bluuebunny/crossref_metadata_2025 huggingface dataset:
Surface structure of imidazolium-based ionic liquids: Quantitative comparison between simulations and high-resolution RBS measurements
Authors: Nakajima Kaoru , Nakanishi Shunto , Lísal Martin , Kimura Kenji
Published: March 2016

Elemental depth profiles of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([CnMIM][TFSI], n = 4, 6, 8) are measured using high-resolution Rutherford backscattering spectroscopy (HRBS). The profiles are compared with the results of molecular dynamics (MD) simulations. Both MD simulations and HRBS measurements show that the depth profiles deviate from the uniform stoichiometric composition in the surface region, showing preferential orientations of ions at the surface. The MD simulations qualitatively reproduce the observed HRBS profiles but the agreement is not satisfactory. The observed discrepancy is ascribed to the capillary waves. By taking account of the surface roughness induced by the capillary waves, the agreement becomes almost perfect.
Hydrodynamic description of an unmagnetized plasma with multiple ion species. II. Two and three ion species plasmas
Authors: Simakov Andrei N. , Molvig Kim
Published: March 2016

Paper I [A. N. Simakov and K. Molvig, Phys. Plasmas 23, 032115 (2016)] obtained a fluid description for an unmagnetized collisional plasma with multiple ion species. To evaluate collisional plasma transport fluxes, required for such a description, two linear systems of equations need to be solved to obtain corresponding transport coefficients. In general, this should be done numerically. Herein, the general formalism is used to obtain analytical expressions for such fluxes for several specific cases of interest: a deuterium-tritium plasma; a plasma containing two ion species with strongly disparate masses, which agrees with previously obtained results; and a three ion species plasma made of deuterium, tritium, and gold. These results can be used for understanding the behavior of the aforementioned plasmas, or for verifying a code implementation of the general multi-ion formalism.
The filament forming reactions of vimentin tetramers studied in a serial-inlet microflow device by small angle x-ray scattering
Authors: Saldanha Oliva , Brennich Martha E. , Burghammer Manfred , Herrmann Harald , Köster Sarah
Published: March 2016

The structural organization of metazoan cells and their shape are established through the coordinated interaction of a composite network consisting of three individual filament systems, collectively termed the cytoskeleton. Specifically, microtubules and actin filaments, which assemble from monomeric globular proteins, provide polar structures that serve motor proteins as tracks. In contrast, intermediate filaments (IFs) assemble from highly charged, extended coiled coils in a hierarchical assembly mechanism of lateral and longitudinal interaction steps into non-polar structures. IF proteins are expressed in a distinctly tissue-specific way and thereby serve to generate the precise plasticity of the respective cells and tissues. Accordingly, in the cell, numerous parameters such as pH and salt concentration are adjusted such that the generation of functional networks is ensured. Here, we transfer the problem for the mesenchymal IF protein vimentin to an in vitro setting and combine small angle x-ray scattering with microfluidics and finite element method simulations. Our approach is adapted to resolve the early assembly steps, which take place in the sub-second to second range. In particular, we reveal the influence of ion species and concentrations on the assembly. By tuning the flow rates and thus concentration profiles, we find a minimal critical salt concentration for the initiation of the assembly. Furthermore, our analysis of the surface sensitive Porod regime in the x-ray data reveals that the formation of first assembly intermediates, so-called unit length filaments, is not a one-step reaction but consists of distinct consecutive lateral association steps followed by radial compaction as well as smoothening of the surface of the full-width filament.
Multipole electrodynamic ion trap geometries for microparticle confinement under standard ambient temperature and pressure conditions
Authors: Mihalcea Bogdan M. , Giurgiu Liviu C. , Stan Cristina , Vişan Gina T. , Ganciu Mihai , Filinov Vladimir , Lapitsky Dmitry , Deputatova Lidiya , Syrovatka Roman
Published: March 2016

Trapping of microparticles and aerosols is of great interest for physics and chemistry. We report microparticle trapping in case of multipole linear Paul trap geometries, operating under standard ambient temperature and pressure conditions. An 8- and 12-electrode linear trap geometries have been designed and tested with an aim to achieve trapping for larger number of particles and to study microparticle dynamical stability in electrodynamic fields. We report emergence of planar and volume ordered structures of microparticles, depending on the a.c. trapping frequency and particle specific charge ratio. The electric potential within the trap is mapped using the electrolytic tank method. Particle dynamics is simulated using a stochastic Langevin equation. We emphasize extended regions of stable trapping with respect to quadrupole traps, as well as good agreement between experiment and numerical simulations.
Ion wake field effects on the dust-ion-acoustic surface mode in a semi-bounded Lorentzian dusty plasma
Authors: Lee Myoung-Jae , Jung Young-Dae
Published: March 2016

The dispersion relation for the dust ion-acoustic surface waves propagating at the interface of semi-bounded Lorentzian dusty plasma with supersonic ion flow has been kinetically derived to investigate the nonthermal property and the ion wake field effect. We found that the supersonic ion flow creates the upper and the lower modes. The increase in the nonthermal particles decreases the wave frequency for the upper mode whereas it increases the frequency for the lower mode. The increase in the supersonic ion flow velocity is found to enhance the wave frequency for both modes. We also found that the increase in nonthermal plasmas is found to enhance the group velocity of the upper mode. However, the nonthermal particles suppress the lower mode group velocity. The nonthermal effects on the group velocity will be reduced in the limit of small or large wavelength limit.
Capacitive radio frequency discharges with a single ring-shaped narrow trench of various depths to enhance the plasma density and lateral uniformity
Authors: Ohtsu Y. , Matsumoto N. , Schulze J. , Schuengel E.
Published: March 2016

Spatial structures of the electron density and temperature in ring-shaped hollow cathode capacitive rf plasma with a single narrow trench of 2 mm width have been investigated at various trench depths of D = 5, 8, 10, 12, and 15 mm. It is found that the plasma density is increased in the presence of the trench and that the radial profile of the plasma density has a peak around the narrow hollow trench near the cathode. The density becomes uniform further away from the cathode at all trench depths, whereas the electron temperature distribution remains almost uniform. The measured radial profiles of the plasma density are in good agreement with a theoretical diffusion model for all the trench depths, which explains the local density increase by a local enhancement of the electron heating. Under the conditions investigated, the trench of 10 mm depth is found to result in the highest plasma density at various axial and radial positions. The results show that the radial uniformity of the plasma density at various axial positions can be improved by using structured electrodes of distinct depths rather than planar electrodes.
Wide angle terahertz sensing with a cross-dipole frequency selective surface
Authors: Rodríguez-Ulibarri P. , Kuznetsov S. A. , Beruete M.
Published: March 2016

In this work, a terahertz sensor based on a cross dipole frequency selective surface is analyzed and experimentally tested. The sensing structure is optimized for operation at the fundamental band-stop resonance near 0.7 THz and characterized under normal and oblique incidence. The sensing performance as a function of the incidence angle and the wave polarization is evaluated with good agreement between simulations and measurements. It is shown that a figure of merit for the proposed sensor can be enhanced from 0.2 up to 0.6 due to switching from normal to oblique excitation, which yields the maximum performance for TM polarization at the incidence angle of 70°. The presented results demonstrate a wide angle operation regime in THz sensing that opens up an alternative approach in improving capabilities of sensing devices.
Temperature dependence of in-plane magnetic anisotropy and anisotropic magnetoresistance in (Ga,Mn)As codoped with Li
Authors: Miyakozawa Shohei , Chen Lin , Matsukura Fumihiro , Ohno Hideo
Published: March 2016

We evaluate the temperature dependence of in-plane magnetic anisotropy and anisotropic magnetoresistance (AMR) in (Ga,Mn)As codoped with Li by magnetotransport measurements. We find that the signs of in-plane uniaxial anisotropy and AMR change at the same temperature of ∼75 K, and that the sign of planar Hall effect does not depend on temperature.
Phonon processes in vertically aligned silicon nanowire arrays produced by low-cost all-solution galvanic displacement method
Authors: Banerjee Debika , Trudeau Charles , Gerlein Luis Felipe , Cloutier Sylvain G.
Published: March 2016

The nanoscale engineering of silicon can significantly change its bulk optoelectronic properties to make it more favorable for device integration. Phonon process engineering is one way to enhance inter-band transitions in silicon's indirect band structure alignment. This paper demonstrates phonon localization at the tip of silicon nanowires fabricated by galvanic displacement using wet electroless chemical etching of a bulk silicon wafer. High-resolution Raman micro-spectroscopy reveals that such arrayed structures of silicon nanowires display phonon localization behaviors, which could help their integration into the future generations of nano-engineered silicon nanowire-based devices such as photodetectors and solar cells.
Ionic sieving through Ti3C2(OH)2 MXene: First-principles calculations
Authors: Berdiyorov Golibjon R. , Madjet Mohamed E. , Mahmoud Khaled A.
Published: March 2016

Recent experiments revealed a great potential of MXene nanosheets for water desalination applications as ultrathin, high-flux, and size/charge-selective sieving membranes. Here, we conduct first-principles density functional theory calculations to explore possible mechanisms for the charge-selective ionic transport through Ti3C2(OH)2 MXene. We find that the charge selectivity originates from the charged nature of the MXene layers. For example, due to the electrostatic interactions, ions of different charge states have different energy barriers for the intercalation between the MXene layers. In addition, the system shows dynamic response to the intercalating ions, even in their hydrated states, by changing the interlayer spacing. Our findings highlight the importance of membrane surface charges on the ion sieving performance.
Spatial distribution of transferred charges across the heterointerface between perovskite transition metal oxides LaNiO3 and LaMnO3
Authors: Kitamura Miho , Horiba Koji , Kobayashi Masaki , Sakai Enju , Minohara Makoto , Mitsuhashi Taichi , Fujimori Atsushi , Nagai Takuro , Fujioka Hiroshi , Kumigashira Hiroshi
Published: March 2016

To investigate the interfacial charge-transfer phenomena between perovskite transition metal oxides LaNiO3 (LNO) and LaMnO3 (LMO), we have performed in situ x-ray absorption spectroscopy (XAS) measurements on LNO/LMO multilayers. The Ni-L2,3 and Mn-L2,3 XAS spectra clearly show the occurrence of electron transfer from Mn to Ni ions in the interface region. Detailed analysis of the thickness dependence of these XAS spectra has revealed that the spatial distribution of the transferred charges across the interface is significantly different between the two constituent layers. The observed spatial distribution is presumably described by the charge spreading model that treats the transfer integral between neighboring transition metal ions and the Coulomb interaction, rather than the Thomas–Fermi screening model.
Giant Dirac point shift of graphene phototransistors by doped silicon substrate current
Authors: Shimatani Masaaki , Ogawa Shinpei , Fujisawa Daisuke , Okuda Satoshi , Kanai Yasushi , Ono Takao , Matsumoto Kazuhiko
Published: March 2016

Graphene is a promising new material for photodetectors due to its excellent optical properties and high-speed response. However, graphene-based phototransistors have low responsivity due to the weak light absorption of graphene. We have observed a giant Dirac point shift upon white light illumination in graphene-based phototransistors with n-doped Si substrates, but not those with p-doped substrates. The source-drain current and substrate current were investigated with and without illumination for both p-type and n-type Si substrates. The decay time of the drain-source current indicates that the Si substrate, SiO2 layer, and metal electrode comprise a metal-oxide-semiconductor (MOS) capacitor due to the presence of defects at the interface between the Si substrate and SiO2 layer. The difference in the diffusion time of the intrinsic major carriers (electrons) and the photogenerated electron-hole pairs to the depletion layer delays the application of the gate voltage to the graphene channel. Therefore, the giant Dirac point shift is attributed to the n-type Si substrate current. This phenomenon can be exploited to realize high-performance graphene-based phototransistors.
High-performance back-channel-etched thin-film transistors with amorphous Si-incorporated SnO2 active layer
Authors: Liu Xianzhe , Ning Honglong , Chen Jianqiu , Cai Wei , Hu Shiben , Tao Ruiqiang , Zeng Yong , Zheng Zeke , Yao Rihui , Xu Miao , Wang Lei , Lan Linfeng , Peng Junbiao
Published: March 2016

In this report, back-channel-etched (BCE) thin-film transistors (TFTs) were achieved by using Si-incorporated SnO2 (silicon tin oxide (STO)) film as active layer. It was found that the STO film was acid-resistant and in amorphous state. The BCE-TFT with STO active layer exhibited a mobility of 5.91 cm2/V s, a threshold voltage of 0.4 V, an on/off ratio of 107, and a steep subthreshold swing of 0.68 V/decade. Moreover, the device had a good stability under the positive/negative gate-bias stress.
Energy storage and polarization switching kinetics of (001)-oriented Pb0.97La0.02(Zr0.95Ti0.05)O3 antiferroelectric thick films
Authors: Liu C. , Lin S. X. , Qin M. H. , Lu X. B. , Gao X. S. , Zeng M. , Li Q. L. , Liu J.-M.
Published: March 2016

For antiferroelectric (AFE) energy storage, the stability of energy storage density and conversion efficiency against wide temperature (T) range and broad frequency (f) band is highly preferred. In this work, we investigate the energy storage and associated kinetics of polarization switching in (001)-textured AFE Pb0.97La0.02(Zr0.95Ti0.05)O3 (PLZT 2/95/5) thick films prepared by sol-gel method. A recoverable energy storage density (Wre) of ∼26.8 J/cm3 and an energy conversion efficiency (η) as high as ∼62.5% have been obtained under an electric field of 1.85 MV/cm and room temperature. Both the Wre and η are only weakly T-dependent up to 280 °C and weakly f-dependent ranging from 20 Hz to 10 kHz. The high frequency stability originates from the rapid polarization switching as identified by the nucleation-limited-switching theory, suggesting a characteristic switching time as short as ∼3 ns, favorable for applications in pulse energy storage.
Comparison of Conventional and Microwave Heating for Evaluation of Microwave Effects
Authors: Bana Péter , Greiner István
Published: March 2016

In microwave-assisted organic synthesis, the question of microwave effects is still debated. Proper examination of these hypothesized phenomena is encumbered by some specific features of microwave heating. We devise a convenient method to eliminate most of the irreproducibility observed in microwave-heated organic transformations by thermal conditioning of the microwave reactor cavity. To show the utility of this approach, we investigated a reaction of 2-chloropyridine, in which microwave conditions were shown to be beneficial by previous studies. Using our method to ensure proper reproducibility together with fibre optic temperature measurement, the observed differences were traced back to large hidden thermal differences, while non-thermal effects could not be detected in the comparison experiments.
Breaking the diffraction limit of light-sheet fluorescence microscopy by RESOLFT
Authors: Hoyer Patrick , de Medeiros Gustavo , Balázs Bálint , Norlin Nils , Besir Christina , Hanne Janina , Kräusslich Hans-Georg , Engelhardt Johann , Sahl Steffen J. , Hell Stefan W. , Hufnagel Lars
Published: March 2016

Significance

Light-sheet fluorescence microscopy (LSFM) is an imaging modality in which a sample is illuminated from the side by a beam engineered into a wide and relatively thin “sheet.” This allows highly parallelized planewise scanning of volumes with inherent optical sectioning, offering a good balance between spatial and temporal resolution with reduced photostress. Unfortunately, the axial extent of the illuminated section is ultimately limited by diffraction. Here, we show that a RESOLFT [reversible saturable/switchable optical (fluorescence) transitions] strategy neutralizes the resolution-limiting role of diffraction in LSFM. While other LS strategies exist, which run into new hard axial limits of resolution, LS-RESOLFT is conceptually diffraction-unlimited and can be developed toward molecular-scale resolution.
Viral serine palmitoyltransferase induces metabolic switch in sphingolipid biosynthesis and is required for infection of a marine alga
Authors: Ziv Carmit , Malitsky Sergey , Othman Alaa , Ben-Dor Shifra , Wei Yu , Zheng Shuning , Aharoni Asaph , Hornemann Thorsten , Vardi Assaf
Published: March 2016

Significance

This work investigates the metabolic basis of the interactions between the cosmopolitan bloom-forming algaEmiliania huxleyiand its specific large DNA virus. We demonstrate some of the basic metabolic principles used by the EhV virus to “engineer” its host sphingolipid metabolism, to produce a unique suite of virus-specific lipids. These sphingolipids were essential for the virus assembly and infectivity. These results present novel insight into the chemical “arm race” at sea that coevolved around a unique metabolic pathway. Furthermore, it may provide important evolutionary and biochemical insights into sphingolipid biosynthesis and its functional role in other host–pathogen interactions (e.g. HIV, hepatitis C virus, dengue virus).
Success in School for Justice-Involved Girls: Do Specific Aspects of Developmental Immaturity Matter?
Authors: Haney-Caron Emily , Goldstein Naomi E. S. , Giallella Christy L. , Kemp Kathleen , Romaine Christina Riggs
Published: March 2016

Developmental immaturity (DI) may help explain some of the variability in aspects of academic achievement among girls in the juvenile justice system, a population with high rates of truancy, dropout, and school failure. This study examined the relationships among the decision making and independent functioning components of DI, verbal intelligence, and academic achievement within this population. Using data from 60 girls in residential juvenile justice facilities, multiple regression analyses indicated that verbal IQ moderated the relationship between the DI construct of decision making and academic achievement. Self-reported school attendance and number of previous arrests did not significantly mediate the relationship between DI and academic achievement. These results may indicate that the decision-making factor of DI may be particularly important, and, if results are replicated, future intervention efforts could focus more on improving this skill within this juvenile justice population. Additionally, the overall importance of the full DI construct is an important area of future study.
Relational Pathways to Substance Misuse and Drug-Related Offending in Women: The Role of Trauma, Insecure Attachment, and Shame
Authors: Kreis Mette K. F. , Gillings Kirsty , Svanberg Jenny , Schwannauer Matthias
Published: March 2016

Dysfunctional relationships are highlighted as a potential mediator between women's substance misuse and offending, but few studies have explored how. This qualitative study explored the role of interpersonal relationships to substance misuse and offending in women, and underlying psychological processes involved. Seven women offenders in community treatment for heroin dependence were interviewed. Data were analyzed using social constructivist grounded theory. A provisional model was constructed of the interconnection between family disconnection, dysfunctional intimate partner relationships, loss of children, and substance misuse and drug-related offending, within the context of complex trauma, insecure attachment, and shame. The potential significance of shame to women's substance misuse and offending has had little prior investigation. Interventions for women offenders with heroin addiction may need to consider all these relational psychological processes to adequately address recidivism risk.
Gender Matters: An Introduction to the Special Issues on Women and Girls
Authors: de Vogel Vivienne , Nicholls Tonia L.
Published: March 2016

Girls and women represent a minority of forensic mental health and prison populations. However, studies worldwide suggest that there has been a steady increase in the number of girls and women being managed by forensic mental health services and correctional agencies over the past two decades. The vast majority of research in the forensic mental health field, however, remains steadfastly focused on male populations. As such, there are growing concerns about whether the theoretical knowledge we have on male offenders is sufficiently valid and useful for female offenders. There remain substantial gaps in knowledge and debate regarding the importance of gender differences, for instance, in developmental pathways to offending and in violence risk factors and assessment. There is a similar paucity of knowledge on the efficacy of treatment in female offenders and a need for treatment programs that are specifically responsive to the needs and issues of these girls and women. These special issues of the International Journal of Forensic Mental Health dedicated to gender issues in the forensic field marks a substantial effort to enlarge the empirical and theoretical knowledge on (violent) offending, assessment, and treatment in girls and women. In this introduction article, we aim to highlight the relevance of studying gender differences in the forensic field and to provide a brief overview of important gender issues in developmental pathways to offending, gender differences and similarities in the nature of offending, assessment and treatment in forensic mental health care and the criminal justice system. Finally, we provide recommendations for practitioners, researchers, and policymakers to move forward on this topic in the forensic field.
Variation in the Effective Range of a Stereo-Video Lander in Relation to Near-Seafloor Water Clarity, Ambient Light and Fish Length
Authors: Hannah Robert W. , Blume Matthew T. O.
Published: March 2016

We studied how variation in seafloor water clarity, ambient light, and fish fork length influenced the maximum detection range of fish with a stereo-video lander on three temperate reefs of different depths (12–40, 44–91, and 144–149 m). Although the results are somewhat approximate and specific to the camera system, the methods we used can be applied to any stereo remote underwater visual survey system. In the 52 total lander deployments distributed between nearshore, mid-shelf and deep-shelf reefs in Oregon waters, seafloor light levels varied over 4 orders of magnitude, primarily as a function of depth. The seafloor scattering index was higher (low water clarity) and highly variable at the nearshore reef and lower (high water clarity) and less variable at the deeper reefs. In the 15 deployments with sufficient numbers of fish for detection range analysis, the mean maximum range of detection across species varied from 3.89 to 4.23 m at the deep-shelf reef, 3.32–5.55 m at the mid-shelf reef, and 1.57–3.42 m at the nearshore reef. Multiple regression analysis of the analyzed deployments showed a strong negative relationship between mean maximum detection range and the scattering index but no relationship with loge of seafloor ambient light. The lack of a light effect showed that the artificial lights were adequately illuminating the field of view in which fish were identifiable, potentially an important system test for sampling across a range of seafloor light levels. Analysis of detection range versus fish fork length for Blue Rockfish Sebastes mystinus and Deacon Rockfish S. diaconus from a single deployment showed a reduction in detection range for 10–20-cm fish of about 1.15 m relative to the detection range of 25–45-cm fish, or about 41%.

Received September 29, 2015; accepted December 14, 2015
EBglmnet: a comprehensive R package for sparse generalized linear regression models
Authors: Huang Anhui , Liu Dianting
Published: March 2016

EBglmnet is an R package implementing empirical Bayesian method with both lasso (EBlasso) and elastic net (EBEN) priors for generalized linear models. In our previous studies, both EBlasso and EBEN outperformed other state-of-the-art methods such as lasso and elastic net in inferring sparse genotype and phenotype associations, in which the number of covariates is typically much larger than the sample size. While high density genetic markers can be easily obtained nowadays in genetics and population analysis thanks to the advancements in molecular high throughput technologies, EBglmnet will be a very useful tool for statistical modeling in this area.

Availability and implementation

EBglmnet package is freely available from the R archive CRAN (http://cran.r-project.org/).
Distribution of megafaunal species in the Southwestern Atlantic: key ecological areas and opportunities for marine conservation
Authors: González Carman V. , Mandiola A. , Alemany D. , Dassis M. , Seco Pon J. P. , Prosdocimi L. , Ponce de León A. , Mianzan H. , Acha E. M. , Rodríguez D. , Favero M. , Copello S.
Published: March 2016

During the last centuries, populations of marine megafauna—such as seabirds, turtles, and mammals—were intensively exploited. At present, other threats such as bycatch and pollution affect these species, which play key ecological roles in marine ecosystems as apex consumers and/or nutrient transporters. This study analyses the distribution of six megafaunal species (Chelonia mydas, Caretta caretta, Dermochelys coriacea, Thalassarche melanophris, Otaria flavescens, and Arctocephalus australis) coexisting in the Southwestern Atlantic to discuss their protection in terms of current management strategies in the region. Through the prediction of the species potential distributions and their relation to bathymetry, sea temperature and oceanographic fronts, key ecological areas are defined from a multi-taxa perspective. Information on the distribution of 70 individuals (18 sea turtles, 19 albatrosses, and 33 otariids) was obtained through satellite tracking conducted during 2007–2013 and analysed using a Geographic Information System and maximum entropy models. During the autumn–winter period, megafaunal species were distributed over the continental shelves of Argentina, Uruguay, and Brazil, mainly over the Argentine Exclusive Economic Zone and the Argentina-Uruguay Common Fishing Zone. Despite some differences, all megafaunal species seems to have similar environmental requirements during the autumn–winter period. Mostly waters shallower than 50 m were identified as key ecological areas, with the Río de la Plata as the habitat with the highest suitability for all the species. This area is highly productive and sustains the main coastal fisheries of Uruguay and Argentina, yet its role as a key ecological area for megafaunal species has been underestimated until now. This approach provides a basis to analyse the effect of anthropic activities on megafaunal species through risk maps and, ultimately, to generate knowledge to improve national and bi-national management plans between Argentina and Uruguay.
Remote sensing of habitat characteristics using echo metrics and image-based seabed classes
Authors: Cutter George R. , Stierhoff Kevin L. , Demer David A.
Published: March 2016

The seabed can be classified using data from vertical, split-beam echosounders. This was demonstrated recently using a model parameterized with acoustic estimates of slope, roughness, normal-incidence backscattering strength, and variation of backscattering strength by frequency and incidence angle. These seabed classifications were interpreted and validated using published surficial geology maps, but the acoustic data indicated greater spatial variability. Here, classifications of sediment grain or feature size are ascribed to areas ∼10 m2. First, images of the seabed in the study area are ascribed, based on per cent coverage, to seven primary classes ranging from mud through high-relief rock, and 25 primary–secondary classes. Then, a refined seabed classifier, based on the acoustic model parameters is trained, using a nearest-neighbours algorithm, on a subset of the class data. The classifier accurately predicts 96% of the primary classes, and 93% of the primary–secondary classes from an independent data subset. These methods should be useful for characterizing, mapping, and quantifying potential seabed habitat domains of demersal fish and benthic invertebrates.
The role of climate and fisheries on the temporal changes in the Bothnian Bay foodweb
Authors: Pekcan-Hekim Zeynep , Gårdmark Anna , Karlson Agnes M. L. , Kauppila Pirkko , Bergenius Mikaela , Bergström Lena
Published: March 2016

Climate change, eutrophication, and fishing are main pressures associated with changes in the abiotic and biotic environment in several sub-basins of the Baltic Sea. Identifying the nature of such changes is of relative importance for fisheries and environmental management. The Bothnian Bay is the northernmost sub-basin in the Baltic Sea and the responses of the foodweb to long-term changes in combined pressures have not been investigated. In this study, we explore long-term changes in the Bothnian Bay foodweb, represented by key species across all trophic levels over the past 34 years, and identify potential environmental and anthropogenic drivers. The results indicate that salinity is the most important driver to explain changes in the composition of the offshore biota in the Bothnian Bay. These changes are probably driven by indirect effects of salinity rather than bottom-up effects. A decline in the herring spawning-stock biomass was most plausibly attributed to an increased competition for food due to a parallel increase in vendace, which uses the same food resources (zooplankton and zoobenthos) and may benefit from declining salinity due to its limnic origin. A strong increase in the abundance of grey seal and ringed seal populations was seen in the late 2000s but was not related to any of the pressure variables analysed. Temperature and nutrients were not identified as important drivers of changes in the overall biota. Our study explores correlative relationships between variables and identifies potential interactions in the foodweb to generate hypotheses for further studies.
Preliminary analysis of the sequential simultaneous integrated boost technique for intensity-modulated radiotherapy for head and neck cancers
Authors: Miyazaki Masayoshi , Nishiyama Kinji , Ueda Yoshihiro , Ohira Shingo , Tsujii Katsutomo , Isono Masaru , Masaoka Akira , Teshima Teruki
Published: March 2016

The aim of this study was to compare three strategies for intensity-modulated radiotherapy (IMRT) for 20 head-and-neck cancer patients. For simultaneous integrated boost (SIB), doses were 66 and 54 Gy in 30 fractions for PTVboost and PTVelective, respectively. Two-phase IMRT delivered 50 Gy in 25 fractions to PTVelective in the First Plan, and 20 Gy in 10 fractions to PTVboost in the Second Plan. Sequential SIB (SEQ-SIB) delivered 55 Gy and 50 Gy in 25 fractions, respectively, to PTVboost and PTVelective using SIB in the First Plan and 11 Gy in 5 fractions to PTVboost in the Second Plan. Conformity indexes (CIs) (mean ± SD) for PTVboost and PTVelective were 1.09 ± 0.05 and 1.34 ± 0.12 for SIB, 1.39 ± 0.14 and 1.80 ± 0.28 for two-phase IMRT, and 1.14 ± 0.07 and 1.60 ± 0.18 for SEQ-SIB, respectively. CI was significantly highest for two-phase IMRT. Maximum doses (Dmax) to the spinal cord were 42.1 ± 1.5 Gy for SIB, 43.9 ± 1.0 Gy for two-phase IMRT and 40.3 ± 1.8 Gy for SEQ-SIB. Brainstem Dmax were 50.1 ± 2.2 Gy for SIB, 50.5 ± 4.6 Gy for two-phase IMRT and 47.4 ± 3.6 Gy for SEQ-SIB. Spinal cord Dmax for the three techniques was significantly different, and brainstem Dmax was significantly lower for SEQ-SIB. The compromised conformity of two-phase IMRT can result in higher doses to organs at risk (OARs). Lower OAR doses in SEQ-SIB made SEQ-SIB an alternative to SIB, which applies unconventional doses per fraction.
Nol12 is a multifunctional endonuclease at the nexus of RNA and DNA metabolism
Authors: Scott D. D. , Trahan C. , Zindy P.J. , Aguilar L.C. , Delubac M.Y. , Wei K. E. , Oeffinger M.
Published: March 2016

Endo‐ and exonucleases are major contributors to RNA metabolism through their diverse roles in maturation and turnover of different species of RNA as well as transcription. Recent data suggests RNA nucleases also affect genome stability programs and act along DNA repair pathways. Here, we describe Nol12 as a multifunctional RNA/DNA endonuclease found in different subcellular compartments - the nucleoplasm, where it co-localizes with the RNA/DNA helicase Dhx9 and paraspeckles, nucleoli as well as GW/P-bodies. We show that Nol12 is required for a key step in ribosomal RNA processing, separating large and small subunit precursors at site 2, rerouting ribosome biogenesis via an alternative pathway in its absence to ensure ribosome production. Furthermore, loss of Nol12 results in increased oxidized DNA levels followed by a rapid p53-independent ATR-Chk1-mediated apoptotic response, suggesting a role for Nol12 in the prevention or resolution of oxidative DNA damage. Identification of a complex Nol12 interactome, which includes NONO, Dhx9 and DNA-PK, further supports its diverse functions in RNA metabolism and DNA maintenance, establishing Nol12 as a multifunctional endonuclease.
Macroscopic coherent structures in a stochastic neural network: from interface dynamics to coarse-grained bifurcation analysis
Authors: Avitabile Daniele , Wedgwood Kyle C. A.
Published: March 2016

We study coarse pattern formation in a cellular automaton modelling a spatially-extended stochastic neural network. The model, originally proposed by Gong and Robinson [36], is known to support stationary and travelling bumps of localised activity. We pose the model on a ring and study the existence and stability of these patterns in various limits using a combination of analytical and numerical techniques. In a purely deterministic version of the model, posed on a continuum, we construct bumps and travelling waves analytically using standard interface methods from neural fields theory. In a stochastic version with Heaviside firing rate, we construct approximate analytical probability mass functions associated with bumps and travelling waves. In the full stochastic model posed on a discrete lattice, where a coarse analytic description is unavailable, we compute patterns and their linear stability using equation-free methods. The lifting procedure used in the coarse time-stepper is informed by the analysis in the deterministic and stochastic limits. In all settings, we identify the synaptic profile as a mesoscopic variable, and the width of the corresponding activity set as a macroscopic variable. Stationary and travelling bumps have similar meso- and macroscopic profiles, but different microscopic structure, hence we propose lifting operators which use microscopic motifs to disambiguate between them. We provide numerical evidence that waves are supported by a combination of high synaptic gain and long refractory times, while meandering bumps are elicited by short refractory times.
Implementing rapid, robust, cost-effective, patient-centred, routine genetic testing in ovarian cancer patients
Authors: George Angela , Riddell Daniel , Seal Sheila , Talukdar Sabrina , Mahamdallie Shazia , Ruark Elise , Cloke Victoria , Slade Ingrid , Kemp Zoe , Gore Martin , Strydom Ann , Banerjee Susana , Hanson Helen , Rahman Nazneen ,   for the Mainstreaming Cancer Genetics (MCG) Programme
Published: March 2016

Background:

Advances in DNA sequencing have made gene testing fast and affordable, but adaptation of clinical services to capitalise on this for patient benefit has been slow. Ovarian cancer exemplifies limitations of current systems and potential benefits of increased gene testing. Approximately 15% of ovarian cancer patients have a germline mutation inBRCA1orBRCA2(collectively termed ‘BRCA’) and this has substantial implications for their personal management and that of their relatives. However, in most countries implementation of BRCA testing in ovarian cancer has been inconsistent and largely unsuccessful.

Methods:

We developed a mainstream pathway in which BRCA testing was undertaken by cancer team members after 30 minutes online training. Patients with a mutation were sent a genetic appointment with their results. Cascade testing to relatives was performed via standard clinical genetic procedures.

Findings:

207 women with ovarian cancer were offered gene testing through the mainstream pathway and all accepted. 33 (16%) had a BRCA mutation. The result informed management of 79% (121/154) women with active disease including 97% (32/33) women with a mutation. All mutation-positive women and ~3.5 relatives per family have been seen in genetics. Patient and clinician feedback was very positive. >95% found the pathway to be simple and effective. The pathway offers considerable reduction in time (~5-fold) and resource requirements (~13-fold) compared to the traditional genetic pathway. We estimate it would deliver £2.6M NHS cost savings per year, and would allow implementation of national testing recommendations with existing infrastructure.

Interpretation:

Mainstream genetic testing is effective, efficient and patient-centred and offers a mechanism for large-scale implementation of BRCA gene testing in cancer patients. The principles could be applied in many other countries and to many other areas of genomic medicine.
Hybrid systems approach to modeling stochastic dynamics of cell size
Authors: Vargas-Garcia Cesar Augusto , Singh Abhyudai
Published: March 2016

A ubiquitous feature of all living cells is their growth over time followed by division into two daughter cells. How a population of genetically identical cells maintains size homeostasis, i.e., a narrow distribution of cell size, is an intriguing fundamental problem. We model size using a stochastic hybrid system, where a cell grows exponentially over time and probabilistic division events are triggered at discrete time intervals. Moreover, whenever these events occur, size is randomly partitioned among daughter cells. We first consider a scenario, where a timer (i.e., cell-cycle clock) that measures the time since the last division event regulates cellular growth and the rate of cell division. Analysis reveals that such a timer-driven system cannot achieve size homeostasis, in the sense that, the cell-to-cell size variation grows unboundedly with time. To explore biologically meaningful mechanisms for controlling size we consider three different classes of models: i) a size-dependent growth rate and timer-dependent division rate; ii) a constant growth rate and size-dependent division rate and iii) a constant growth rate and division rate that depends both on the cell size and timer. We show that each of these strategies can potentially achieve bounded intercellular size variation, and derive closed-form expressions for this variation in terms of underlying model parameters. Finally, we discuss how different organisms have adopted the above strategies for maintaining cell size homeostasis.
iFORM: incorporating Find Occurrence of Regulatory Motifs
Authors: Ren Chao , Chen Hebing , Liu Feng , Li Hao , Bo Xiaochen , Shu Wenjie
Published: March 2016

Motivation

Accurately identifying binding sites of transcription factors (TFs) is crucial to understand the mechanisms of transcriptional regulation and human disease.

Results

We present incorporating Find Occurrence of Regulatory Motifs (iFORM), an easy-to-use tool for scanning DNA sequence with TF motifs described as position weight matrices (PWMs). iFORM achieves higher accuracy and sensitivity by integrating the results from five classical motif discovery programs based on Fisher’s combined probability test. We have used iFORM to provide accurate results on a variety of data in the ENCODE Project and the NIH Roadmap Epigenomics Project, and has demonstrated its utility to further understand individual roles of functional elements.

Availability

iFORM can be freely accessed athttps://github.com/wenjiegroup/iFORM.

Contact

shuwj@bmi.ac.cnandboxc@bmi.ac.cn
Characterisation of consumers of traditional foods: the case of Mexican fresh cheeses
Authors: Hidalgo-Milpa Minerva , Arriaga-Jordán Carlos Manuel , Cesín-Vargas Alfredo , Espinoza-Ortega Angélica
Published: March 2016

Purpose

– The purpose of this paper is to characterize consumers of traditional foods, taking as case study fresh cheeses produced in a village, in Central Mexico.

Design/methodology/approach

– Semi-structured interviews were applied to a sample of 150 consumers, selected by non-probabilistic convenience sampling. A factorial analysis by principal component analysis was performed to the data, followed by a cluster analysis.

Findings

– Four factors were obtained, named: artisanship, health and well-being, liking, and satisfaction with the purchase. Three consumer groups were identified: practical, in the process of valorization, and with liking and tradition. The socioeconomic characteristics of consumers do not have a relationship in the classification of groups. It is concluded that the consumption of fresh cheeses is due to a number of social and cultural attributes, and in lesser proportion, to economic aspects.

Originality/value

– At present, as part of life in a dynamic society, people have the power of choice in the food they consume, a process that involves cultural, social, economic, political, and ideological aspects, established by the consumers themselves, or by a determined social group to which they belong. This has not been researched in Mexico. Being an emerging economy immersed in a rapid process of globalization, studies like this contribute in similar countries of Latin America and other places to find ways to valorize local foods and products that play important roles in the development of rural communities.
Determining Turkish consumers’ consumption satisfaction with Erzurum Civil cheese
Authors: Uzundumlu Ahmet Semih , Topcu Yavuz
Published: March 2016

Purpose

– The purpose of this paper is to determine redesigned product profiles to maximize Erzurum Civil cheese consumption satisfaction of Turkish consumers under an ordinal utility approach.

Design/methodology/approach

– Data were obtained from a survey conducted in Erzurum in 2014. A conjoint analysis was used to determine the utilities of each level along with the relative importance of Erzurum Civil cheese attributes for measuring the consumption satisfaction as an indicator of the purchase decision and priorities of Turkish consumers.

Findings

– The results of the study clearly highlighted that Erzurum Civil cheese consumption satisfaction was maximized with the augmented and actual product images redesigned by a private-labelled and local-branded simple product with the highest and medium prices based on organic production techniques for heavy and light consumers, respectively. However, medium consumers appreciated the core benefit obtained from the credence quality attributes supported by the generic branded simple cheese with the lowest price purchased directly from the farmstead villages. Eventually, these marketing tactics and strategies could increase demand, maximizing the cheese consumption and satisfaction of Turkish consumers in each cluster. They could also provide greater consumption satisfaction to Turkish consumers as well as bigger marginal contributions to the market dynamics of the food supply chain.

Originality/value

– This study was the first research conducted on Erzurum Civil cheese consumption satisfaction of Turkish consumers using innovative approaches and brand designations, such as Protected Designation of Origin, Protected Geographical Indication, and Traditional Specialty Guaranteed in Turkey using the conjoint and k-mean cluster analyses techniques.
Simulating compliance behaviour for effective inspection strategies using agent based modelling
Authors: van Asselt Esther , Osinga Sjoukje , Bremmers Harry
Published: March 2016

Purpose

– The purpose of this paper is to simulate compliance behaviour of entrepreneurs in the Netherlands based on the Table of Eleven: 11 factors determining compliance (based on economic, cognitive, social and institutional factors).

Design/methodology/approach

– An Agent-Based Model (ABM) was developed that could incorporate both individual and group behaviour and allowed to evaluate the effect of various intervention strategies. For this purpose, a case study on the compliance of pig farmers with antibiotics legislation in the Netherlands was used.

Findings

– The effect of social factors (acceptance of legislation and social influence) on compliance levels was tested as well as the number of inspectors. This showed that the model can help to choose the most optimal intervention strategy depending on the input parameters.

Research limitations/implications

– Further expansion of the model may be necessary, e.g. including economic factors, in order to reflect real-life situations more closely.

Practical implications

– The model can be used by inspection services to effectively implement their control programme.

Originality/value

– The developed ABM is a first attempt to simulate compliance behaviour and as such contributes to the current limited knowledge on effective intervention strategies.