bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimal microwave absorption of hierarchical cobalt dendrites enhanced by multiple dielectric and magnetic resonance
Authors: Wen S. L. , Liu Y. , Zhao X. C. , Cheng J. W.
Published: August 2014

In this paper, we reported the microwave performance of three-dimensional hierarchical cobalt dendrites dispersed in the paraffin matrix (70 wt. %) in the frequency range of 2–18 GHz. The cobalt dendrites presented multiple dielectric relaxation and magnetic resonances, contributing to broaden the microwave absorption bandwidth. The calculated reflection loss shows that the cobalt dendrites have optimal microwave absorption. The maximum reflection loss reaches −58.60 dB at 13.75 GHz with a matching thickness of 1.4 mm. Meanwhile, an effective absorption bandwidth of 5.03 GHz from 11.34 to 16.37 GHz was obtained, possessing a better microwave absorption than earlier reported materials. The cobalt dendrites have potential application as candidate for microwave absorption.
Influence of magnetic electrodes thicknesses on the transport properties of magnetic tunnel junctions with perpendicular anisotropy
Authors: Cuchet Léa , Rodmacq Bernard , Auffret Stéphane , Sousa Ricardo C. , Dieny Bernard
Published: August 2014

The influence of the bottom and top magnetic electrodes thicknesses on both perpendicular anisotropy and transport properties is studied in (Co/Pt)/Ta/CoFeB/MgO/FeCoB/Ta magnetic tunnel junctions. By carefully investigating the relative magnetic moment of the two electrodes as a function of their thicknesses, we identify and quantify the presence of magnetically dead layers, likely localized at the interfaces with Ta, that is, 0.33 nm for the bottom electrode and 0.60 nm for the top one. Critical thicknesses (spin-reorientation transitions) are determined as 1.60 and 1.65 nm for bottom and top electrodes, respectively. The tunnel magnetoresistance ratio reaches its maximum value, as soon as both effective (corrected from dead layer) electrode thicknesses exceed 0.6 nm.
Graphene spin diode: Strain-modulated spin rectification
Authors: Wang Yunhua , Liu Yulan , Wang B.
Published: August 2014

Strain effects on spin transport in a ferromagnetic/strained/normal graphene junction are explored theoretically. It is shown that the spin-resolved Fermi energy range can be controlled by the armchair direction strain because the strain-induced pseudomagnetic field suppresses the current. The spin rectification effect for the bias reversal occurs because of a combination of ferromagnetic exchange splitting and the broken spatial symmetry of the junction. In addition, the spin rectification performance can be tuned remarkably by manipulation of the strains. In view of this strain-modulated spin rectification effect, we propose that the graphene-based ferromagnetic/strained/normal junction can be used as a tunable spin diode.
Mechanical annealing in the flow of supercooled metallic liquid
Authors: Zhang Meng , Dai Lan Hong , Liu Lin
Published: August 2014

Flow induced structural evolution in a supercooled metallic liquid Vit106a (Zr58.5Cu15.6Al10.3Ni12.8Nb2.8, at. %) was investigated via uni-axial compression combined with differential scanning calorimeter (DSC). Compression tests at strain rates covering the transition from Newtonian flow to non-Newtonian flow and at the same strain rate 2 × 10−1 s−1 to different strains were performed at the end of glass transition (Tg-end = 703 K). The relaxation enthalpies measured by DSC indicate that the samples underwent non-Newtonian flow contain more free volume than the thermally annealed sample (703 K, 4 min), while the samples underwent Newtonian flow contain less, namely, the free volume of supercooled metallic liquids increases in non-Newtonian flow, while decreases in Newtonian flow. The oscillated variation of the relaxation enthalpies of the samples deformed at the same strain rate 2 × 10−1 s−1 to different strains confirms that the decrease of free volume was caused by flow stress, i.e., “mechanical annealing.” Micro-hardness tests were also performed to show a similar structural evolution tendency. Based on the obtained results, the stress-temperature scaling in the glass transition of metallic glasses are supported experimentally, as stress plays a role similar to temperature in the creation and annihilation of free volume. In addition, a widening perspective angle on the glass transition of metallic glasses by exploring the 3-dimensional stress-temperature-enthalpy phase diagram is presented. The implications of the observed mechanical annealing effect on the amorphous structure and the work-hardening mechanism of metallic glasses are elucidated based on atomic level stress model.
Correlation of photothermal conversion on the photo-induced deformation of amorphous carbon nitride films prepared by reactive sputtering
Authors: Harata T. , Aono M. , Kitazawa N. , Watanabe Y.
Published: August 2014

The photo-induced deformation of hydrogen-free amorphous carbon nitride (a-CNx) films was investigated under visible-light illumination. The films gave rise to photothermal conversion by irradiation. In this study, we investigated the effects of thermal energy generated by irradiation on the deformation of a-CNx/ultrathin substrate bimorph specimens. The films were prepared on both ultrathin Si and SiO2 substrates by reactive radio-frequency magnetron sputtering from a graphite target in the presence of pure nitrogen gas. The temperature of the film on the SiO2 substrate increased as the optical band-gap of the a-CNx was decreased. For the film on Si, the temperature remained constant. The deformation degree of the films on Si and SiO2 substrates were approximately the same. Thus, the deformation of a-CNx films primarily induced by photon energy directly.
Optical waveguiding properties into porous gallium nitride structures investigated by prism coupling technique
Authors: Alshehri Bandar , Lee Seung-Min , Kang Jin-Ho , Gong Su-Hyun , Ryu Sang-Wan , Cho Yong-Hoon , Dogheche Elhadj
Published: August 2014

In order to modulate the refractive index and the birefringence of Gallium Nitride (GaN), we have developed a chemical etching method to perform porous structures. The aim of this research is to demonstrate that optical properties of GaN can be tuned by controlling the pores density. GaN films are prepared on sapphire by metal organic chemical vapor deposition and the microstructure is characterized by transmission electron microscopy, and scanning electron microscope analysis. Optical waveguide experiment is demonstrated here to determine the key properties as the ordinary (n0) and extraordinary (ne) refractive indices of etched structures. We report here the dispersion of refractive index for porous GaN and compare it to the bulk material. We observe that the refractive index decreases when the porous density p is increased: results obtained at 0.975 μm have shown that the ordinary index n0 is 2.293 for a bulk layer and n0 is 2.285 for a pores density of 20%. This value corresponds to GaN layer with a pore size of 30 nm and inter-distance of 100 nm. The control of the refractive index into GaN is therefore fundamental for the design of active and passive optical devices.
Ferroelectric field-effect transistors based on multi-walled carbon nanotube micron-wide stripe arrays
Authors: Song H. J. , Liu P. P. , Zhong X. L. , Li B. , Chen T. , Wang F. , Wang J. B. , Zhou Y. C.
Published: August 2014

Ferroelectric field-effect transistors (FeFETs) with multiwall carbon nanotube (MWCNT) micron-wide stripe arrays as channel and (Bi,Nd)4Ti3O12 films as insulator were developed and fabricated. The prepared stripe arrays MWCNT-FeFETs possess excellent properties such as large “on” current, high Ion/Ioff ratio, high channel carrier mobility, and wide memory window. These good performances are mainly attributed to the use of the MWCNT micron-wide stripe arrays channel. The spaces between MWCNT stripes can inhibit the function of the mixed metallic nanotubes in MWCNTs and, thus, improve the semiconductor property of channel layer, and sequentially improve the Ion/Ioff ratio. In addition, the stripe arrays and CNTs within stripes have very high density; therefore, the metallic nanotubes within stripes can transfer many carriers and, thereby, display large “on” current and high channel carrier mobility.
Alternative process for thin layer etching: Application to nitride spacer etching stopping on silicon germanium
Authors: Posseme N. , Pollet O. , Barnola S.
Published: August 2014

Silicon nitride spacer etching realization is considered today as one of the most challenging of the etch process for the new devices realization. For this step, the atomic etch precision to stop on silicon or silicon germanium with a perfect anisotropy (no foot formation) is required. The situation is that none of the current plasma technologies can meet all these requirements. To overcome these issues and meet the highly complex requirements imposed by device fabrication processes, we recently proposed an alternative etching process to the current plasma etch chemistries. This process is based on thin film modification by light ions implantation followed by a selective removal of the modified layer with respect to the non-modified material. In this Letter, we demonstrate the benefit of this alternative etch method in term of film damage control (silicon germanium recess obtained is less than 6 A), anisotropy (no foot formation), and its compatibility with other integration steps like epitaxial. The etch mechanisms of this approach are also addressed.
Alignment of the diamond nitrogen vacancy center by strain engineering
Authors: Karin Todd , Dunham Scott , Fu Kai-Mei
Published: August 2014

The nitrogen vacancy (NV) center in diamond is a sensitive probe of magnetic field and a promising qubit candidate for quantum information processing. The performance of many NV-based devices improves by aligning the NV(s) parallel to a single crystallographic direction. Using ab initio theoretical techniques, we show that NV orientation can be controlled by high-temperature annealing in the presence of strain under currently accessible experimental conditions. We find that (89 ± 7)% of NVs align along the [111] crystallographic direction under 2% compressive biaxial strain (perpendicular to [111]) and an annealing temperature of 970 °C.
Wideband plasmonic focusing metasurfaces
Authors: Saeidi Chiya , Weide Daniel van der
Published: August 2014

We present a technique for designing wideband focusing metasurfaces. The proposed metasurface consists of unit cells of nanoparticle-based spatial phase shifters distributed over a planar surface. The topology of each spatial phase shifter is based on the design of plasmonic frequency selective surfaces. A true ab-initio design procedure for the proposed reflectarray is also proposed for the desired bandwidth and center frequency. A reflectarray for focusing the entire red spectrum (75 nm) is designed, with full-wave simulation results demonstrating desired focusing.
Optimization of indirect magnetoelectric effect in thin-film/substrate/piezoelectric-actuator heterostructure using polymer substrate
Authors: Gueye Mouhamadou , Zighem Fatih , Faurie Damien , Belmeguenai Mohamed , Mercone Silvana
Published: August 2014

Indirect magnetoelectric effect has been studied in magnetostrictive-film/substrate/piezoelectric-actuator heterostructures. Two different substrates have been employed: a flexible substrate (Young's modulus of 4 GPa) and a rigid one (Young's modulus of 180 GPa). A clear optimization of the indirect magnetoelectric coupling, studied by micro-strip ferromagnetic resonance, has been highlighted when using the polymer substrate. However, in contrast to the rigid substrate, the flexible substrate also leads to an a priori undesirable and huge uniaxial anisotropy which seems to be related to a nonequibiaxial residual stress inside the magnetostrictive film. The “strong” amplitude of this nonequibiaxiallity is due to the large Young's modulus mismatch between the polymer and the magnetostrictive film which leads to a slight curvature along a given direction during the elaboration process and thus to a large magnetoelastic anisotropy.
Volume and surface propellant heating in an electrothermal radio-frequency plasma micro-thruster
Authors: Greig A. , Charles C. , Paulin N. , Boswell R. W.
Published: August 2014

The temporal evolution of neutral gas temperature over the first 5 min of operation for an electrothermal radio-frequency micro-thruster with nitrogen (N2) propellant was measured using rovibrational band matching of the second positive N2 system. Three distinct periods of gas heating were identified with time constants of τ1 = 8 × 10−5 s, τ2 = 8 s, and τ3 = 100 s. The fast heating (τ1) is attributed to volumetric heating processes within the discharge driven by ion-neutral collisions. The slow heating (τ3) is from ion neutralization and vibrational de-excitation on the walls creating wall heating. The intermediate heating mechanism (τ2) is yet to be fully identified although some theories are suggested.
Adaptation to Climate Change: Professional Networks and Reinforcing Institutional Environments
Authors: Hovik Sissel , Naustdalslid Jon , Reitan Marit , Muthanna Tone
Published: August 2014

The paper studies processes of adaptation to a changing climate in the water supply and wastewater sector in five Norwegian municipalities. Our case illustrates that the combination of characteristics of climate adaptation as a policy issue, institutional characteristics related to the vertical organization of the water sector in Norway, and characteristics of the professional network between local and national levels of governance seem to have been conducive to problem awareness and proactive approaches to problem solving. Our findings contradict the general picture drawn in the literature concluding that adaptation efforts are mainly reactive and internally related to the sector. We identify important mechanisms related to the production of policy solutions in governance networks mediating knowledge between different institutional levels. By these observations, the paper should contribute to the debate about the working of governance networks, and in particular to the knowledge about factors that are conducive to effective network governance.
Neglected Aspects of Regional Policy: A Retrospective View
Authors: Parr John B
Published: August 2014

The primary focus is on three aspects of regional policy that have tended to be taken for granted in the past. To set the discussion in context, several important background issues are examined. Of the three neglected aspects to be considered here, the first explores the bases or justifications for regional policy and the implications of these. Important in this connection are the possible trade-offs between efficiency and equity. A second aspect deals with the various modes of intervention in regional policy, and a distinction is drawn between direct or conventional regional policy and indirect regional policy, the latter not generally being thought of as regional in character. The third neglected aspect is concerned with the varying extent to which space is accorded an importance in regional policy. Attention is directed to a situation where the question of space has been given inadequate treatment, and also to a case where it has exerted a predominant influence. This leads on to a consideration of the ‘competition’ between space-based and space-neutral emphases of present development strategies, starting with the place prosperity versus people prosperity debate.
Chronic conditions, financial burden and pharmaceutical pricing: insights from Australian consumers
Authors: Whitty Jennifer A. , Sav Adem , Kelly Fiona , King Michelle A. , McMillan Sara S. , Kendall Elizabeth , Wheeler Amanda J.
Published: August 2014

Objective To explore the perceptions of Australian consumers and carers about the financial burden associated with medicines used for the treatment of chronic conditions. Method Semi-structured interviews were undertaken with individuals (n = 97) who identified as having a chronic condition(s) (n = 70), cared for someone with a chronic condition(s) (n = 8), or both (n = 19). Participants included individuals identifying with an Aboriginal or Torres Strait Islander (n = 23) or Culturally and Linguistically Diverse (n = 19) background. Data were analysed using the constant comparison method and reported thematically. Results Participants described substantial costs associated with medicines use, along with aggravating factors, including the duration and number of medicines used, loss of employment, lack of pricing consistency between pharmacies and the cost of dose administration aids. Consequences included impacts on medicine adherence, displacement of luxury items and potentially a reduced financial incentive to work. Understanding and beliefs related to pharmaceutical pricing policy varied and a range of proactive strategies to manage financial burden were described by some participants. Conclusions The financial burden associated with medicines used for the management of chronic conditions by Australian consumers is substantial. It is compounded by the ongoing need for multiple medicines and indirect effects associated with chronic conditions, such as the impact on employment. What is known about the topic? Medicines are a common form of treatment in chronic conditions. The financial burden related to medicines use, including co-payments, is associated with reduced adherence and other cost-coping strategies. Out of pocket costs for prescription medicines are relatively high in Australia compared with some other countries, including New Zealand and the United Kingdom. Australian consumers with chronic illness are likely to be at particular risk of financial burden associated with medicines use. What does this paper add? This paper explores the perceptions of consumers and carers around the financial burden associated with the use of medicines for the treatment of chronic conditions in Australia. It draws on the experiences and perceptions of a diverse group of consumers in Australia who identify as having, or caring for someone with, a chronic condition(s). What are the implications for practitioners? Health professionals who assist consumers to manage their medicines need to be aware of the potential for financial burden associated with medicines use and its potential impact on adherence. There is a need for health professionals to educate and assist consumers with chronic conditions to ensure they can navigate the health system to maximum benefit and receive financial entitlements for which they are eligible.
Effectiveness of 'rehabilitation in the home' service
Authors: Bharadwaj Sneha , Bruce David
Published: August 2014

Objectives Rehabilitation in the home (RITH) services increasingly provide hospital substitution services. This study examines clinical outcomes in a large metropolitan RITH service in Western Australia. Methods The 2010 database of Fremantle Hospital RITH service was interrogated to identify the clinical profile of cases, length of stay (LOS) and clinical outcomes. Negative outcomes included death or unexpected hospital readmission. Multiple logistic regression modelling was used to explore associations with negative outcomes. This study was reviewed by the Institutional Review Board which deemed it not to require ethics approval. Results There were 1348 cases managed by RITH: 70.6% were aged ≥ 65 years; elective joint replacement (29.7%), medical conditions (20%), stroke (13%), hip fractures (10%) were major contributors. The majority (93.3%) were discharged after a median of 9 days. Negative outcomes occurred in 90 cases (6.7%), including five deaths (0.4%) and 85 readmissions (6.3%). Independent associations with negative outcomes included older age (odds ratio (OR) (95% CI); 1.02, P = 0.006), orthopaedic conditions (OR 1.91, P = 0.004) and longer inpatient LOS (OR 1.96, P = 0.003). Age above 80 years was independently associated with risk of negative outcome (OR 2.99, P = 0.004). Conclusions RITH had a low rate of negative outcomes. The database proved useful for monitoring quality of service provision. What is known about the topic? Rehabilitation in the home environment has proven cost effective for multiple conditions, particularly stroke and elective joint surgery, among others, facilitating better quality of life, with reduced rates of delirium and mortality. Overall there are few negative outcomes and death is rare. What does this paper add? Although RITH services are widely utilised as bed substitution services, there is scant literature on clinical outcomes while within the service. This study focuses on frequency of good and poor clinical outcomes in a well-established RITH service in Western Australia, suggesting pattern recognition of an at-risk cohort by identifying potentially useful predictors of poor outcome. What are the implications for practitioners? RITH services are a safe alternative for many, including older people. Health administration databases are useful tools to monitor clinical outcomes. Clinical indicators such as older age, long hospital stay and orthopaedic diagnoses may be useful predictors of poor outcomes in such services.
The community network: an Aboriginal community football club bringing people together
Authors: Thorpe Alister , Anders Wendy , Rowley Kevin
Published: August 2014

There are few empirical studies about the role of Aboriginal sporting organisations in promoting wellbeing. The aim of the present study was to understand the impact of an Aboriginal community sporting team and its environment on the social, emotional and physical wellbeing of young Aboriginal men, and to identify barriers and motivators for participation. A literature review of the impact of sport on the health and wellbeing of Aboriginal participants was conducted. This informed a qualitative study design with a grounded theory approach. Four semistructured interviews and three focus groups were completed with nine current players and five past players of the Fitzroy Stars Football Club to collect data about the social, emotional and physical wellbeing impact of an Aboriginal football team on its Aboriginal players. Results of the interviews were consistent with the literature, with common concepts emerging around community connection, cultural values and identity, health, values, racism and discrimination. However, the interviews provided further detail around the significance of cultural values and community connection for Aboriginal people. The complex nature of social connections and the strength of Aboriginal community networks in sports settings were also evident. Social reasons were just as important as individual health reasons for participation. Social and community connection is an important mechanism for maintaining and strengthening cultural values and identity. Barriers and motivators for participation in Aboriginal sports teams can be complex and interrelated. Aboriginal sports teams have the potential to have a profound impact on the health of Aboriginal people, especially its players, by fostering a safe and culturally strengthening environment and encompassing a significant positive social hub for the Aboriginal community.
Energetically significant networks of coupled interactions within an unfolded protein
Authors: Cho Jae-Hyun , Meng Wenli , Sato Satoshi , Kim Eun Young , Schindelin Hermann , Raleigh Daniel P.
Published: August 2014

Significance

Unfolded and partially unfolded proteins participate in a wide range of biological processes from pathological aggregation to the regulation of normal cellular activity. Characterization of nonnative states is critical for the understanding of these processes, yet comparatively little is known about their energetics and their structural propensities under native conditions. We demonstrate that energetically important interactions, which involve multiple residues and which include significant nonnative effects, can form in the denatured state ensemble (DSE) of globular proteins, and can involve residues that are distant in sequence and spatially well separated in the native structure. Mutations that alter the energetics of the DSE can impact the analysis of cooperativity and folding, and could modulate the propensity to aggregate.
Assessment of Fat Reserves Adequacy in the First Migrant Silver American Eels of a Large-Scale Stocking Experiment
Authors: Couillard Catherine M. , Verreault Guy , Dumont Pierre , Stanley David , Threader Ron W.
Published: August 2014

An experimental stocking program in the St. Lawrence River–Lake Ontario system provided a unique opportunity to compare reproductive fitness of migrant silver American Eels Anguilla rostrata from the stocking program (SM) and wild migrants (WM), both of which were grown in the same location. Body size, muscle lipid stores, oocyte development, and morphometric indices of silvering were compared between SM and WM eels captured in the St. Lawrence River estuary. Migrant eels from the stocking program were smaller than wild migrants from the estuary, but their size was similar to migrating wild silver American Eels from their site of original capture on the Atlantic coast of New Brunswick and Nova Scotia. A bioenergetic model was used to estimate the costs of migration and reproduction and the duration of migration. The adequacy of the measured lipid reserves to meet these estimated energetic costs was assessed for SM and WM eels. Gonad maturation and stage of silvering for SM eels were less advanced than that for WM eels, and they had lower initial muscle fat reserves and higher estimated energetic requirements for migration as a consequence of their smaller size. It was estimated that 100% of the SM eels would not have adequate fat reserves for migration and reproduction, whereas 57% of the WM eels would have adequate reserves. Smaller-sized SM eels would take 1.6 times longer to reach the spawning grounds than WM eels and, thus, may not arrive in synchrony with these wild migrants. Thus, smaller-sized, out-migrating, stocked eels from the upper St. Lawrence River are less likely than wild migrants to complete successfully their migration and reproduction. These results support the recommendation to source and stock American Eels at sites where they have similar life strategies to increase the likelihood of successful silver eel escapement.

Received November 27, 2013; accepted April 9, 2014
Toward Enhancing 12-Step Facilitation among Young People: A Systematic Qualitative Investigation of Young Adults’ 12-Step Experiences
Authors: Labbe Allison K. , Slaymaker Valerie , Kelly John F.
Published: August 2014

Background

12-Step Facilitation (TSF) interventions designed to enhance rates of engagement with 12-step mutual-help organizations (MHOs) have shown efficacy among adults, but research provides little guidance on how to adapt TSF strategies for young people.

Methods

To inform TSF strategies for youth, this study used qualitative methods to investigate the self-reported experiences of 12-step participation, and reasons for nonattendance and discontinuation among young adults (18–24 years; N = 302). Responses to open-ended questions following residential treatment were coded into rationally derived domains.

Results

Young adults reported that cohesiveness, belonging, and instillation of hope were the most helpful aspects of attending 12-step groups; meeting structure and having to motivate oneself to attend meetings were the most common aspects young adults liked least; logistical barriers and low recovery motivation and interest were the most common reasons for discontinued attendance; and perceptions that one did not have a problem or needed treatment were cited most often as reasons for never attending.

Conclusions

Findings may inform and enhance strategies intended to engage young people with community-based recovery-focused 12-step MHOs and ultimately improve recovery outcomes.
Two-sided BGG resolutions of admissible representations
Authors: Arakawa Tomoyuki
Published: August 2014

We prove the conjecture of Frenkel, Kac and Wakimoto on the existence of two-sided BGG resolutions of

G
G

-integrable admissible representations of affine Kac-Moody algebras at fractional levels. As an application we establish the semi-infinite analogue of the generalized Borel-Weil theorem for minimal parabolic subalgebras which enables an inductive study of admissible representations.
BioTextQuest
+
: a knowledge integration platform for literature mining and concept discovery
Authors: Papanikolaou Nikolas , Pavlopoulos Georgios A. , Pafilis Evangelos , Theodosiou Theodosios , Schneider Reinhard , Satagopam Venkata P. , Ouzounis Christos A. , Eliopoulos Aristides G. , Promponas Vasilis J. , Iliopoulos Ioannis
Published: August 2014

Summary: The iterative process of finding relevant information in biomedical literature and performing bioinformatics analyses might result in an endless loop for an inexperienced user, considering the exponential growth of scientific corpora and the plethora of tools designed to mine PubMed ® and related biological databases. Herein, we describe BioTextQuest + , a web-based interactive knowledge exploration platform with significant advances to its predecessor (BioTextQuest), aiming to bridge processes such as bioentity recognition, functional annotation, document clustering and data integration towards literature mining and concept discovery. BioTextQuest + enables PubMed and OMIM querying, retrieval of abstracts related to a targeted request and optimal detection of genes, proteins, molecular functions, pathways and biological processes within the retrieved documents. The front-end interface facilitates the browsing of document clustering per subject, the analysis of term co-occurrence, the generation of tag clouds containing highly represented terms per cluster and at-a-glance popup windows with information about relevant genes and proteins. Moreover, to support experimental research, BioTextQuest + addresses integration of its primary functionality with biological repositories and software tools able to deliver further bioinformatics services. The Google-like interface extends beyond simple use by offering a range of advanced parameterization for expert users. We demonstrate the functionality of BioTextQuest + through several exemplary research scenarios including author disambiguation, functional term enrichment, knowledge acquisition and concept discovery linking major human diseases, such as obesity and ageing.

Availability: The service is accessible at http://bioinformatics.med.uoc.gr/biotextquest .

Contact:  g.pavlopoulos@gmail.com or georgios.pavlopoulos@esat.kuleuven.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers
Authors: Ohue Masahito , Shimoda Takehiro , Suzuki Shuji , Matsuzaki Yuri , Ishida Takashi , Akiyama Yutaka
Published: August 2014

Summary: The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of >97% strong scaling.

Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock .

Contact:  akiyama@cs.titech.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online
First Report of Rice stripe necrosis virus Infecting Rice in Burkina Faso
Authors: Sereme D. , Neya B. J. , Bangratz M. , Brugidou C. , Ouedraogo I.
Published: August 2014

Rice stripe necrosis virus (RSNV) was first described in 1977 as a new virus infecting rice in Cote d'Ivoire (3) and was subsequently observed in Liberia, Nigeria, and Sierra Leone (2). RSNV is a soil-borne virus transmitted by the fungus Polymyxa graminis (1) and belongs to the genus Benyvirus (4). During a survey carried out in April of 2013, severe symptoms characterized by seedling death, severe plant malformation, and foliar striping were observed on rice plants in an experimental field of INERA at Banfora located in western Burkina Faso. Disease incidence in the field was estimated to be 80 ± 5%. The symptoms of disease were successfully transmitted to the susceptible rice (Oryza sativa) cultivar IR64 by soil transmission experiments (1). RSNV was detected by ELISA using a polyclonal antiserum (1), kindly provided by Dr. Denis Fargette, IRD, Montpellier, France. Total nucleic acid was extracted with TRIzol reagent (Invitrogen) from IR64 and field infected samples. The presence of the virus was confirmed by RT-PCR using primers 5′-CATCTTGTCGAGATGAG-3′ and 5′-GCGTTGTCTTTATCAGTG-3′ for specific sequences flanking the RNA2 CP gene. The RT-PCR product was directly sequenced and the sequence was deposited in GenBank (Accession No. LK023710). Sequence analysis showed that the CP gene of the RSNV isolate from Burkina Faso shared the highest nucleotide sequence identity (97.6%) with the known RSNV CP gene sequence from the Colombian isolate (EU099845) available in GenBank, confirming the presence of RSNV in the rice crops in Burkina Faso. To our knowledge, this is the first confirmed report of RSNV in Burkina Faso. Further studies are needed to determine its incidence and spread in the country. Detection of RSNV in Burkina Faso signals the urgent need for adoption of appropriate measures to restrict the spread and impact of this virus within Africa.

References: (1) C. Fauquet and J. C. Thouvenel. Proc. Acad. Sci. Ser. D 296:575, 1983. (2) C. Fauquet et al. Develop. Appl. Biol. 2:71, 1988. (3) D. Louvel and J.-M. Bidaux. Agronomie Tropicale 32:257, 1977. (4) I. Lozano and F. Morales. Eur. J. Plant Pathol. 124:673, 2009.
Intraoperative Transitions of Anesthesia Care and Postoperative Adverse Outcomes
Authors: Saager Leif , Hesler Brian D. , You Jing , Turan Alparslan , Mascha Edward J. , Sessler Daniel I. , Kurz Andrea
Published: August 2014

Background:

Transfers of patient care and responsibility among caregivers, “handovers,” are common. Whether handovers worsen patient outcome remains unclear. The authors tested the hypothesis that intraoperative care transitions among anesthesia providers are associated with postoperative complications.

Methods:

From the records of 138,932 adult Cleveland Clinic (Cleveland, Ohio) surgical patients, the authors assessed the association between total number of anesthesia handovers during a case and an adjusted collapsed composite of in-hospital mortality and major morbidities using multivariable logistic regression.

Results:

Anesthesia care transitions were significantly associated with higher odds of experiencing any major in-hospital mortality/morbidity (incidence of 8.8, 11.6, 14.2, 17.0, and 21.2% for patients with 0, 1, 2, 3, and ≥4 transitions; odds ratio 1.08 [95% CI, 1.05 to 1.10] for an increase of 1 transition category, P < 0.001). Care transitions among attending anesthesiologists and residents or nurse anesthetists were similarly associated with harm (odds ratio 1.07 [98.3% CI, 1.03 to 1.12] for attending [incidence of 9.4, 13.9, 17.4, and 21.5% for patients with 0, 1, 2, and ≥3 transitions] and 1.07 [1.04 to 1.11] for residents or nurses [incidence of 9.4, 13.0, 15.4, and 21.2% for patients with 0, 1, 2, and ≥3 transitions], both P < 0.001). There was no difference between matched resident only (8.5%) and nurse anesthetist only (8.8%) cases on the collapsed composite outcome (odds ratio, 1.00 [98.3%, 0.93 to 1.07]; P = 0.92).

Conclusion:

Intraoperative anesthesia care transitions are strongly associated with worse outcomes, with a similar effect size for attendings, residents, and nurse anesthetists.
Insights into DNA hydroxymethylation in the honeybee from in-depth analyses of TET dioxygenase
Authors: Wojciechowski Marek , Rafalski Dominik , Kucharski Robert , Misztal Katarzyna , Maleszka Joanna , Bochtler Matthias , Maleszka Ryszard
Published: August 2014

In mammals, a family of TET enzymes producing oxidized forms of 5-methylcytosine (5mC) plays an important role in modulating DNA demethylation dynamics. In contrast, nothing is known about the function of a single TET orthologue present in invertebrates. Here, we show that the honeybee TET (AmTET) catalytic domain has dioxygenase activity and converts 5mC to 5-hydroxymethylcytosine (5hmC) in a HEK293T cell assay.In vivo, the levels of 5hmC are condition-dependent and relatively low, but in testes and ovaries 5hmC is present at approximately 7–10% of the total level of 5mC, which is comparable to that reported for certain mammalian cells types. AmTET is alternatively spliced and highly expressed throughout development and in adult tissues with the highest expression found in adult brains. Our findings reveal an additional level of flexible genomic modifications in the honeybee that may be important for the selection of multiple pathways controlling contrasting phenotypic outcomes in this species. In a broader context, our study extends the current, mammalian-centred attention to TET-driven DNA hydroxymethylation to an easily manageable organism with attractive and unique biology.
NxTrim: optimized trimming of Illumina mate pair reads
Authors: O’Connell Jared , Schulz-Trieglaff Ole , Carlson Emma , Hims Matthew M. , Gormley Niall A. , Cox Anthony J.
Published: August 2014

Motivation

Mate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance spanned by each pair of reads, potentially allowing larger repeats to be bridged and resolved. The Illumina Nextera Mate Pair (NMP) protocol employs a circularisation-based strategy that leaves behind 38bp adapter sequences which must be computationally removed from the data. While “adapter trimming” is a well-studied area of bioinformatics, existing tools do not fully exploit the particular properties of NMP data and discard more data than is necessary.

Results

We present NxTrim, a tool that strives to discard as little sequence as possible from NMP reads. The sequence either side of the adapter site is triaged into “virtual libraries” of mate pairs, paired-end reads and single-ended reads. When combined, these data boost coverage and can substantially improve the de novo assembly of bacterial genomes.

Availability

The source code is available athttps://github.com/sequencing/NxTrim

Contact

acox@illumina.com
How to make a kin selection model when marginal fitness is non-linear?
Authors: Schonmann R.H. , Boyd R. , Vicente R.
Published: August 2014

We observe that the Taylor-Frank method for making kin selection models when fitnesswis a nonlinear function of a continuous actor’s phenotypeyand the average phenotypezin its social environment requiresw(y, z) to be differentiable (as a function of two variables, i.e., jointly inyandz). This means that even ifw(y, z) is non-linear globally, locally it must be close to linear, meaning that its graph must be well approximated by a plane. When more than two individuals interact, this assumption is only satisfied when the marginal fitness of the actor is a linear function of the fraction of individuals in its social environment that share its phenotype. This assumption sometimes fails for biologically important fitness functions, for instance in microbial data and the theory of repeated n-person games. In these cases, the Taylor-Frank methodology cannot be used, and a more general form of direct fitness must replace it, to decide when a social mutant allele can invade a monomorphic population.
Can the site-frequency spectrum distinguish exponential population growth from multiple-merger coalescents?
Authors: Eldon Bjarki , Birkner Matthias , Blath Jochen , Freund Fabian
Published: August 2014

The ability of the site-frequency spectrum (SFS) to reflect the particularities of gene genealogies exhibiting multiple mergers of ancestral lines as opposed to those obtained in the presence of population growth is our focus. An excess of singletons is a well-known characteristic of both population growth and multiple mergers. Other aspects of the SFS, in particular the weight of the right tail, are, however, affected in specific ways by the two model classes. Using an approximate likelihood method and minimum-distance statistics, our estimates of statistical power indicate that exponential and algebraic growth can indeed be distinguished from multiple merger coalescents, even for moderate sample size, if the number of segregating sites is high enough. A normalized version of the SFS is also used as a summary statistic in an approximate Bayesian computation (ABC) approach. The results give further positive evidence as to the general eligibility of the SFS to distinguish between the different histories.
Structure of the calcium pyrophosphate monohydrate phase (Ca2P2O7·H2O): towards understanding the dehydration process in calcium pyrophosphate hydrates
Authors: Gras Pierre , Ratel-Ramond Nicolas , Teychéné Sébastien , Rey Christian , Elkaim Erik , Biscans Béatrice , Sarda Stéphanie , Combes Christèle
Published: August 2014

Calcium pyrophosphate hydrate (CPP, Ca2P2O7·nH2O) and calcium orthophosphate compounds (including apatite, octacalcium phosphateetc.) are among the most prevalent pathological calcifications in joints. Even though only two dihydrated forms of CPP (CPPD) have been detectedin vivo(monoclinic and triclinic CPPD), investigations of other hydrated forms such as tetrahydrated or amorphous CPP are relevant to a further understanding of the physicochemistry of those phases of biological interest. The synthesis of single crystals of calcium pyrophosphate monohydrate (CPPM; Ca2P2O7·H2O) by diffusion in silica gel at ambient temperature and the structural analysis of this phase are reported in this paper. Complementarily, data from synchrotron X-ray diffraction on a CPPM powder sample have been fitted to the crystal parameters. Finally, the relationship between the resolved structure for the CPPM phase and the structure of the tetrahydrated calcium pyrophosphate β phase (CPPT-β) is discussed.
A new heteroleptic cuprous complex with strong yellow photoluminescence
Authors: Xu Kaijie , Hong Mingwei , Zhang Yicheng , Song Li , Chai Wenxiang
Published: August 2014

In the title heteroleptic cuprous complex, (acetonitrile-κN)({2-[2-(diphenylphosphanyl)phenoxy]phenyl}diphenylphosphane-κ2P,P′)[2-(pyridin-4-yl-κN)-1,3-benzoxazole]copper(I) hexafluoridophosphate, [Cu(C36H28OP2)(CH3CN)(C12H8N2O)]PF6, conventionally abbreviated [Cu(POP)(CH3CN)(4-PBO)]PF6, where POP is the diphosphane ligand {2-[2-(diphenylphosphanyl)phenoxy]phenyl}diphenylphosphane and 4-PBO is the N-containing ligand 2-(pyridin-4-yl)-1,3-benzoxazole, the asymmetric unit consists of a hexafluoridophosphate anion and a whole mononuclear cation, where the CuIcentre is coordinated by two P atoms from the POP ligand, by one N atom from the 4-PBO ligand and by the N atom of the coordinated acetonitrile molecule, giving rise to a CuP2N2distorted tetrahedral coordination geometry. The electronic absorption, photoluminescence and thermal stability properties of this complex have been studied on as-synthesized samples, which had previously been examined by powder X-ray diffraction. A yellow emission signal is attributed to an excited state arising from metal-to-ligand charge transfer (MLCT).
Biologics are more potent than other treatment modalities for improvement of quality of life in psoriasis patients
Authors: Takahashi Hidetoshi , Iinuma Shin , Tsuji Hitomi , Honma Masaru , Iizuka Hajime
Published: August 2014

Although mental health is hampered in various skin disorders, few studies regarding anxiety in psoriasis patients are available, and specifically, no evaluation exists between mental health and psoriasis severity or the patients' quality of life. To examine the relation between mental health, psoriasis severity and patient's quality of life, 119 psoriasis vulgaris patients were assessed for anxiety using the General Health Questionnaire (GHQ)‐30. Psoriasis area and severity index (PASI) and Dermatological Life Quality Index (DLQI) scores were also measured. The average total GHQ‐30 score was significantly decreased from 4.41 to 2.11 (52.2% decrease) in biologics‐treated patients. That of patients treated with other systemic agents decreased from 4.36 to 3.32 (23.9% decrease) and that of those treated with topical agents from 4.21 to 3.48 (17.3% decrease). In the biologics‐treated group five of the six categories of GHQ‐30, i.e. general illness, somatic symptoms, sleep disturbance, social dysfunction, and anxiety and dysphoria, were significantly decreased after the treatment. In contrast, in the other systemic treatment and topical treatment groups, three of the six categories, general illness, somatic symptoms, and sleep disturbance were significantly decreased. There was a significant correlation between GHQ‐30 and DLQI, but not with PASI. The psoriasis patients show impaired mental health and among various treatment modalities biologics are superior to other systemic or topical treatments for improving the defective mental state.
HLA‐C*12:02 is a susceptibility factor in late‐onset type of psoriasis in Japanese
Authors: Mabuchi Tomotaka , Ota Tami , Manabe Yasuaki , Ikoma Norihiro , Ozawa Akira , Terui Tadashi , Ikeda Shigaku , Inoko Hidetoshi , Oka Akira
Published: August 2014

Psoriasis is thought to be a multifactorial disease triggered by both genetic and environmental factors. The HLA‐C locus on chromosome 6p21.33 remains the strongest susceptibility candidate locus in psoriasis. The strong association between psoriasis and the HLA‐Cw6 allele has been well documented in various races. It is known that psoriatic patients with early onset are more likely to be familial and associated with HLA‐Cw6. Familial occurrence of Japanese psoriasis is smaller than other populations. Furthermore, males are predominant over females in Japanese psoriasis. We investigated the relation between HLA‐C alleles and age of onset, and in each gender for Japanese psoriasis, and discuss male predominance in the incidence of psoriasis in Japan. Four hundred forty six unrelated Japanese patients with psoriasis vulgaris and 557 sex‐ and age‐matched unrelated Japanese healthy controls were investigated by genotyping. We confirmed the association between early‐onset type of psoriasis with HLA‐C*06:02 allele in Japanese. In addition, we detected the association between the late‐onset type of psoriasis and the HLA‐C*12:02 allele in Japanese. No significant differences in allele frequency were observed between females and males. Our results suggest that there is no genetic factor effect on male predominance in Japanese. In contract, the effect of environmental risk factors on the onset of Japanese psoriatic patients is stronger in males than in females. As a result, male predominant in psoriasis may occur in Japan.