bluuebunny/crossref_metadata_2025 huggingface dataset:
Characteristics and TB treatment outcomes in TB patients with viral hepatitis, New York City, 2000–2010
Authors: BUSHNELL G. , STENNIS N. L. , DROBNIK A. M. , PROOPS D. C. , AHUJA S. D. , BORNSCHLEGEL K. , FULD J.
Published: November 2014

Literature surrounding the burden of and factors associated with hepatitis B virus (HBV) and hepatitis C virus (HCV) infection in persons with tuberculosis (TB) disease remains limited and focused on populations outside the USA. Cross-matched New York City (NYC) TB and viral hepatitis surveillance data were used to estimate the proportion of NYC adults diagnosed with TB from 2000 to 2010 with a report of viral hepatitis infection and to describe the impact of viral hepatitis infection on TB treatment completion and death. For 9512 TB patients, HCV infection was reported in 4·2% and HBV infection in 3·7%; <1% of TB patients had both HCV and HBV infection. The proportion of TB patients with HCV infection to die before TB treatment completion was larger than in TB patients without a viral hepatitis report (21%vs. 9%); this association remained when stratified by HIV status. There was no significant difference in death before treatment completion for TB patients with HBV infection compared to TB patients without a viral hepatitis report when stratified by HIV status. These findings reinforce the importance of hepatitis testing and providing additional support to TB patients with viral hepatitis infection.
Addendum to ‘The Katětov construction modified for a T0-quasi-metric space’
Authors: KÜNZI HANS-PETER A. , SANCHIS MANUEL
Published: November 2014

It is known that if K is a compact subset of the (separable complete) metric Urysohn space (${\mathbb U}$, d) and f is a Katětov function on the subspace K of (${\mathbb U}$, d), then there is z ∈ ${\mathbb U}$ such that d(z, x) = f(x) for all x ∈ K.

Answering a question of Normann, we show in this article that the supseparable bicomplete q-universal ultrahomogeneous T0-quasi-metric space (q${\mathbb U}$, D) recently discussed by the authors satisfies a similar property for Katětov function pairs on subsets that are compact in the associated metric space (q${\mathbb U}$, Ds).
A light-weight integration of automated and interactive theorem proving
Authors: KANSO KARIM , SETZER ANTON
Published: November 2014

In this paper, aimed at dependently typed programmers, we present a novel connection between automated and interactive theorem proving paradigms. The novelty is that the connection offers a better trade-off between usability, efficiency and soundness when compared to existing techniques. This technique allows for a powerful interactive proof framework that facilitates efficient verification of finite domain theorems and guided construction of the proof of infinite domain theorems. Such situations typically occur with industrial verification. As a case study, an embedding of SAT and CTL model checking is presented, both of which have been implemented for the dependently typed proof assistant Agda.

Finally, an example of a real world railway control system is presented, and shown using our proof framework to be safe with respect to an abstract model of trains not colliding or derailing. We demonstrate how to formulate safety directly and show using interactive theorem proving that signalling principles imply safety. Therefore, a proof by an automated theorem prover that the signalling principles hold for a concrete system implies the overall safety. Therefore, instead of the need for domain experts to validate that the signalling principles imply safety they only need to make sure that the safety is formulated correctly. Therefore, some of the validation is replaced by verification using interactive theorem proving.
Correcting Bias Caused by Missing Data in the Estimate of the Effect of Apolipoprotein ε4 on Cognitive Decline
Authors: Hall Charles B. , Lipton Richard B. , Katz Mindy J. , Wang Cuiling
Published: November 2014

Longitudinal administration of neuropsychological instruments are often used to assess age-related changes in cognition. Informative loss to follow-up may bias the results of these studies. Herein, we use auxiliary data to adjust for informative loss to follow-up. In the Einstein Aging Study, memory was assessed annually in a community sample of adults age 70+, free of dementia at baseline, using the free recall from the Free and Cued Selective Reminding Test, andviatelephone using the Memory Impairment Screen for Telephone (the auxiliary data). Joint linear mixed models were used to assess how the effect of the APOE ε4 genotype may be affected by informative missingness in the in-person data. A total of 620 EAS participants contributed 2085 person years of follow-up to the analyses. Memory decline rates estimated in joint models were 19% greater in ε4 negative participants and 27% greater in ε4 positive participants compared to traditional approaches; the effect of APOE ε4 on memory decline was 37% greater. Joint modeling methods can help address bias caused by informative missing data in the estimation of the effect of risk factors on cognitive change, and may be applicable to a broader range of outcomes in longitudinal aging studies. (JINS, 2014,20, 1–6)
Structure Identification in High-Resolution Transmission Electron Microscopic Images: An Example on Graphene
Authors: Vestergaard Jacob S. , Kling Jens , Dahl Anders B. , Hansen Thomas W. , Wagner Jakob B. , Larsen Rasmus
Published: November 2014

A connection between microscopic structure and macroscopic properties is expected for almost all material systems. High-resolution transmission electron microscopy is a technique offering insight into the atomic structure, but the analysis of large image series can be time consuming. The present work describes a method to automatically estimate the atomic structure in two-dimensional materials. As an example graphene is chosen, in which the positions of the carbon atoms are reconstructed. Lattice parameters are extracted in the frequency domain and an initial atom positioning is estimated. Next, a plausible neighborhood structure is estimated. Finally, atom positions are adjusted by simulation of a Markov random field model, integrating image evidence and the strong geometric prior. A pristine sample with high regularity and a sample with an induced hole are analyzed. False discovery rate-controlled large-scale simultaneous hypothesis testing is used as a statistical framework for interpretation of results. The first sample yields, as expected, a homogeneous distribution of carbon–carbon (C–C) bond lengths. The second sample exhibits regions of shorter C–C bond lengths with a preferred orientation, suggesting either strain in the structure or a buckling of the graphene sheet. The precision of the method is demonstrated on simulated model structures and by its application to multiple exposures of the two graphene samples.
CLASSIFICATION OF UNIVALENT HARMONIC MAPPINGS ON THE UNIT DISK WITH HALF-INTEGER COEFFICIENTS
Authors: PONNUSAMY SAMINATHAN , QIAO JINJING
Published: November 2014

Let${\mathcal{S}}$denote the set of all univalent analytic functions$f$of the form$f(z)=z+\sum _{n=2}^{\infty }a_{n}z^{n}$on the unit disk$|z|<1$. In 1946, Friedman [‘Two theorems on Schlicht functions’,Duke Math. J.13(1946), 171–177] found that the set${\mathcal{S}}_{\mathbb{Z}}$of those functions in${\mathcal{S}}$which have integer coefficients consists of only nine functions. In a recent paper, Hiranuma and Sugawa [‘Univalent functions with half-integer coefficients’,Comput. Methods Funct. Theory13(1) (2013), 133–151] proved that the similar set obtained for functions with half-integer coefficients consists of only 21 functions; that is, 12 more functions in addition to these nine functions of Friedman from the set${\mathcal{S}}_{\mathbb{Z}}$. In this paper, we determine the class of all normalized sense-preserving univalent harmonic mappings$f$on the unit disk with half-integer coefficients for the analytic and co-analytic parts of$f$. It is surprising to see that there are only 27 functions out of which only six functions in this class are not conformal. This settles the recent conjecture of the authors. We also prove a general result, which leads to a new conjecture.
Which plan to choose? The determinants of pension system choice for public school teachers
Authors: GOLDHABER DAN , GROUT CYRUS
Published: November 2014

This paper examines a natural experiment in which Washington State teachers were offered the opportunity to choose between enrolling in a traditional defined benefit (DB) plan and a hybrid plan with DB and defined contribution (DC) components. We find plan preference is weakly related to estimates of the relative financial benefits of being in either the DB or hybrid system and strongly related to teacher age. Importantly, we also find that the majority of teachers prefer the hybrid plan, and that teachers opting into the hybrid plan tend to be more effective based on student output measures of teacher productivity. These results suggest that policy shifts toward pension systems that include DC options do not necessarily make teaching a less desirable profession, particularly for the most productive employees.
Facile synthesis of a pyrrole-fused dibenzo[a,e]pentalene and its application as a new extended, ladder-type fused aromatic system
Authors: Li Cheng , Liu Chunming , Li Yan , Zhu Xiaozhang , Wang Zhaohui
Published: November 2014

A novel ladder-type pyrrole-fused dibenzo[a,e]pentalene is synthesizedviadouble intermolecular Pd-catalyzed cascade crossover annulations.
One-pot cascade synthesis of N-methoxyisoquinolinediones via Rh(iii)-catalyzed carbenoid insertion C–H activation/cyclization
Authors: Shi Jingjing , Zhou Jie , Yan Yunnan , Jia Jinlong , Liu Xuelei , Song Huacan , Xu H. Eric , Yi Wei
Published: November 2014

A mild and efficient method for one-pot synthesis ofN-methoxyisoquinolinedionesviaRh(iii)-catalyzed carbenoid insertion C–H activation/cyclization has been developed.
The role of an active site Mg2+in HDV ribozyme self-cleavage: insights from QM/MM calculations
Authors: Mlýnský Vojtěch , Walter Nils G. , Šponer Jiří , Otyepka Michal , Banáš Pavel
Published: November 2014

The specific position and coordination of active site Mg2+ion have a significant direct impact on the self-cleavage reaction in HDV ribozyme.
A first-principles study of the III–IV–V semiconductor nanosheets
Authors: Bhattacharya Amrita , Bhattacharya Saswata , Das G. P.
Published: November 2014

Alloying the III–V and IV–IV sheets leads to III–IV–V nano-composites, such as the BC2N sheet, having a lower band gap than their parent III–V counterparts while having higher cohesive energies.
Solvent-free oxidation of dec-1-ene using gold/graphite catalyst using an in situ generated oxidant
Authors: Gupta Upendra Nath , Alshammari Hamed , Dummer Nicholas F. , Jenkins Robert L. , Bethell Donald , Hutchings Graham J.
Published: November 2014

The oxidation of dec-1-ene is investigated under solvent-free conditions using gold nanoparticles supported on graphite and in a batch reactor in the presence of a radical initiator using oxygen from air as the terminal oxidant.
Indole-based novel small molecules for the modulation of bacterial signalling pathways
Authors: Biswas Nripendra Nath , Kutty Samuel K. , Barraud Nicolas , Iskander George M. , Griffith Renate , Rice Scott A. , Willcox Mark , Black David StC. , Kumar Naresh
Published: November 2014

Indole basedN-acylatedl-homoserine lactone (AHL) mimics were developed as quorum sensing (QS) inhibitors for Gram-negative bacteriaPseudomonas aeruginosaand can be used as novel antimicrobial agents.
Transesterification of dimethyl carbonate with phenol to diphenyl carbonate over hexagonal Mg(OH)2 nanoflakes
Authors: Wang Qiang , Li Chunhong , Guo Ming , Luo Shengjun , Hu Changwen
Published: November 2014

Hexagonal Mg(OH)2 nanoflakes were synthesized, which showed excellent catalytic activities for the transesterification of dimethyl carbonate with phenol.
Gold-catalyzed highly efficient benzylation of alcohols with N-Cbz-N-benzyl-propargylamine
Authors: Zhao Jing-Rui , Yuan Xiaolong , Wang Zhaoyan , Chen Shiwu , Zhang Zhan-Xin , Xue Weihua
Published: November 2014

Functional group tolerance under mild conditions eliminates the need for base additives or hygroscopic promoters.
Preparation of an organic–inorganic polyurethane–Al2O3anion exchange fibrous composite and its application in the development of a membrane electrode for the determination of chromium(vi) in water
Authors: Baig Umair , Sanagi Mohd Marsin , Khan Asif Ali
Published: November 2014

An ion-selective electrode was developed using a polyurethane–Al2O3organic–inorganic fibrous composite for the determination of Cr(vi) in water.
Shape-dependent photocatalytic activity of Bi5O7I caused by facets synergetic and internal electric field effects
Authors: Su Yurong , Wang Hui , Ye Liqun , Jin Xiaoli , Xie Haiquan , He Chaozheng , Bao Keyan
Published: November 2014

The shape-dependent photocatalytic activity of Bi5O7I is caused by facets synergetic and internal electric field effects.
Three 3D coordination polymers based on [1,1′:4′,1′′-terphenyl]-2′,4,4′′,5′-tetracarboxylate demonstrating magnetic properties and selective sensing of Al3+/Fe3+over mixed ions
Authors: Kang Bei-Bei , Wei Na , Han Zheng-Bo
Published: November 2014

Three 3D coordination polymers have been synthesized by using the 1,1′:4′,1′′-terphenyl]-2′,4,4′′,5′-tetracarboxylate acid and Cd(ii),Co(ii) and Mn(ii), the Cd(ii) complex shows selective sensing Al3+/Fe3+ over the mixed metal ions.
Dispersive liquid–liquid microextraction for preconcentration and determination of phenytoin in real samples using response surface methodology-high performance liquid chromatography
Authors: Pourbasheer Eslam , Sadafi Samira , Ganjali Mohammad Reza , Abbasghorbani Maryam
Published: November 2014

In the present study, dispersive liquid–liquid microextraction (DLLME) was developed for preconcentration and determination of phenytoin in real samples by high performance liquid chromatography (HPLC).
Total synthesis of cruciferane via epoxidation/tandem cyclization sequence
Authors: Ghosh Suman Kr , Nagarajan Rajagopal
Published: November 2014

The total synthesis of alkaloid cruciferane is performed in three steps with an overall yield of 60.3%.
Kinetic and thermodynamic studies on methylene blue biosorption using corn-husk
Authors: Paşka Oana Maria , Păcurariu Cornelia , Muntean Simona Gabriela
Published: November 2014

A low-cost waste biomass derived from corn plant (husk) was tested as an alternative to other expensive treatment options, for the removal of methylene blue (MB), from aqueous solutions.
Synthesis and characterization of TiO2 nanotube supported Rh-nanoparticle catalysts for regioselective hydroformylation of vinyl acetate
Authors: Shi Yukun , Hu Xiaojing , Zhu Baolin , Wang Shurong , Zhang Shoumin , Huang Weiping
Published: November 2014

Three procedures: the impregnation-borohydride reduction procedure, the impregnation-alcohol reduction procedure and the impregnation-photoreducing procedure, were utilized for preparing TiO2 nanotube supported rhodium nanoparticle catalysts.
Regularizing the molecular potential in electronic structure calculations. I. SCF methods
Authors: Bischoff Florian A.
Published: November 2014

We present a method to remove the singular nuclear potential in a molecule and replace it with a regularized potential that is more amenable to be represented numerically. The singular nuclear potential is canceled by the similarity-transformed kinetic energy operator giving rise to an effective nuclear potential that contains derivative operators acting on the wave function. The method is fully equivalent to the non-similarity-transformed version. We give numerical examples within the framework of multi-resolution analysis for medium-sized molecules.
Regularizing the molecular potential in electronic structure calculations. II. Many-body methods
Authors: Bischoff Florian A.
Published: November 2014

In Paper I of this series [F. A. Bischoff, “Regularizing the molecular potential in electronic structure calculations. I. SCF methods,” J. Chem. Phys. 141, 184105 (2014)] a regularized molecular Hamilton operator for electronic structure calculations was derived and its properties in SCF calculations were studied. The regularization was achieved using a correlation factor that models the electron-nuclear cusp. In the present study we extend the regularization to correlated methods, in particular the exact solution of the two-electron problem, as well as second-order many body perturbation theory. The nuclear and electronic correlation factors lead to computations with a smaller memory footprint because the singularities are removed from the working equations, which allows coarser grid resolution while maintaining the precision. Numerical examples are given.
Distributed generation dynamic planning using covariance matrix adaptation evolutionary strategy method considering uncertainties
Authors: Sadeghi Mahmood , Kalantar Mohsen
Published: November 2014

This paper presents a Distributed Generation (DG) expansion dynamic planning problem considering uncertainties related to the economic conditions and intermittent nature of the DG units in order to reduce the total costs of the distribution system. The electricity price and fuel price are the economic effective parameters in DG planning studies. The variations and stochastic conditions of these parameters during the planning period are analyzed in this paper. In order to cover the uncertainties related to these parameters, and since these parameters are dependent to the global economic variations, all of the possible scenarios of these parameters during the planning period are produced using Monte Carlo Simulation (MCS) and the generated scenarios are reduced with backward reduction program using GAMS software. The Covariance Matrix Adaptation Evolutionary Strategy (CMAES) which is a new and strong strategy in evolutionary algorithms is introduced in this paper. A modified version of this algorithm, presented in this paper, is used to solve the DG planning problem. The results of covariance matrix adaptation evolutionary strategy is compared with the known genetic algorithm (GA). The defined problem is applied on the 9 bus test distribution system. The results show a significant reduction in the total annual costs of the distribution system.
Charge noise, spin-orbit coupling, and dephasing of single-spin qubits
Authors: Bermeister Adam , Keith Daniel , Culcer Dimitrie
Published: November 2014

Quantum dot quantum computing architectures rely on systems in which inversion symmetry is broken, and spin-orbit coupling is present, causing even single-spin qubits to be susceptible to charge noise. We derive an effective Hamiltonian for the combined action of noise and spin-orbit coupling on a single-spin qubit, identify the mechanisms behind dephasing, and estimate the free induction decay dephasing times T2* for common materials such as Si and GaAs. Dephasing is driven by noise matrix elements that cause relative fluctuations between orbital levels, which are dominated by screened whole charge defects and unscreened dipole defects in the substrate. Dephasing times T2* differ markedly between materials and can be enhanced by increasing gate fields, choosing materials with weak spin-orbit, making dots narrower, or using accumulation dots.
Fano collective resonance as complex mode in a two-dimensional planar metasurface of plasmonic nanoparticles
Authors: Campione Salvatore , de Ceglia Domenico , Guclu Caner , Vincenti Maria A. , Scalora Michael , Capolino Filippo
Published: November 2014

Fano resonances are features in transmissivity/reflectivity/absorption that owe their origin to the interaction between a broad bright resonance and a dark (i.e., sub-radiant) narrower one. They may emerge in the optical properties of planar two-dimensional (2D) periodic arrays (metasurfaces) of plasmonic nanoparticles. In this letter, we provide a thorough assessment of their nature for the general case of normal and oblique plane wave incidence, highlighting when a Fano resonance is affected by the mutual coupling in an array and its capability to support free modal solutions. We analyze the representative case of a metasurface of plasmonic nanoshells at ultraviolet frequencies and compute its absorption under TE- and TM-polarized, oblique plane-wave incidence. In particular, we find that plasmonic metasurfaces display two distinct types of resonances observable as absorption peaks: one is related to the Mie electric dipolar resonance of each nanoparticle and the other is due to the forced excitation of free modes with small attenuation constant, usually found at oblique incidence. The latter is thus an array-induced collective Fano resonance. This realization opens up to manifold flexible designs at optical frequencies mixing individual and collective resonances. We explain the physical origin of such Fano resonances using the modal analysis through which we calculate the free modes with complex wavenumber supported by the metasurface. We define equivalent array dipolar polarizabilities that are directly related to the absorption physics at oblique incidence and show a direct dependence between array modal phase and attenuation constants and Fano resonances. We thus provide a more complete picture of Fano resonances that may lead to the design of filters, energy-harvesting devices, photodetectors, and sensors at ultraviolet frequencies. Similar resonances may be also extended to the visible range with an appropriate choice of geometries and materials.
Time resolved diagnostics of ions in colliding carbon plasmas
Authors: Singh Ravi Pratap , Gupta Shyam L. , Thareja Raj K.
Published: November 2014

We report a comparative study of the dynamic behaviour of ions at different pressures in laser ablated colliding and single plasma plumes using 2D imaging, optical emission spectroscopy (OES) and a retarding field analyser (RFA). 2D imaging shows the splitting of plasma plumes due to different velocities of various plasma species. OES shows enhancement in abundance of ionic species with their presence for a longer time in colliding plume. C2 molecular formation is seen at later time in colliding plume compared to single plume and is attributed to dominating collisional processes in the colliding region of the plumes. The time of flight distribution of ions traced by the RFA shows the variation with change in fluence as well as ambient pressure for both colliding and single plume. Time of flight analysis of ions also shows the appearance of a fast peak in ion signal due to acceleration of ions at larger fluence.
Some remarks on the entropy for algebraic actions of amenable groups
Authors: Chung Nhan-Phu , Thom Andreas
Published: November 2014

In this short note we study the entropy for algebraic actions of certain amenable groups. The possible values for this entropy are studied. Various fundamental results about certain classes of amenable groups are re-proved using elementary arguments and the entropy invariant. We provide a natural decomposition of the entropy into summands contributed by individual primes and a summand corresponding to

∞
\infty

. These results extend previous work by Lind and Ward on

p
p

-adic entropy.
Distinct profiling of antimicrobial peptide families
Authors: Khamis Abdullah M. , Essack Magbubah , Gao Xin , Bajic Vladimir B.
Published: November 2014

Motivation: The increased prevalence of multi-drug resistant (MDR) pathogens heightens the need to design new antimicrobial agents. Antimicrobial peptides (AMPs) exhibit broad-spectrum potent activity against MDR pathogens and kills rapidly, thus giving rise to AMPs being recognized as a potential substitute for conventional antibiotics. Designing new AMPs using current in-silico approaches is, however, challenging due to the absence of suitable models, large number of design parameters, testing cycles, production time and cost. To date, AMPs have merely been categorized into families according to their primary sequences, structures and functions. The ability to computationally determine the properties that discriminate AMP families from each other could help in exploring the key characteristics of these families and facilitate the in-silico design of synthetic AMPs.

Results: Here we studied 14 AMP families and sub-families. We selected a specific description of AMP amino acid sequence and identified compositional and physicochemical properties of amino acids that accurately distinguish each AMP family from all other AMPs with an average sensitivity, specificity and precision of 92.88%, 99.86% and 95.96%, respectively. Many of our identified discriminative properties have been shown to be compositional or functional characteristics of the corresponding AMP family in literature. We suggest that these properties could serve as guides for in-silico methods in design of novel synthetic AMPs. The methodology we developed is generic and has a potential to be applied for characterization of any protein family.

Contact:  vladimir.bajic@kaust.edu.sa

Supplementary information:  Supplementary data are available at Bioinformatics online.
Near-infrared spectroscopy of M dwarfs. I. CO molecule as an abundance indicator of carbon
Authors: Tsuji Takashi , Nakajima Tadashi
Published: November 2014

Based on the near-infrared spectra of 42 M dwarfs, carbon abundances are determined from the ro-vibrational lines of the CO (2–0) band. We apply Teff values based on the angular diameters if available or use the Teff values in a log Teff–M3.4 relation (M3.4 is the absolute magnitude at 3.4 μm based on the WISE W1 flux and the Hipparcos parallax) to estimate Teff values of objects for which angular diameters are unknown. Also, we discuss briefly the HR diagram of low-mass stars. On the observed spectrum of the M dwarf, the continuum is depressed by the numerous weak lines of H2O and only the depressed continuum or the pseudo-continuum can be seen. On the theoretical spectrum of the M dwarf, the true continuum can be evaluated easily but the pseudo-continuum can also be evaluated accurately thanks to the recent H2O line database. Then spectroscopic analysis of the M dwarf can be done by referring to the pseudo-continuum both on the observed and theoretical spectra. Since the basic principle of the spectroscopic analysis should be the same whether the true- or pseudo-continuum is referred to, the difficulty related to the continuum in cool stars can in principle be overcome. Then, the numerous CO lines can be excellent abundance indicators of carbon, since almost all the carbon atoms are in stable CO molecules which suffer little effect of the uncertainties in photospheric structure, and carbon abundances in late-type stars can best be determined in M dwarfs rather than in solar type stars. The resulting C/Fe ratios for most M dwarfs are nearly constant at about the solar value based on the classical high carbon abundance rather than on the recently revised lower value. This result implies that the solar carbon abundance is atypical for its metallicity among the stellar objects in the solar neighborhood if the downward revised carbon abundance is correct.
A jump persistent turning walker to model zebrafish locomotion
Authors: Mwaffo Violet , Anderson Ross P. , Butail Sachit , Porfiri Maurizio
Published: November 2014

Zebrafish are gaining momentum as a laboratory animal species for the investigation of several functional and dysfunctional biological processes. Mathematical models of zebrafish behaviour are expected to considerably aid in the design of hypothesis-driven studies by enabling preliminaryin silicotests that can be used to infer possible experimental outcomes without the use of zebrafish. This study is motivated by observations of sudden, drastic changes in zebrafish locomotion in the form of large deviations in turn rate. We demonstrate that such deviations can be captured through a stochastic mean reverting jump diffusion model, a process that is commonly used in financial engineering to describe large changes in the price of an asset. The jump process-based model is validated on trajectory data of adult subjects swimming in a shallow circular tank obtained from an overhead camera. Through statistical comparison of the empirical distribution of the turn rate against theoretical predictions, we demonstrate the feasibility of describing zebrafish as a jump persistent turning walker. The critical role of the jump term is assessed through comparison with a simplified mean reversion diffusion model, which does not allow for describing the heavy-tailed distributions observed in the fish turn rate.
Evolution on neutral networks accelerates the ticking rate of the molecular clock
Authors: Manrubia Susanna , Cuesta José A.
Published: November 2014

Large sets of genotypes give rise to the same phenotype, because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as the genotype mutates into another one on the same set. By linking every pair of genotypes that are mutually accessible through mutation, genotypes organize themselves into neutral networks (NNs). These networks are known to be heterogeneous and assortative, and these properties affect the evolutionary dynamics of the population. By studying the dynamics of populations on NNs with arbitrary topology, we analyse the effect of assortativity, of NN (phenotype) fitness and of network size. We find that the probability that the population leaves the network is smaller the longer the time spent on it. This progressive ‘phenotypic entrapment’ entails a systematic increase in the overdispersion of the process with time and an acceleration in the fixation rate of neutral mutations. We also quantify the variation of these effects with the size of the phenotype and with its fitness relative to that of neighbouring alternatives.
Enhanced adhesion of bioinspired nanopatterned elastomers via colloidal surface assembly
Authors: Akerboom Sabine , Appel Jeroen , Labonte David , Federle Walter , Sprakel Joris , Kamperman Marleen
Published: November 2014

We describe a scalable method to fabricate nanopatterned bioinspired dry adhesives using colloidal lithography. Close-packed monolayers of polystyrene particles were formed at the air/water interface, on which polydimethylsiloxane (PDMS) was applied. The order of the colloidal monolayer and the immersion depth of the particles were tuned by altering the pH and ionic strength of the water. Initially, PDMS completely wetted the air/water interface outside the monolayer, thereby compressing the monolayer as in a Langmuir trough; further application of PDMS subsequently covered the colloidal monolayers. PDMS curing and particle extraction resulted in elastomers patterned with nanodimples. Adhesion and friction of these nanopatterned surfaces with varying dimple depth were studied using a spherical probe as a counter-surface. Compared with smooth surfaces, adhesion of nanopatterned surfaces was enhanced, which is attributed to an energy-dissipating mechanism during pull-off. All nanopatterned surfaces showed a significant decrease in friction compared with smooth surfaces.
Eyespots deflect predator attack increasing fitness and promoting the evolution of phenotypic plasticity
Authors: Prudic Kathleen L. , Stoehr Andrew M. , Wasik Bethany R. , Monteiro Antónia
Published: November 2014

Some eyespots are thought to deflect attack away from the vulnerable body, yet there is limited empirical evidence for this function and its adaptive advantage. Here, we demonstrate the conspicuous ventral hindwing eyespots found onBicyclus anynanabutterflies protect against invertebrate predators, specifically praying mantids. Wet season (WS) butterflies with larger, brighter eyespots were easier for mantids to detect, but more difficult to capture compared to dry season (DS) butterflies with small, dull eyespots. Mantids attacked the wing eyespots of WS butterflies more frequently resulting in greater butterfly survival and reproductive success. With a reciprocal eyespot transplant, we demonstrated the fitness benefits of eyespots were independent of butterfly behaviour. Regardless of whether the butterfly was WS or DS, large marginal eyespots pasted on the hindwings increased butterfly survival and successful oviposition during predation encounters. In previous studies, DSB. anynanaexperienced delayed detection by vertebrate predators, but both forms suffered low survival once detected. Our results suggest predator abundance, identity and phenology may all be important selective forces forB. anynana. Thus, reciprocal selection between invertebrate and vertebrate predators across seasons may contribute to the evolution of theB. anynanapolyphenism.
The relative importance of direct and indirect effects of hunting mortality on the population dynamics of brown bears
Authors: Gosselin Jacinthe , Zedrosser Andreas , Swenson Jon E. , Pelletier Fanie
Published: November 2014

There is increasing evidence of indirect effects of hunting on populations. In species with sexually selected infanticide (SSI), hunting may decrease juvenile survival by increasing male turnover. We aimed to evaluate the relative importance of direct and indirect effects of hunting via SSI on the population dynamics of the Scandinavian brown bear (Ursus arctos). We performed prospective and retrospective demographic perturbation analyses for periods with low and high hunting pressures. All demographic rates, except yearling survival, were lower under high hunting pressure, which led to a decline in population growth under high hunting pressure (λ= 0.975; 95% CI = 0.914–1.011). Hunting had negative indirect effects on the population through an increase in SSI, which lowered cub survival and possibly also fecundity rates. Our study suggests that SSI could explain 13.6% of the variation in population growth. Hunting also affected the relative importance of survival and fecundity of adult females for population growth, with fecundity being more important under low hunting pressure and survival more important under high hunting pressure. Our study sheds light on the importance of direct and indirect effects of hunting on population dynamics, and supports the contention that hunting can have indirect negative effects on populations through SSI.
Direct and indirect causal effects of heterozygosity on fitness-related traits in Alpine ibex
Authors: Brambilla Alice , Biebach Iris , Bassano Bruno , Bogliani Giuseppe , von Hardenberg Achaz
Published: November 2014

Heterozygosity–fitness correlations (HFCs) are a useful tool to investigate the effects of inbreeding in wild populations, but are not informative in distinguishing between direct and indirect effects of heterozygosity on fitness-related traits. We tested HFCs in male Alpine ibex (Capra ibex) in a free-ranging population (which suffered a severe bottleneck at the end of the eighteenth century) and used confirmatory path analysis to disentangle the causal relationships between heterozygosity and fitness-related traits. We tested HFCs in 149 male individuals born between 1985 and 2009. We found that standardized multi-locus heterozygosity (MLH), calculated from 37 microsatellite loci, was related to body mass and horn growth, which are known to be important fitness-related traits, and to faecal egg counts (FECs) of nematode eggs, a proxy of parasite resistance. Then, using confirmatory path analysis, we were able to show that the effect of MLH on horn growth was not direct but mediated by body mass and FEC. HFCs do not necessarily imply direct genetic effects on fitness-related traits, which instead can be mediated by other traits in complex and unexpected ways.
Ecological dynamics of emerging bat virus spillover
Authors: Plowright Raina K. , Eby Peggy , Hudson Peter J. , Smith Ina L. , Westcott David , Bryden Wayne L. , Middleton Deborah , Reid Peter A. , McFarlane Rosemary A. , Martin Gerardo , Tabor Gary M. , Skerratt Lee F. , Anderson Dale L. , Crameri Gary , Quammen David , Jordan David , Freeman Paul , Wang Lin-Fa , Epstein Jonathan H. , Marsh Glenn A. , Kung Nina Y. , McCallum Hamish
Published: November 2014

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility.
Predator-induced phenotypic plasticity within- and across-generations: a challenge for theory?
Authors: Walsh Matthew R. , Cooley Frank , Biles Kelsey , Munch Stephan B.
Published: November 2014

Much work has shown that the environment can induce non-genetic changes in phenotype that span multiple generations. Theory predicts that predictable environmental variation selects for both increased within- and across-generation responses. Yet, to the best of our knowledge, there are no empirical tests of this prediction. We explored the relationship between within- versus across-generation plasticity by evaluating the influence of predator cues on the life-history traits ofDaphnia ambigua. We measured the duration of predator-induced transgenerational effects, determined when transgenerational responses are induced, and quantified the cues that activate transgenerational plasticity. We show that predator exposure during embryonic development causes earlier maturation and increased reproductive output. Such effects are detectable two generations removed from predator exposure and are similar in magnitude in response to exposure to cues emitted by injured conspecifics. Moreover, all experimental contexts and traits yielded a negative correlation between within- versus across-generation responses. That is, responses to predator cues within- and across-generations were opposite in sign and magnitude. Although many models address transgenerational plasticity, none of them explain this apparent negative relationship between within- and across-generation plasticities. Our results highlight the need to refine the theory of transgenerational plasticity.
Characterization of Sporohalobacter salinus sp. nov., an anaerobic, halophilic, fermentative bacterium isolated from a hypersaline lake
Authors: Ben Abdallah Manel , Karray Fatma , Mhiri Najla , Cayol Jean-Luc , Tholozan Jean-Luc , Alazard Didier , Sayadi Sami
Published: November 2014

Halophilic, obligately anaerobic, Gram-stain-negative bacterial strains were isolated from a sediment sample taken from under the salt crust of El-Jerid hypersaline lake in southern Tunisia by using tryptone or glucose as the substrate. One strain, CEJFT1BT, was characterized phenotypically and phylogenetically. Cells were non-motile, non-spore-forming, short rods. Strain CEJFT1BT was able to grow in the presence of 5–30 % (w/v) NaCl (optimum 20 %) and at 30–60 °C (optimum 45 °C). It grew at pH 5.5–7.8 and the optimum pH for growth was 6.8. The isolate required yeast extract for growth. Substrates utilized by strain CEJFT1BT as the sole carbon source included glucose, fructose, sucrose, pyruvate, Casamino acids and starch. Individual amino acids such as glutamate, lysine, methionine, serine, tyrosine, and amino acid mixtures formed by the Stickland reaction such as alanine-glycine, valine-proline, leucine-proline, isoleucine-proline were also utilized. Products of glucose fermentation were acetate (major product), butyrate, H2 and CO2. The genomic DNA G+C content of strain CEJFT1BT was 32.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CEJFT1BT should be assigned to the genus

Sporohalobacter

. The sequence similarity between strain CEJFT1BT and

Sporohalobacter lortetii

was 98.5 %, but DNA–DNA hybridization between the two strains revealed a relatedness value of 56.4 %, indicating that they are not related at the species level. The combination of phylogenetic analysis, DNA–DNA hybridization data, and differences in substrate utilization support the view that strain CEJFT1BT represents a novel species of the genus

Sporohalobacter

, for which the name Sporohalobacter salinus sp. nov. is proposed. The type strain is CEJFT1BT ( = DSM 26781T = JCM 19279T).
Control system design and testing for a small‐scale autonomous helicopter
Authors: Kim Seongpil , Budiyono Agus , Lee Jang‐Ho , Kim DooHyun , Joon Yoon Kwang
Published: November 2014

Purpose

The purpose of this paper is to conduct the design, development and testing of a controller for an autonomous small‐scale helicopter.

Design/methodology/approach

The hardware in the loop simulation (HILS) platform is developed based on the nonlinear model of JR Voyager G‐260 small‐scale helicopter. Autonomous controllers are verified using the HILS environment prior to flight experiments.

Findings

The gains of the multi‐loop cascaded control architecture can be effectively optimized within the HILS environment. Various autonomous flight operations are achieved and it is demonstrated that the prediction from the simulations is in a good agreement with the result from the flight test.

Research limitations/implications

The synthesized controller is effective for the particular test‐bed. For other small‐scale helicopters (with different size and engine specifications), the controller gains must be tuned again.

Practical implications

This work represents a practical control design and testing procedures for an autonomous small‐scale helicopter flight control. The autonomous helicopter can be used for various missions ranging from film making, agriculture and volcanic surveillance to power line inspection.

Originality/value

The research addresses the need for systematic design, development and testing of controller for a small‐scale autonomous helicopter by utilizing HILS environment.
An examination of five open access online state encyclopedias
Authors: Koenig Johnson Jennifer
Published: November 2014

Purpose – ‐‐ The purpose of this paper is to examine and evaluate five open access state encyclopedias.Design/methodology/approach ‐‐ Each encyclopedia is discussed and evaluated separately in regard to the following categories: web design, search functionality, features, scope, and currency.Findings ‐‐ The paper finds that, while many of the evaluated state encyclopedias provide different types of information with varying web design and structure, the end product is the same: offering free, authoritative articles and other media for anyone to access on a given topic related to the selected state. While some encyclopedias are continuously updated with new material and have better interfaces, features, and search functions, each site is valuable for the authoritative information it provides.Originality/value ‐‐ The state encyclopedias discussed are all open access resources that provide scholarly, authoritative information in an easily accessible format. Through evaluation of the web design, search features, currency, and scope and content, librarians can assist their users with searching and locating information in these encyclopedias.
Using images to capture and share service users' spirituality
Authors: Bryce Hazel , Lorraine
Published: November 2014

This article explores some of the images and words that service users choose to capture and represent their unique spirituality. It was written using material that service users produced as part of two projects focusing on spirituality and hope. The first project involved a group where service users were given a camera to capture something that represented their spirituality. The second project involved producing material for an art exhibition entitled Growing Hope, that was showcased in Sheffield as part of World Mental Health Day 2009.The article is written by Hazel Bryce, an occupational therapist working in an assertive outreach team (SORT) in Sheffield, and Lorraine, a service user who worked on the two projects and who has an interest in spirituality. They reflect together on the process of being involved in the projects and the meaning of this piece of work. The article was written together to try to capture a range of perspectives.
Assessment of communication in people with learning disabilities
Authors: Taylor Cathy
Published: November 2014

Thorough assessment of communication is of utmost importance for successful working with people with learning disabilities. Indeed, recent legislation now makes it incumbent on professionals working with people with learning disabilities to address issues of communication, both their own communication to clients and that of their clients. There are clear associations between learning disabilities, emotional, behavioural and psychiatric problems, and impaired communication. The nature of the communication impairments experienced by individuals with learning disabilities is likely to be complex, with cumulative and inter‐related features associated with the general developmental delay, the phenotypical presentation in a particular syndrome, the presence of specific linguistic impairments and the indirect impact of other difficulties on communication skills. A number of parameters need to be addressed in a communication assessment in order to take account of the complexity and dynamism of the communication process. They concern not only the underlying developmental and communication impairments affecting particular areas of functioning, but also many aspects of the wider context in which the communication takes place.
Psychiatric and mental state assessment in learning disabilities
Authors: Al‐Sheikh Alaa , O'Hara Jean
Published: November 2014

Mental health assessment in people with learning disability can be a challenging process for clinicians. The more severe the cognitive impairment and level of learning disability, the less likely it is that the clinician can reliably confirm the diagnosis of a psychiatric disorder. Coordinated, multi‐modal interdisciplinary team assessment is the way forward, as it draws together the bio‐psychosocial model of interviewing and mental health care planning. In this article we go through the psychiatric assessment structure and highlight the differences in assessing people with learning disability compared with their peers in the general population. We give special consideration to mental health assessments in emergency settings, and to people with challenging behaviour.
Psychiatric and behavioural assessment scales for adults with learning disabilities
Authors: Unwin Gemma , Deb Shoumitro
Published: November 2014

The paper reports on a review of assessment scales commonly used for assessment of psychiatric illnesses or behaviour problems in adults with learning disabilities. Initially, a literature search was conducted to identify relevant peer‐reviewed journal publications pertaining to relevant scales. Those scales with more publications were reviewed with reference to the scale composition and psychometric properties. In total, eight behaviour scales, one psychiatric illness scale and three combined behaviour and psychiatric illness scales are reviewed.