bluuebunny/crossref_metadata_2025 huggingface dataset:
Solubility study of tobramycin in room temperature ionic liquids: an experimental and computational based study
Authors: Cunningham Richard , Forero-Martinez Nancy C. , Hardacre Christopher , Youngs Tristan G. A. , Migaud Marie E.
Published: November 2016

Herein, we present a computational and experimental study assessing the solubility of tobramycin1in a series of hydrophilic room temperature ionic liquids (RTIL).
Investigating high-school chemical kinetics: the Greek chemistry textbook and students' difficulties
Authors: Gegios Theodoros , Salta Katerina , Koinis Spyros
Published: November 2016

In this study we present an analysis of how the structure and content of the Greek school textbook approach the concepts of chemical kinetics, and an investigation of the difficulties that 11th grade Greek students face regarding these concepts. Based on the structure and content of the Greek textbook, a tool was developed and applied to students in the form of test questions in order to investigate the difficulties that they encounter with concepts and facts of chemical kinetics. Our results indicate that the textbook presentation at several points does not take into consideration basic findings of chemistry education research, which could improve the understanding of the content, and that a large proportion of Greek students show low comprehension levels of the concepts and facts of chemical kinetics. Given the important role of the school textbook in the learning process, it seems that the structure and content of the textbook do not facilitate the conceptual understanding of the subject matter, and together with other factors contribute to the difficulties that students face regarding concepts in chemical kinetics.
Luminescent chemosensors by using cyclometalated iridium(iii) complexes and their applications
Authors: Ma Dik-Lung , Lin Sheng , Wang Wanhe , Yang Chao , Leung Chung-Hang
Published: November 2016

This review describes recent examples of cyclometalated iridium(iii) metal complexes that act as luminescent chemosensors for cations, anions or small molecules.
Metal-free O–H/C–H difunctionalization of phenols by o-hydroxyarylsulfonium salts in water
Authors: Chen Dengfeng , Feng Qingyuan , Yang Yunqin , Cai Xu-Min , Wang Fei , Huang Shenlin
Published: November 2016

Polyfunctional aromatic rings have been constructed by direct functionalization of C–H and O–H bonds to C–S and C–O bonds under mild and green conditions.
Local heterojunctions of atomic Pt clusters boost the oxygen reduction activity of Rucore@Pdshell nanocrystallites
Authors: Wang Jeng Han , Wang Kuan-Wen , Chen Tian-Lin , Wang Chia-Hsin , Huang Yu-Ming , Hsu Yang-Yang , Chen Tsan-Yao
Published: November 2016

Atomic scale Pt clusters attract the valence electron from sublayer crystallites to facilitate oxygen reduction kinetics at core–shell NPs.
Controllable synthesis of single crystalline Sn-based oxides and their application in perovskite solar cells
Authors: Yeom Eun Joo , Shin Seong Sik , Yang Woon Seok , Lee Seon Joo , Yin Wenping , Kim Dasom , Noh Jun Hong , Ahn Tae Kyu , Seok Sang Il
Published: November 2016

We synthesized single-crystalline Sn-based oxides for use as electron-transporting layers (ETLs) in perovskite solar cells (PSCs).
Reprecipitation synthesis of luminescent CH3NH3PbBr3/NaNO3 nanocomposites with enhanced stability
Authors: Yang Gaoling , Fan Qingsong , Chen Bingkun , Zhou Qingchao , Zhong Haizheng
Published: November 2016

A facile one-step method was developed to fabricate luminescent CH3NH3PbBr3/NaNO3 nanocomposites. Due to the space localization and protection of the tight inorganic salt matrix, the nanocomposites show a longer PL lifetime and enhanced thermal, light, and solvent stability.
LDPC coded lossy forwarding scheme for cooperative wireless networks
Authors: Jayakody D.N.K.
Published: November 2016

A new methodology for lossy forwarding based on a novel technique known as soft angular modulation is investigated. In this new relay (R) scheme, the soft symbols are embedded into phases at the R. This is more advantageous as to forward real values (under bandwidth constraints) via wireless channels is refrained. This makes the proposed scheme practically feasible. The proposed system provides a means of using distributed low‐density parity‐check coding. This also precludes the amplitudes of generated symbols descent to zero, as happens with most of the existing soft forwarding (or lossy) methods. Ordinarily, such schemes suffer from error propagation to the destination when the signal‐to‐noise ratio of the source (S)–R link is low; however, the system avoids this problem by regenerating soft versions of the S symbols at the R. Simulation results demonstrate that the proposed scheme can maintain very good performance.
Disrupting the world of Disability: The Next Generation of Assistive Technologies and Rehabilitation Practices
Authors: Holloway Catherine , Dawes Helen
Published: November 2016

Designing, developing and deploying assistive technologies at a scale and cost which makes them accessible to people is challenging. Traditional models of manufacturing would appear to be insufficient at helping the world's 1 billion disabled people in accessing the technologies they require. In addition, many who receive assistive technologies simply abandon them as they do not meet their needs. In this study the authors explore the changing world of design for disability. A landscape which includes the rise of the maker movement, the role of ubiquitous sensing and the changing role of the ‘user’ to one of designer and maker. The authors argue they are on the cusp of a revolution in healthcare provision, where the population will soon have the ability to manage their own care with systems in place for diagnosis, monitoring, individualised prescription and action/reaction. This will change the role of the clinician from that of diagnostician, gatekeeper and resource manager/deliverer to that of consultant informatics manager and overseer; perhaps only intervening to promote healthy behaviour, prevent crisis and react at flash moments.
Typical synergistic effect of graphite nanoplatelets and carbon nanotubes and its influence on polymer‐based dielectric composites
Authors: Zhao Hang , Yang Minhao , He Delong , Liu Yu , Bai Jintao , Wang Hui , Chen Haowei , Bai Jinbo
Published: November 2016

Graphite nanoplatelets (GNPs) with their intrinsic two‐dimensional structure make an excellent compromise of advantages of both graphite and graphene. Due to their outstanding inherent properties, GNPs have been widely used as the functional fillers to improve certain performances of polymer‐based composites. However, the multi‐layer stacked construction of GNPs could form aggregations easily, which limits their application in polymer‐based dielectric composites. Here, the authors exhibit a polydimethylsilicone (PDMS)‐based nanocomposite which loading equivalent carbon nanotubes (CNTs) and GNPs as co‐loading fillers, whose dielectric properties are improved significantly. The composites were fabricated through a highly‐shearing mechanical mixing process. During the mixing process, both intrinsic CNTs entanglements and GNPs stacked aggregation could be ameliorated due to the interaction between these two types of fillers. Compared with the GNPs solely loaded composites, a small quantity of CNTs addition endows GNPs/CNTs/PDMS ternary composites with a significantly decreased percolation threshold (fc ∼ 1.7 vol.%). Both GNPs and CNTs, these two representative conductive carbon constructions with high aspect ratios are able to effectively enhance the establishing efficiency of internal conductive network inner composites. These results indicate that the development of internal conductive network and dielectric performance of nanocomposites are able to be optimised through the strategy of taking advantage of the synergistic effect of multi‐type fillers reasonably.
Energy storage properties of PVDF terpolymer/PMMA blends
Authors: Chu Baojin , Zhou Yang
Published: November 2016

Dielectrics can be used to store electric energy in capacitors and high‐energy density of the materials is desirable to reduce the size or weight of capacitors. To improve the energy storage properties of poly(vinylidene fluoride–trifluoroethylene–chlorofluoroethylene) [P(VDF–TrFE–CFE)] terpolymer, P(VDF–TrFE–CFE)/poly(methyl methacrylate) (PMMA) blends were investigated in this study. By adding a small amount of PMMA into PVDF terpolymer (<5 wt%), the dielectric breakdown field of the blends can be improved as a result of the enhancement of elastic modulus of the blends. For the blends with <2.5 wt% PMMA, though their dielectric properties are reduced, under the same electric field, the energy density of the blends is almost the same as that of PVDF terpolymer. Consequently, the energy storage performance of the terpolymer can be improved by blending with a small amount of PMMA.
Surface‐modified barium titanate by MEEAA for high‐energy storage application of polymer composites
Authors: Shen Yanbin , Luo Suibin , Yu Shuhui , Sun Rong , Wong Ching‐Ping
Published: November 2016

In this study, 2‐[2‐(2‐methoxyethoxy)ethoxy]acetic acid (MEEAA) was used to modify the surface of barium titanate nanoparticles (BT NPs) to enhance the compatibility and dispersion of the BT ceramic fillers in polymer matrix. A uniform coating layer with a thickness about 2 nm was formed on the surface of BT after modification. The poly(vinylidene fluoride)‐hexafluoropropene [P(VDF‐HFP)] composites filled with MEEAA‐modified BT NPs achieved higher permittivity(∼13 at 3.0 vol% filler) and discharged energy density than that of the untreated BT filled composite. The maximum discharge energy density of 7.8 J/cm3 was obtained in the nanocomposites with 3 vol% MEEAA‐modified BT NPs at electric field of 425 kV/mm, which is 77% higher than that of 4.4 J/cm3 of pure P(VDF‐HFP) film at electric field of 420 kV/mm.
Integrated model predictive control with reduced switching frequency for modular multilevel converters
Authors: Dekka Apparao , Wu Bin , Yaramasu Venkata , Zargari Navid R.
Published: November 2016

The indirect model predictive control (I‐MPC) is one of the reduced computational predictive strategies, used to control the modular multilevel converter (MMC). This approach operates at higher switching frequency, which is not desirable for high‐power applications. This study proposes an integrated solution for MMC by combining predictive control with the classical energy balancing approach. To implement the predictive algorithm, a detailed three‐phase MMC model is presented. The three‐phase model includes the zero sequence voltage to reduce the switching frequency of submodules. In addition, the output power quality is enhanced, while operating at reduced switching frequency. The performance of integrated approach is experimentally validated on a laboratory prototype under balanced and unbalanced conditions. In addition, the performance of integrated approach is compared with the existing methodology in terms of output current ripple, switching frequency, computational complexity, and total harmonic distortion.
Modelling the low‐frequency dielectric response test of insulation oil
Authors: Wang Dongyang , Zhou Lijun , Chen Xuejiao , Jiang Junfei , Wang Lujia
Published: November 2016

The frequency domain dielectric response method has been one of the most effective approaches for condition assessment of an electrical insulation system. The low‐frequency part is more effective for diagnosing the moisture content and aging status of oil‐paper insulation. To facilitate the study of the low‐frequency dielectric spectrum of oil‐paper insulation, a model applicable to the low‐frequency dielectric response of insulation oil is proposed in this study, which is based on the ionic motion of insulation oil. The creation of charge carriers under field test conditions mainly derives from the dissociation of ionic pairs. During testing, ionic motion of insulation oil is jointly affected by thermal diffusion and the electric field; moreover, dissociation and recombination of negative and positive ions also occur. Therefore, the above factors were all considered in the modelling process. The applicability of the model is verified against measured results. For further interpreting the proposed model, the characteristics of the ionic concentration distribution, the relation between ionic distribution and dielectric properties, and the application of the proposed model are analysed.
Influence of partial substitution for CB with MWNTs on performance of CB‐filled NR composites
Authors: Zhang Huan , Wei Yintao , Kang Zhenran , Zhao Guizhe , Liu Yaqing
Published: November 2016

The effects of substituting carbon black (CB) with multiwall carbon nanotubes (MWNTs) on the structure and properties of natural rubber (NR)/CB composites is explored. Compared with NR/CB composites, NR/MWNTs/CB presents better filler dispersity and dynamic properties of the MWNT up to a certain concentration, as confirmed by scanning electron microscope, dynamic mechanical analyser and rubber processing analyser. Sample with 1 phr MWNTs shows obviously the highest tensile strength, 28.60 MPa, and almost the lowest heat build‐up, only 9.6°C, and it is attributed to that not only large cross‐link density and better filler dispersity but also high effective elasticity and large filler–rubber interaction. However, when the concentration is much higher, MWNTs tend to aggregate and lead to the poor efficiency to enhance the dynamic properties of rubber composites or even deteriorate the properties.
Synthesis of double‐shelled hollow silica sphere with single‐shelled hollow silica sphere and cetyltrimethyl ammonium bromide as dual templates
Authors: Zhou Gaoxin , Zhang Zhilong , Chen Bo , Wang Ying , Ding Yu , Zhang Xiaolu , Ji Min
Published: November 2016

In this work, single‐shelled hollow mesoporous silica nanoparticles (SHMSNs) were first fabricated via template method and surface‐protected etching strategy with the aid of cetyltrimethyl ammonium bromide (CTAB). Then, double‐shelled hollow mesoporous silica nanoparticles (DHMSNs) were successfully synthesised based on single‐shelled hollow mesoporous silica. The etching procedure using sodium carbonate as etchant, the surface‐protected etching time and the influence of CTAB were discussed in detail. Experimental results showed that a warm and effective etching process could be achieved at 39°C for 3 h with CTAB protection. The resulting SHMSNs and DHMSNs were characterised by transmission electron microscope, scanning electron microscope, and nitrogen adsorption–desorption isotherms. In addition, it was proved that SHMSNs and DHMSNs possessed a well‐defined hollow structure and uniform size. It is believed that the nanostructure feature some implication for creating other hollow structures.
Synthesis of transferable nanoporous PtFe/Au film with enhanced electrocatalytic activity
Authors: Yin Yingying , Zhao Jianwei , Qin Lirong , Yang Yu , He Lizhong
Published: November 2016

An ordered nanoporous PtFe/Au film is synthesised via a simple two‐step strategy based on sputtering and electrochemical deposition onto anodic aluminium oxide template. The morphology image of PtFe/Au film is characterised. The results reveal that the prepared porous film consists of ordered hexagonal array of nanoholes with a pore diameter of 40 nm and a periodic distance of 120 nm. PtFe/Au film after dissolving the template can maintain its integrality and is transferable. The PtFe/Au nanoporous film based electrode shows high catalytic activity for oxidation of methanol in alkaline ambiance which making it more attractive for fuel cell operations.
Novel Mutation in PLA2G6 Gene in a Patient with Infantile Neuroaxonal Dystrophy
Authors: Veerapandiyan Aravindhan , Chaudhari Amit , Aravindhan Akilandeswari , Hayes-Rosen Caroline
Published: November 2016

Infantile neuroaxonal dystrophy (INAD) is an autosomal recessive disorder that causes psychomotor regression. Clinicopathological features include truncal hypotonia followed by spastic quadriparesis, strabismus, nystagmus, cerebellar ataxia, bulbar dysfunction, and cerebellar atrophy. INAD is associated with a variety of mutations in the PLA2G6 gene that encodes the group VI calcium-independent phospholipase A2 protein which is important in cell membrane homeostasis. Defects in this protein cause axonal dystrophy. We report a 2-year-old boy with INAD who was found to have a novel deletion c.1019_1025del7 leading to a frame shift in the PLA2G6 gene. We suggest that this change may be an addition to the array of mutations causing INAD.
Engineering interface-type resistance switching based on forming current compliance in ITO/Ga2O3:ITO/TiN resistance random access memory: Conduction mechanisms, temperature effects, and electrode influence
Authors: Pan Chih-Hung , Chang Ting-Chang , Tsai Tsung-Ming , Chang Kuan-Chang , Chen Po-Hsun , Chang-Chien Shi-Wang , Chen Min-Chen , Huang Hui-Chun , Wu Huaqiang , Deng Ning , Qian He , Sze Simon M.
Published: November 2016

In this paper, an ITO/Ga2O3:ITO/TiN structured resistance random access memory is introduced. Either interface or filament conduction mechanism can be induced depending on the forming compliance current, which has not been investigated before. Material analyses and electrical I–V measurements on this ITO/Ga2O3:ITO/TiN have also been carried out. The interface conduction mechanism was confirmed by a size-effect experiment, where resistance varied inversely to via size. In addition, the current fitting results show that Schottky emission dominates the on- and off-state currents. All physical mechanisms of device resistive switching behaviors are explained by our models and also confirmed by I–V characteristics.
Dynamics of heteromolecular filament formation
Authors: Dear Alexander J. , Michaels Thomas C. T. , Knowles Tuomas P. J.
Published: November 2016

The self-assembly of molecular building blocks into linear filaments is a common form of self-organization in nature and underlies the formation of supra-molecular polymers in a variety of contexts, including in both functional and aberrant biology. To date, attention has focused mainly on homomolecular assembly phenomena; however, it has recently become apparent that heteromolecular assemblies can be common, and, for instance, pathological protein filaments such as amyloid aggregates form in vivo in environments supporting copolymerization. Here, we present a general kinetic scheme for heteromolecular filament formation and derive closed-form analytical expressions that describe the dynamics of such systems. Our results reveal the existence of a demixing transition time controlled by the relative rates of depletion of the different aggregating species, after which predominantly homomolecular polymers are formed even when the initial solution is heteromolecular. Furthermore, these results may be applied to the analysis of experimental kinetic data on the aggregation of mixtures of proteins, to determine which fundamental reaction steps occur between unlike proteins, and to provide accurate estimates of their rate constants.
Observation of longitudinal quadrupole ion bunch oscillations in an electrostatic ion beam trap
Authors: Saha K. , Gangwar R. K. , Heber O. , Rappaport M. L. , Zajfman D.
Published: November 2016

Ions in an ion bunch trapped inside an Electrostatic Ion Beam Trap (EIBT) exhibit collective oscillations within the bunch under the influence of an external driving force. These internal oscillations have been measured explicitly using a new method with a particle detector outside the EIBT. In this approach, the evolving ion bunch is monitored along the entire trap length, in contrast to the localized single point measurements that are often carried out in other techniques. In the present study, quadrupole oscillations have been measured for the first time in an EIBT along with the dipole oscillations that were measured previously. The frequency of the quadrupole oscillation is found to be about twice the dipole oscillation frequency. This is in agreement with the prediction of a theoretical model.
Effect of β-stabilizer elements on stacking faults energies and ductility of α-titanium using first-principles calculations
Authors: Salloom R. , Banerjee R. , Srinivasan S. G.
Published: November 2016

The effect of W, Mo, V, Ta, and Nb, five common β-stabilizing substitutional elements, on α-Ti stacking fault energy has been studied using first principle calculations. The generalized stacking fault energy (GSFE) curves have been determined for different concentrations of β-stabilizers at the fault plane using supercells with up to 360 atoms. Both basal and prismatic slip systems with the stable (γSF) and unstable (γUSF) stacking faults and twinning fault energies were determined. All the alloying elements reduce the stacking fault energy for Ti for both basal and prismatic slip. At higher concentration of 25 at. % of V, Ta, and Nb at the slip plane, the basal slip becomes more favorable than the prismatic slip in Ti. Ti-Mo and Ti-W systems also show a significant shift in the GSFE curve towards a higher shear deformation strain along 〈011¯0〉 due to the change in bond character between Ti and those two elements. Using Rice criterion, which employs γS/γUSF ratio to estimate ductility, we show that all the alloying elements likely improve the ductility of α-Ti with Ti-25 at. % Nb exhibiting the most ductile behavior. However, according to the Tadmor and Bernstein model, all the alloying elements considered here do not improve the partial dislocation emission or the twinning propensity in spite of decreasing the stacking fault energies for α-Ti and. Hence, a better empirical model that incorporates changes in the character of directional bonding upon alloying is needed to estimate how alloying influences ductility in hcp metals.
Analytic study of a rolling sphere on a rough surface
Authors: Florea Olivia A. , Rosca Ileana C.
Published: November 2016

In this paper it is realized an analytic study of the rolling’s sphere on a rough horizontal plane under the action of its own gravity. The necessities of integration of the system of dynamical equations of motion lead us to find a reference system where the motion equations should be transformed into simpler expressions and which, in the presence of some significant hypothesis to permit the application of some original methods of analytical integration. In technical applications, the bodies may have a free rolling motion or a motion constrained by geometrical relations in assemblies of parts and machine parts. This study involves a lot of investigations in the field of tribology and of applied dynamics accompanied by experiments. Multiple recordings of several trajectories of the sphere, as well as their treatment of images, also followed by statistical processing experimental data allowed highlighting a very good agreement between the theoretical findings and experimental results.
Synthesis and Characterisation of Hierarchically Porous HZSM-5 as Catalysts for the Synthesis of 2,3,5-Trimethyl-1,4-benzoquinone
Authors: Shen Yu , Wang Fumin , Yang Chaoqun , Zhang Xubin
Published: October 2016

Hierarchical HZSM-5 were synthesised by controlled desilication in alkaline medium and characterised by field-emission scanning electron microscopy, X-ray diffraction, transmission electron microscopy, inductively coupled plasma–atomic emission spectrometry, N2 adsorption–desorption, and Fourier transform infrared spectroscopy. The catalytic performance of HZSM-5 towards the selective oxidation of 2,3,6-trimethylphenol by H2O2 was evaluated. Recyclability tests were also carried out. The results showed that 2,3,5-trimethyl-1,4-benzoquinone was produced in high yields (i.e. 90 %), corresponding to a 2,3,6-trimethylphenol percentage of 98 %. The N2 adsorption–desorption and XRD studies suggested that mesopores with an average size of 5 nm were produced and that the structural character of HZSM-5 was preserved after desilication. Transmission electron microscopy analysis of the spent catalyst indicated good stability of the hierarchical structure. The Fourier transform infrared spectroscopy studies revealed the development of acid sites. The combined results suggested that the nature of the solvent, intrinsic acidity, and shape selectivity of the hierarchical structure of the catalyst ensured high catalytic properties.
Molecules and morphology unite Sarcophaga (Stackelbergeola) Rohdendorf and S. (Rohdendorfisca) Grunin within megadiverse Sarcophaga Meigen (sensu lato) (Diptera, Sarcophagidae)
Authors: Zhang Ming , Buenaventura Eliana , Pape Thomas , Zhang Dong
Published: October 2016

The largest genus of the family Sarcophagidae (Insecta, Diptera), Sarcophaga Meigen (sensu lato), has ~160 subgenera; however, the validity and phylogenetic relationships of these are still unclear, impeding progress in evolutionary studies. This study presents a phylogenetic hypothesis for selected subgenera of Sarcophaga s.l. based on COI sequences (685 bp) for 87 species representing 27 valid subgenera. The subgenera Stackelbergeola Rohdendorf and Rohdendorfisca Grunin are reconsidered in the light of new molecular, morphological and biological data. The female is described for the first time for a representative of both subgenera, and Sarcophaga (Rohdendorfisca) flagellifera (Grunin) is shown to be a parasitoid of tettigoniid grasshoppers. As the male of Sarcophaga (Stackelbergeola) sushkini (Rohdendorf) is insufficiently documented in the literature, a redescription is provided based on material from Xinjiang, thereby providing the first record of this subgenus and species from China. Detailed documentation through photographs, scanning electron microscopy and illustrations of the adult morphology is also provided. The subgenera Stackelbergeola and Rohdendorfisca are shown to be monophyletic, together forming a monophylum supported by molecular and morphological data, and they are placed in a wider phylogenetic context of the megadiverse genus Sarcophaga s.l.
Pseudoscorpions of the family Feaellidae (Pseudoscorpiones : Feaelloidea) from the Pilbara region of Western Australia show extreme short-range endemism
Authors: Harvey Mark S. , Abrams Kym M. , Beavis Amber S. , Hillyer Mia J. , Huey Joel A.
Published: October 2016

The phylogenetic relationships of the Australian species of Feaellidae are assessed with a molecular analysis using mitochondrial (CO1) and nuclear (ITS2) data. These results confirm the morphological analysis that three previously undescribed species occur in the Pilbara bioregion, which are named and described: Feaella (Tetrafeaella) callani, sp. nov., F. (T.) linetteae, sp. nov. and F. (T.) tealei, sp. nov. The males of these three species, as well as males of F. anderseni Harvey and other unnamed species from the Kimberley region of north-western Australia, have a pair of enlarged, thick-walled bursa that are not found in other feaellids. Despite numerous environmental impact surveys for short-range endemic invertebrates in the Pilbara, very few specimens have been collected, presumably due to their relictual distributions, restricted habitat preferences and low densities. http://zoobank.org/urn:lsid:zoobank.org:pub:131F0587-F2EE-405F-BE5A-772F072D9915
Graphical Function Mapping as a New Way to Explore Cause-and-Effect Chains
Authors: Evans Mary Anne
Published: November 2016

Graphical function mapping provides a simple method for improving communication within interdisciplinary research teams and between scientists and nonscientists. This article introduces graphical function mapping using two examples and discusses its usefulness. Function mapping projects the outcome of one function into another to show the combined effect. Using this mathematical property in a simpler, even cartoon-like, graphical way allows the rapid combination of multiple information sources (models, empirical data, expert judgment, and guesses) in an intuitive visual to promote further discussion, scenario development, and clear communication.

El mapeo gráfico-funcional ofrece un método simple para mejorar la comunicación hacia el interior de los grupos de investigación interdisciplinaria, así como también entre los científicos y los no científicos. En este artículo se introduce el mapeo gráfico-funcional, usando dos ejemplos y se discute su utilidad. El mapeo funcional proyecta el resultado de una función en otra para mostrar el efecto combinado. El uso de esta propiedad matemática traducido de una manera gráfica sencilla, incluso caricaturizada, permite una rápida combinación de múltiples fuentes de información (modelos, datos empíricos, juicios expertos y tanteos) dentro de un contexto visual intuitivo que promueve la discusión, el desarrollo de escenarios y una comunicación más eficiente.

La fonction de mapping graphique fournit une méthode simple pour améliorer la communication au sein des équipes de recherche interdisciplinaires et entre scientifiques et non-scientifiques. Cet article présente la fonction de mapping graphique à l'aide de deux exemples et discute de son utilité. La fonction de mapping graphique projette le résultat d'une fonction dans un autre pour en montrer l'effet combiné. L'utilisation de cette propriété mathématique de manière graphique simple, même caricaturale, permet la combinaison rapide de multiples sources d'information (modèles, données empiriques, jugement d'expert, et suppositions) dans un visuel intuitif pour promouvoir davantage la discussion, l'élaboration de scénarios, et une communication claire.
Mental Health Court Participants' Perspectives of Success: What Key Outcomes Are We Missing?
Authors: Canada Kelli E. , Ray Brad
Published: November 2016

Mental health court research has largely assessed program effectiveness using criminal recidivism as an indicator of success. The present study expands this literature by exploring mental health court participants' perceptions of how the mental health court impacted them. We analyzed in-depth interviews with 26 participants from 2 different mental health courts using thematic analysis. Participants identified four salient successes that they perceived to result from mental health court participation: improved psychiatric stability, sobriety, improved relationships, and increased engagement in life and mental health. While reduced substance use and “staying out of trouble” were seen as successes, participants also reported recovery-oriented outcomes like improved relationships with family, mood stability, increased patience, ability to care about others, and greater understanding of mental illness as measures of their success. Although recidivism is an indicator of success, future mental health court research would benefit from utilizing additional measures of success that span criminal justice, recovery, and mental health outcomes.
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
Authors: Fortin Jean-Philippe , Triche Timothy J. , Hansen Kasper D
Published: November 2016

The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC (‘EPIC’) array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 (‘450k’) and EPIC platforms. We introduce the single-sample Noob (ssNoob) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data.

Availability and Implementation

The minfi package version 1.19.12 or higher is available for all platforms from the Bioconductor project.

Supplementary information

Supplementary data are available at Bioinformatics online.
A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm
Authors: Fresno Cristóbal , González Germán Alexis , Merino Gabriela Alejandra , Flesia Ana Georgina , Podhajcer Osvaldo Luis , Llera Andrea Sabina , Fernández Elmer Andrés
Published: November 2016

Motivation

The PAM50 classifier is used to assign patients to the highest correlated breast cancer subtype irrespectively of the obtained value. Nonetheless, all subtype correlations are required to build the risk of recurrence (ROR) score, currently used in therapeutic decisions. Present subtype uncertainty estimations are not accurate, seldom considered or require a population-based approach for this context.

Results

Here we present a novel single-subject non-parametric uncertainty estimation based on PAM50’s gene label permutations. Simulations results (n = 5228) showed that only 61% subjects can be reliably ‘Assigned’ to the PAM50 subtype, whereas 33% should be ‘Not Assigned’ (NA), leaving the rest to tight ‘Ambiguous’ correlations between subtypes. The NA subjects exclusion from the analysis improved survival subtype curves discrimination yielding a higher proportion of low and high ROR values. Conversely, all NA subjects showed similar survival behaviour regardless of the original PAM50 assignment. We propose to incorporate our PAM50 uncertainty estimation to support therapeutic decisions.

Availability and Implementation

Source code can be found in ‘pbcmc’ R package at Bioconductor.

Supplementary information

Supplementary data are available at Bioinformatics online.
Eastern Baltic cod recruitment revisited—dynamics and impacting factors
Authors: Köster Friedrich W. , Huwer Bastian , Hinrichsen Hans-Harald , Neumann Viola , Makarchouk Andrei , Eero Margit , Dewitz Burkhard V. , Hüssy Karin , Tomkiewicz Jonna , Margonski Piotr , Temming Axel , Hermann Jens-Peter , Oesterwind Daniel , Dierking Jan , Kotterba Paul , Plikshs Maris
Published: October 2016

The Eastern Baltic cod abundance started rapidly to increase in the mid-2000s as evidenced by analytical stock assessments, due to increased recruitment and declining fishing mortality. Since 2014, the analytical stock assessment is not available, leaving the present stock status unclear and casting doubts about the magnitude of the recent increase in recruitment. Earlier studies identified main factors impacting on cod reproductive success to be related to the loss of two out of three spawning areas in the 1980s caused by lack of major Baltic inflows with a concurrent reduction in salinity and oxygen. Other important factors include prey availability for first-feeding larvae, egg predation by sprat and herring and cannibalism on juveniles, all in one way or the other related to the prevailing hydrographic conditions. These factors cannot explain increased reproductive success in the last decade, as the period was characterized by an absence of large-scale Baltic inflows since 2003 and persistent anoxic conditions in the bottom water of the deep Baltic basins. This questions the perception of the increased recruitment in later years and challenges our present understanding of cod recruitment dynamics in the Baltic Sea. In this contribution, we review evidence from the recent literature supplemented by information from latest research cruises to elucidate whether cod reproductive success indeed has increased during the last decade, and we suggest the key processes responsible for the recent dynamics in cod recruitment and outline directions for future research.
Adaptive full-order and reduced-order observers for one-sided Lur'e systems with set-valued mappings
Authors: Shi Min-Jie , Huang Jun , Chen Liang , Yu Lei
Published: November 2016

This article proposes an adaptive observer design method for one-sided Lipschitz Lur'e differential inclusion systems with unknown parameters. First, under some assumptions, we design an adaptive full-order observer for the system. Then, under the same assumptions, a reduced-order observer is proved to be valid. Finally, we simulate an example to show the effectiveness of the presented method under the background of rotor system.
Historical Durability of Resistance to Wheat Diseases in Kansas
Authors: Bockus William W. , De Wolf Erick D. , Gill Bikram S. , Jardine Douglas J. , Stack James P. , Bowden Robert L. , Fritz Allan K. , Martin T. Joe
Published: November 2016

In Kansas, estimated annual losses from wheat diseases averaged 16% from 1976 through 1988; however, losses have declined to 10% in recent years. This decline is mainly due to emphasis on developing cultivars with resistance to important diseases. Data from annual KSU extension publications were used to track disease ratings over time for individual wheat cultivars to eight diseases to draw inferences on the durability of deployed resistance. The duration of durability of resistance to leaf rust has been short for some cultivars but moderate for others. Conversely, the duration of durability of resistance to stem and stripe rusts has been long, although a recent virulence shift in the stripe rust pathogen indicates only moderate duration. Duration of durability of resistance toward tan spot, Septoria tritici blotch, wheat soilborne mosaic, and wheat spindle streak mosaic has been long. Resistance to wheat streak mosaic has been of long duration in some cultivars but others have shown only moderate duration of durability. The effort by breeders to produce cultivars with resistance to diseases in Kansas has resulted in an annual savings of about $58 million. Just as important as the incorporation of resistance into those cultivars is the moderate to long duration of durability of the resistance contributing to effective management of these diseases.

Accepted for publication 22 June 2011. Published 2 August 2011.
Estimating Population Densities of Root Lesion Nematodes, Pratylenchus spp., from Soil Samples Using Dual Active and Passive Assays
Authors: MacGuidwin Ann E. , Bender Breann E.
Published: November 2016

Root lesion nematodes are versatile parasites that move freely between root and soil habitats. Most laboratories conduct separate assays for soil or root tissue, using time-of-year as the selecting factor. We used a dual assay that simultaneously extracts nematodes from soil and root fragments in soil samples to identify the value of soil versus root tests using 920 research samples collected 1 April to 15 May, and 853 clinic samples collected year round. Nematodes were recovered from both soil and root fragments regardless of the time of year or origin of the sample. When the data were summarized by cohort, the mean percentage of nematodes recovered from root fragments was 65% for the research samples, 59% for clinic samples submitted 1 March to 15 June, 56% for clinic samples submitted 16 June to 31 July, and 49% for clinic samples submitted after 1 August. Both the incidence and population density of root lesion nematodes was underestimated if only the soil or only the root fraction was considered, indicating the need for testing methods that consider both habitats. The variability among samples for the distribution of nematodes between root and soil habitats was high, negating the option of running one assay and using a constant scaling factor to account for the other.

Accepted for publication 30 October 2012. Published 20 November 2012.
Modeling Cognitive Processes with Neural Reinforcement Learning
Authors: Bosch S.E. , Seeliger K. , van Gerven M.A.J.
Published: October 2016

Artificial neural networks (ANNs) have seen renewed interest in the fields of computer science, artificial intelligence and neuroscience. Recent advances in improving the performance of ANNs open up an exciting new avenue for cognitive neuroscience research. Here, we propose that ANNs that learn to solve complex tasks based on reinforcement learning, can serve as a universal computational framework for analyzing the neural and behavioural correlates of cognitive processing. We demonstrate this idea on a challenging probabilistic categorization task, where neural network dynamics are linked to human behavioural and neural data as identical tasks are solved.
The neural basis of precise visual short-term memory for complex recognisable objects
Authors: Veldsman Michele , Mitchell Daniel J. , Cusack Rhodri
Published: November 2016

Recent evidence suggests that visual short-term memory (VSTM) capacity estimated using simple objects, such as colours and oriented bars, may not generalise well to more naturalistic stimuli. More visual detail can be stored in VSTM when complex, recognisable objects are maintained compared to simple objects. It is not yet known if it is recognisability that enhances memory precision, nor whether maintenance of recognisable objects is achieved with the same network of brain regions supporting maintenance of simple objects.

We used a novel stimulus generation method to parametrically warp photographic images along a continuum, allowing separate estimation of the precision of memory representations and the number of items retained. The stimulus generation method was also designed to create unrecognisable, though perceptually matched, stimuli, to investigate the impact of recognisability on VSTM. We adapted the widely-used change detection and continuous report paradigms for use with complex, photographic images.

Across three functional magnetic resonance imaging (fMRI) experiments, we demonstrated greater precision for recognisable objects in VSTM compared to unrecognisable objects. This clear behavioural advantage was not the result of recruitment of additional brain regions, or of stronger mean activity within the core network. Representational similarity analysis revealed greater variability across item repetitions in the representations of recognisable, compared to unrecognisable complex objects. We therefore propose that a richer range of neural representations support VSTM for complex recognisable objects.
Starting from the end: what to do when restricted data is released
Authors: Teperek Marta , Morgan Rhys , Ellefson Michelle , Kingsley Danny
Published: November 2016

Repository managers can never be one hundred percent sure of the security ofhosted research data. Even assuming that human errors and technical faults will never happen, repositories can be subject to hacking attacks. Therefore, repositories accepting personal/sensitive data (or other forms of restricted data) should have workflows in place with defined procedures to be followed should things go wrong and restricted data is inappropriately released. In this paper wewill report on our considerations and procedures when restricted data from ourinstitution was inappropriately released.
Standard Issue: Copy number heterogeneity of JC virus standards discovered through next-generation sequencing
Authors: Greninger Alexander L. , Bateman Allen C. , Atienza Ederlyn E. , Wendt Sharon , Jerome Keith R. , Cook Linda
Published: November 2016

Quantitative PCR is a diagnostic mainstay of clinical virology, and accurate quantitation of viral load among labs requires the use of international standards. However, the use of multiple passages of viral isolates to obtain sufficient material for international standards may result in genomic changes that complicate their use as quantitative standards. We performed next-generation sequencing to gain single-nucleotide resolution and relative copy number of JC virus (JCV) clinical standards. Strikingly, the WHO international standard and ExactTMv1/v2 prototype standards for JCV showed 8-fold and 4-fold variation in genomic coverage between different loci in the viral genome, respectively, due to large deletions in the large T-antigen region. No such variation was seen for a clinical sample with high copy-number of JCV nor a plasmid control. Intriguingly, several of the JCV standards sequenced in this study with large T-antigen deletions were cultured in cell lines immortalized using SV40 T-antigen, suggesting the possibility of trans-complementation in cell culture. Using a cut-off of 2% variant allele fraction for junctional reads to define the presence of a strain, 11 different strains were present in the WHO standard. In summary, targeting of different regions of the same international standard could result in up to an 8-fold difference in quantitation. We recommend the use of next-generation sequencing to validate standards in clinical virology.
Identifying Migrant Origins Using Genetics, Isotopes, and Habitat Suitability
Authors: Ruegg Kristen C. , Anderson Eric C. , Harrigan Ryan J. , Paxton Kristina L. , Kelly Jeff , Moore Frank , Smith Thomas B.
Published: November 2016

Identifying migratory connections across the annual cycle is important for studies of migrant ecology, evolution, and conservation. While recent studies have demonstrated the utility of high-resolution SNP-based genetic markers for identifying population-specific migratory patterns, the accuracy of this approach relative to other intrinsic tagging techniques has not yet been assessed.

Here, using a straightforward application of Bayes' Rule, we develop a method for combining inferences from high-resolution genetic markers, stable isotopes, and habitat suitability models, to spatially infer the breeding origin of migrants captured anywhere along their migratory pathway. Using leave-one-out cross validation, we compare the accuracy of this combined approach with the accuracy attained using each source of data independently.

Our results indicate that when each method is considered in isolation, the accuracy of genetic assignments far exceeded that of assignments based on stable isotopes or habitat suitability models. However, our joint assignment method consistently resulted in small, but informative increases in accuracy and did help to correct misassignments based on genetic data alone. We demonstrate the utility of the combined method by identifying previously undetectable patterns in the timing of migration in a North American migratory songbird, the Wilson's warbler.

Overall, our results support the idea that while genetic data provides the most accurate method for tracking animals using intrinsic markers when each method is considered independently, there is value in combining all three methods. The resulting methods are provided as part of a new computationally-efficient R-package, GIAIH, allowing broad application of our statistical framework to other migratory animal systems.
Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast
Authors: Cheng Jun , Maier Kerstin C. , Avsec Žiga , Rus Petra , Gagneur Julien
Published: November 2016

The stability of mRNA is one of the major determinants of gene expression. Although a wealth of sequence elements regulating mRNA stability has been described, their quantitative contributions to half-life are unknown. Here, we built a quantitative model forSaccharomyces cerevisiaebased on functional mRNA sequence features that explains 60% of the half-life variation between genes and predicts half-life at a median relative error of 30%. The model revealed a new destabilizing 3’UTR motif, ATATTC, which we functionally validated. Codon usage proves to be the major determinant of mRNA stability. Nonetheless, single-nucleotide variations have the largest effect when occurring on 3’UTR motifs or upstream AUGs. Analyzing mRNA half-life data of 34 knockout strains showed that the effect of codon usage not only requires functional decapping and deadenylation, but also the 5’-to-3’ exonuclease Xrn1, the non-sense mediated decay genes, but not no-go decay. Altogether, this study quantitatively delineates the contributions of mRNA sequence features on stability in yeast, reveals their functional dependencies on degradation pathways, and allows accurate prediction of half-life from mRNA sequence.