroup of PC patients. These are then tested in primary patient‐derived xenografts and cell lines from the above deeply characterized cohort. In addition, we return information to treating clinicians that influences patient care and are launching a clinical trial called IMPaCT (Individualized Molecular Pancreatic Cancer Therapy). This umbrella design trial randomizes patients with metastatic disease to either standard first‐line therapy with gemcitabine, or a molecular phenotype‐guided approach using next‐generation sequencing strategies to screen for actionable mutations defined through the ICGC effort.
Primate abundance and habitat preferences on the lower Urubamba and Tambo rivers, central–eastern Peruvian Amazonia
Authors: Aquino Rolando , Cornejo Fanny M. , Heymann Eckhard W. 
Published: May 2013

AbstractWe report information on population density, group size, and habitat preferences of primates along the lower Río Urubamba and in the Río Urubamba–Río Tambo interfluvium, in central–eastern Peruvian Amazonia, an area that has been little explored with regard to its primate fauna. During 425 km of transect walks in October–November 2008 and April–May 2009 totally 174 groups of nine primate species were encountered, the most common beingCallicebus brunneus(45 groups),Saguinus imperator(41 groups), andAotus nigriceps(26 groups). Group sizes were smallest forA. nigricepsandC. brunneus(mean of 2.8 and 2.9, respectively) and largest forSaimiri boliviensis(mean 15.6). Population densities were lowest forLagothrix cana(3.3 individuals/km2) and highest forA. nigriceps(31.1 individuals/km2). Groups ofC. brunneus,S. imperator,S. boliviensis,Cebus albifrons, andCebus apellawere most frequently (83 % of sightings) encountered in semi-dense or in open primary forest that included stands of bamboo (Guadua sarcocarpa) or where bamboo was a very common species.
Retracted: Novel Imidazolium‐Based Gemini Surfactants: Synthesis, Surface Properties, Corrosion Inhibition and Biocidal Activity Against Sulfate‐Reducing Bacteria
Authors: Aiad Ismail , Emam Dalia , El‐Deeb Ali , Abd‐Alrahman Eman 
Published: May 2013

AbstractThree novel imidazolium‐based gemini surfactants had been synthesized and characterized using different spectroscopic techniques. The surface properties of the synthesized surfactants were determined using surface tension measurements at 20 °C. The surface parameters including critical micelle concentration (CMC), πCMC, Pc20, Γmax and Amin were determined. The synthesized compounds were evaluated as corrosion inhibitors for carbon steel in 0.5 M HCl solution using the weight loss and polarization techniques. The biological activity of these surfactants was evaluated against sulfate reducing bacteria using most probable number method. The results indicate that the synthesized compounds have good surface properties and are proper corrosion inhibitors for low carbon steel, with a high inhibition efficiency observed around their CMC. These compounds exhibit a significant biocidal activity against sulfate reducing bacteria.
A Review of Emergency Medical Services Events in US National Parks From 2007 to 2011
Authors: DeClerck Matthieu P. , Atterton Laurie M. , Seibert Thomas , Cushing Tracy A. 
Published: May 2013

Objective Outdoor recreation is growing in the United States, with more than 279 million annual visitors to areas controlled by the National Park Service (NPS). Emergency medical needs in these parks are overseen by the National Park's rangers within the NPS Emergency Medical Services (EMS) system. This study examines medical and traumatic emergencies throughout the NPS over a 5-year period to better understand the types of events and fatalities rangers encounter, both regionally and on a national scale. Methods This is a retrospective review of the annual EMS reports published by the 7 NPS regions from 2007 to 2011. The following were compared and examined at a regional and national level: medical versus traumatic versus first aid events, cardiac events and outcomes, use of automated external defibrillators, and medical versus traumatic fatalities. Results The national incidence of EMS events was 45.9 events per 1 million visitors. Medical, traumatic, and first aid events composed 29%, 28%, and 43% of reports, respectively. Of medical episodes, 1.8% were cardiac arrests, of which 64.2% received automated external defibrillator treatment; 29.1% of cardiac arrests survived to hospital discharge. Of fatalities, 61.4% were traumatic in nature and the remaining 38.5% were nontraumatic (medical). Regional differences were found for all variables. Conclusions On a national level, the NPS experiences an equal number of medical and traumatic EMS events. This differs from past observed trends that reported a higher incidence of traumatic events than medical events in wilderness settings. Cardiac events and automated external defibrillator usage are relatively infrequent. Traumatic fatalities are more common than medical fatalities in the NPS. Regional variations in events likely reflect differences in terrain, common activities, proximity to urban areas, and access to definitive care between regions. These data can assist the NPS in targeting the regions with the greatest number of incidents and fatalities for prevention, ranger training, and visitor education.
The quasi-geostrophic theory of the thermal shallow water equations
Authors: Warneford Emma S. , Dellar Paul J. 
Published: May 2013

AbstractThe thermal shallow water equations provide a depth-averaged description of motions in a fluid layer that permits horizontal variations in material properties. They typically arise through an equivalent barotropic approximation of a two-layer system, with a spatially varying density contrast due to an evolving temperature field in the active layer. We formalize a previous derivation of the quasi-geostrophic (QG) theory of these equations, by performing a direct asymptotic expansion for small Rossby number. We then present a second derivation as the small Rossby number limit of a balanced model that projects out high-frequency dynamics due to inertia-gravity waves. This latter derivation has wider validity, not being restricted to mid-latitude$\beta $-planes. We also derive their local energy conservation equation from the QG limit of a thermal shallow water pseudo-energy conservation equation. This derivation involves the ageostrophic correction to the leading-order geostrophic velocity that is eliminated in the usual derivation of a closed evolution equation for the QG potential vorticity. Finally, we derive the non-canonical Hamiltonian structure of the thermal QG equations from a decomposition in Rossby number of a pseudo-energy and Poisson bracket for the thermal shallow water equations.