bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of annulated bis-indoles through Au(i)/Brønsted acid-catalyzed reactions of (1H-indol-3-yl)(aryl)methanols with 2-(arylethynyl)-1H-indoles
Authors: Inamdar Suleman M. , Gonnade Rajesh G. , Patil Nitin T.
Published: December 2016

A general method to access annulated bis-indoles from (1H-indol-3-yl)(aryl)methanols and 2-(arylethynyl)-1H-indoles under the catalysis of the Ph3PAuOTf/Brønsted acid binary catalyst system has been developed.
Cost-effective approach for structural evolution of Si-based multicomponent for Li-ion battery anodes
Authors: Hong Dongki , Ryu Jaegeon , Shin Sunghee , Park Soojin
Published: December 2016

Al2O3passivated porous Si particles with novel electrochemical properties were successfully demonstrated as outstanding anodes.
A multifunctional poly-N-vinylcarbazole interlayer in perovskite solar cells for high stability and efficiency: a test with new triazatruxene-based hole transporting materials
Authors: Su Pei-Yang , Huang Li-Bo , Liu Jun-Min , Chen Yi-Fan , Xiao Li-Min , Kuang Dai-Bin , Mayor Marcel , Su Cheng-Yong
Published: December 2016

Coupling of a polymer-protection method with the molecular design of a novel HTM in PSCs: a PVK-protection approach and triazatruxene-based HTMs are developed.
Dimension engineering on cesium lead iodide for efficient and stable perovskite solar cells
Authors: Liao Jin-Feng , Rao Hua-Shang , Chen Bai-Xue , Kuang Dai-Bin , Su Cheng-Yong
Published: December 2016

Dimension engineering is developed to form 2D BA2CsPb2I7 by introducing a bulky ammonium cation, which exhibits superior structural and compositional stability.
Designing nanocomposites using supercritical CO2 to insert Ni nanoparticles into the pores of nanopatterned BaTiO3 thin films
Authors: Castro Alichandra , Morère Jacobo , Cabañas Albertina , Ferreira Liliana P. , Godinho Margarida , Ferreira Paula , Vilarinho Paula M.
Published: December 2016

Supercritical CO2 deposition: a tool to achieve multifunctional materials starting from a porous platform.
Foundational Resources and Terminology for Supervision and Mentorship
Authors: Robke Darlene D.
Published: December 2016

Growth in the professions of speech pathology and audiology has led to an increased need for supervision as well as the degree of interest and the request for guidance regarding supervision. Speech-language pathologists (SLPs) and audiologists may be uncertain of the responsibilities of their roles as supervisors, lack necessary training, and develop unrealistic expectations of their supervisees. These new supervisors may have a limited understanding about the complexity of the supervisory process (ASHA, 2008b). This article provides a review of the literature on supervision and offers an initial reference guide for those who are new to supervising professionals and supports their understanding of supervision and mentorship. The review and compilation of information is meant to serve a useful quick start reference guide that may be utilized to help new supervisors navigate through the “collaborative process of supervision” (ASHA, 2008a, p.1). This compendium of information is meant to serve as a general content overview and is not intended to be all inclusive. Instead, it is intended to be a functional resource that provides a glossary of commonly utilized terms, offers some insight into the principals and concepts of the supervision and touches on current issues that may arise across settings.
The Why, Who, What, When, and How of Supervision
Authors: Wright Janice , Needham Christie
Published: December 2016

Many therapists find themselves in the role of supervisor in their career. However, not many supervisors have formal training in supervision. In fact, as a supervisor, we may not even have a clear understanding of the following basic questions: why supervise, who can supervise, who to supervise, when to supervisor, why supervise, or how to supervise. This article explores the roles and responsibilities of the supervisor in both in the supervision of the clinical fellow (CF) and the supervision of the student. The answers to these questions become an essential foundation to creating a supportive and effective supervisor to supervisee relationship.
Student Misconceptions and Vocabulary Mix-ups: Speech Science at the Nexus
Authors: Boyce Suzanne
Published: December 2016

Purpose

The immediate purpose of this article is to describe how the meaning of terms used in the speech science classroom may conflict with different terminology used in ordinary conversation and in more specialized areas of practice. The ultimate aim is to enable teachers to head off these potential confusions when teaching speech science, and to consider such confusions when untangling wrong answers from students.

Method

Several examples of confusing terminology are discussed: Resonance, Constriction, Aspiration.

Conclusion

Students and teachers have a hard job of disentangling the terminology used in the communication disorders classroom. Teachers should be aware of these potential confusions and take steps to reduce or elucidate them.
Broadband white light emission from Ce:AlN ceramics: High thermal conductivity down-converters for LED and laser-driven solid state lighting
Authors: Wieg A. T. , Penilla E. H. , Hardin C. L. , Kodera Y. , Garay J. E.
Published: December 2016

We introduce high thermal conductivity aluminum nitride (AlN) as a transparent ceramic host for Ce3+, a well-known active ion dopant. We show that the Ce:AlN ceramics have overlapping photoluminescent (PL) emission peaks that cover almost the entire visible range resulting in a white appearance under 375 nm excitation without the need for color mixing. The PL is due to a combination of intrinsic AlN defect complexes and Ce3+ electronic transitions. Importantly, the peak intensities can be tuned by varying the Ce concentration and processing parameters, causing different shades of white light without the need for multiple phosphors or light sources. The Commission Internationale de l’Eclairage coordinates calculated from the measured spectra confirm white light emission. In addition, we demonstrate the viability of laser driven white light emission by coupling the Ce:AlN to a readily available frequency tripled Nd-YAG laser emitting at 355 nm. The high thermal conductivity of these ceramic down-converters holds significant promise for producing higher power white light sources than those available today.
Perturbative triples correction for local pair natural orbital based explicitly correlated CCSD(F12*) using Laplace transformation techniques
Authors: Schmitz Gunnar , Hättig Christof
Published: December 2016

We present an implementation of pair natural orbital coupled cluster singles and doubles with perturbative triples, PNO-CCSD(T), which avoids the quasi-canonical triples approximation (T0) where couplings due to off-diagonal Fock matrix elements are neglected. A numerical Laplace transformation of the canonical expression for the perturbative (T) triples correction is used to avoid an I/O and storage bottleneck for the triples amplitudes. Results for a test set of reaction energies show that only very few Laplace grid points are needed to obtain converged energy differences and that PNO-CCSD(T) is a more robust approximation than PNO-CCSD(T0) with a reduced mean absolute deviation from canonical CCSD(T) results. We combine the PNO-based (T) triples correction with the explicitly correlated PNO-CCSD(F12*) method and investigate the use of specialized F12-PNOs in the conventional triples correction. We find that no significant additional errors are introduced and that PNO-CCSD(F12*)(T) can be applied in a black box manner.
Experimental and ab initio characterization of HC3N+ vibronic structure. II. High-resolution VUV PFI-ZEKE spectroscopy
Authors: Gans Bérenger , Lamarre Nicolas , Broquier Michel , Liévin Jacques , Boyé-Péronne Séverine
Published: December 2016

Vacuum-ultraviolet pulsed-field-ionization zero-kinetic-energy photoelectron spectra of X+Π2←XΣ+1 and B+Π2←XΣ+1 transitions of the HC314N and HC315N isotopologues of cyanoacetylene have been recorded. The resolution of the photoelectron spectra allowed us to resolve the vibrational structures and the spin-orbit splittings in the cation. Accurate values of the adiabatic ionization potentials of the two isotopologues (EI/hc(HC314N)=93 909(2) cm−1 and EI/hc(HC315N)=93 912(2) cm−1), the vibrational frequencies of the ν2, ν6, and ν7 vibrational modes, and the spin-orbit coupling constant (ASO = −44(2) cm−1) of the X+Π2 cationic ground state have been derived from the measurements. Using ab initio calculations, the unexpected structure of the B+Π2←XΣ+1 transition is tentatively attributed to a conical intersection between the A+ and B+ electronic states of the cation.
Reductions in finite-dimensional integrable systems and special points of classical r-matrices
Authors: Skrypnyk T.
Published: December 2016

For a given 𝔤 ⊗ 𝔤-valued non-skew-symmetric non-dynamical classical r-matrices r(u, v) with spectral parameters, we construct the general form of 𝔤-valued Lax matrices of finite-dimensional integrable systems satisfying linear r-matrix algebra. We show that the reduction in the corresponding finite-dimensional integrable systems is connected with “the special points” of the classical r-matrices in which they become degenerated. We also propose a systematic way of the construction of additional integrals of the Lax-integrable systems associated with the symmetries of the corresponding r-matrices. We consider examples of the Lax matrices and integrable systems that are obtained in the framework of the general scheme. Among them there are such physically important systems as generalized Gaudin systems in an external magnetic field, ultimate integrable generalization of Toda-type chains (including “modified” or “deformed” Toda chains), generalized integrable Jaynes-Cummings-Dicke models, integrable boson models generalizing Bose-Hubbard dimer models, etc.
Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations
Authors: Amin Md. Asif , Halder Ritaban , Ghosh Catherine , Jana Biman , Bhattacharyya Kankan
Published: December 2016

Effect of ethanol on the size and structure of a protein cytochrome C (Cyt C) is investigated using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. For FCS studies, Cyt C is covalently labeled with a fluorescent probe, alexa 488. FCS studies indicate that on addition of ethanol, the size of the protein varies non-monotonically. The size of Cyt C increases (i.e., the protein unfolds) on addition of alcohol (ethanol) up to a mole fraction of 0.2 (44.75% v/v) and decreases at higher alcohol concentration. In order to provide a molecular origin of this structural transition, we explore the conformational free energy landscape of Cyt C as a function of radius of gyration (Rg) at different compositions of water-ethanol binary mixture using MD simulations. Cyt C exhibits a minimum at Rg ∼ 13 Å in bulk water (0% alcohol). Upon increasing ethanol concentration, a second minimum appears in the free energy surface with gradually larger Rg up to χEtOH ∼ 0.2 (44.75% v/v). This suggests gradual unfolding of the protein. At a higher concentration of alcohol (χEtOH > 0.2), the minimum at large Rg vanishes, indicating compaction. Analysis of the contact map and the solvent organization around protein indicates a preferential solvation of the hydrophobic residues by ethanol up to χEtOH = 0.2 (44.75% v/v) and this causes the gradual unfolding of the protein. At high concentration (χEtOH = 0.3 (58% v/v)), due to structural organization in bulk water-ethanol binary mixture, the extent of preferential solvation by ethanol decreases. This causes a structural transition of Cyt C towards a more compact state.
Numerical simulations of the breakup of emulsion droplets inside a spraying nozzle
Authors: Feigl Kathleen , Baniabedalruhman Ahmad , Tanner Franz X. , Windhab Erich J.
Published: December 2016

Numerical simulations are used to investigate the breakup of emulsion drops within a spraying nozzle. The simulations are performed by solving a two-phase flow problem in the nozzle in which individual drops are tracked through the flow field. A modified version of an OpenFOAM® solver is used as a basis for the simulations. The numerical algorithm employs the finite volume method for solving the mass and momentum conservation equations and a volume-of-fluid approach for capturing the fluid-fluid interface. Dynamic meshing is used to maintain a sufficiently refined mesh around a drop as it moves through the flow field. The dispersed phase is Newtonian, while a Newtonian and a shear-thinning non-Newtonian continuous phase are used. The simulations show two types of breakup behavior. Larger drops break up via tipstreaming in which small drops are detached from the tail of the mother drop, while smaller drops break up via filament fracturing in which the daughter drops were formed via pinching at several locations along the stretched drop. The critical drop sizes and critical capillary numbers are determined for each continuous phase fluid along various streamlines. It is found that for both continuous phase fluids, there is an initial rapid decrease in these quantities as the distance from the centerline of the nozzle increases, i.e., as strain rates and stress increase, before leveling off. Moreover, closer to the centerline, these quantities are larger for the Newtonian continuous phase than for the non-Newtonian one, even though the strain rates and stresses are larger for the Newtonian fluid. This is explained in terms of the viscosity ratios reached within the die. Finally, proper scaling of the stresses produces a master critical drop size and critical capillary number curve for the two continuous phase fluids.
Enhancing the injection locking range of spin torque oscillators through mutual coupling
Authors: Romera M. , Talatchian P. , Lebrun R. , Merazzo K. J. , Bortolotti P. , Vila L. , Costa J. D. , Ferreira R. , Freitas P. P. , Cyrille M.-C. , Ebels U. , Cros V. , Grollier J.
Published: December 2016

We investigate how the ability of the vortex oscillation mode of a spin-torque nano-oscillator to lock to an external microwave signal is modified when it is coupled to another oscillator. We show experimentally that the mutual electrical coupling can lead to locking range enhancements of a factor 1.64. Furthermore, we analyze the evolution of the locking range as a function of the coupling strength through experiments and numerical simulations. By uncovering the mechanisms at stake in the locking range enhancement, our results will be useful for designing spin-torque nano-oscillator arrays with high sensitivities to external microwave stimuli.
Passive wireless strain measurement based upon the Villari effect and giant magnetoresistance
Authors: Windl Roman , Bruckner Florian , Abert Claas , Huber Christian , Vogler Christoph , Huber Thomas , Oezelt Harald , Suess Dieter
Published: December 2016

A passive wireless radio frequency-identification (RFID) stress/strain sensor is presented. Stress is transformed into a change of magnetic field by utilizing an amorphous metal ribbon. This magnetic field change is measured by a giant magnetoresistance magnetic field sensor and converted into a digital value with a RFID chip for wireless access. Standard metal foil strain gauges have a gauge factor GF from around 2 to 5 and suffer from the disadvantage of a physically connected power supply and measurement equipment. For the presented sensor, a strain range of −10 μmm to 190 μmm results in a linear sensor response, a gauge factor of GF ≈ 245, and a detectivity of 4.10 nmm1Hz. The detectivity of the presented sensor is similar to the detectivity of a reference metal foil strain gauge. Due to low power consumption and easy signal analysis, this sensor is well suited for long term strain measurement inside closed spaces. RFID adds features like multiple tag detection, wireless passive operation and a user data storage.
Valley splitting of single-electron Si MOS quantum dots
Authors: Gamble John King , Harvey-Collard Patrick , Jacobson N. Tobias , Baczewski Andrew D. , Nielsen Erik , Maurer Leon , Montaño Inès , Rudolph Martin , Carroll M. S. , Yang C. H. , Rossi A. , Dzurak A. S. , Muller Richard P.
Published: December 2016

Silicon-based metal-oxide-semiconductor quantum dots are prominent candidates for high-fidelity, manufacturable qubits. Due to silicon's band structure, additional low-energy states persist in these devices, presenting both challenges and opportunities. Although the physics governing these valley states has been the subject of intense study, quantitative agreement between experiment and theory remains elusive. Here, we present data from an experiment probing the valley states of quantum dot devices and develop a theory that is in quantitative agreement with both this and a recently reported experiment. Through sampling millions of realistic cases of interface roughness, our method provides evidence that the valley physics between the two samples is essentially the same.
A general method for baseline-removal in ultrafast electron powder diffraction data using the dual-tree complex wavelet transform
Authors: René de Cotret Laurent P. , Siwick Bradley J.
Published: December 2016

The general problem of background subtraction in ultrafast electron powder diffraction (UEPD) is presented with a focus on the diffraction patterns obtained from materials of moderately complex structure which contain many overlapping peaks and effectively no scattering vector regions that can be considered exclusively background. We compare the performance of background subtraction algorithms based on discrete and dual-tree complex (DTCWT) wavelet transforms when applied to simulated UEPD data on the M1–R phase transition in VO2 with a time-varying background. We find that the DTCWT approach is capable of extracting intensities that are accurate to better than 2% across the whole range of scattering vector simulated, effectively independent of delay time. A Python package is available.
Discursive construction of Lithuania's “others:” the case of Belarus
Authors: Kesylytė-Alliks Eglė
Published: December 2016

This article analyzes discursive representations of Lithuania and of Belarus as Lithuania's “Other” in the context of the recent political crisis in Ukraine. Focusing on the media discourse of Lithuanian intellectuals regarding the historical Grand Duchy of Lithuania (GDL) and its legacy, it examines how Belarus and its role vis-à-vis Lithuania have been depicted. The analysis is informed by the discourse-historical approach within critical discourse analysis, using thematic content and argumentation schemes for studying the images ascribed to the GDL, Belarus, and Lithuania in the selected texts. Focus in the discourse of intellectuals on the GDL as a historical homeland is found to shift from history as a scholarly endeavor to the politics of history and the uses of the past in today's political projects. Belarus and the GDL emerge as topics not only historically and politically salient but also potentially dangerous for Lithuania within the setting of the events in Ukraine.
In situ neutron diffraction measurement of strain relaxation in welds during heat treatment
Authors: Alipooramirabad Houman , Paradowska Anna , Lavigne Olivier , Ghomashchi Reza , Reid Mark
Published: December 2016

Neutron diffraction (ND) is commonly used to investigate the stress redistribution before and after post-weld heat treatment (PWHT) in welded structures. However, there is a lack of information on the evaluations of strains during PWHT. The present work employed in situ ND to measure the relaxation of residual strains during conventional PWHT in multi-pass high-strength low-alloy steel welds. It was found that strain relaxation occurs principally during the heating stage of the heat treatment. The findings have important economic bearings and can be used to characterise comparable material combinations and optimise the PWHT process for high-strength low-alloy weld joints. This unique information also provides a valuable benchmark for the finite element modelling of this complex process.
Character-complexity effects in Chinese reading and visual search: A comparison and theoretical implications
Authors: Yu Lili , Zhang Qiaoming , Priest Caspian , Reichle Erik D , Sheridan Heather
Published: December 2016

Three eye-movement experiments were conducted to examine how the complexity of characters in Chinese words (i.e., number of strokes per character) influences their processing and eye-movement behaviour. In Experiment 1, English speakers with no significant knowledge of Chinese searched for specific low-, medium-, and high-complexity target characters in a multi-page narrative containing characters of varying complexity (3–16 strokes). Fixation durations and skipping rates were influenced by the visual complexity of both the target characters and the characters being searched even though participants had no knowledge of Chinese. In Experiment 2, native Chinese speakers performed the same character-search task, and a similar pattern of results was observed. Finally, in Experiment 3, a second sample of native Chinese speakers read the same text used in Experiments 1 and 2, with text characters again exhibiting complexity effects. These results collectively suggest that character-complexity effects on eye movements may not be due to lexical processing per se but may instead reflect whatever visual processing is required to know whether or not a character corresponds to an episodically represented target. The theoretical implications of this for our understanding of normal reading are discussed.
Performance differences between electroacoustic and electric alone cochlear stimulation using complex tests in noise. A pilot study
Authors: Cantore Italo , De Nicola Carmen , Santandrea Alessandro , Carelli Gabriella , Valente Paola , Santandrea Lorenzo , Cantore Rocco
Published: December 2016

Objectives:

Hybrid cochlear implants enable very interesting performances in bisyllabic words recognition, mainly in noisy conditions. In this paper, we studied patients with implants performing some very difficult timbric tasks in quiet and noisy conditions.

Methods:

We studied three adult patients with hybrid implants (group A-hybrid implants) and three adult patients with traditional ones (group B-traditional implants). We made the following tests (in quiet and noise): bisyllabic words recognition; voice kind recognition; common melodies identification and recognition; musical instrument identification and recognition.

Results:

Mean results in quiet: test 1: 35% A, 47% B; test 2: 92% A, 42% B; test 3: identification scores 88% A, 100% B, recognition scores: 37.5% A, 50% B; test 4 identification scores 50% A, 20% B, recognition scores 30% A, 20% B. As for tests in noise: test 1: 28% A, 46% B; test 2: 75% A, 25% B; test 3: identification 81% A, 87.5% B and recognition 56% A, 50% B; test 4: identification 60% A, 30% B and recognition 50% A, 20% B.

Conclusion:

Patients with hybrid implants seem to have better results, mainly in noisy timbric tasks. This could be explained by the better quality of low frequency stimulation and could be an encouragement for further studies and a larger diffusion of this kind of implant in the future.
A statistical study of giant molecular clouds traced by 13CO, C18O, CS, and CH3OH in the disk of NGC 1068 based on ALMA observations
Authors: Tosaki Tomoka , Kohno Kotaro , Harada Nanase , Tanaka Kunihiko , Egusa Fumi , Izumi Takuma , Takano Shuro , Nakajima Taku , Taniguchi Akio , Tamura Yoichi
Published: December 2016

We present 1${^{\prime\prime}_{.}}$4 (98 pc) resolution ALMA observations of 13CO(J = 1–0), C18O(J = 1–0), CS(J = 2–1), and CH3OH(JK = 2K–1K) molecular rotational lines in the central 1΄ (4.2 kpc) diameter region of NGC 1068 to study the physical and chemical properties of giant molecular clouds (GMCs) and to test whether these GMC-scale properties are linked to the larger-scale galactic environment. Using the derived 13CO cube, we have identified 187 high-significance (>8 σ) GMCs by employing the CLUMPFIND algorithm. The molecular gas masses of GMCs ($M_{\rm ^{13}CO}$), derived from the 13CO data, range from 1.8 × 104 M⊙ to 4.2 × 107 M⊙. A mass function of GMCs in NGC 1068 has been obtained for the first time at ∼100 pc resolution. We find the slope of the mass function γ = −1.25 ± 0.07 for a mass range of $M_{\rm ^{13}CO} \ge 10^{5}$ M⊙. This is shallower than the GMCs in the disk regions of the Milky Way, M 51, and NGC 300. Further, we find that the high mass cut-off of the GMC mass function occurs at $M_{\rm ^{13}CO} \sim 6 \times 10^{7}$ M⊙, which is an order of magnitude larger than that in the nuclear bar region of M 51, indicating that the more massive clouds dominate the mass budget in NGC 1068. The observed C18O(J = 1–0)/13CO(J = 1–0) intensity ratios are found to be fairly uniform (0.27 ± 0.05) among the identified GMCs. In contrast, the CH3OH(JK = 2K–1K)/13CO(J = 1–0) ratios exhibit striking spatial variation across the disk, with the smallest values around the bar-end (<0.03), and larger ratios along the spiral arms (∼0.1–0.2). We find that GMCs with detectable methanol emission tend to have systematically larger velocity widths than those without methanol emission, suggesting that (relatively weak) shocks are responsible for the enhancement of the CH3OH/13CO ratios of GMCs in the disk of NGC 1068.
The Vascular Pathogen Verticillium longisporum Does Not Affect Water Relations and Plant Responses to Drought Stress of Its Host, Brassica napus
Authors: Lopisso Daniel Teshome , Knüfer Jessica , Koopmann Birger , von Tiedemann Andreas
Published: December 2016

Verticillium longisporum is a host-specific vascular pathogen of oilseed rape (Brassica napus L.) that causes economic crop losses by impairing plant growth and inducing premature senescence. This study investigates whether plant damage through Verticillium stem striping is due to impaired plant water relations, whether V. longisporum affects responses of a susceptible B. napus variety to drought stress, and whether drought stress, in turn, affects plant responses to V. longisporum. Two-factorial experiments on a susceptible cultivar of B. napus infected or noninfected with V. longisporum and exposed to three watering levels (30, 60, and 100% field capacity) revealed that drought stress and V. longisporum impaired plant growth by entirely different mechanisms. Although both stresses similarly affected plant growth parameters (plant height, hypocotyl diameter, and shoot and root dry matter), infection of B. napus with V. longisporum did not affect any drought-related physiological or molecular genetic plant parameters, including transpiration rate, stomatal conductance, photosynthesis rate, water use efficiency, relative leaf water content, leaf proline content, or the expression of drought-responsive genes. Thus, this study provides comprehensive physiological and molecular genetic evidence explaining the lack of wilt symptoms in B. napus infected with V. longisporum. Likewise, drought tolerance of B. napus was unaffected by V. longisporum, as was the level of disease by drought conditions, thus excluding a concerted action of both stresses in the field. Although it is evident that drought and vascular infection with V. longisporum impair plant growth by different mechanisms, it remains to be determined by which other factors V. longisporum causes crop loss.
Spatial Genetic Structure of Coffee-Associated Xylella fastidiosa Populations Indicates that Cross Infection Does Not Occur with Sympatric Citrus Orchards
Authors: Francisco Carolina S. , Ceresini Paulo C. , Almeida Rodrigo P. P. , Coletta-Filho Helvécio D.
Published: December 2016

Xylella fastidiosa, an economically important plant-pathogenic bacterium, infects both coffee and citrus trees in Brazil. Although X. fastidiosa in citrus is well studied, knowledge about the population structure of this bacterium infecting coffee remains unknown. Here, we studied the population structure of X. fastidiosa infecting coffee trees in São Paulo State, Brazil, in four regions where citrus is also widely cultivated. Genotyping of over 500 isolates from coffee plants using 14 genomic microsatellite markers indicated that populations were largely geographically isolated, as previously found with populations of X. fastidiosa infecting citrus. These results were supported by a clustering analysis, which indicated three major genetic groups among the four sampled regions. Overall, approximately 38% of isolates showed significant membership coefficients not related to their original geographical populations (i.e., migrants), characterizing a significant degree of genotype flow among populations. To determine whether admixture occurred between isolates infecting citrus and coffee plants, one site with citrus and coffee orchards adjacent to each other was selected; over 100 isolates were typed from each host plant. No signal of natural admixture between citrus- and coffee-infecting isolates was found; artificial cross-infection assays with representative isolates also yielded no successful cross infection. A comparison determined that X. fastidiosa populations from coffee have higher genetic diversity and allelic richness compared with citrus. The results showed that coffee and citrus X. fastidiosa populations are effectively isolated from each other and, although coffee populations are spatially structured, migration has an important role in shaping diversity.
Differentiation of human induced pluripotent or embryonic stem cells decreases the DNA damage response
Authors: Mujoo Kalpana , Pandita Raj K. , Tiwari Anjana , Charaka Vijay , Chakraborty Sharmistha , Hittelman Walter N. , Horikoshi Nobuo , Hunt Clayton R. , Khanna Kum Kum , Kots Alexander Y. , Butler E. Brian , Murad Ferid , Pandita Tej K.
Published: December 2016

Genomic integrity is critical for preservation of stem cell function and is, maintained through a robust DNA damage response (DDR) with systemized DNA DSB repair by either the non-homologous end joining (NHEJ) pathway or the homologous recombination (HR) pathway. To examine DDR during stem cell differentiation, human embryonic (hES) and induced pluripotent stem (IPS) cells were exposed to DNA damaging agents and DNA damage signaling/repair measured. Differentiated cells displayed a higher frequency of residual DNA damage, chromosomal aberrations, cells with delayed γ-H2AX foci disappearance and a reduced number of RAD51 foci. Factors impacting DNA DSB repair by HR formed reduced foci in differentiated cells. The reduction in repairosome foci formation after DNA damage was not due to changes in HR protein levels, which were unchanged by differentiation. Differentiated cells also displayed a higher frequency of stalled DNA replication forks and decreased firing of new replication origins from transient inhibition of DNA synthesis by hydroxyurea treatment. In addition, we observed that differentiated cells exhibit a higher frequency of R-loops. A similar decline in DDR was observed as early stage mouse astrocytes differentiated into later stage astrocytes. Our studies thus suggest that DSB repair by homologous recombination is increasingly impaired during stem cell differentiation while the NHEJ pathway is minimally altered.
New Insights into the Dynamics of Swarming Bacteria: A Theoretical Study
Authors: Hansmann David , Fier Guido , Buceta Rubén C.
Published: December 2016

In the present work we simulate the basic two-dimensional dynamics of swarmingE. colibacteria on the surface of a moderately soft agar plate. Individual bacteria are modelled by self-propelled ridged bodies (agents), which interact with each other only through inelastic collision and with the highly viscous environment through damping forces. The motion of single agents is modelled closely corresponding to the behaviour of swimming bacteria. The dynamics of the model were adjusted to reproduce the experimental measurements of swimmingE. coliK-12. Accordingly, simulations with loosely packed agents (ρ≈0) show typical run-and-tumble statistics. In contrast, simulations with densely packed agents (ρ≈0.3-0.7) are dominated by interactions (collisions) between agents which lead to the emergence of swarming behaviour. In addition, we model the motion of single agents on the base of modified run-and-tumble dynamics, where the bacteria do not turn actively during the tumble. We show that simulations with densely packed modified agents lead as well the emergence of swarming behaviour, if rotational diffusion is considered.
Deep sequencing of natural and experimental populations ofDrosophila melanogasterreveals biases in the spectrum of new mutations
Authors: Assaf Zoe June , Tilk Susanne , Park Jane , Siegal Mark L. , Petrov Dmitri A.
Published: December 2016

Mutations provide the raw material of evolution, and thus our ability to study evolution depends fundamentally on whether we have precise measurements of mutational rates and patterns. Here we explore the rates and patterns of mutations using i)de novomutations fromDrosophila melanogastermutation accumulation lines and ii) polymorphisms segregating at extremely low frequencies. The first, mutation accumulation (MA) lines, are the product of maintaining flies in tiny populations for many generations, therefore rendering natural selection ineffective and allowing new mutations to accrue in the genome. In addition to generating a novel dataset of sequenced MA lines, we perform a meta-analysis of all published MA studies inD. melanogaster, which allows more precise estimates of mutational patterns across the genome. In the second half of this work, we identify polymorphisms segregating at extremely low frequencies using several publicly available population genomic data sets from natural populations ofD. melanogaster. Extremely rare polymorphisms are difficult to detect with high confidence due to the problem of distinguishing them from sequencing error, however a dataset of true rare polymorphisms would allow the quantification of mutational patterns. This is due to the fact that rare polymorphisms, much likede novomutations, are on average younger and also relatively unaffected by the filter of natural selection. We identify a high quality set of ~70,000 rare polymorphisms, fully validated with resequencing, and use this dataset to measure mutational patterns in the genome. This includes identifying a high rate of multi-nucleotide mutation events at both short (~5bp) and long (~1kb) genomic distances, showing that mutation drives GC content lower in already GC-poor regions, and finding that the context-dependency of the mutation spectrum predicts long-term evolutionary patterns at four-fold synonymous sites. We also show thatde novomutations from independent mutation accumulation experiments display similar patterns of single nucleotide mutation, and match well the patterns of mutation found in natural populations.
GeNNet: An Integrated Platform for Unifying Scientific Workflow Management and Graph Databases for Transcriptome Data Analysis
Authors: Costa Raquel L. , Gadelha Luiz M. R. , Ribeiro-Alves Marcelo , Porto Fabio
Published: December 2016

Background

There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced may additionally be integrated with other biological databases, such as Protein-Protein Interactions and annotations. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managingthe resulting data and its respective metadata are challenging tasks. Running in-silico experiments to structure and compose the information as needed for analysis is a daunting task. Different programsmay need to be applied and different files are produced during the experiment cycle. In this context,the availability of a platform supporting experiment execution is paramount.

Results

We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. GeNNet includes pre-loaded biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and geneset enrichment analysis. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment. As a result, we obtained differentially expressed genes for which biological functions were analyzed. The results are integrated into GeNNet-DB, a database about genes, clusters, experiments and their properties and relationships.The resulting graph database is explored with queries that demonstrate the expressiveness of this data model for reasoning about gene regulatory networks.

Conclusions

GeNNet is the first platform to integrate the analytical process of transcriptome data with graph database. It provides a comprehensive set of tools that would otherwise be challenging for non-expert users to install and use. Developers as well can add new functionality to each component of GeNNet. The resulting data allows for testing previous hypotheses about an experiment as well as exploring new ones through the interactive graph database environment. It enables the analysis of different data on humans, rhesus, mice and rat coming from Affymetrix platforms.
Direct tomography imaging for inelastic X-ray scattering experiments at high pressure
Authors: Sahle Ch. J. , Rosa A. D. , Rossi M. , Cerantola V. , Spiekermann G. , Petitgirard S. , Jacobs J. , Huotari S. , Moretti Sala M. , Mirone A.
Published: December 2016

A method to separate the non-resonant inelastic X-ray scattering signal of a micro-metric sample contained inside a diamond anvil cell (DAC) from the signal originating from the high-pressure sample environment is described. Especially for high-pressure experiments, the parasitic signal originating from the diamond anvils, the gasket and/or the pressure medium can easily obscure the sample signal or even render the experiment impossible. Another severe complication for high-pressure non-resonant inelastic X-ray measurements, such as X-ray Raman scattering spectroscopy, can be the proximity of the desired sample edge energy to an absorption edge energy of elements constituting the DAC. It is shown that recording the scattered signal in a spatially resolved manner allows these problems to be overcome by separating the sample signal from the spurious scattering of the DAC without constraints on the solid angle of detection. Furthermore, simple machine learning algorithms facilitate finding the corresponding detector pixels that record the sample signal. The outlined experimental technique and data analysis approach are demonstrated by presenting spectra of the SiL2,3-edge and OK-edge of compressed α-quartz. The spectra are of unprecedented quality and both the OK-edge and the SiL2,3-edge clearly show the existence of a pressure-induced phase transition between 10 and 24 GPa.
Sub-pixel motion estimation using phase correlation: comparisons and evaluations
Authors: Ren Jie , Zhao Huimin , Ren Jinchang , Cheng Shi
Published: December 2016

Purpose

Effective and robust motion estimation with sub-pixel accuracy is essential in many image processing and computer vision applications. Due to its computational efficiency and robustness in the presence of intensity changes as well as geometric distortions, phase correlation in the Fourier domain provides an attractive solution for global motion estimation and image registration. The paper aims to discuss these issues.

Design/methodology/approach

In this paper, relevant sub-pixel strategies are categorized into three classes, namely, single-side peak interpolation, dual-side peak interpolation and curve fitting. The well-known images “Barbara” and “Pentagon” were used to evaluate the performance of eight typical methods, in which Gaussian noise was attached in the synthetic data.

Findings

For eight such typical methods, the tests using synthetic data have suggested that considering dual-side peaks in interpolation or fitting helps to produce better results. In addition, dual-side interpolation outperforms curve fitting methods in dealing with noisy samples. Overall, Gaussian-based dual-side interpolation seems the best in the experiments.

Originality/value

Based on the comparisons of eight typical methods, the authors can have a better understanding of the phase correlation for motion estimation. The evaluation can provide useful guidance in this context.
Moving object detection based on optical flow and neural network fusion
Authors: Qin Haiqun , Zhen Ziyang , Ma Kun
Published: December 2016

Purpose

The purpose of this paper is to meet the large demand for the new-generation intelligence monitoring systems that are used to detect targets within a dynamic background.

Design/methodology/approach

A dynamic target detection method based on the fusion of optical flow and neural network is proposed.

Findings

Simulation results verify the accuracy of the moving object detection based on optical flow and neural network fusion. The method eliminates the influence caused by the movement of the camera to detect the target and has the ability to extract a complete moving target.

Practical implications

It provides a powerful safeguard for target detection and targets the tracking application.

Originality/value

The proposed method represents the fusion of optical flow and neural network to detect the moving object, and it can be used in new-generation intelligent monitoring systems.
Juvenile concentrations of IGF‐1 predict life‐history trade‐offs in a wild mammal
Authors: Lewin Nora , Swanson Eli M. , Williams Barry L. , Holekamp Kay E.
Published: December 2016

Early postnatal development can have profound effects on life‐history traits later in life. One mechanism hypothesized to mediate this relationship is the anabolic hormone, insulin‐like growth factor‐1 (IGF‐1). IGF‐1 contributes importantly to postnatal growth, and thus offers a means by which environmental and genetic variation might direct organismal development, reproduction and survival.

We tested whether juvenile concentrations of IGF‐1 can predict intraspecific variation in life‐history traits later in life using longitudinal data from free‐living female spotted hyenas (Crocuta crocuta).

We found that juvenile concentrations of IGF‐1 predicted heavier juvenile mass, which in turn predicted greater survival to reproductive maturity. However, independent of mass, higher juvenile concentrations of IGF‐1 predicted earlier age at first parturition and reduced longevity in adulthood.

Our results highlight the importance of early postnatal development as a determination period in mammals and suggest that concentrations of IGF‐1 during this sensitive period can be used to predict important later‐life trade‐offs between growth, reproductive fitness and life span in wild, long‐lived animals.

A lay summary is available for this article.
Introduction: The Progressive Dilemma in British Politics
Authors: Diamond Patrick , Kenny Michael , Liddle Roger
Published: December 2016

This special edition reflects on the contemporary relevance of the insights and concerns of David Marquand's book The Progressive Dilemma. In this Introduction, the editors set the scene for these reflections. They consider the structural changes that have occurred in politics since the 1990s: the impact of globalisation, the erosion of class identities, the rise of ‘identity politics’ and the continued fragmentation of the party system. There has been no reconciliation between the parties of the centre‐left, nor any re‐examination of the ‘liberal tradition’ and the potential for a new synthesis with revisionist social democracy. On the one hand, Corbynism is a radicalised metropolitan species of liberalism, while on the other there are plenty in Labour who stress the need for the party to re‐engage with the traditional, socially conservative values of the working class in a new ‘postliberal’ appeal. Yet the authors argue that those who broadly identify with progressive causes in British politics—animated by the various overlapping strands of social liberalism, social democracy and liberal socialism—have still to work out how to address the historic failings that Marquand so eloquently exposed, to create a new and inspiring intellectual vision that unites and energises the left and centre‐left.
Ethics as an Enabler of Public Policy
Authors: Goodin Robert E.
Published: December 2016

Ethics constrains us. But ethics can also act as an ‘enabler’, helping to secure compliance with public policies. Basing policies on ethical principles helps the public know what is required of them by public policies. Framing policies in those ways also primes people to think in terms of their own ethically based reasons for action. Basing policies on ethical principles can assist in securing the cooperation of potential veto players by creating cooperative norms and a culture of trust.
Electrofishing method improves evaluation of amphibian larvae abundance: a case of “beaver rivers”
Authors: DGEBUADZE Yury Y. , BASHINSKIY Ivan V.
Published: December 2016

There are many locations in Russia where Eurasian beaver (Castor fiber) populations have been restored. As a keystone species, beavers provide wide‐ranging direct and indirect impacts on aquatic ecosystems. In particular, beaver‐created ponds are sites for spawning and nursery places for tadpoles of the brown frogs (genus Rana). Because of such impacts, study techniques for assessing aquatic organism abundance are being developed. We compared two methods for estimating tadpole abundance: traditional catches by dipnet and electrofishing. Our results show that the dipnet catch data for the shallower ponds with larger water surface area were five times lower than that obtained by electrofishing. Therefore, we conclude that dipnet catches are not suitable for comparing the relative abundance of tadpoles in the two beaver ponds that were studied.
Circulating fibroblast activation protein and dipeptidyl peptidase 4 in rheumatoid arthritis and systemic sclerosis
Authors: Sinnathurai Premarani , Lau Wendy , Vieira de Ribeiro Ana Julia , Bachovchin William W. , Englert Helen , Howe Graydon , Spencer David , Manolios Nicholas , Gorrell Mark D.
Published: December 2016

Aim

To quantify circulating fibroblast activation protein (cFAP) and dipeptidyl peptidase 4 (cDPP4) protease activities in patients with rheumatoid arthritis (RA), systemic sclerosis (SSc), and a control group with mechanical back pain and to correlate plasma levels with disease characteristics.

Methods

Plasma was collected from patients with RA (n = 73), SSc (n = 37) and control subjects (n = 26). DPP4 and FAP were quantified using specific enzyme activity assays.

Results

Median cDPP4 was significantly lower in the RA group (P = 0.02), and SSc group (P = 0.002) compared with controls. There were no significant differences in median cFAP between the three groups. DPP4 and FAP demonstrated a negative correlation with inflammatory markers and duration of disease. There were no associations with disease subtypes in RA, including seropositive and erosive disease. Decreased cDPP4 was found in SSc patients with myositis. Plasma FAP was lower in RA patients receiving prednisone (P = 0.001) or leflunomide (P = 0.04), but higher with biologic agents (P = 0.01). RA patients receiving leflunomide also had decreased cDPP4 (P = 0.014). SSc patients receiving prednisone (P = 0.02) had lower cDPP4 but there was no association with cFAP.

Conclusions

No association was found between cFAP and RA or SSc. Plasma DPP4 was decreased in RA and SSc when compared with controls. cDPP4 and cFAP correlated negatively with inflammatory markers and there were no significant correlations with disease characteristics in this RA cohort.