bluuebunny/crossref_metadata_2025 huggingface dataset:
High mobility, hole transport materials for highly efficient PEDOT:PSS replacement in inverted perovskite solar cells
Authors: Neophytou Marios , Griffiths Jack , Fraser James , Kirkus Mindaugas , Chen Hu , Nielsen Christian B. , McCulloch Iain
Published: April 2017

Herein, we report novel triarylamine based hole transporting materials (HTM) with high mobilities for perovskite solar cells.
Metal oxide semiconductor 3D printing: preparation of copper(ii) oxide by fused deposition modelling for multi-functional semiconducting applications
Authors: Salea Ahamad , Prathumwan Rat , Junpha Jedsada , Subannajui Kittitat
Published: April 2017

A CuO semiconductor was fabricated by FDM printing and sintering technique. The obtained CuO can be used as a multifunctional semiconductor.
Correction: Pore-size-tuned host–guest interactions in Co-MOFs via in situ microcalorimetry: adsorption and magnetism
Authors: Qiao Chengfang , Sun Lin , Zhang Sheng , Liu Ping , Chang Liangliang , Zhou Chunsheng , Wei Qing , Chen Sanping , Gao Shengli
Published: April 2017

Correction for ‘Pore-size-tuned host–guest interactions in Co-MOFs via in situ microcalorimetry: adsorption and magnetism’ by Chengfang Qiao et al., J. Mater. Chem. C, 2017, 5, 1064–1073.
Toxic mechanisms of microcystins in mammals
Authors: McLellan Nicole L. , Manderville Richard A.
Published: April 2017

This review discusses mechanisms of toxicity, particularly those observed in liver tissue, mediated by microcystins (MCs) produced by cyanobacteria.
Biosafety study and mechanism comparison on two types of silica with different nanostructures
Authors: Zhang Yang , Chen Xianhui , Zhao Bo , Wu Hounan , Yuan Lan , Zhang Hua , Dai Wenbing , He Bing , Xing Gengmei , Zhang Qiang , Wang Xueqing
Published: April 2017

This research suggests the biosafety and possible mechanisms of silica A200 and S350, which are frequently used in oral drug delivery systems.
Coal combustion related fine particulate matter (PM2.5) induces toxicity in Caenorhabditis elegans by dysregulating microRNA expression
Authors: Wu Qiuli , Han Xiaoxiao , Wang Di , Zhao Fang , Wang Dayong
Published: April 2017

We employed anin vivoassay system ofCaenorhabditis elegansto determine if and which microRNAs (miRNAs) were dysregulated upon exposure to coal combustion related fine particulate matter (PM2.5) by profiling the miRNAs using SOLiD sequencing.
Anti-inflammatory, Antipyretic, and Antinociceptive Effects of a Cressa cretica Aqueous Extract
Authors: Abdallah Heba , Elshamy Abdelsamed , El Gendy Abd , Abd El-Gawad Ahmed , Omer Elsayed , De Leo Marinella , Pistelli Luisa
Published: April 2017

Cressa cretica is a widely grown halophytic plant traditionally used for the treatment of different ailments. Previous investigations reported its biological activity on a wide spectrum of diseases. In this study, in vivo antinociceptive, anti-inflammatory, and antipyretic activities of C. cretica aqueous extract whole plant were evaluated. In addition, the total polyphenol content, the total flavonoid content, and the chemical characterization of the extract were performed. C. cretica showed writhing inhibition in acetic acid-induced peripheral nociception of 43 and 48 % at doses of 50 and 100 mg/kg, respectively. The same doses increased latency time in a hot plate model of central analgesia by 66 and 78 % compared to the control group, respectively. The acute anti-inflammatory effect of the extract was explored in the carrageenan-induced rat hind paw test. The inhibition of paw volume was better than that of the standard drug indomethacin. C. cretica significantly decreased rectal temperature in the rats injected with Brewerʼs yeast. C. cretica aqueous extract showed both central and peripheral antinociceptive activities and was effective as an anti-inflammatory and antipyretic. Phenolic compounds, including chlorogenic acids and flavonol glycosides, were identified by HPLC-PDA-ESI-MS techniques. These findings indicate the medicinal importance of this traditionally used plant as a therapeutic remedy for different ailments.
Potential of Bryophyllum pinnatum as a Detrusor Relaxant: An in Vitro Exploratory Study
Authors: Bachmann Simon , Betschart Cornelia , Gerber Julia , Fürer Karin , Mennet Mónica , Hamburger Matthias , Potterat Olivier , von Mandach Ursula , Simões-Wüst Ana
Published: April 2017

An earlier prospective, randomised, placebo-controlled clinical trial had suggested that Bryophyllum pinnatum might have potential in the treatment of overactive bladder. Here we investigated the effects of B. pinnatum leaf press juice, fractions enriched in flavonoids and bufadienolides, and a flavonoid aglycon mixture and individual aglycons on detrusor contractility as a major target in overactive bladder treatment. The strength of the detrusor contractions was investigated using porcine muscle strips stimulated with KCl. B. pinnatum leaf press juice increased the contraction force of muscle strips. Treatment with the flavonoid-enriched fraction had almost no effect on contractility, while the bufadienolide-enriched fraction and flavonoid aglycons led to a concentration-dependent lowering of the contraction force. The data indicate that several components of B. pinnatum leaf press juice may contribute to the inhibitory effect on detrusor contractility, which in turn provides support to overactive bladder treatment with B. pinnatum.
Development of a bio-magnetic measurement system and sensor configuration analysis for rats
Authors: Kim Ji-Eun , Kim In-Seon , Kim Kiwoong , Lim Sanghyun , Kwon Hyukchan , Kang Chan Seok , Ahn San , Yu Kwon Kyu , Lee Yong-Ho
Published: April 2017

Magnetoencephalography (MEG) based on superconducting quantum interference devices enables the measurement of very weak magnetic fields (10–1000 fT) generated from the human or animal brain. In this article, we introduce a small MEG system that we developed specifically for use with rats. Our system has the following characteristics: (1) variable distance between the pick-up coil and outer Dewar bottom (∼5 mm), (2) small pick-up coil (4 mm) for high spatial resolution, (3) good field sensitivity (45∼ 80fT/cm/Hz), (4) the sensor interval satisfies the Nyquist spatial sampling theorem, and (5) small source localization error for the region to be investigated. To reduce source localization error, it is necessary to establish an optimal sensor layout. To this end, we simulated confidence volumes at each point on a grid on the surface of a virtual rat head. In this simulation, we used locally fitted spheres as model rat heads. This enabled us to consider more realistic volume currents. We constrained the model such that the dipoles could have only four possible orientations: the x- and y-axes from the original coordinates, and two tangentially layered dipoles (local x- and y-axes) in the locally fitted spheres. We considered the confidence volumes according to the sensor layout and dipole orientation and positions. We then conducted a preliminary test with a 4-channel MEG system prior to manufacturing the multi-channel system. Using the 4-channel MEG system, we measured rat magnetocardiograms. We obtained well defined P-, QRS-, and T-waves in rats with a maximum value of 15 pT/cm. Finally, we measured auditory evoked fields and steady state auditory evoked fields with maximum values 400 fT/cm and 250 fT/cm, respectively.
Atomistic simulations of wetting properties and water films on hydrophilic surfaces
Authors: Kanduč Matej , Netz Roland R.
Published: April 2017

We use molecular simulations to investigate the wetting behavior of water at flat polar surfaces. Introducing a computational procedure based on thermodynamic integration methods, we determine the equilibrium water film thickness on the surface at given vapor density as well as the corresponding change of the surface free energy. The wetting film is relevant on polar surfaces near the wetting transition and significantly alters the surface contact angle. For thin films, the surface free energy change increases linearly with the thickness, as predicted by simple thermodynamic arguments. For thick films we observe deviations from linearity, which we rationalize by the formation of hydrogen bonds between water molecules in the film. Our approach provides an efficient and accurate technique to calculate the wetting properties of surface layers, which we verify by simulating water droplets on the surfaces.
Structure-preserving second-order integration of relativistic charged particle trajectories in electromagnetic fields
Authors: Higuera A. V. , Cary J. R.
Published: April 2017

Time-centered, hence second-order, methods for integrating the relativistic momentum of charged particles in an electromagnetic field are derived. A new method is found by averaging the momentum before use in the magnetic rotation term, and an implementation is presented that differs from the relativistic Boris Push only in the method for calculating the Lorentz factor. This is shown to have the same second-order accuracy in time as that found by splitting the electric acceleration and magnetic rotation (Boris Push) and that found by averaging the velocity in the magnetic rotation term (Vay's method) [J.-L. Vay, Phys. Plasmas 15, 056701 (2008)]. All three methods are shown to conserve energy when there is no electric field. The Boris Push and the current method are shown to be volume-preserving, while Vay's method and the current method preserve the E→×B→ velocity. Thus, of these second-order relativistic momentum integrations, only the integrator introduced here both preserves volume and gives the correct E→×B→ velocity. While all methods have error that is second-order in time, they deviate from each other by terms that increase as the motion becomes relativistic. Numerical results show that Vay's method develops energy errors near resonant orbits of a test problem that neither volume-preserving integrator does.
Metadynamic metainference: Convergence towards force field independent structural ensembles of a disordered peptide
Authors: Löhr Thomas , Jussupow Alexander , Camilloni Carlo
Published: April 2017

Metadynamic metainference has been recently introduced as a theoretical framework to determine structural ensembles by combining and weighting their noise multiple sources of experimental data with molecular mechanics force fields and metadynamics simulations. Here we build upon these initial developments to further extend and streamline the computational approach. We also show that metadynamic metainference can actually determine a structural ensemble for a disordered peptide that is essentially independent from the employed force field. We further show that it is possible to use a very computationally efficient implicit solvent force field in the place of very expensive state-of-the-art explicit solvent ones without a significant loss in accuracy.
Sausage instabilities on top of kinking lengthening current-carrying magnetic flux tubes
Authors: von der Linden Jens , You Setthivoine
Published: April 2017

We theoretically explore the possibility of sausage instabilities developing on top of a kink instability in lengthening current-carrying magnetic flux tubes. Observations indicate that the dynamics of magnetic flux tubes in our cosmos and terrestrial experiments can involve topological changes faster than time scales predicted by resistive magnetohydrodynamics. Recent laboratory experiments suggest that hierarchies of instabilities, such as kink and Rayleigh-Taylor, could be responsible for initiating fast topological changes by locally accessing two-fluid and kinetic regimes. Sausage instabilities can also provide this coupling mechanism between disparate scales. Flux tube experiments can be classified by the flux tube's evolution in a configuration space described by a normalized inverse aspect-ratio k¯ and current-to-magnetic flux ratio λ¯. A lengthening current-carrying magnetic flux tube traverses this k¯–λ¯ space and crosses stability boundaries. We derive a single general criterion for the onset of the sausage and kink instabilities in idealized magnetic flux tubes with core and skin currents. The criterion indicates a dependence of the stability boundaries on current profiles and shows overlapping kink and sausage unstable regions in the k¯–λ¯ space with two free parameters. Numerical investigation of the stability criterion reduces the number of free parameters to a single one that describes the current profile and confirms the overlapping sausage and kink unstable regions in k¯–λ¯ space. A lengthening, ideal current-carrying magnetic flux tube can therefore become sausage unstable after it becomes kink unstable.
X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization
Authors: Schieferstein Jeremy M. , Pawate Ashtamurthy S. , Sun Chang , Wan Frank , Sheraden Paige N. , Broecker Jana , Ernst Oliver P. , Gennis Robert B. , Kenis Paul J. A.
Published: April 2017

Elucidating and clarifying the function of membrane proteins ultimately requires atomic resolution structures as determined most commonly by X-ray crystallography. Many high impact membrane protein structures have resulted from advanced techniques such as in meso crystallization that present technical difficulties for the set-up and scale-out of high-throughput crystallization experiments. In prior work, we designed a novel, low-throughput X-ray transparent microfluidic device that automated the mixing of protein and lipid by diffusion for in meso crystallization trials. Here, we report X-ray transparent microfluidic devices for high-throughput crystallization screening and optimization that overcome the limitations of scale and demonstrate their application to the crystallization of several membrane proteins. Two complementary chips are presented: (1) a high-throughput screening chip to test 192 crystallization conditions in parallel using as little as 8 nl of membrane protein per well and (2) a crystallization optimization chip to rapidly optimize preliminary crystallization hits through fine-gradient re-screening. We screened three membrane proteins for new in meso crystallization conditions, identifying several preliminary hits that we tested for X-ray diffraction quality. Further, we identified and optimized the crystallization condition for a photosynthetic reaction center mutant and solved its structure to a resolution of 3.5 Å.
A split-cavity design for the incorporation of a DC bias in a 3D microwave cavity
Authors: Cohen Martijn A. , Yuan Mingyun , de Jong Bas W. A. , Beukers Ewout , Bosman Sal J. , Steele Gary A.
Published: April 2017

We report on a technique for applying a DC bias in a 3D microwave cavity. We achieve this by isolating the two halves of the cavity with a dielectric and directly using them as DC electrodes. As a proof of concept, we embed a variable capacitance diode in the cavity and tune the resonant frequency with a DC voltage, demonstrating the incorporation of a DC bias into the 3D cavity with no measurable change in its quality factor at room temperature. We also characterize the architecture at millikelvin temperatures and show that the split cavity design maintains a quality factor Qi ∼ 8.8 × 105, making it promising for future quantum applications.
Transverse forces on dust particles in a magnetized sheath with crossed electric and magnetic fields
Authors: Melzer A. , Puttscher M.
Published: April 2017

Recent experimental findings on the transverse forces acting on dust particles in a discharge under moderate magnetic fields [Puttscher and Melzer, Phys. Plasmas (1994–present) 21, 123704 (2014)] are compared to model calculations. Using the sheath model of Pandey et al. [Phys. Plasmas 18, 053703 (2011)], Mehdipour et al. [Phys. Plasmas 17, 123708 (2010)], and Foroutan et al. [Phys. Plasmas 16, 103703 (2009)], first, the plasma parameters of a magnetized sheath are calculated. From that, the horizontal forces on dust particles along or opposite to the E→×B→ direction are determined. The experiments show a complex dependence of these forces on gas pressure in the discharge, magnetic field strength, and particle size. From the model, this complex behavior of the dust particles can be recovered with good agreement with the experimental findings.
Energetic particle modes of q = 1 high-order harmonics in tokamak plasmas with monotonic weak magnetic shear
Authors: Ren Zhen-Zhen , Wang Feng , Fu G. Y. , Shen Wei , Wang Zheng-Xiong
Published: April 2017

Linear and nonlinear simulations of high-order harmonics q=1 energetic particle modes excited by trapped energetic particles in tokamaks are carried out using kinetic/magnetohydrodynamic hybrid code M3D-K. It is found that with a flat safety factor profile in the core region, the linear growth rate of high-order harmonics (m=n>1) driven by energetic trapped particles can be higher than the m/n=1/1 component. The high m=n>1 modes become more unstable when the pressure of energetic particles becomes higher. Moreover, it is shown that there exist multiple resonant locations satisfying different resonant conditions in the phase space of energetic particles for the high-order harmonics modes, whereas there is only one precessional resonance for the m/n=1/1 harmonics. The fluid nonlinearity reduces the saturation level of the n=1 component, while it hardly affects those of the high n components, especially the modes with m=n=3,4. The frequency of these modes does not chirp significantly, which is different with the typical fishbone driven by trapped particles. In addition, the flattening region of energetic particle distribution due to high-order harmonics excitation is wider than that due to m/n=1/1 component, although the m/n=1/1 component has a higher saturation amplitude.
Numerical simulation to study transient self-focusing and gigahertz acoustic generation in collisional plasma
Authors: Hussain Saba , Sharma Swati , Singh Ram Kishor , Uma R. , Sharma R. P.
Published: April 2017

This paper presents the study of a coupled system of equations for a laser beam and an ion acoustic wave (IAW) in a collisional plasma through numerical simulation. The pump beam has been perturbed by a periodic perturbation that leads to the nonlinear evolution of the laser beam. The filamentation of the laser beam has been found to change appreciably with varying perturbation number. It was observed that the frequency spectra of the IAW lie in the gigahertz (GHz) domain. For the sake of better understanding of the physical process involved, a simplified model has been developed. The model contains spatial harmonics (obtained through simulation) at different times, by which the time dependent localization of the beam has been investigated.
Thin-film GaN Schottky diodes formed by epitaxial lift-off
Authors: Wang Jingshan , Youtsey Chris , McCarthy Robert , Reddy Rekha , Allen Noah , Guido Louis , Xie Jinqiao , Beam Edward , Fay Patrick
Published: April 2017

The performance of thin-film GaN Schottky diodes fabricated using a large-area epitaxial lift-off (ELO) process is reported in this work. Comparison of the device characteristics before and after lift-off processing reveals that the Schottky barrier height remains unchanged by the liftoff processing and is consistent with expectations based on metal-semiconductor work function differences, with a barrier height of approximately 1 eV obtained for Ni/Au contacts on n− GaN. However, the leakage current in both reverse and low-forward-bias regimes is found to improve significantly after ELO processing. Likewise, the ideality factor of the Schottky diodes also improves after ELO processing, decreasing from n = 1.12–1.18 before ELO to n = 1.04–1.10 after ELO. A possible explanation for the performance improvement obtained for Schottky diodes after substrate removal by ELO processing is the elimination of leakage paths consisting of vertical leakage along threading dislocations coupled with lateral conduction through the underlying n+ buffer layer that is removed in the ELO process. Epitaxial liftoff with GaN may enable significant improvement in device performance and economics for GaN-based electronics and optoelectronics.
« Obscur à soi-même », obscur au lecteur ?
Authors: Rey Pierre-Louis
Published: April 2017

Though Camus admires Faulkner, he differs from him in his accomplished novels, in as far as he lets no doubt emerge about his characters’ identity or the reality of events revealed in the plot. This is all the more evident because the short sentences in his novel L’Étranger contrast with the intricate and often abstruse parts of The Sound and the Fury. However, when Camus explores the most indefinable aspects of his self in the last chapter of Le Premier Homme, he regenerates his écriture in such a way that the resemblance critics had found with the American writer, in retrospect, seemed to be justified.
Residual stress relief in the aluminium alloy 7075
Authors: Robinson J. S. , Pirling T. , Truman C. E. , Panzner T.
Published: April 2017

The residual stresses in heat-treated 7075 aluminium alloy blocks have been characterised using two neutron diffraction strain scanning instruments. The influence of uniaxial cold compression on relieving the residual stress has been determined. Systematically increasing the magnitude of cold compression from 1 to 10% has been shown to have a small beneficial effect on the final residual stress distribution, by reducing the magnitude of the range in the triaxial residual stresses. The effect of an overaging precipitation treatment on the residual stress has also been characterised, and this was found to have a significant stress relieving influence (25–40%). A relationship between the width of the {311} diffraction peaks and the amount of cold compression was also observed.
Assessing Reservoir Largemouth Bass Standardized Boat Electrofishing: Effect of Catchability on Density and Size Structure Indices
Authors: Tyszko Stephen M. , Hangsleben Matt A. , Zweifel Richard D. , Pritt Jeremy J. , Conroy Joseph D.
Published: April 2017

Understanding catchability—the fraction of a stock caught by a defined unit of effort—is crucial to using fisheries assessment data to index abundance. We conducted mark–recapture experiments to estimate catchability and evaluate standard boat electrofishing methods for assessing populations of Largemouth Bass Micropterus salmoides. We then used a resampling analysis to test for differences in bass CPUE (fish/h and fish/km) between two high-density reservoirs and one low-density reservoir and among surveys within each reservoir. We compared scenarios using surveys conducted only during (1) the standard time period (mid-April to mid-May) and (2) the entire assessment period (early April to mid-June). We considered the percentage of significant differences in CPUE between the high-density and low-density reservoirs to represent statistical power (i.e., the ability to detect a difference in CPUE when a difference actually exists) and the percentage of significant differences in CPUE between surveys in the same reservoir to represent the false-positive rate (i.e., the detection of a difference in CPUE when no difference in density exists). Catchability and CPUE were greatest and least variable during recapture events conducted during the standard period. The mean catchability of sub–stock length Largemouth Bass (150–200 mm) and memorable-length bass (≥510 mm) was significantly less than those for other length categories. Statistical power exceeded 80%, and the false-positive rate was generally less than 10% for sampling during the standard period at as few as six electrofishing sites. When including samples from outside the standard period, power was lower and the false-positive rate was as high as 60%. Power and false-positive rate were similar whether effort was measured in time or distance. Our results emphasize that standardized springtime boat electrofishing assessments validly index Largemouth Bass density and size structure.

Received October 7, 2016; accepted February 2, 2017 Published online April 24, 2017
Which factors to induce hearing loss in professional musicians? Extensive literature review and histopathology findings can answer it
Authors: Di Stadio A.
Published: April 2017

Objective:

To evaluate the determining factors of noise-induced sensorineural hearing loss (SNHL) in professional musicians (PMs).

Methods:

An extensive review using Pubmed, Medscape and Google scholar research was performed and studies with the following keywords were selected: ‘hearing loss, tinnitus, hyperacusis, music, classical music, rock music, pop music, musicians, orchestra, music student, professional musician, non-professional musician, music exposure and temporary hearing loss’. A histopathology study from individuals who during life were musician in orchestra was described.

Results:

Eighty to ninety per cent of PMs are affected from noise-induced SNHL at 3000–8000 Hz frequencies. The range of the frequency of SNHL was correlated with the frequency of the specific frequency of the musical instrument and to the sound intensity which they were exposed. The two temporal bones studied, showed a severely loss hair cells at the basal turn of both cochleae and moderate loss of hair cells in medial and apical turn.

Conclusion:

The review and the results of the temporal bones (TBs) findings show that the intensity and frequency range are the more relevant factors causing noise-induced high frequency SNHL. The time exposed to sound, instead, can impact the low frequency range as supported by temporal bone results.
Discovery and genotyping of novel sequence insertions in many sequenced individuals
Authors: Kavak Pınar , Lin Yen-Yi , Numanagić Ibrahim , Asghari Hossein , Güngör Tunga , Alkan Can , Hach Faraz
Published: April 2017

Motivation

Despite recent advances in algorithms design to characterize structural variation using high-throughput short read sequencing (HTS) data, characterization of novel sequence insertions longer than the average read length remains a challenging task. This is mainly due to both computational difficulties and the complexities imposed by genomic repeats in generating reliable assemblies to accurately detect both the sequence content and the exact location of such insertions. Additionally, de novo genome assembly algorithms typically require a very high depth of coverage, which may be a limiting factor for most genome studies. Therefore, characterization of novel sequence insertions is not a routine part of most sequencing projects.

There are only a handful of algorithms that are specifically developed for novel sequence insertion discovery that can bypass the need for the whole genome de novo assembly. Still, most such algorithms rely on high depth of coverage, and to our knowledge there is only one method (PopIns) that can use multi-sample data to “collectively” obtain a very high coverage dataset to accurately find insertions common in a given population.

Result

Here, we present Pamir, a new algorithm to efficiently and accurately discover and genotype novel sequence insertions using either single or multiple genome sequencing datasets. Pamir is able to detect breakpoint locations of the insertions and calculate their zygosity (i.e. heterozygous versus homozygous) by analyzing multiple sequence signatures, matching one-end-anchored sequences to small-scale de novo assemblies of unmapped reads, and conducting strand-aware local assembly. We test the efficacy of Pamir on both simulated and real data, and demonstrate its potential use in accurate and routine identification of novel sequence insertions in genome projects.

Availability and implementation

Pamir is available at https://github.com/vpc-ccg/pamir.

Supplementary information

Supplementary data are available at Bioinformatics online.
Retrograde accretion discs in high-mass Be/X-ray binaries
Authors: Christodoulou D. M. , Laycock S. G. T. , Kazanas D.
Published: April 2017

We have compiled a comprehensive library of all X-ray observations of Magellanic pulsars carried out by XMM–Newton, Chandra and RXTE in the period 1997–2014. In this work, we use the data from 53 high-mass Be/X-ray binaries in the Small Magellanic Cloud to demonstrate that the distribution of spin-period derivatives versus spin periods of spinning-down pulsars is not at all different from that of the accreting spinning-up pulsars. The inescapable conclusion is that the up and down samples were drawn from the same continuous parent population; therefore, Be/X-ray pulsars that are spinning down over periods spanning 18 yr are, in fact, accreting from retrograde discs. The presence of prograde and retrograde discs in roughly equal numbers supports a new evolutionary scenario for Be/X-ray pulsars in their spin period–period derivative diagram.
COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information
Authors: Zhang Chengxin , Freddolino Lydia , Zhang Yang
Published: April 2017

The COFACTOR web server is a unified platform for structure-based multiple-level protein function predictions. By structurally threading low-resolution structural models through the BioLiP library, the COFACTOR server infers three categories of protein functions including gene ontology, enzyme commission and ligand-binding sites from various analogous and homologous function templates. Here, we report recent improvements of the COFACTOR server in the development of new pipelines to infer functional insights from sequence profile alignments and protein–protein interaction networks. Large-scale benchmark tests show that the new hybrid COFACTOR approach significantly improves the function annotation accuracy of the former structure-based pipeline and other state-of-the-art functional annotation methods, particularly for targets that have no close homology templates. The updated COFACTOR server and the template libraries are available at http://zhanglab.ccmb.med.umich.edu/COFACTOR/.
Glomerular disease frequencies by race, sex and region: results from the International Kidney Biopsy Survey
Authors: O'Shaughnessy Michelle M , Hogan Susan L , Thompson Bawana D , Coppo Rosanna , Fogo Agnes B , Jennette J Charles
Published: April 2017

Background

Large-scale studies comparing glomerular disease frequencies across continents are lacking.

Methods

We surveyed 29 nephropathology laboratories in four continents using a standardized data collection form. We obtained recent consecutive kidney biopsy diagnosis frequencies at each center and summary demographics for each diagnosis. This report focuses on glomerular disease frequencies by region and race/ethnicity.

Results

Among 42 603 glomerular disease diagnoses reported (median age 47 years, 52% male, 57% white), from a total of 60 340 diagnoses, glomerular disease subtype frequencies differed considerably by continent. Diabetic glomerulosclerosis (GS; 19.1%) and focal segmental glomerulosclerosis (FSGS; 19.1%) predominated in North America; lupus nephritis (38.1%) and FSGS (15.8%) predominated in Latin America; IgA nephropathy (IgAN; 22.1%) and FSGS (14.9%) predominated in Europe; and IgAN (39.5%) and lupus nephritis (16.8%) predominated in Asia. After stratifying by race, diabetic GS (17.4% versus 4.3%, P < 0.001) and FSGS (17.3% versus 11.8%, P < 0.001) were more, and lupus nephritis less (15.8% versus 45.6%, P < 0.001), frequent among Latinos in North versus Latin America; FSGS was more (13.1% versus 7.1%, P < 0.001), and IgAN less (27.4% versus 40.5%, P < 0.001), frequent among Asians in North America versus Asia; and FSGS (18.9% versus 13.5%, P < 0.001) and diabetic GS (18.7% versus 6.5%, P < 0.001) were more, and IgAN less (14.4% versus 25.4%, P < 0.001), frequent among whites in North America versus Europe.

Conclusions

We determined that glomerular disease frequencies differed by continent, even among patients of similar race/ethnicity. Regional environmental and lifestyle factors, and local biopsy policies, might influence glomerular disease epidemiology independently of race/ethnicity.
Flow Diverters for Treatment of 160 Ophthalmic Segment Aneurysms: Evaluation of Safety and Efficacy in a Multicenter Cohort
Authors: Griessenauer Christoph J. , Piske Ronie L. , Baccin Carlos E. , Pereira Benedito J.A. , Reddy Arra S. , Thomas Ajith J. , Abud Thiago G. , Ogilvy Christopher S.
Published: April 2017

BACKGROUND: Treatment of ophthalmic segment aneurysms (OSA) remains challenging. Flow diverter stents (FDS) have evolved as a promising endovascular treatment option for aneurysms of the internal carotid artery and are associated with high occlusion rates and a favorable morbidity and mortality profile.

OBJECTIVE: To determine safety and efficacy of FDS for OSA in a large, multicenter cohort.

METHODS: A retrospective analysis of prospectively maintained databases of 127 consecutive patients harboring 160 OSA treated with FDS was performed. Aneurysms were classified based on location and morphology. Follow-up with digital subtraction angiography (DSA) was performed 6 to 18 months after treatment.

RESULTS: Follow-up DSA was available for 101 (63.1%) aneurysms with a mean follow-up of 18 months. Complete occlusion was observed in 90 aneurysms (89.1%), near-complete occlusion (>95%) in 3 (3%), and incomplete occlusion (<95%) in 8 aneurysms (7.9%). One aneurysm was retreated with another FDS (0.9%). No risk factors for incomplete occlusion were identified. The OA was occluded at the latest follow-up in 6 cases (7.1%). Permanent morbidity occurred in 4 patients (3.1%), and there was no mortality related to the FDS procedure.

CONCLUSION: Treatment of OSA with FDS was found to be safe and effective. The retreatment rate was extremely low and aneurysms that occluded did not reanalyze.
Risk of Venous Thromboembolism and Operative Duration in Patients Undergoing Neurosurgical Procedures
Authors: Bekelis Kimon , Labropoulos Nicos , Coy Shannon
Published: April 2017

BACKGROUND: The association of operative duration with the risk of venous thromboembolism (VTE) has not been quantified in neurosurgery.

OBJECTIVE: To investigate the association of surgical duration for several neurosurgical procedures and the incidence of VTE.

METHODS: We performed a retrospective cohort study involving patients who underwent neurosurgical procedures from 2005 to 2012 and were registered in the American College of Surgeons National Quality Improvement Project registry. In order to control for confounding, we used multivariable regression models, and propensity score conditioning.

RESULTS: During the study period, there were 94 747 patients, who underwent neurosurgical procedures, and met the inclusion criteria. Of these, 1358 (1.0%) developed VTE within 30 days postoperatively. Multivariable logistic regression demonstrated an association of longer operative duration with higher 30-day incidence of VTE (odds ratio [OR], 1.22; 95% confidence interval [CI], 1.19-1.25). Compared with procedures of moderate duration (third quintile, 40-60th percentile), patients undergoing the longest procedures (>80th percentile) had higher odds (OR, 3.15; 95% CI, 2.49-3.99) of developing VTE. The shortest procedures (<20th percentile) were associated with a decreased incidence of VTE (OR, 0.51; 95% CI, 0.27-0.76) in comparison to those of moderate duration. The same associations were present in propensity score-adjusted models, and models stratified by subgroups of cranial, spinal, peripheral nerve, and carotid procedures.

CONCLUSIONS: In a cohort of patients from a national prospective surgical registry, increased operative duration was associated with increased incidence of VTE for neurosurgical procedures. These results can be used by neurosurgeons to inform operative management, and to stratify patients with regard to VTE risk.
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in the surface ocean
Authors: Delmont Tom O. , Quince Christopher , Shaiber Alon , Esen Özcan C. , Lee Sonny TM , Lücker Sebastian , Murat Eren A.
Published: April 2017

Nitrogen fixation in the surface ocean impacts the global climate by regulating the microbial primary productivity and the sequestration of carbon through the biological pump. Cyanobacterial populations have long been thought to represent the main suppliers of the bio-available nitrogen in this habitat. However, recent molecular surveys of nitrogenase reductase gene revealed the existence of rare non-cyanobacterial populations that can also fix nitrogen. Here, we characterize for the first time the genomic content of some of these heterotrophic bacterial diazotrophs (HBDs) inhabiting the open surface ocean waters. They represent new lineages within Planctomycetes and Proteobacteria, a phylum never linked to nitrogen fixation prior to this study. HBDs were surprisingly abundant in the Pacific Ocean and the Atlantic Ocean northwest, conflicting with decades of PCR surveys. The abundance and widespread occurrence of non-cyanobacterial diazotrophs in the surface ocean emphasizes the need to re-evaluate their role in the nitrogen cycle and primary productivity.
The relationship of survivorship and body mass modeled by metabolic and vitality theories
Authors: Anderson James J.
Published: April 2017

The relationship between body mass and survivorship is explained by a model that merges metabolic theory relating metabolism to body mass, and vitality theory relating survival to vitality loss and extrinsic mortality. The resulting metabolic-vitality framework hypothesizes mortality results from replicative senescence of the hematopoietic system and predator-prey interactions. Fitting the metabolic-vitality model to body mass and maximum lifespan data of 494 nonvolant mammals yields allometric relationships of body mass to the vitality parameters, from which full survivorship profiles can be predicted from body mass. Comparisons of the mass-derived vitality parameters to those estimated directly from survival data identifies how intrinsic and extrinsic mortality processes of specific populations deviate from the aggregate. Highlighted findings include a mathematical explanation for the shift from Type I to Type II survivorship curves with decreasing body mass, a quantification of the impact of hunting on wild populations and a quantification of the reduce rate of primate aging relative to the aggregate of mammal populations. Finally, the framework allows explorations of the combined effects of animal aging and predation on survival patterns.
Stationary Analysis the Alternative Splicing Profile Reveals the Splicing Code
Authors: Li Meng
Published: April 2017

Recent works indicated that the regulatory function of RBPs showed context dependent manners, but the details of the regulatory function of most RBPs and importance are unknown. Here we integrated hundreds of eCLIP-seq and RNA-seq from ENCODE project and used RBP-position combinations on events to predict if the events are spliced out or not and the results showed that only a small of them can regulate the alternative splicing process in a degree. We observedSRSF1, LIN28B, FMR1, SRSF7, RBM22, PRPF8, SF3B4, TIA1andhnRNP Mare important features by binding the exon or intron region respectively.SF3B4andRBM22show opposite regulatory function when binding exons downstream and upstream intron. This supports the asymmetric exon decision model that state the exon exclusion pathway compete with the exon inclusion pathway to regulate splicing. We also observed that some peaks locate in exon-exon junction regions and indicate some splicing related RBPs also bind on mRNAs.
Caught between norm and difference: narratives on refugees’ inclusion in organizations
Authors: Ponzoni Elena , Ghorashi Halleh , van der Raad Sylvia
Published: April 2017

Purpose

In this study the authors show how discursive spaces both enable and constrain the inclusion of first-generation refugees. For this purpose the authors analyzed a triptych of narratives from first-generation refugees, employers, and mediators (mediating between organizations and job-seeking refugees). The authors adopted a critical studies approach, paying particular attention to the ways in which meanings are embedded within the normalizing discursive processes. The purpose of this paper is to show the maneuvering capacities of three different groups concerning the inclusion of first-generation refugees.

Design/methodology/approach

The data consist of a selected number of narratives from three groups of actors (refugees, mediators and employers) with the ambition of contrasting their discursive positionings. By including multiple positionings in the process, the authors aimed to reveal “the power effects of particular discursive formations,” which Alvessonet al.(2008) refer to as “positioning practices.” To investigate these patterns, the authors used in-depth interviews and employed an interpretive approach with the focus on the narrations of inclusion and exclusion.

Findings

The major constraint the authors discovered was that, in spite of the “good will” of all parties involved, the normalizing impact of the dominant discourses on migrants and refugees (discourse of lack) often works against other approaches (added value). This creates contradictory expectations toward refugees, limiting the possibilities of inclusion within organizations. The findings of this research show that diversity and inclusion can only be successful in conjunction with critical reflection that questions the taken-for-granted position of privileged groups as a norm reproduced by dominant societal discourses.

Research limitations/implications

In the light of growing urgency for the inclusion of refugees in the European context, it is crucial to rethink the notions of inclusion and exclusion from a critical perspective. The authors believe that the findings of the study could have implications which goes beyond the particular experiences presented in this study.

Originality/value

The authors conclude that diversity talk and practice which does not include reflection on the normalizing power of discourses of otherness does not have a chance of making a long-term impact on inclusion. Although there is a growing body of literature on this topic within critical organization studies, there has been no attention so far for the position of refugees in organizations which makes this paper both unique and urgent.
The European virtual seminar on sustainable development as an opportunity for staff ESD competence development within university curricula
Authors: de Kraker Joop , Dlouhá Jana , Machackova Henderson Laura , Kapitulcinová Dana
Published: April 2017

Purpose

The purpose of this paper is to assess the current and potential value of the European Virtual Seminar on Sustainable Development (EVS) as an opportunity for professional development in Education for Sustainable Development (ESD) for teaching staff at university level.

Design/methodology/approach

The paper presents and reflects on the specific case of EVS, including its competence-based approach and educational staff roles. Particular attention is paid to the development of ESD competences of tutors through participation in EVS, based on the UNECE (2011) competence framework and supported by the results from a small-scale questionnaire. Three major aspects of EVS as a professional opportunity in ESD are elaborated: EVS as an on-the-job training opportunity, EVS as an international staff mobility opportunity and EVS as an active learning and innovation community.

Findings

EVS is an effective opportunity for developing a range of ESD competences, especially for junior university staff. The contribution of EVS to professional development in ESD currently extends to a partnership of ten universities from across Europe, but given its features, the EVS approach has the potential to be adopted at a much larger scale. Possible limitations in scaling up are rigid rules for integration of new courses in curricula and the need to form new EVS-like partnerships.

Practical implications

This case study of EVS shows that Web-based, internationally networked courses with a pedagogical approach and design focused on ESD have a large potential in providing effective opportunities for the development of teachers’ ESD competences, but to realize this potential, active uptake of the approach by the existing networks for ESD in higher education is needed.

Originality/value

The paper presents a promising option to address the observed lack of opportunities within university curricula to acquire and practice ESD competences for teaching staff.
The health of older adults in community activities
Authors: Millard Jack
Published: April 2017

Purpose

The purpose of this paper is to establish whether the inclusion of physical activity (PA) in a community programme setting is more beneficial than the benefit obtained from social participation for older adults.

Design/methodology/approach

A cross-sectional study conducted with a sample of 105 adults age 65+ and older that take part in community activities organised by the Bristol based charity LinkAge. Participants took part in either solely social groups or social groups with a PA component. A self-report questionnaire was composed of measures assessing functional health and well-being, health-related quality of life, functional ability, outcome expectation for exercise, and social support.

Findings

A significantly different and higher score on physical health measures was reported by the physically active group for role physical, physical function, bodily pain, and the physical capacity score. No significant difference was found for health measures that include a mental component. The physically active group reported higher outcome expectations for exercise.

Research limitations/implications

Social activity in community programmes may provide a method to maintain a healthy mental state in older adults, but participation in PA in the same environment is associated with better scores for physical health measures.

Originality/value

Providing greater support for older people to engage in physical and social activities may enable them to maintain a higher quality of life.
Lessons learned from designing and evaluating an educational brain fitness program
Authors: Nicholson Roscoe , O’Brien Catherine
Published: April 2017

Purpose

The purpose of this paper is to provide aging services professional insights into older adult responses to brain fitness programs that may not appear on quantitative program evaluations.

Design/methodology/approach

Qualitative data obtained via observations, instructor interviews and feedback, open-ended responses on course evaluations and participant focus groups.

Findings

Participants come to brain fitness programs with a variety of expectations and preferences about program content. Some are looking for educational content, some wanted to learn memory strategies, and others are looking for drilling or brain games. Participants responded very positively to descriptions of brain fitness research and scientific details. However, presenting such content posed a challenge to non-expert instructors, and efforts should be made to reduce this burden. Instructors can play a valuable role in goal setting, but instructors and participants felt that small rewards for meeting goals were unnecessary. Both instructors and participants felt that peer-to-peer interaction is a particularly valuable component of such courses. Overburdening participants should also be avoided. Organizations offering the program were also found to be adapting the course to better fit the organization’s capacities and the desires of participants.

Research limitations/implications

The participant population is largely Caucasian, well-educated and middle to high socioeconomic status.

Practical implications

Due to the characteristics of the participant population, it is not known which, if any, of the findings apply to a less well-educated, lower income populations, or populations from other racial/ethnic groups.

Originality/value

These insights can assist senior living professionals in successfully creating, adopting or adapting brain fitness programs in order to best meet the needs of the populations that they serve.