bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational Fluid Dynamic (CFD) Simulations of Liquid Steel Infiltration in Porous Ceramic Structures: Dynamics of the Penetrating Melt Surface
Authors: Schwarze Rüdiger , Klostermann Jens
Published: June 2015

Pressure infiltration of liquid steel into an open‐cell porous ceramic structure is a possible production line for a new composite material, which is currently under investigation in a joint research project. The initial phase of processing the new composite is dominated by the infiltration of the free melt surface into the porous structure. During the infiltration, the melt surface is alternately divided and reassembled. A more detailed understanding of this process can help e.g., to avoid disadvantageous capturing of pore‐scale gas bubbles in the final metal‐matrix composite. Numerical investigations of the infiltration process are often based on homogenized Darcy‐type model equations. However, the formulation of sound and reliable numerical models beyond the Darcy‐scale is challenging due to the complex physical nature of these processes.

In this paper, we describe a refined model approach for the behavior of a free surface in an artificial porous foam structure. The numerical model is based on the volume of fluid method for two‐phase flows. Whereas standard numerical discretization methods lead to time‐consuming simulations, a reformulation of the numerics allows a fair compromise between accuracy and efficiency. A comparison between numerical results and corresponding information from a model experiment is given.
Deformations of Working Elements in Oil Free Scroll Vacuum Pumps
Authors: Raykov A. , Burmistrov A. , Salikeev S. , Fomina M. , Kapustin E.
Published: June 2015

The mechanical and thermal causes of deformations of the orbiting and the fixed elements of oil free vacuum pumps are considered. Basic data for deformation calculation are geometric dimensions of the pump and dependence of working chamber volume on the orbiting scroll element rotation angle. Gas temperature and pressure values in each vacuum pump chamber are obtained with the help of a working process mathematical model.

Deformation calculation is carried out by the finite element method realized in the software ANSYS.

It is shown that deformations caused by pressure‐induced mechanical forces do not have considerable influence on the change of radial clearances between the scrolls. They may not be taken into account for pumping characteristics calculation. Thermal‐induced deformations are much greater, and the change of the clearances due to this cause may be 25 % and even larger.
Combustion chemical vapor deposition
Authors: Eigenbrod Volkmar J. , Hensch Christina , Kemper Alexander
Published: June 2015

In this paper, flame‐pyrolytic treatment methods of metal surfaces are compared to vacuum‐based CVD processes. There is a practical consideration of the aforementioned methods. The layers formed were analyzed by scanning electron microscopy, changes in properties such as surface energy and adhesion of subsequent layers of paint were detected by measurement.
Anorganisch‐organische Hybridschichten für die Entspiegelung optischer Oberflächen
Authors: Schulz Ulrike , Munzert Peter , Rickelt Friedrich , Präfke Christiane , Gratzke Nancy , Knopf Heiko , Wolleb Sabrina , Kaiser Norbert
Published: June 2015

Spätestens seit der Entdeckung von entspiegelnden Nanostrukturen auf den Augen nachtfliegender Insekten wird eine solche Struktur auch für die Anwendung auf optischen Oberflächen diskutiert. Auf spritzgegossenen Kunststofflinsen können Antireflexstrukturen relativ einfach durch Plasmaätzen erzeugt werden. Dieses Verfahren wurde nun auf im Vakuum aufgedampfte organische Schichten übertragen. Durch die Kombination organischer Nanostrukturen mit anorganischen Schichten entstehen komplexe Schichtsysteme, die für die Breitbandentspiegelung von Glaslinsen sehr gut geeignet sind.
Transparente und leitfähige Veredelung von Kunststoffoberflächen
Authors: Abendroth Thomas , Liebich Jens , Härtel Paul , Schumm Benjamin , Althues Holger , Kaskel Stefan , Beyer Eckhard
Published: June 2015

In diesem Beitrag werden konventionelle Abscheideverfahren bei Atmosphärendruck genutzt um Glas und Kunststoffoberflächen mit transparent und leitfähigen Schichten zu funktionalisieren.

Durch die Verwendung eines neu entwickelten Transfer‐ und Integrationsverfahrens wird der Schichtherstellungsprozess vom zu beschichtenden Substrat getrennt. Mit diesem Verfahren lassen sich somit temperatursensitive Kunststoffe, wie beispielsweise PET‐Folien, mit FTO‐Schichten veredeln. Neben diesen hoch leitfähigen TCO‐Folien für elektrooptische Anwendungen, lassen sich auch antistatische Kunststoffoberflächen, auf Basis von Kohlenstoffnanoröhren, herstellen.
Gas Permeation through Vacuum Materials
Authors: Vinogradov M. L. , Barchenko V. T. , Lisenkov A. A. , Kostrin D. K. , Babinov N. A.
Published: June 2015

The aim of this research is to study the gas permeability of materials being used to create elements of unmanned aerial vehicles. The measurement system for gas permeation coefficients of composite materials is designed on the basis of a helium leak detector. Due to permeation through the Viton sealing the smallest flow that can be correctly measured by the system is 10‐10 Pa · m3/s. Verification of the system was held on PTFE polymer sample with a known helium permeability value. Gas permeability of three composite materials was studied. The steadystate helium permeation coefficient in [Pa · m3/s] · [m/(m2 · bar)] for high molecular weight polyethylene (HM‐WPE) with 100 nm copper coating is 3.1 · 10‐8, for low pressure polyethylene (HDPE 209‐07) with 100 nm copper coating it is 1.9 · 10‐7; for vacuum‐tight ceramics VK94‐1 with glue K400 layer it is 2.2 · 10‐9. Authors will be glad to measure the gas permeability of new materials that can be provided by readers of this publication.
Concurrent software architectures for exploratory data analysis
Authors: Starič Anže , Demšar Janez , Zupan Blaž
Published: June 2015

Decades ago, increased volume of data made manual analysis obsolete and prompted the use of computational tools with interactive user interfaces and rich palette of data visualizations. Yet their classic, desktop‐based architectures can no longer cope with the ever‐growing size and complexity of data. Next‐generation systems for explorative data analysis will be developed on client–server architectures, which already run concurrent software for data analytics but are not tailored to for an engaged, interactive analysis of data and models. In explorative data analysis, the key is the responsiveness of the system and prompt construction of interactive visualizations that can guide the users to uncover interesting data patterns. In this study, we review the current software architectures for distributed data analysis and propose a list of features to be included in the next generation frameworks for exploratory data analysis. The new generation of tools for explorative data analysis will need to address integrated data storage and processing, fast prototyping of data analysis pipelines supported by machine‐proposed analysis workflows, pre‐emptive analysis of data, interactivity, and user interfaces for intelligent data visualizations. The systems will rely on a mixture of concurrent software architectures to meet the challenge of seamless integration of explorative data interfaces at client site with management of concurrent data mining procedures on the servers. WIREs Data Mining Knowl Discov 2015, 5:165–180. doi: 10.1002/widm.1155

This article is categorized under:

Application Areas > Data Mining Software Tools

Technologies > Computer Architectures for Data Mining
Comparison of Distal Limb Warming With Fluidotherapy and Warm Water Immersion for Mild Hypothermia Rewarming
Authors: Kumar Parveen , McDonald Gerren K. , Chitkara Radhika , Steinman Alan M. , Gardiner Phillip F. , Giesbrecht Gordon G.
Published: June 2015

Objective

The purpose of the study was to determine the effectiveness of Fluidotherapy rewarming through the distal extremities for mildly hypothermic, vigorously shivering subjects. Fluidotherapy is a dry heat modality in which cellulose particles are suspended by warm air circulation.

Methods

Seven subjects (2 female) were cooled on 3 occasions in 8˚C water for 60 minutes, or to a core temperature of 35°C. They were then dried and rewarmed in a seated position by 1) shivering only; 2) Fluidotherapy applied to the distal extremities (46 ± 1°C, mean ± SD); or 3) water immersion of the distal extremities (44 ± 1°C). The order of rewarming followed a balanced design. Esophageal temperature, skin temperature, heart rate, oxygen consumption, and heat flux were measured.

Results

The warm water produced the highest rewarming rate, 6.1°C·h−1, 95% CI: 5.3–6.9, compared with Fluidotherapy, 2.2°C·h−1, 95% CI: 1.4–3.0, and shivering only, 2.0°C·h−1, 95% CI: 1.2–2.8. The Fluidotherapy and warm water conditions increased skin temperature and inhibited shivering heat production, thus reducing metabolic heat production (166 ± 42 W and 181 ± 45 W, respectively), compared with shivering only (322 ± 142 W). Warm water provided a significantly higher net heat gain (398.0 ± 52 W) than shivering only (288.4 ± 115 W).

Conclusions

Fluidotherapy was not as effective as warm water for rewarming mildly hypothermic subjects. Although Fluidotherapy is more portable and technically simpler, it provides a lower rate of rewarming that is similar to shivering only. It does help decrease shivering heat production, lowering energy expenditure and cardiac work, and could be considered in a hospital setting, if convenient.
The Gospel of Jesus' Wife: Textual Evidence of Modern Forgery
Authors: Bernhard Andrew
Published: June 2015

The present essay summarises textual evidence indicating that the Gospel of Jesus' Wife is essentially a ‘patchwork’ of words and short phrases culled from the lone extant Coptic manuscript of the Gospel of Thomas (Nag Hammadi Codex ii), prepared by a forger using Michael W. Grondin's 2002 PDF edition of this manuscript. The text contains at least five tell-tale signs of its modern origin, including the apparent replication of a typographical (and grammatical) error from Grondin's edition. A direct link between it and Grondin's work also seems to be confirmed by the earliest known English translation of the fragment.
Das Heidelberger Frühbehandlungszentrum für junge Menschen in Krisen – ein Modell zur kooperativen Versorgung von Jugendlichen und jungen Erwachsenen
Authors: Kaess Michael , Koch Eginhard , Thomann Philipp A. , Herpertz Sabine C. , Resch Franz
Published: June 2015

Die Adoleszenz bezeichnet die Lebensphase im Übergang zwischen Kindheit und Erwachsenenalter. Sie geht mit erheblichen biologischen und psychosozialen Veränderungen einher und birgt ein erhöhtes Risiko für das Erstauftreten psychischer Erkrankungen. Da eine psychische Störung während der Adoleszenz oftmals zu einer Beeinträchtigung wesentlicher Entwicklungsschritte führt, sind negative Auswirkungen auf den weiteren Lebens- und Krankheitsverlauf sehr häufig. Früherkennung und Frühbehandlung sind daher erklärte gesundheitspolitische Ziele, die jedoch in der Versorgungsrealität nicht immer verwirklicht werden. Ein großes Problem der sogenannten Adoleszentenpsychiatrie ist der Kontinuitätsabbruch der Helfersysteme bei Erreichen der Volljährigkeit. Das Heidelberger Frühbehandlungszentrum stellt seit mehr als 10 Jahren eine Einheit zur interdisziplinären Versorgung von Jugendlichen und Erwachsenen mit psychischen Störungen dar. Die Kliniken für Allgemeine Psychiatrie und Kinder- und Jugendpsychiatrie des Universitätsklinikums Heidelberg versorgen hier gemeinsam junge Menschen in seelischen Krisen. Besondere Kennzeichen des Frühbehandlungszentrums sind: Flexibles Behandlungssetting (stationär, tagesklinisch, ambulant, aufsuchend) mit Behandlerkontinuität; funktionsorientierter Behandlungsansatz mit Fokus auf adoleszenten-typischen Problemen; Kurzzeitbehandlung, psychosoziale Unterstützung mit Weichenstellung und Perspektivklärung. Das Heidelberger Frühbehandlungszentrum stellt ein Beispiel integrativer und interdisziplinärer adoleszentenpsychiatrischer Versorgung dar.
Grb2 monomer–dimer equilibrium determines normal versus oncogenic function
Authors: Ahmed Zamal , Timsah Zahra , Suen Kin M. , Cook Nathan P. , Lee Gilbert R. , Lin Chi-Chuan , Gagea Mihai , Marti Angel A. , Ladbury John E.
Published: June 2015

The adaptor protein growth factor receptor-bound protein 2 (Grb2) is ubiquitously expressed in eukaryotic cells and involved in a multitude of intracellular protein interactions. Grb2 plays a pivotal role in tyrosine kinase-mediated signal transduction including linking receptor tyrosine kinases to the Ras/mitogen-activated protein (MAP) kinase pathway, which is implicated in oncogenic outcome. Grb2 exists in a constitutive equilibrium between monomeric and dimeric states. Here we show that only monomeric Grb2 is capable of binding to SOS and upregulating MAP kinase signalling and that the dimeric state is inhibitory to this process. Phosphorylation of tyrosine 160 (Y160) on Grb2, or binding of a tyrosylphosphate-containing ligand to the SH2 domain of Grb2, results in dimer dissociation. Phosphorylation of Y160 on Grb2 is readily detectable in the malignant forms of human prostate, colon and breast cancers. The self-association/dissociation of Grb2 represents a switch that regulates MAP kinase activity and hence controls cancer progression.
Au(i)-catalyzed synthesis of 8-oxabicyclo[3.2.1]oct-2-enes and 9-oxabicyclo[3.3.1]nona-2,6-dienes from enynol via oxonium/Prins-type cyclization
Authors: Vandavasi Jaya Kishore , Hu Wan-Ping , Boominathan Siva Senthil Kumar , Guo Bing-Chun , Hsiao Cheng-Tien , Wang Jeh-Jeng
Published: June 2015

An AuI catalytic system to synthesise 8-oxabicyclo[3.2.1]oct-2-enes and 9-oxabicyclo[3.3.1]nona-2,6-dienes from enynol via oxonium/Prins-type cyclization.
Photosynthesis of formate from CO2 and water at 1% energy efficiency via copper iron oxide catalysis
Authors: Kang Unseock , Choi Sung Kyu , Ham Dong Jin , Ji Sang Min , Choi Wonyong , Han Dong Suk , Abdel-Wahab Ahmed , Park Hyunwoong
Published: June 2015

Solar conversion of carbon dioxide and water to value-added chemicals remains a challenge.
Editorial: Chemical Ecology
Authors: Schulz Stefan , Kubanek Julia , Piel Joern
Published: June 2015

Stefan Schulz, Julia Kubanek and Joern Piel introduce the Natural Product Reports themed issue on ‘Chemical ecology’.
Improved electrochemical performance of tin-sulfide anodes for sodium-ion batteries
Authors: Lu Ying Ching , Ma Chuze , Alvarado Judith , Dimov Nikolay , Meng Ying Shirley , Okada Shigeto
Published: June 2015

Due to their highly reversible capacity, tin-sulfide-based materials have gained attention as potential anodes for sodium-ion and lithium-ion batteries.
Deep red emission in Eu2+-activated Sr4(PO4)2O phosphors for blue-pumped white LEDs
Authors: Komuro Naoyuki , Mikami Masayoshi , Saines Paul J. , Akimoto Katsuhiro , Cheetham Anthony K.
Published: June 2015

The deep red phosphor Sr4(PO4)2O:Eu2+, which has an excitation peak around 450 nm for blue LED applications, is reported.
Radiographic Comparison between Cervical Spine Lateral and Whole-Spine Lateral Standing Radiographs
Authors: Park Moon Soo , Moon Seong-Hwan , Kim Tae-Hwan , Oh Jae Keun , Kang Hwa Jun , Riew K. Daniel
Published: June 2015

Study Design

Retrospective radiologic study.

Objective

The sagittal alignment of the cervical spine can be evaluated using either a lateral cervical radiograph or a whole-spine lateral view on which the cervical spine is included. To our knowledge, however, no report has compared the two. The purpose of this work is to identify the difference in radiographic parameters between the cervical spine lateral view and the whole-spine lateral view.

Methods

We retrospectively analyzed 59 adult patients suffering from neck pain with cervical spine lateral radiographs and whole-spine lateral radiographs from November 2007 to December 2011. The radiographs were measured using standard techniques to obtain the following parameters from the two different radiographs: occipital–C2 angle, C2–C7 angle, C7–sternal angle, sternal slope, T1 slope, C2 central offset distance, the distance between C2 and C7 plumb lines, C4 anteroposterior (AP) diameter, the ratio of C2 central off distance to C4 AP diameter, the ratio of plumb lines’ distance to C4 AP diameter.

Results

We found that the occipital–C2 angle, sternal slope, and C4 AP diameter were similar, but the C2–C7 angle, C7–sternal angle, T1 slope, C2 central offset distance, distance between C2 and C7 plumb lines, ratio of C2 central off distance to C4 AP diameter, and ratio of plumb lines’ distance to C4 AP diameter were different. However, the error of measurement was greater than the small angular and linear differences between the two views.

Conclusions

Most numerical values of the measured radiographic parameters appear to be different between the two views. However, the two views are comparable because the numerical differences were smaller than the errors of measurement.
Retirement patterns of Australian doctors aged 65 years and older
Authors: Joyce Catherine M. , Wang Wei C. , McDonald Hayley M.
Published: June 2015

Objective To investigate retirements over a 4-year period among Australian general practitioners (GPs) and specialists aged 65 years and over, and factors influencing retirement. Methods Data from Medicine in Australia: Balancing Employment and Life (MABEL) for the years 2009–12 were analysed for 435 GPs and 643 specialists aged 65 years and over at the time of entry to the MABEL survey. Discrete time survival analysis was used. Results The retirement rates were 4.1% (2009), 5.1% (2010), 4.2% (2011) and 10.4% (2012). Retirement was associated with: (1) the intention to leave medical work in 2009 and 2010; (2) working fewer hours in private consulting rooms in 2010 and 2012; (3) having lower job satisfaction in 2009 and 2011; (4) being older in 2009; (5) working fewer hours in a public hospital in 2012; and (6) working fewer hours in a private hospital in 2010. Doctors who intended to reduce their working hours were less likely to retire in 2009. Conclusions Strategies to support doctors at the late career stage to provide their valued contributions to the medical workforce for as long as possible may include increasing job satisfaction and addressing barriers to reducing work hours. What is known about the topic? Much of the available literature provides measures of retirement intentions. What does this paper add? The present study examined actual retirements and the factors associated with them. What are the implications for practitioners? Consideration should be given by policy makers to ensure that doctors are retained for as long as possible as active contributors to the medical workforce in a safe, appropriate manner.
What a great idea! Someone should evaluate that...
Authors: Schmidt David D.
Published: June 2015

How often, as clinicians, do we see a really clever idea implemented in the workplace? In rural health in particular, creative work-around solutions are relatively commonplace. However, the evaluation and promotion of these ideas is less so, and this leads to lost opportunities for perpetuating these clever ideas. This paper explores one rural clinician’s experience of what can happen if, instead of appreciating and complementing a great idea, that step of evaluating the great idea is taken. A reflective narrative was created, beginning with a corridor conversation (‘What a great idea! Someone should evaluate that…’), continuing through a formal research project and ending with the impact of that project and the way its findings were communicated and implemented. The narrative outlines the effect of evaluating one great idea at the individual, workplace, organisational, state and national levels. Clinicians are well placed to identify great ideas in practice. Making the decision to evaluate these ideas can lead to personal growth, professional discovery and organisational benefits. With motivation and organisational support, who knows where evaluation may lead?
Potential economic impact on hospitalisations of the Palliative Care Clinical Studies Collaborative (PaCCSC) ketamine randomised controlled trial
Authors: McCaffrey Nikki , Hardy Janet , Fazekas Belinda , Agar Meera , Devilee Linda , Rowett Debra , Currow David
Published: June 2015

Objective The aim of the present study was to estimate the potential healthcare cost savings associated with reduced prescribing of subcutaneous ketamine for the treatment of chronic cancer pain after publication of the Palliative Care Clinical Studies Collaborative (PaCCSC) ketamine randomised controlled trial (RCT), to provide further reasons to modify ketamine prescribing practice in this setting. Methods Potential cost savings in this setting were estimated from a health system perspective using a 1-year impact model. The model was populated with estimates derived using an epidemiological approach informed by morbidity and prevalence data, the PaCCSC feasibility study, ketamine RCT and national ketamine utilisation survey results, as well as clinical opinion. Results The total estimated annual hospitalisation costs associated with subcutaneous ketamine prescribing were A$3 899 600 (2605 bed-days). A 17% reduction in ketamine prescribing lowered hospitalisation costs to A$3 236 668 (2162 bed-days), a reduction of A$662 932 (443 bed-days) because of reduced in-patient stays associated with ketamine toxicity and prescribing process. Conclusions The findings from the modelled impact analysis suggest that dissemination of the PaCCSC ketamine RCT results may have saved the Australian healthcare system approximately A$663 000 in annual hospitalisation costs and freed up 443 in-patient bed-days, although there was high uncertainty within the study. Wider dissemination over time and targeted, local de-adoption strategies could result in further savings.
A new simple method for estimating the pork carcass mass of primal cuts and lean meat content of the carcass
Authors: Lisiak Dariusz , Duziński Kamil , Janiszewski Piotr , Borzuta Karol , Knecht Damian
Published: June 2015

The aim of this study was to develop regression equations for estimating lean meat content and the mass of primal cuts (ham, loin, shoulder, belly) based on selected linear measurements. The experiment involved a classification of 141 pigs from the Polish commercial pig population, with hot carcass weight ranging between 60 and 120 kg. The study population was characterised by high variability in terms of analysed measurements. Eight measurements were made including: mass of half-carcass, backfat thickness at different points (over shoulder, over last rib, over the middle of M. gluteus medius), width and thickness of the M. longissimus dorsi measured over the last rib, thickness of the lumbar and the gluteal muscle layer located between the spinal cord and beginning of the M. gluteus medius and waist width – the width of the carcass measured at the narrowest point of the lumbar. A subjective five-point scale was used to score difficulties in obtaining linear measurements (workload rate). The lean meat percentage and mass of cuts were determined by dissection. The study enabled equations to be devised for estimating lean meat content with an accuracy greater than most devices used for carcass classification (estimation error 1.67). Regression coefficients for the mass of primal cuts were: 0.92 for ham, 0.87 for loin, 0.87 for shoulder, and 0.74 for belly. The error of equations used to estimate the mass of primal cuts were: 391 g for ham, 447 g for loin, 263 g for shoulder and 257 g for belly. The workload rate for all the developed regression equations ranged from 1.3 to 1.6 points. The outcome of this study was the development of equations to predict carcass value without the need to use expensive classification equipment.
Alkali Metal Hydride Complexes: Well-Defined Molecular Species of Saline Hydrides
Authors: Fohlmeister Lea , Stasch Andreas
Published: June 2015

The first examples of well-defined alkali metal hydride complexes have been synthesised and characterised in recent years, and their properties and underlying principles for their generation and stabilisation are emerging. This article gives an account of the hydrides of the alkali metals (Group 1 metals) and selected ‘-ate’ complexes containing hydrides and alkali metals, and reviews the chemistry of well-defined alkali metal hydride complexes including their syntheses, structures, and characteristics. The properties of the alkali metal hydrides LiH, NaH, KH, RbH, and CsH are dominated by their ionic NaCl structure. Stable, soluble, and well-defined LiH and NaH complexes have been obtained by metathesis and β-hydride elimination reactions that require suitable ligands with some steric bulk and the ability to coordinate to several metal ions. These novel hydride complexes reward with higher reactivity and different properties compared with their parent ionic solids.
Yield gain due to fungicide application in varieties of winter wheat (Triticum aestivum) resistant and susceptible to leaf rust
Authors: Morgounov Alex , Akin Beyhan , Demir Lütfi , Keser Mesut , Kokhmetova Alma , Martynov Sergey , Orhan Şinasi , Özdemir Fatih , Özseven Ïzzet , Sapakhova Zagipa , Yessimbekova Minura
Published: June 2015

In three independent experiments in Turkey and Kazakhstan, winter wheat germplasm with variable degrees of resistance to leaf rust was subjected to fungicide protection. The yield loss of genotypes susceptible to leaf rust varied from 30% to 60% depending on the environment and severity of infection. Genotypes completely or moderately resistant to leaf rust also responded positively to fungicide protection, with average yield increases in the range 10–30%. This increase was observed even in one season without leaf rust infection. The main character affected by fungicide was 1000-kernel weight. There was stable expression of the magnitude of yield gain in resistant genotypes in different seasons, confirming genetic variation for this trait. Possible mechanisms of yield gain from fungicide protection in resistant genotypes are related to a positive physiological effect of the chemical used as well as a possible ‘cost of resistance’ to wheat plants. The magnitude of yield gain by resistant germplasm justifies its capture in breeding programs to develop varieties resistant to diseases and with greater benefits from the fungicide protection.
Role of arbuscular mycorrhizal symbiosis in phosphorus-uptake efficiency and aluminium tolerance in barley growing in acid soils
Authors: Seguel Alex , Barea José Miguel , Cornejo Pablo , Borie Fernando
Published: June 2015

Arbuscular mycorrhizal fungi (AMF) play an important role in protecting plant growth against such stresses as phytotoxic aluminium (Al) in soil. To understand some of the AMF interactions that relate to amelioration of Al phytotoxicity and phosphorus (P)-uptake efficiency in barley (Hordeum vulgare L.), this study examined the effect of soil Al levels and mycorrhizal symbiosis on plant response, including root colonisation, AMF propagules and glomalin production. A greenhouse experiment was conducted using two native barley cultivars, Sebastián and Aurora, grown in an acidic soil at two Al-saturation levels (80% Al-sat, unlimed soil; 7% Al-sat, limed soil) with and without AMF propagules. Root dry weight, total and colonised root lengths, and root P and Al contents were determined at 60 and 150 days after sowing. AMF spore density, total hyphal length, glomalin-related soil protein (GRSP) and Al bound to GRSP (Al-GRSP) were analysed at final harvest. AM root colonisation was not inhibited in limed soil, mycorrhizal propagule numbers increased at high Al levels, and Al-GRSP ranged from 5.6% to 8.3% of the total GRSP weight. These values also increased in unlimed soil, particularly those associated with cv. Aurora. Root Al concentration correlated inversely with AMF spores (r = –0.85, P < 0.001) and Al-GRSP (r = –0.72, P < 0.01), but only in plants growing in limed soil. Conversely, the AMF treatments in which Al was present showed a greater relationship between total root length and both root Al (r = –0.72, P < 0.01) and root P (r = 0.66, P < 0.01) concentrations. Sebastián showed a greater response to lime, whereas Aurora responded better to mycorrhizal presence. The relative growth rate of roots, P uptake efficiency and mycorrhizal parameters such as root colonisation, spores, hyphae and GRSP showed Aurora to be more Al-tolerant than Sebastián. In conclusion, the greater rate of increase of AM propagules, GRSP and Al-GRSP associated with cv. Aurora supports the hypothesis that AMF play an important role in the Al-tolerance capacity and P-uptake efficiency of H. vulgare growing in soils with high Al levels.
Online self-management for gay men living with HIV: a pilot study
Authors: Millard Tanya , McDonald Karalyn , Girdler Sonya , Slavin Sean , Elliot Julian
Published: June 2015

Background
The aim of this pilot study was to assess the feasibility, acceptability and effectiveness of Positive Outlook, an online self-management program for gay men living with HIV in Australia. Methods: Two pilot studies were conducted, a small feasibility study (Pilot 1) followed by a pilot randomised controlled study (Pilot 2). Pilot 1 employed a pre and post-test design and included 10 men. Within- and between-group differences were evaluated in Pilot 2, which involved 37 participants randomly assigned to receive the Positive Outlook Program or usual care. We report on feasibility, acceptability and a range of preliminary efficacy outcomes, including health education impact, HIV-related quality of life and HIV-related self-efficacy. Results: The program was well accepted by participants with some decline in engagement with the discussion boards witnessed over the duration of the program. Overall, intervention group participants demonstrated improvements in the majority of efficacy outcome measures, including HIV-related quality of life, self-efficacy, self-management skills, social support and adjustment to HIV. Conclusion: These pilot studies demonstrated that an online program to facilitate self-management among gay men living with HIV is both feasible and well accepted by participants who persisted with the program per protocol. Preliminary data suggest that the Positive Outlook program has the potential to enhance participants’ quality of life, self-efficacy and health related outcomes, and demonstrates the need for further study with a larger sample.
A second peak in genital warts in later life suggests that behavioural factors explain a second peak in human papillomavirus prevalence in older women
Authors: Chow Eric P. F. , Fairley Christopher K.
Published: June 2015

An age-based pattern of human papillomavirus (HPV) was observed among unvaccinated women in Australia, with a second peak occurring when women were in their early 50s. A similar age-based pattern for genital warts was also observed among unvaccinated Australian women, with the first peak (8.4%) occurring at age 15–20 years, which then declined gradually to 4.8% when women were aged 41–45 years; this then increased to 5.4% when women were aged 46–50 years. This data suggests that behavioural factors may explain the changes in HPV occurrence.
Relationships between fire danger and the daily number and daily growth of active incidents burning in the northern Rocky Mountains, USA
Authors: Freeborn Patrick H. , Cochrane Mark A. , Jolly W. Matt
Published: June 2015

Daily National Fire Danger Rating System (NFDRS) indices are typically associated with the number and final size of newly discovered fires, or averaged over time and associated with the likelihood and total burned area of large fires. Herein we used a decade (2003–12) of NFDRS indices and US Forest Service (USFS) fire reports to examine daily relationships between fire danger and the number and growth rate of wildfires burning within a single predictive service area (PSA) in the Northern Rockies, USA. Results demonstrate that daily associations can be used to: (1) extend the utility of the NFDRS beyond the discovery date of new fires; (2) examine and justify the temporal window within which daily fire danger indices are averaged and related to total burned area; (3) quantify the probability of managing an active incident as a function of fire danger; and (4) quantify the magnitude and variability of daily fire growth as a function of fire danger. The methods herein can be extended to other areas with a daily history of weather and fire records, and can be used to better inform fire management decisions or to compare regional responses of daily fire activity to changes in fire danger.
The Effect of the Fresh Fruit and Vegetable Program on Childhood Obesity
Authors: Qian Yiwei , Nayga Rodolfo M. , Thomsen Michael R. , Rouse Heather L.
Published: June 2015

This paper investigates how the Fresh Fruit and Vegetable Program (FFVP), a nutrition assistance program that provides funding for the distribution of free fresh fruits and vegetables to students in participating schools, affects childhood obesity using a panel data set of Arkansas public schoolchildren with two different approaches. First, we combine matching methodology and difference‐in‐differences (DID) analysis. Second, we use the synthetic control method to compare each FFVP participating school to a similar, albeit synthetic, control school. Both analyses show that FFVP program causes an economically meaningful reduction in the obesity outcome of participating children.
GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications
Authors: Laird Matthew R. , Langille Morgan G.I. , Brinkman Fiona S.L.
Published: June 2015

Motivation: A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations.

Results: GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general.

Availability and implementation: GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/.

Contact:  brinkman@sfu.ca
An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics
Authors: Lan Shiwei , Palacios Julia A. , Karcher Michael , Minin Vladimir N. , Shahbaba Babak
Published: June 2015

Motivation: The field of phylodynamics focuses on the problem of reconstructing population size dynamics over time using current genetic samples taken from the population of interest. This technique has been extensively used in many areas of biology but is particularly useful for studying the spread of quickly evolving infectious diseases agents, e.g. influenza virus. Phylodynamic inference uses a coalescent model that defines a probability density for the genealogy of randomly sampled individuals from the population. When we assume that such a genealogy is known, the coalescent model, equipped with a Gaussian process prior on population size trajectory, allows for nonparametric Bayesian estimation of population size dynamics. Although this approach is quite powerful, large datasets collected during infectious disease surveillance challenge the state-of-the-art of Bayesian phylodynamics and demand inferential methods with relatively low computational cost.

Results: To satisfy this demand, we provide a computationally efficient Bayesian inference framework based on Hamiltonian Monte Carlo for coalescent process models. Moreover, we show that by splitting the Hamiltonian function, we can further improve the efficiency of this approach. Using several simulated and real datasets, we show that our method provides accurate estimates of population size dynamics and is substantially faster than alternative methods based on elliptical slice sampler and Metropolis-adjusted Langevin algorithm.

Availability and implementation: The R code for all simulation studies and real data analysis conducted in this article are publicly available at http://www.ics.uci.edu/∼slan/lanzi/CODES.html and in the R package phylodyn available at https://github.com/mdkarcher/phylodyn.

Contact:  S.Lan@warwick.ac.uk or babaks@uci.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Chimira: analysis of small RNA sequencing data and microRNA modifications
Authors: Vitsios Dimitrios M. , Enright Anton J.
Published: June 2015

Summary: Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3′-modifications (e.g. uridylation, adenylation), 5′-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface.

Availability and implementation: Chimira has been developed as a web application and it is accessible here: http://www.ebi.ac.uk/research/enright/software/chimira.

Contact:  aje@ebi.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
LFQC: a lossless compression algorithm for FASTQ files
Authors: Nicolae Marius , Pathak Sudipta , Rajasekaran Sanguthevar
Published: June 2015

Motivation: Next Generation Sequencing (NGS) technologies have revolutionized genomic research by reducing the cost of whole genome sequencing. One of the biggest challenges posed by modern sequencing technology is economic storage of NGS data. Storing raw data is infeasible because of its enormous size and high redundancy. In this article, we address the problem of storage and transmission of large FASTQ files using innovative compression techniques.

Results: We introduce a new lossless non-reference based FASTQ compression algorithm named Lossless FASTQ Compressor. We have compared our algorithm with other state of the art big data compression algorithms namely gzip, bzip2, fastqz (Bonfield and Mahoney, 2013), fqzcomp (Bonfield and Mahoney, 2013), Quip (Jones et al., 2012), DSRC2 (Roguski and Deorowicz, 2014). This comparison reveals that our algorithm achieves better compression ratios on LS454 and SOLiD datasets.

Availability and implementation: The implementations are freely available for non-commercial purposes. They can be downloaded from http://engr.uconn.edu/rajasek/lfqc-v1.1.zip.

Contact:  rajasek@engr.uconn.edu
Characterization of Dietary Fiber Polysaccharides from Dehulled Common Buckwheat (Fagopyrum esculentum) Seeds
Authors: Wefers Daniel , Bunzel Mirko
Published: June 2015

Buckwheat is a pseudocereal that has gained increasing interest of industry and consumers over the past decade. Little, however, is known about its dietary fiber composition and nonstarch polysaccharide structures. Analysis of the monosaccharide composition indicated large amounts of pectic polysaccharides in both insoluble and soluble fiber from buckwheat. Methylation analysis gave further insights into the structures of the polysaccharides. The corresponding partially methylated alditol acetates suggested only low amounts of galactans. Xyloglucans were the main hemicellulosic polysaccharides in the insoluble fiber fraction. Highly branched arabinans, exclusively substituted at position O3, were of higher abundance. These results were confirmed by screening endo‐arabinanase and endo‐galactanase liberated oligosaccharides with high‐performance anion‐exchange chromatography with pulsed amperometric detection and LC‐MS2. Application of this method also demonstrated highly branched arabinan areas within the pectic polysaccharides. Only low amounts of fiber associated hydroxycinnamic acids and diferulic acids were liberated by alkaline treatment, and no evidence was found for their attachment to polysaccharides, suggesting only a minor impact of these structural elements on fiber structures in dehulled buckwheat seeds.
First Report of Pythium spinosum as a Pathogen of Watermelon and in Association with a Dieback of Watermelon in Southwest Florida
Authors: Hendricks K. E. , Roberts P. D.
Published: June 2015

The objective of the study was to elucidate the identity of pathogens associated with a dieback of mature watermelon vines in Southwest Florida. This is the first report of Pythium spinosum associated with dieback of watermelon in Southwest Florida.

Accepted for publication 23 March 2015. Published 1 May 2015.
Identification of Races of Colletotrichum orbiculare on Muskmelon in South Carolina
Authors: Keinath Anthony P.
Published: June 2015

Anthracnose caused by the fungus Colletotrichum orbiculare was observed on commercial cantaloupe grown in South Carolina for the first time in decades. Isolates from leaves were inoculated onto standard differential cultivars, and races 1, 2, and 2B were identified. This is the first report of C. orbiculare race 2B from South Carolina.

Accepted for publication 27 March 2015. Published 1 May 2015.
First Report of Phytophthora Fruit Rot on Bitter Gourd (Mormodica charantia) and Sponge Gourd (Luffa cylindrica) Caused by Phytophthora capsici
Authors: Kousik Chandrasekar S. , Parada Camilo , Quesada-Ocampo Lina
Published: June 2015

Luffa sponge (smooth gourd) and bitter gourds (bitter melon) are specialty vegetables grown in the U.S. on a small scale for select markets. Luffa gourds are also grown for sponges. In Sept. 2014, heavy rainfall resulted in rot of >50% of bitter gourd and >25% on sponge gourd in a field in Charleston, SC. The microbe causing the fruit rot was identified using microscopy and molecular tools. Prior to this study it was not known if this microbe could cause fruit rot of bitter gourd. This knowledge will be useful to suggest management strategies.

Accepted for publication 17 March 2015. Published 6 May 2015.
Monitoring of a Single Point Mutation in the PvCesA3 Allele Conferring Resistance to Carboxylic Acid Amide Fungicides in Plasmopara viticola Populations In Yamanashi Prefecture, Japan
Authors: Aoki Yoshinao , Kawagoe Yumi , Fujimori Nozomi , Tanaka Sayumi , Suzuki Shunji
Published: June 2015

The use of the carboxylic acid amide (CAA) fungicide mandipropamid to manage grapevine downy mildew in vineyards in Japan has been increasing since 2010, because of widespread quinone outside inhibitor fungicide resistance in the Plasmopara viticola population. However, CAA fungicide resistance in P. viticola is becoming a serious problem worldwide. In 2013, we monitored for the presence of a single point mutation at codon 1105 of the cellulose synthase gene PvCesA3, which confers resistance to mandipropamid in P. viticola samples collected from four vineyards in Yamanashi prefecture in Japan. Five out of 157 samples were found to be heterozygotes, carrying both the mutated and nonmutated PvCesA3 alleles. Although CAA fungicide-resistant P. viticola isolates have not been reported yet in Japan, the emergence of heterozygous P. viticola populations indicates the potential risk of emergence of resistant homozygotes.

Accepted for publication 14 March 2015. Published 1 May 2015
Decision Models for Fungicide Applications for Soybean Rust
Authors: Kelly Heather M. , Wright David L. , Dufault Nicholas S. , Marois James J.
Published: June 2015

Soybean rust (SBR), caused by Phakopsora pachyrhizi, can be a devastating disease to southeastern U.S. soybean (Glycine max) production. Fungicides can be applied to avoid yield loss, but growers need to know when an application will be most beneficial. To better understand and manage SBR epidemics in the southeastern U.S., fungicide application decision models were developed and validated. Application decision models were developed based on SBR presence and hours of leaf wetness or amount of cumulative rain and compared to non-treated controls and applications based on crop growth stage. The models were evaluated in 2009, 2010, and 2011. High disease pressure and conducive weather conditions in 2009 resulted in significantly greater disease severity and lower yields in non-treated plots compared to treated plots. In 2010 and 2011, low disease pressure and drought conditions resulted in no significant differences in disease severity or yields among most treatments. Results indicate two fungicide applications during early reproductive stage can reduce yield loss due to SBR, but subsequent applications need to be determined based on disease pressure, weather conditions, and crop growth stage.

Accepted for publication 1 March 2015. Published 1 May 2015.
U-shaped Osteotomy Around the Descending Palatine Artery to Prevent Posterior Osseous Interference for Superior/Posterior Repositioning of the Maxilla in Le Fort I Osteotomy
Authors: Omura Susumu , Iwai Toshinori , Honda Koji , Shibutani Naoki , Fujita Koichi , Yamashita Yosuke , Takasu Hikaru , Murata Shogo , Tohnai Iwai
Published: June 2015

In maxillary orthognathic surgery, superior repositioning of the maxilla is sometimes difficult, and removal of bony interference, especially around the descending palatine artery (DPA), is very time-consuming in cases of severe maxillary impaction. Posterior repositioning of the maxilla for removal of bony interference between the posterior maxilla and the pterygoid process is also technically difficult. Because the most common site of hemorrhage in Le Fort I osteotomy is the posterior maxilla, this bone removal is a source of frustration for surgeons in DPA injury. When the DPA is injured during bone removal and ligation is performed, aseptic necrosis of the maxilla may occur. Therefore, a simple and safe method for maxillary superior/posterior repositioning is required to remove osseous interference around the DPA. The authors describe here U-shaped osteotomy around the DPA to prevent posterior osseous interference for superior/posterior repositioning of the maxilla in Le Fort I osteotomy.