bluuebunny/crossref_metadata_2025 huggingface dataset:
Frequency of Serous Otitis Media in Children without Otolaryngological Symptoms
Authors: Kocyigit Murat , Ortekin Safiye , Cakabay Taliye , Ozkaya Guven , Bezgin Selin , Adali Mustafa
Published: June 2016

Introduction Otitis media with effusion is the fluid in the middle ear with no signs or symptoms of acute ear infection.

Objective This study aims to research the frequency of serous otitis media in patients referred to the pediatric clinic between 3–16 years of age without any active ear, nose, and throat complaints.

Methods This study included 589 children patients (280 boys, 309 girls; mean age: 9.42; range 3–16) who were administered to the pediatric clinic without otolaryngologic complaints. Patients underwent examination with flexible nasopharyngoscopy for adenoid hypertrophy. An otorhinolaryngologist examined all children on both ears using an otoscope and tested with tympanometry. We used tympanometry results to diagnose SOM.

Results The study included 589 patients that underwent fiber optic examination of the nasopharynx with an endoscope. Adenoid vegetation was present in 58 patients (9.8%) and was not detected in 531 patients (90.2%). We found serous otitis media in 94 (15.9%) patients. We obtained Type A tympanogram in 47 (81%) of 58 patients with adenoid vegetation, 6 (10.3%) Type B, and 5 (8.6%) Type C. When comparing 58 patients with adenoid vegetation with 538 patients without adenoid vegetation for serous otitis media, the frequency was not statistically significant (p > 0.05).

Conclusion We believe that in children without any ear, nose, and throat complaints, it is possible to detect serous otitis media with adenoid vegetation. Thus, pediatric patients should undergo screening at regular intervals.
A spacetime with pseudo-projective curvature tensor
Authors: Mallick Sahanous , Suh Young Jin , De Uday Chand
Published: June 2016

The object of the present paper is to study spacetimes admitting pseudo-projective curvature tensor. At first we prove that a pseudo-projectively flat spacetime is Einstein and hence it is of constant curvature and the energy momentum tensor of such a spacetime satisfying Einstein’s field equation with cosmological constant is covariant constant. Next, we prove that if the perfect fluid spacetime with vanishing pseudo-projective curvature tensor obeys Einstein’s field equation without cosmological constant, then the spacetime has constant energy density and isotropic pressure, and the perfect fluid always behaves as a cosmological constant and also such a spacetime is infinitesimally spatially isotropic relative to the unit timelike vector field U. Moreover, it is shown that a pseudo-projectively flat spacetime satisfying Einstein’s equation without cosmological constant for a purely electromagnetic distribution is an Euclidean space. We also prove that under certain conditions a perfect fluid spacetime with divergence-free pseudo-projective curvature is a Robertson-Walker spacetime and the possible local cosmological structure of such a spacetime is of type I, D or O. We also study dust-like fluid spacetime with vanishing pseudo-projective curvature tensor.
Lateral critical Casimir force in two–dimensional inhomogeneous Ising strip. Exact results
Authors: Nowakowski Piotr , Napiórkowski Marek
Published: June 2016

We consider two–dimensional Ising strip bounded by two planar, inhomogeneous walls. The inhomogeneity of each wall is modeled by a magnetic field acting on surface spins. It is equal to +h1 except for a group of N1 neighboring surface spins where it is equal to −h1. The inhomogeneities of the upper and lower wall are shifted with respect to each other by a lateral distance L. Using exact diagonalization of the transfer matrix, we study both the lateral and normal critical Casimir forces as well as magnetization profiles for different temperature regimes: below the wetting temperature, between the wetting and the critical temperature, and above the critical temperature. The lateral critical Casimir force acts in the direction opposite to the shift L, and the excess normal force is always attractive. Upon increasing the shift L we observe, depending on the temperature regime, three different scenarios of breaking of the capillary bridge of negative magnetization connecting the inhomogeneities of the walls across the strip. As long as there exists a capillary bridge in the system, the magnitude of the excess total critical Casimir force is almost constant, with its direction depending on L. By investigating the bridge morphologies we have found a relation between the point at which the bridge breaks and the inflection point of the force. We provide a simple argument that some of the properties reported here should also hold for different models of the strip with the same type of inhomogeneity.
Note: An iterative algorithm to improve colloidal particle locating
Authors: Jensen K. E. , Nakamura N.
Published: June 2016

Confocal microscopy of colloids combined with digital image processing has become a powerful tool in soft matter physics and materials science. Together, these techniques enable locating and tracking of more than half a million individual colloidal particles at once. However, despite improvements in locating algorithms that improve position accuracy, it remains challenging to locate all particles in a densely packed, three dimensional colloid without erroneously identifying the same particle more than once. We present a simple iterative algorithm that mitigates both the “missed particle” and “double counting” problems while simultaneously reducing sensitivity to the specific choice of input parameters. It is also useful for analyzing images with spatially varying brightness in which a single set of input parameters is not appropriate for all particles. The algorithm is easy to implement and compatible with existing particle locating software.
Linear development of controlled disturbances in the supersonic boundary layer on a swept wing at Mach 2
Authors: Kosinov A. D. , Kolosov G. L. , Semionov N. V. , Yermolaev Yu. G.
Published: June 2016

Experimental results are presented on the linear development of a wave train in a three-dimensional supersonic boundary layer on a swept wing with 45°-sweep angle at Mach number M = 2.0. Artificial disturbances in the boundary layer were excited by periodical glow discharge mainly at frequencies 10 and 20 kHz. The maximum of the controlled pulsation amplitude was localized in the boundary layer in normal to the swept-wing surface direction for spatial amplitude distributions as well as for the amplitude wave spectra. The asymmetry of the wave characteristics of the unstable disturbances in the boundary layer of a swept wing caused by the presence of crossflow is confirmed. The stability characteristics, including dispersion relations and amplification rates over a wide range of wave inclination angles, are obtained for disturbances with prescribed frequencies 10 and 20 kHz.
Quantum dynamics of a vibronically coupled linear chain using a surrogate Hamiltonian approach
Authors: Lee Myeong H. , Troisi Alessandro
Published: June 2016

Vibronic coupling between the electronic and vibrational degrees of freedom has been reported to play an important role in charge and exciton transport in organic photovoltaic materials, molecular aggregates, and light-harvesting complexes. Explicitly accounting for effective vibrational modes rather than treating them as a thermal environment has been shown to be crucial to describe the effect of vibronic coupling. We present a methodology to study dissipative quantum dynamics of vibronically coupled systems based on a surrogate Hamiltonian approach, which is in principle not limited by Markov approximation or weak system-bath interaction, using a vibronic basis. We apply vibronic surrogate Hamiltonian method to a linear chain system and discuss how different types of relaxation process, intramolecular vibrational relaxation and intermolecular vibronic relaxation, influence population dynamics of dissipative vibronic systems.
An efficient and numerically stable procedure for generating sextic force fields in normal mode coordinates
Authors: Sibaev M. , Crittenden D. L.
Published: June 2016

In this paper, we outline a general, scalable, and black-box approach for calculating high-order strongly coupled force fields in rectilinear normal mode coordinates, based upon constructing low order expansions in curvilinear coordinates with naturally limited mode-mode coupling, and then transforming between coordinate sets analytically. The optimal balance between accuracy and efficiency is achieved by transforming from 3 mode representation quartic force fields in curvilinear normal mode coordinates to 4 mode representation sextic force fields in rectilinear normal modes. Using this reduced mode-representation strategy introduces an error of only 1 cm−1 in fundamental frequencies, on average, across a sizable test set of molecules. We demonstrate that if it is feasible to generate an initial semi-quartic force field in curvilinear normal mode coordinates from ab initio data, then the subsequent coordinate transformation procedure will be relatively fast with modest memory demands. This procedure facilitates solving the nuclear vibrational problem, as all required integrals can be evaluated analytically. Our coordinate transformation code is implemented within the extensible PyPES library program package, at http://sourceforge.net/projects/pypes-lib-ext/.
Efficient expulsion of magnetic flux in superconducting radiofrequency cavities for high Q applications
Authors: Posen S. , Checchin M. , Crawford A. C. , Grassellino A. , Martinello M. , Melnychuk O. S. , Romanenko A. , Sergatskov D. A. , Trenikhina Y.
Published: June 2016

Even when cooled through its transition temperature in the presence of an external magnetic field, a superconductor can expel nearly all external magnetic flux. This paper presents an experimental study to identify the parameters that most strongly influence flux trapping in high purity niobium during cooldown. This is critical to the operation of superconducting radiofrequency cavities, in which trapped flux degrades the quality factor and therefore cryogenic efficiency. Flux expulsion was measured on a large survey of 1.3 GHz cavities prepared in various ways. It is shown that both spatial thermal gradient and high temperature treatment are critical to expelling external magnetic fields, while surface treatment has minimal effect. For the first time, it is shown that a cavity can be converted from poor expulsion behavior to strong expulsion behavior after furnace treatment, resulting in a substantial improvement in quality factor. Microscopic investigations are performed to study the relevant changes in the material from this treatment. Future plans are described to build on this result in order to optimize treatment for future cavities.
Nitrogen-concentration modulated interfacial and electrical properties of sputtering-derived HfGdON gate dielectric
Authors: Ma Rui , Liu Mao , He Gang , Fang Ming , Shang Guoliang , Fei Guangtao , Zhang Lide
Published: June 2016

HfGdON thin films with different N concentrations have been deposited on Si (100) substrates using a radio frequency magnetron sputtering by changing the flow rate of N2 during deposition. Results have indicated that N doping could partly suppress the formation of the low-k SiOx interfacial layer in the interfacial region, which induces the evolution of the composition of interfacial layer changes from SiOx to the mixture of SiOx and silicate. Reduction in band gap and valence band offset and increment in conduction band offset have been detected with the increase of N doping content. Moreover, the best electrical properties including the highest dielectric constant (∼21.69), no obvious ΔVfb as well as the lowest leakage current density have been obtained with HfGdON films deposited at a N2 flow rate of 7 sccm. It can be concluded that N doping content should be carefully controlled to meet the best performance requirement for future complementary metal-oxide-semiconductor device.
Reduced photoconductivity observed by time-resolved terahertz spectroscopy in metal nanofilms with and without adhesion layers
Authors: Alberding Brian G. , Kushto Gary P. , Lane Paul A. , Heilweil Edwin J.
Published: June 2016

Non-contact, optical time-resolved terahertz spectroscopy has been used to study the transient photoconductivity of nanometer-scale metallic films deposited on the fused quartz substrates. Samples of 8 nm thick gold or titanium show an instrument-limited (ca. 0.5 ps) decrease in conductivity following photoexcitation due to electron-phonon coupling and subsequent increased lattice temperatures which increases charge carrier scattering. In contrast, for samples of 8 nm gold with a 4 nm adhesion layer of titanium or chromium, a ca. 70 ps rise time for the lattice temperature increase is observed. These results establish the increased transient terahertz transmission sign change of metallic compared to semiconductor materials. The results also suggest nanoscale gold films that utilize an adhesion material do not consist of distinct layers.
Out-of-phase Andreev transports in a double-quantum-dot Cooper-pair splitter
Authors: Gong Wei-Jiang , Wang Xiao-Qi , Zhu Yu-Lian , Gao Zhen , Wu Hai-Na
Published: June 2016

We investigate the Andreev transports through a double-quantum-dot Cooper-pair splitter with an additional direct coupling between the dots. It is found that when finite magnetic flux is applied through this structure, its induced phase adjusts the local and crossed Andreev reflections in different manners. Moreover, in the presence of appropriate magnetic flux, the crossed Andreev reflection can be efficiently enhanced, accompanied by the suppression of the local Andreev reflection. Such a result exists in both the linear and nonlinear transport regions, even in the case of strong intradot Coulomb interaction. Therefore, such a work provides a promising scheme to enhance the splitting of the Cooper pair.
A recognition method research based on the heart sound texture map
Authors: Cheng Huizhong , Cheng Xie-feng , Li Yunyi , Li Wei
Published: June 2016

In order to improve the Heart Sound recognition rate and reduce the recognition time, in this paper, we introduces a new method for Heart Sound pattern recognition by using Heart Sound Texture Map. Based on the Heart Sound model, we give the Heart Sound time-frequency diagram and the Heart Sound Texture Map definition, we study the structure of the Heart Sound Window Function principle and realization method, and then discusses how to use the Heart Sound Window Function and the Short-time Fourier Transform to obtain two-dimensional Heart Sound time-frequency diagram, propose corner correlation recognition algorithm based on the Heart Sound Texture Map according to the characteristics of Heart Sound. The simulation results show that the Heart Sound Window Function compared with the traditional window function makes the first (S1) and the second (S2) Heart Sound texture clearer. And the corner correlation recognition algorithm based on the Heart Sound Texture Map can significantly improve the recognition rate and reduce the expense, which is an effective Heart Sound recognition method.
Dissolved organic carbon and dissolved organic nitrogen concentrations and exports upstream and downstream of the Dallas–Fort Worth metropolis, Texas, USA
Authors: Aitkenhead-Peterson J. A. , Steele M. K.
Published: June 2016

Concentrations and export of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) from terrestrial landscapes to near-coastal zones vary with land use. Information on (DOC) and (DON) concentrations and exports from urban ecosystems is sparse; thus, their source from within urbanised watersheds such as soil or vegetation or from permitted sewage discharge is unknown. We examined DOC and DON concentrations and exports in four gauged subwatersheds in the humid subtropical, upper Trinity River basin, upstream and downstream of the Dallas–Fort Worth metropolis in Texas, USA. Annual average DOC concentrations ranged from 5.7±0.4 to 6.4±0.8mgL–1 and DON concentrations ranged from 0.31±0.05 to 0.33±0.14mgL–1. Dissolved organic carbon exports, which included permitted sewage discharge, ranged from 522kgkm–2 year–1 above Dallas–Fort Worth to 3637kgkm–2 year–1 below Dallas–Fort Worth. Permitted effluent discharge contributed between 1 and 35% of DOC loading above and below the Dallas–Fort Worth metropolis. DON exports ranged from 27 to 179kgkm–2 year–1 above and below Dallas–Fort Worth respectively. There was difficulty apportioning permitted effluent-discharge contribution to DON because of the transformations among nitrogen-species. A moderate but significant relationship was found between DOC and sodium concentrations (R2=0.45; P<0.0001; n=40) and between DOC and potassium concentrations (R2=0.45; P<0.0001; n=40). Dissolved organic nitrogen also displayed a significant relationship with sodium (R2=0.33; P<0.001; n=40) and potassium (R2=0.59; P<0.001; n=40), suggesting that increases in these cations to aquatic ecosystems may induce increases in DOC and DON concentrations. Although DOC export was significantly correlated with medium-density urban land use (r=0.96; P<0.05: n=4), DON export was not (r=0.93; P>0.05; n=4), suggesting that land-management practices and permitted point-source discharges have a significant effect on aquatic DOC and DON concentrations and exports derived from urban watersheds.
Alpha and beta diversity of freshwater meiofauna at different spatial scales in a Neotropical lotic system
Authors: Araújo T. Q. , Checon H. H. , Garraffoni A. R. S.
Published: June 2016

Meiofaunal assemblages are important components of benthic communities in freshwater habitats, but studies about their ecology are scarce. In the present study we investigated the spatial and temporal distribution patterns of freshwater meiofaunal taxa, in a lotic system in south-eastern Brazil, assessing α and β diversities through additive partitioning of diversity. At each of six sampling sites, a 50-m transect was divided into five equal sections. Two random samples were collected in each section. Local spatial scales (α and β1) and among areas (β3) made the highest contribution to overall richness, but seasonal variation could be seen. Non-randomness patterns were observed, especially at the lowest and highest spatial scales, showing the effects of local intraspecific aggregation and environmental variability among areas. Temporal scale analysis showed that diversity was highly aggregated at the monthly scale, but sampling location affected these results. Community composition results highlighted the contrasting conditions found at the sampling sites, highlighting β3 as an important component of γ diversity across spatial scales. The effects of different levels of environmental degradation and precipitation on community composition and meiofaunal abundance affected the ability of the community to recover and recolonise the meiobenthos.
A review of biodiversity outcomes from possum-focused pest control in New Zealand
Authors: Byrom Andrea E. , Innes John , Binny Rachelle N.
Published: June 2016

Worldwide, introduced vertebrate pests impact primary production, native biodiversity, and human health. In New Zealand, extensive pest control (~10 million ha) is undertaken to protect native biota and to prevent losses to the primary sector from wildlife vectors of bovine tuberculosis (TB), primarily possums (Trichosurus vulpecula). Control is conducted by TBfree New Zealand and by conservation agencies. Remote, forested terrain is treated using the toxin 1080 via aerial delivery in bait with a return time of ~5 years. Ground-based control is conducted annually using traps and/or poison bait. Possums are controlled to very low abundance by these operations. Aerial 1080 is effective against another forest-dwelling vertebrate pest, the ship rat (Rattus rattus). Possum control has reduced TB rates, but collateral benefits for native biodiversity have not been quantified, making it difficult to demonstrate a return on investment. We review information from 47 accounts of responses of native biota to possum control. Of these, 60% quantified responses to aerial 1080; the remainder were ground-based. Possum control benefited vegetation by increasing foliage and fruit production, and by reducing tree mortality. Controlling ship rats and possums together improved bird populations, but rats recovered rapidly and long-term outcomes for rat-vulnerable birds are unknown.Large-bodied invertebrates also benefited from extensive pest control. We conducted a meta-analysis of 84 response measures from 35 of these 47 studies in order to provide a quantitative assessment of these findings. The analysis demonstrated that both ground and aerial control of this invasive pest in New Zealand has provided substantial collateral benefits for native biota. Few studies have taken advantage of decades of extensive pest control in New Zealand to monitor ecosystem-level outcomes, which have received only short-term attention thus far. Non-treatment experimental controls and replicate sites that enable validated assessments of outcomes for native biota are vital. Future studies would benefit from a standardised set of biodiversity indicators from a range of taxonomic and functional groupings, and from standardising experimental designs so individual studies can contribute to future meta-analyses, to strengthen the evidence base for the impacts of invasive pests on native biota in New Zealand and worldwide.
The multimodal approach in audiovisual translation
Authors: Taylor Christopher
Published: June 2016

This paper will explore the multimodal approach to audiovisual translation (AVT). It must first be stressed, however, that most research on multimodality has not as yet focused on questions of translation. The Routledge Handbook of Multimodal Analysis (Jewitt 2009), which contains articles by most of the leading figures in the field, while representing a major step forward in multimodal studies, does not tackle translation head on. The word ‘translation’ does not even appear in the index. Over a relatively short time span, most of the major contributions to the field have been more purely linguistically based and intent on providing keys to the understanding of the interplay of semiotic resources such as words, images, gesture, music, light, etc. (see O’Toole 1994; Kress and van Leeuwen 1996; Martinec 2000; Unsworth 2001; Baldry and Thibault 2006, etc.). The work of these scholars, however, has provided an impetus to developing ideas on how to exploit multimodal analyses in the area of AVT. Thibault’s work, for example, on the ‘multimodal transcription’ provided this author with the basis for investigating how the integration of semiotic modalities in a film text could assist the subtitler in making those all-important decisions on what to retain and what to discard when faced with time constraints. Other scholars have studied the co-articulation of words and image in their discussion of how different modalities realize social functions and make meaning (O’Halloran 2008; Bednarek 2010), emphasising the importance of supplementing purely linguistic analyses with studies of all the other semiotic resources that make up a multimodal text. Findings will inevitably be reported verbally but the analyses need to explore the concept of integration and how other resources can interact with language and, crucially, how translators can be made sensitive to the entire semiotic impact of a multimodal text.
Imagined spectators
Authors: O’Sullivan Carol
Published: June 2016

This article considers theoretical and methodological questions of language and translation policy in the dissemination of audiovisual products across languages. This is an area where scholarly research is inevitably playing catch-up with rapid change both in the language industries and in film and television production. For example, we have a general sense of ‘dubbing territories’ and ‘subtitling territories’ but in reality the picture is more complex. Norms changed in the course of the home entertainment revolution, with the arrival of the DVD format in the late 1990s ostensibly increasing viewer choice and flexibility of translation provision. The relocation of much audiovisual material to an online environment has also generated fundamental changes in the way that works circulate, with volunteer translators and automated translation processes playing a larger role. Policy developments in access translation have meant that there have also been great changes relatively recently in the availability of SDH subtitling, audio description and other modes of access translation.

This is a very broad field which raises many compelling research questions. At the same time, its very breadth does not lend itself to a comprehensive overview. The article will therefore aim to provide an orientation to, rather than a summary of, the theoretical and methodological challenges of research on this topic.
Methods for measuring 1/1 error field in Wendelstein 7-X stellarator
Authors: Bozhenkov S.A. , Lazerson S. , Otte M. , Gates D.A. , Sunn Pedersen T. , Wolf R.C.
Published: June 2016

Wendelstein 7-X is an optimized helical axis stellarator that came into operation at the end of 2015. A m/n  =  5/5 island chain is used in most of its configurations to form a divertor. This island chain at

ι

=
1

is sensitive to symmetry-breaking error fields, with the resonant 1/1 field being of particular concern because of its influence on the divertor heat flux distribution. Measurement and compensation of the 1/1 mode is therefore necessary. Experimentally, vacuum error fields in W7-X will be studied with a flux surface mapping diagnostic. In this paper numerical simulations for planning and analysing such measurements are presented. Two methods for determining the 1/1 mode are considered: measurement of the island width and measurement of a helical shift of the magnetic axis. Measurement of the resonant island width is a sensitive technique, but the island structure is also affected by other co-resonant components. A complementary method is to measure a helical shift of the magnetic axis in a configuration close to the resonance. This method has a simple interpretation and isolates the 1/1 error field from higher order resonant modes.
The use of plant community attributes to detect habitat quality in coastal environments
Authors: Del Vecchio Silvia , Slaviero Antonio , Fantinato Edy , Buffa Gabriella
Published: June 2016

The monitoring of biodiversity has mainly focused on the species level. However, researchers and land managers are making increasing use of complementary assessment tools that address higher levels of biological organization, i.e. communities, habitats and ecosystems. Recently, a variety of frameworks have been proposed for assessing the conservation status of communities or ecosystems. Among the various criteria proposed, all the protocols suggest considering (i) spatial aspects (range and area), and (ii) qualitative aspects of specific structures and functions. However, changes to ecological function are difficult to quantify and many protocols end up by using qualitative criteria. The aim of this work was to test the efficacy of some plant community attributes for the detection of vegetation quality in sand dune plant communities. We chose plant community attributes that either help to distinguish a habitat from others (diagnostic components) or play a significant role in habitat function and persistence over time. We used a diachronic approach by contrasting up-to-date vegetation data with data from previous studies carried out within the same areas. Changes in species composition were detected through detrended correspondence analyses (detrended correspondence analyses), Multi-Response Permutation Procedures and Indicator Species Analysis, while structural changes were analyzed by comparing species richness, total species cover, ecological groups of species and growth forms through null models. Ecological groups such as native focal species and aliens, and growth forms proved their efficacy in discriminating between habitat types and in describing their changes over time. The approach used in this study may provide an instrument for the assessment of plant community quality that can be applied to other coastal ecosystems.
CART—a chemical annotation retrieval toolkit
Authors: Deghou Samy , Zeller Georg , Iskar Murat , Driessen Marja , Castillo Mercedes , van Noort Vera , Bork Peer
Published: June 2016

Motivation: Data on bioactivities of drug-like chemicals are rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to prevailing ambiguity between chemical names and identifiers and a lack of cross-references between databases.

Results: To address this challenge, we have developed CART, a Chemical Annotation Retrieval Toolkit. As a key functionality, it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data.

Availability and Implementation: CART is available as a Galaxy web service (cart.embl.de). Source code and an easy-to-install command line tool can also be obtained from the web site.

Contact: bork@embl.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
SETH detects and normalizes genetic variants in text
Authors: Thomas Philippe , Rocktäschel Tim , Hakenberg Jörg , Lichtblau Yvonne , Leser Ulf
Published: June 2016

Summary: Descriptions of genetic variations and their effect are widely spread across the biomedical literature. However, finding all mentions of a specific variation, or all mentions of variations in a specific gene, is difficult to achieve due to the many ways such variations are described. Here, we describe SETH, a tool for the recognition of variations from text and their subsequent normalization to dbSNP or UniProt. SETH achieves high precision and recall on several evaluation corpora of PubMed abstracts. It is freely available and encompasses stand-alone scripts for isolated application and evaluation as well as a thorough documentation for integration into other applications.

Availability and Implementation: SETH is released under the Apache 2.0 license and can be downloaded from http://rockt.github.io/SETH/.

Contact:  thomas@informatik.hu-berlin.de or leser@informatik.hu-berlin.de
RANKS: a flexible tool for node label ranking and classification in biological networks
Authors: Valentini Giorgio , Armano Giuliano , Frasca Marco , Lin Jianyi , Mesiti Marco , Re Matteo
Published: June 2016

Summary:  RANKS is a flexible software package that can be easily applied to any bioinformatics task formalizable as ranking of nodes with respect to a property given as a label, such as automated protein function prediction, gene disease prioritization and drug repositioning. To this end RANKS provides an efficient and easy-to-use implementation of kernelized score functions, a semi-supervised algorithmic scheme embedding both local and global learning strategies for the analysis of biomolecular networks. To facilitate comparative assessment, baseline network-based methods, e.g. label propagation and random walk algorithms, have also been implemented.

Availability and Implementation: The package is available from CRAN: https://cran.r-project.org/. The package is written in R, except for the most computationally intensive functionalities which are implemented in C.

Contact:  valentini@di.unimi.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge
Authors: Lu Yang Young , Chen Ting , Fuhrman Jed A , Sun Fengzhu
Published: June 2016

Motivation

The advent of next-generation sequencing technologies enables researchers to sequence complex microbial communities directly from the environment. Because assembly typically produces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analysis. OTU clustering is also referred to as binning. We present COCACOLA, a general framework automatically bin contigs into OTUs based on sequence composition and coverage across multiple samples.

Results

The effectiveness of COCACOLA is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT. The superior performance of COCACOLA relies on two aspects. One is using L1 distance instead of Euclidean distance for better taxonomic identification during initialization. More importantly, COCACOLA takes advantage of both hard clustering and soft clustering by sparsity regularization. In addition, the COCACOLA framework seamlessly embraces customized knowledge to facilitate binning accuracy. In our study, we have investigated two types of additional knowledge, the co-alignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both. We find that both co-alignment and linkage information further improve binning in the majority of cases. COCACOLA is scalable and faster than CONCOCT, GroopM, MaxBin and MetaBAT.

Availability and implementation

The software is available at https://github.com/younglululu/COCACOLA.

Supplementary information

Supplementary data are available at Bioinformatics online.
Perceived Physical Appearance: Assessing Measurement Equivalence in Black, Latino, and White Adolescents
Authors: Epperson Anna E. , Depaoli Sarah , Song Anna V. , Wallander Jan L. , Elliott Marc N. , Cuccaro Paula , Tortolero Emery Susan , Schuster Mark
Published: June 2016

Objective This aim of this study was to examine whether the construct of physical appearance perception differed among the three largest racial/ethnic groups in the United States using an adolescent sample. Methods Black (46%), Latino (31%), and White (23%) adolescents in Grade 10 from the Healthy Passages study (N = 4,005) completed the Harter’s Self-Perception Profile for Adolescents–Physical Appearance Scale (SPPA–PA) as a measure of physical appearance perception. Results Overall, Black adolescents had a more positive self-perception of their physical appearance than Latino and White adolescents. However, further analysis using measurement invariance testing revealed that the construct of physical appearance perception, as measured by SPPA–PA, was not comparable across the three racial/ethnic groups in both males and females. Conclusions These results suggest that observed differences may not reflect true differences in perceptions of physical appearance. Measures that are equivalent across racial/ethnic groups should be developed to ensure more precise measurement and understanding.
Active Trigger Points in the Cervical Musculature Determine the Altered Activation of Superficial Neck and Extensor Muscles in Women With Migraine
Authors: Florencio Lidiane L. , Ferracini Gabriela N. , Chaves Thais C. , Palacios-Ceña María , Ordás-Bandera Carlos , Speciali José G. , Falla Deborah , Grossi Débora B. , Fernández-de-las-Peñas César
Published: June 2016

Objective:

Previous studies have demonstrated the presence of active trigger points (TrPs) in women with migraine reproducing their headache attacks. No study has investigated whether these TrPs can alter cervical muscle function in migraine. Our objective was to analyze differences in the activation of superficial neck flexor and extensor muscles in women with migraine considering the presence of active TrPs in the splenius capitis (SC), the upper trapezius (UT), and the sternocleidomastoid (SCM) muscles.

Methods:

Surface electromyography (EMG) was recorded from the superficial flexors (SCM and anterior scalene) and the extensor (SC, UT) muscles bilaterally as participants performed a staged task of cranio-cervical flexion (CCF; 5 contractions representing a progressive increase in CCF range of motion) in 70 women with migraine. They were stratified according to the presence or the absence of active TrPs in the SCM, the SC, or the UT musculature. A comparison of EMG normalized root mean square (RMS) values was conducted with a 2×5 analysis of covariance with the task level as the within-subject variable, group stratified by active TrPs as the between-subjects variable and the presence of neck pain as a covariable.

Results:

All patients exhibited active TrPs in their cervical muscles, which reproduced their migraine. Women with migraine exhibiting active TrPs in the SCM (P<0.01), the UT (P<0.05), or the SC (P<0.05) muscles had lower normalized RMS values of their superficial neck flexors than those without active TrPs in the same muscles. In addition, individuals exhibiting active TrPs in the SC and the UT (both, P<0.05) muscles had higher normalized RMS values in the SC muscle than those without active TrPs in the same muscles.

Conclusions:

The presence of active TrPs in the cervical musculature determines an altered activation of superficial neck and extensor muscles during low-load, isometric CCF contractions in women with migraine.
All Fatigue is Not Created Equal
Authors: Boggero Ian A. , Rojas-Ramirez Marcia V. , Carlson Charles R.
Published: June 2016

Objectives:

Fatigue is known to be a pathway through which depression, psychological distress, pain intensity, and sleep disturbance influence pain interference, but the independent effects of fatigue on pain interference after controlling for these variables remains unknown. In addition, no study to date has tested whether fatigue subtypes of general fatigue, mental fatigue, emotional fatigue, physical fatigue, or vigor differentially predict pain interference.

Methods:

The current study tested these associations using archival medical data of 2133 chronic orofacial pain patients, who completed a battery of psychological questionnaires at the time of their first appointment at an orofacial pain clinic.

Results:

Hierarchical linear regression analysis revealed that after controlling for depression, psychological distress, sleep disturbance, pain intensity, and demographic variables, fatigue predicted higher pain interference (B=0.70, SE=0.17, P<0.001, η2=0.01). Physical fatigue (B=1.70, SE=0.48, P<0.001, η2=0.01) and vigor (B=−3.24, SE=0.47, P<0.001, η2=0.03) were independently associated with pain interference after controlling for the aforementioned variables.

Discussion:

The findings suggest that fatigue is an important independent predictor of pain interference and not merely a mediator. These findings also suggest that not all fatigue is created equal. Interventions aimed at reducing pain interference should target specific fatigue symptoms of physical fatigue and vigor. Future research investigating the independent associations of fatigue subtypes on pain outcomes may help clarify the nature of the interrelationships between pain and fatigue.
The Association Between Corticomotor Excitability and Motor Skill Learning in People With Painful Hand Arthritis
Authors: Parker Rosalind S. , Lewis Gwyn N. , Rice David A. , McNair Peter J.
Published: June 2016

Objectives:

Previous studies have shown a tendency for reduced motor cortex inhibition in chronic pain populations. People with chronic pain also routinely demonstrate motor deficiencies, including skill learning. The goals of the current study were to (1) provide a thorough analysis of corticomotor and intracortical excitability in people with chronic arthritic hand pain, and (2) examine the relationship between these measures and performance on a motor skill learning task.

Methods:

Twenty-three people with arthritic hand pain and 20 pain-free controls participated in a cross-sectional study. Transcranial magnetic stimulation was used to assess corticomotor and intracortical excitability of the first dorsal interosseus muscle. Participants then completed a 30-minute motor skill training task involving the index finger of the same hand.

Results:

Hand arthritis participants showed evidence of reduced intracortical inhibition and enhanced facilitation, which correlated with duration of hand pain. Arthritis participants were initially poorer at the motor skill task but over the total training time performance was equivalent between groups. There were no associations found between measures of intracortical excitability and motor skill learning.

Discussion:

Our findings are the first to provide evidence of cortical disinhibition in people with painful arthritis, as previously demonstrated in other chronic pain populations. Cortical excitability changes may progress the longer pain persists, with increased pain duration being associated with greater cortical disinhibition. There was no evidence that these changes in cortical excitability are related to impaired motor function or skill learning.
Outcome of the unaffected contralateral hip in unilateral slipped capital femoral epiphysis: a report comparing prophylactic fixation with observation
Authors: Bhattacharjee Atanu , Freeman Robert , Roberts Andrew P. , Kiely Nigel T.
Published: June 2016

This was a retrospective review of 80 patients with unilateral slipped capital femoral epiphysis treated with either prophylactic fixation or observation. The unaffected hip of 44 patients (mean age 12.6 years) were subjected to simultaneous prophylactic fixation and 36 patients (mean age 13.4 years) were managed by observation. Fisher’s exact test showed a significantly high incidence of sequential slip of unaffected hips in the observation group in comparison with prophylactic fixation (P=0.002). No cases had avascular necrosis or chondrolysis. Prophylactic fixation significantly reduces the incidence of sequential slip. It outweighs the minimal surgical risks compared with its benefit in the prevention of further sequential slip.
Craniocervical spinal instability after type 1 Arnold Chiari decompression: a case report
Authors: Camino Willhuber Gaston O. , Bosio Santiago T. , Puigdevall Miguel H. , Halliburton Carolina , Sola Carlos A. , Maenza Ruben A.
Published: June 2016

To present and describe an unusual case of spinal instability after craniocervical spinal decompression for a type-1 Chiari malformation. Type-1 Chiari malformation is a craniocervical disorder characterized by tonsillar displacement greater than 5 mm into the vertebral canal; posterior fossa decompression is the most common surgical treatment for this condition. Postoperative complications have been described: cerebrospinal fluid leak, pseudomeningocele, aseptic meningitis, wound infection, and neurological deficit. However, instability after decompression is unusual. A 9-year-old female presented with symptomatic torticollis after cervical decompression for a type-1 Chiari malformation. Spinal instability was diagnosed; craniocervical stabilization was performed. After a 12-month follow-up, spinal stability was achieved, with a satisfactory clinical neck alignment. We present a craniocervical instability secondary to surgical decompression; clinical and radiological symptoms, and definitive treatment were described.
Early MRI Detection and Closed Bone Graft Epiphysiodesis May Alter the Course of Avascular Necrosis Following Unstable Slipped Capital Femoral Epiphysis
Authors: Napora Joshua K. , Gilmore Allison , Son-Hing Jochen P. , Grimberg Dominic C. , Thompson George H. , Liu Raymond W.
Published: June 2016

Background:

Unstable slipped capital femoral epiphysis (SCFE) has an increased incidence of avascular necrosis (AVN). Early identification and surgical intervention for AVN may help preserve the femoral head.

Methods:

We retrospectively reviewed 48 patients (50 hips) with unstable SCFE managed between 2000 and 2014. AVN was diagnosed based on 2 different postoperative protocols. Seventeen patients (17 hips) had a scheduled magnetic resonance imaging (MRI) between 1 and 6 months from initial surgery, and the remaining 31 patients (33 hips) were evaluated by plain radiographs alone. If AVN was diagnosed, we offered core decompression and closed bone graft epiphysiodesis (CBGE) to mitigate its affects. At final follow-up, we assessed progression of AVN using the Steinberg classification.

Results:

Overall 13 hips (26%) with unstable SCFEs developed AVN. MRI revealed AVN in 7 of 17 hips (41%) at a mean of 2.5 months postoperatively (range, 1.0 to 5.2 mo). Six hips diagnosed by MRI received surgical intervention (4 CBGE, 1 free vascularized fibula graft, and 1 repinning due to screw cutout) at a mean of 4.1 months (range, 1.3 to 7.2 mo) postoperatively. None of the 4 patients treated with CBGE within 2 months postoperatively progressed to stage IVC AVN. The 2 patients treated after 4 months postoperatively both progressed to stage VC AVN.

Plain radiographs demonstrated AVN in 6 of 33 hips (18%) at a mean of 6.8 months postoperatively (range, 2.1 to 21.1 mo). One patient diagnosed with stage IVB AVN at 2.4 months had screw cutout and received CBGE at 2.5 months from initial pinning. The remaining 5 were not offered surgical intervention. Five of the 6 radiographically diagnosed AVN, including the 1 treated with CBGE, progressed to stage IVC AVN or greater.

Conclusions:

Although all patients with positive MRI scans developed radiographic AVN, none of the 4 patients treated with CBGE within 2 months after pinning developed grade IVC or greater AVN. Early MRI detection and CBGE may mitigate the effects of AVN after SCFE.

Level of Evidence:

Level III—retrospective comparative study.