bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining 2D and 3D features to improve road detection based on stereo cameras
Authors: Cai Guorong , Su Songzhi , He Wenli , Wu Yundong , Li Shaozi
Published: April 2018

Road detection is a fundamental component of autonomous driving systems since it provides validspace and candidate regions of objects for driving decision. The core of roaddetection methods is extracting effective and discriminative features. Sincetwo‐dimensional (2D) and 3D features are complementary, the authors propose arobust multi‐feature combination and optimisation framework for stereo imagepairs, called Feature++. First, several 2D and 3D features such as Gabor andplane are, respectively, extracted after the generation of 2D super‐pixel and a3D depth image from stereo matching. Second, the combined features are fed intoa three‐layer shallow neural network classifier to decide whether a super‐pixelis road region or not. Finally, the classified results are further refined usingfully connected conditional random field (CRF), taking the content informationinto consideration. We extensively evaluate the performance of four 2D features,four 3D features, and their combinations. Experiments conducted on the KITTIROAD benchmark show that (i) the combinations of 2D and 3D features greatlyimprove the road detection performance and (ii) using CRF as a refinement stepis necessary. Overall, their proposed ‘Feature + +’ method outperforms mostmanually designed features, and is comparable with state‐of‐the‐art methods thatare based on deep learning methods.
Convolutional neural network in network (CNNiN): hyperspectral image classification and dimensionality reduction
Authors: Shamsolmoali Pourya , Zareapoor Masoumeh , Yang Jie
Published: April 2018

Classification is a principle technique in hyperspectral images (HSIs), where a label is assigned to each pixel based on its characteristics. However, due to lack of labelled training instances in HSIs and also its ultra‐high dimensionality, deep learning approaches need a special consideration for HSI classification. As one of the first works in the HSI classification, this study proposes a novel network pipeline called convolutional neural network in network (which is deeper than the existing approaches) by jointly utilising the spatial and spectral information and produces high‐level features from the original HSI. This can occur by using spatial–spectral relationships of individual pixel vector at the initial component of the proposed pipeline; the extracted features are then combined to form a joint spatial–spectral feature map. Finally, a recurrent neural network is trained on the extracted features which contain wealthy spectral and spatial properties of the HSI to predict the corresponding label of each vector. The model has been tested on two large scale hyperspectral datasets in terms of classification accuracy, training error, and computational time.
Design of a randomised arrangement AMC surfaces for RCS reduction based on equivalent circuit modelling
Authors: Varkani Ali Ramezani , Firouzeh Zaker Hossein , Nezhad Abolghasem Zeidaabadi
Published: April 2018

This study aims to present a thin and broadband meta‐surface for both mono‐static and bi‐static radar cross‐section (RCS) reduction being able to operate in large range of incident angles and different polarisations. Meta‐surfaces are formed through the combination of two artificial magnetic conductor (AMC) cells arranged in periodic and randomised fashions in order to suppress the scattered fields in low levels in all directions as well as minimising the maximum RCS of the metallic surface. By appropriate design of each AMC, and using equivalent circuit method, the reflection coefficients of these surfaces are designed in a way to reach 180 (±37°) phase difference over a wide range of frequencies and incident angles. The bandwidth for 10 dB mono‐static RCS reduction is about 53% for both periodic and randomised structures at the normal incidence. It is illustrated that the randomised arrangement structure has 3 dB lower maximum bi‐static RCS compared with the periodic structure. Finally, the periodic and randomised arrangement prototypes are fabricated and measurements of their mono‐static RCS are conducted. The validity of the study design is fulfilled by achieving an acceptable agreement between the measured and simulated results.
Modelling and regulation of two mechanical systems
Authors: Rubio José de Jesús , Pieper Jeff , Meda‐Campaña Jesús A. , Aguilar Arturo , Rangel Vanya I. , Gutierrez Guadalupe Juliana
Published: April 2018

In this work, the modelling and regulation of two mechanical systems are studied. The model is employed to describe the system dynamic behaviour. The regulator is employed to force the system states to track constantly wanted signals. The stability of the advised regulator is analysed via the Lyapunov technique. The recommended strategy is applied to a magnetic generator and in a hexarotor.
Dual‐edge triggered JK flip‐flop with comprehensive analysis in quantum‐dot cellular automata
Authors: Zhang Yongqiang , Xie Guangjun , Lv Hongjun
Published: April 2018

Quantum‐dot cellular automata (QCA), a new computing paradigm at nanoscale, may be a prospective substitution of conventional complementary metal oxide semiconductor (CMOS)‐based integrated circuits. A new dual‐edge triggered JK flip‐flop based on a novel dual‐edge triggered structure with less fundamental building gates is proposed in QCA domain in this study. To get a more robust triggered structure, the probabilistic transfer matrix is employed to analyse the reliability of the structure. The functionalities of the dual‐edge triggered structure and JK flip‐flop are verified with QCADesigner, a simulation tool widely used. By arranging the clock zones serially and QCA cells logically, compared with previous circuits, both of the proposed triggered structure and JK flip‐flop perform well in terms of cells count, area, complexity, QCA cost and power dissipation at different tunnelling energy levels at 2 K temperature, respectively.
Thick turbulent gas disks with magnetocentrifugal winds in active galactic nuclei
Authors: Vollmer B. , Schartmann M. , Burtscher L. , Marin F. , Hönig S. , Davies R. , Goosmann R.
Published: April 2018

Infrared high-resolution imaging and interferometry show that the dust distribution is frequently elongated along the polar direction of an AGN. In addition, interferometric mm line observations have revealed a bipolar outflow in a direction nearly perpendicular to the nuclear disk. To explain these findings, we developed a model scenario for the inner ~30 pc of an AGN. The structure of the gas within this region is entirely determined by the gas inflow from larger scales. We assumed a rotating thick gas disk between about one and ten parsec. External gas accretion adds mass and injects energy via gas compression into this gas disk and drives turbulence. We extended the description of a massive turbulent thick gas disk developed in a recent paper by adding a magnetocentrifugal wind. Our disks are assumed to be strongly magnetized via equipartition between the turbulent gas pressure and the energy density of the magnetic field. In a second step, we built 3D density cubes based on the analytical model, illuminated them with a central source, and made radiative transfer calculations. In a third step, we calculated mid-infrared (MIR) visibility amplitudes and compared them to available interferometric observations. We show that magnetocentrifugal winds starting from a thin and thick gas disk are viable in active galaxy centers. The magnetic field associated with this thick gas disk plays a major role in driving a magnetocentrifugal wind at a distance of ~1 pc from the central black hole. Once the wind is launched, it is responsible for the transport of angular momentum and the gas disk can become thin. A magnetocentrifugal wind is also expected above the thin magnetized gas disk. The structure and outflow rate of this wind is determined by the properties of the thick gas disk. The outflow scenario can account for the elongated dust structures, outer edges of the thin maser disks, and molecular outflows observed in local AGN. The models reproduce the observed terminal wind velocities, the scatter of the MIR – intrinsic X-ray correlation, and point source fractions. An application of the model to the Circinus galaxy and NGC 1068 shows that the infrared spectral energy distribution, available MIR interferometric observations, and optical polarization can be reproduced in a satisfactory way, provided that (i) a puff-up at the inner edge of the thin disk is present and (ii) a local screen with an optical depth of τV ~ 20 in form of a local gas filament and/or a warp of the thick disk hide a significant fraction of both nuclei. Our thick disk, wind, thin disk model is thus a promising scenario for local Seyfert galaxies.
Photometric survey of 67 near-Earth objects
Authors: Ieva S. , Dotto E. , Mazzotta Epifani E. , Perna D. , Rossi A. , Barucci M. A. , Di Paola A. , Speziali R. , Micheli M. , Perozzi E. , Lazzarin M. , Bertini I.
Published: April 2018

Context. The near-Earth object (NEO) population is a window into the original conditions of the protosolar nebula, and has the potential to provide a key pathway for the delivery of water and organics to the early Earth. In addition to delivering the crucial ingredients for life, NEOs can pose a serious hazard to humanity since they can impact the Earth. To properly quantify the impact risk, physical properties of the NEO population need to be studied. Unfortunately, NEOs have a great variation in terms of mitigation-relevant quantities (size, albedo, composition, etc.) and less than 15% of them have been characterized to date.

Aims. There is an urgent need to undertake a comprehensive characterization of smaller NEOs (D< 300 m) given that there are many more of them than larger objects; their small sizes make them intrinsically fainter and therefore harder to study. One of the main aims of the NEOShield-2 project (2015–2017), financed by the European Community in the framework of the Horizon 2020 program, is therefore to retrieve physical properties of a wide number of NEOs in order to design impact mitigation missions and assess the consequences of an impact on Earth.

Methods. We carried out visible photometry of NEOs, making use of the DOLORES instrument at the Telescopio NazionaleGalileo(TNG, La Palma, Spain) in order to derive visible color indexes and the taxonomic classification for each target in our sample.

Results. We attributed for the first time the taxonomical complex of 67 objects obtained during the first year of the project. While the majority of our sample belong to the S-complex, carbonaceous C-complex NEOs deserve particular attention. These NEOs can be located in orbits that are challenging from a mitigation point of view, with high inclination and low minimum orbit intersection distance (MOID). In addition, the lack of carbonaceous material we see in the small NEO population might not be due to an observational bias alone.
Gastric peroral endoscopic myotomy for the treatment of refractory gastroparesis: a multicenter international experience
Authors: Kahaleh Michel , Gonzalez Jean-Michel , Xu Ming-ming , Andalib Iman , Gaidhane Monica , Tyberg Amy , Saumoy Monica , Baptista Marchena Alberto Jose , Barthet Marc
Published: April 2018

Background Gastroparesis is a difficult-to-treat motility disorder with a poor response to medical therapy. Gastric peroral endoscopic pyloromyotomy (G-POEM) has been offered as a novel therapy in the treatment of refractory gastroparesis. We present a multicenter case series of our experience with G-POEM.

Methods This is an international multicenter case series of patients who underwent G-POEM for the treatment of gastroparesis. The severity of gastroparesis was assessed by delayed gastric emptying scintigraphy (GES) and an elevated gastroparesis cardinal symptoms index (GCSI). Patients then underwent G-POEM using the submucosal tunneling technique. The primary endpoint was improvement in the GCSI score and improvement in gastric emptying on repeat scintigraphy. Secondary endpoints were technical success, complication rate, procedure duration, and length of hospital stay post-procedure.

Results G-POEM was technically successful in all 33 patients. Symptomatic improvement was seen in 28/33 patients (85 %), with a decrease in symptom score by GCSI from 3.3 to 0.8 at follow-up (P < 0.001). The mean procedure duration was 77.6 minutes (37 – 255 minutes). Mean GES improved significantly from 222.4 minutes to 143.16 minutes (P < 0.001). Complications were minimal and included bleeding (n = 1) and an ulcer (n = 1) treated conservatively. The mean length of hospital stay post-procedure was 5.4 days (1 – 14 days). The mean follow-up duration was 11.5 months (2 – 31 months).

Conclusion G-POEM is a technically feasible, safe, and successful procedure for the treatment of refractory gastroparesis. A further multicenter comparative study should be performed to compare this technique to laparoscopic pyloromyotomy.
Diagnostik und Behandlungsstrategien bei Morel-Lavallée-Läsionen im Wirbelsäulen- und Beckenbereich
Authors: Becker Christopher , Kammerlander Christian , Greiner Axel , Sommer Fabian , Linhart Christoph , Böcker Wolfgang , Rubenbauer Bianka , Weidert Simon
Published: April 2018

Hintergrund Die Morel-Lavallée-Verletzung ist eine typische Weichteilverletzung bei Beckenfrakturen. Ihre Versorgungsstrategie im Zusammenhang mit Wirbelfrakturen und osteosynthetischer Versorgung von Wirbelfrakturen wurde bislang noch nicht hinreichend untersucht. Das Ziel dieser Studie war es, Diagnose- und Therapieprinzipien von Becken- und Wirbelfrakturen in Kombination mit Morel-Lavallée-Verletzungen zu analysieren.

Methoden Literaturanalyse via Medline und PubMed. Insgesamt wurden 197 Studien und Fallberichte analysiert. Nach der Analyse blieben 19 Studien/Fallberichte übrig, welche die Einschlusskriterien erfüllten.

Ergebnisse Es existieren verschiedene Diagnoseverfahren bezogen auf die Morel-Lavallée-Verletzung, wie bspw. Ultraschall, CT oder MRT. In Kombination mit Becken- und Wirbelfrakturen erscheint der Ultraschall als geeignete Methode, eine Morel-Lavallée-Verletzung zu diagnostizieren. Einige Autoren tendieren zum offenen Débridement, wenngleich andere Autoren ein perkutanes Vorgehen propagieren. Offenes Débridement und Vakuumversiegelung wird bei spät diagnostizierten Morel-Lavallée-Verletzungen empfohlen, wenn keine Primärnaht initial durchführbar ist. Die Frakturversorgung sollte zeitgleich mit der Versorgung der Morel-Lavallée-Verletzung erfolgen. Breitspektrum-Cephalosporine in Kombination mit Aminoglykosiden oder Piperacillin/Tazobactam sollten zur antibiotischen Abdeckung eingesetzt werden.

Schlussfolgerung Radikales Débridement und Einlegen einer Drainage wird insbesondere bei spät diagnostizierter Morel-Lavallée-Verletzung empfohlen. Programmiert durchgeführte Ultraschalluntersuchungen sollten vom frakturumgebenden Weichteil erfolgen. Wenn die Morel-Lavallée-Verletzung innerhalb von 2 Tagen diagnostiziert wird, kann ein perkutanes Vorgehen mit zeitgleicher Fraktur- und Morel-Lavallée-Behandlung erfolgen. Bei verzögerter Diagnosestellung (> 2 Tage) sollte eine offene Behandlung im Sinne eines offenen Débridements, offener Frakturversorgung und bestenfalls Primärnaht durchgeführt werden.
Selective Diacetoxylation of Disubstituted 1,2,3-Triazoles through Palladium-Catalyzed C–H Activation
Authors: Cheng Huiling , Jiang Yubo , Yang Jianhua , Zhao Fen , Liu Yaowen , Luo Fang
Published: April 2018

A simple and efficient selective diacetoxylation of 1,4-disubstituted 1,2,3-triazoles by Pd-catalyzed C–H bond activation is described. PhI(OAc)2 was used as an acetyloxy source to convert aromatic sp2 C–H bonds into C–O bonds with high selectivity by employing a 1,2,3-triazole ring as an elegant directing group. A range of 1,2,3-triazoles bearing two acetyloxy groups can be readily synthesized by the reaction.
Synthesis of Aromatic Disulfonic Acids for Water-Soluble Dibenzo­thiophene Derivatives
Authors: McCulla Ryan , Omlid Sara , Isor Ankita , Sulkowski Kathryn , Chintala S. , Petroff John
Published: April 2018

There is a need for efficient methods for the synthesis of water-soluble dibenzothiophene (DBT) and dibenzothiophene S-oxide (DBTO) derivatives to allow for the study of atomic oxygen in biological applications. Attaining water-solubility of aromatic compounds is effectively achieved through functionalization with sulfonic acid groups. Three approaches for the synthesis were considered. An indirect approach was unsuccessful. A modular approach was found to be highly effective for one DBTO disulfonic acid derivative (>99% pure). The direct approach was the most straightforward and highest-yielding route. Additionally, a highly effective, scalable, and improved purification method was identified for disulfonic acid DBT and DBTO derivatives, allowing for the isolation of positional isomers and other modifications by using reverse-phase high-performance flash chromatography.
"It’s a (Kinetic) Trap!" – Selectively Differentiating Allylic Azide
Isomers
Authors: Topczewski Joseph , Porter Matthew
Published: April 2018

Allylic azides are known to undergo the Winstein rearrangement and are often isolated as an equilibrating mixture of isomers. While this process has been known for almost 60 years, very few synthetic applications of this process have been reported. The absence of methods exploiting these intermediates likely stems from a paucity of approaches for gaining the required selectivity to differentiate the isomers. Our lab has made some progress in leveraging this unusual reaction into practical synthetic methodology. Presented herein is a summary of our lab’s recent accomplishments in selectively trapping allylic azides.

1 Introduction

2 Background: Allylic Azides

3 Dynamic Cyclization of Imidates

4 Summary and Outlook
Beyond ideological platitudes: socialism and psychiatry in Eastern Europe
Authors: Savelli Mat
Published: April 2018

For both contemporaneous commentators and historians, psychiatry within what was Communist Europe has largely been discussed through the prism of politics and ideology. Recently, scholars have begun to debate the extent to which psychiatric practices within post-WWII Eastern Europe were beholden to the ideological aspirations of the political elite. This paper enters into these debates by suggesting the need for more nuance in how historians analyse the relationship between ideology and psychiatry in this context. Specifically, it argues that there is a need to differentiate between psychiatric practices that were socialist by design—where professional knowledge was theoretically guided by ideological considerations—and those that were socialist by default—where practices were shaped by the socialist context without being meaningfully inspired by ideology. In order to demonstrate these distinctions, this paper reflects upon psychiatric developments within Communist Yugoslavia (1945–1991). By drawing a clearer distinction between “socialist by design” and “socialism by default”, it becomes easier to reconnect Eastern Europe to the broader historiography of twentieth century psychiatry, while simultaneously providing new insights into the experience of state-sponsored Communism.
Emergence of Landauer transport from quantum dynamics: A model Hamiltonian approach
Authors: Pal Partha Pratim , Ramakrishna S. , Seideman Tamar
Published: April 2018

The Landauer expression for computing current-voltage characteristics in nanoscale devices is efficient but not suited to transient phenomena and a time-dependent current because it is applicable only when the charge carriers transition into a steady flux after an external perturbation. In this article, we construct a very general expression for time-dependent current in an electrode-molecule-electrode arrangement. Utilizing a model Hamiltonian (consisting of the subsystem energy levels and their electronic coupling terms), we propagate the Schrödinger wave function equation to numerically compute the time-dependent population in the individual subsystems. The current in each electrode (defined in terms of the rate of change of the corresponding population) has two components, one due to the charges originating from the same electrode and the other due to the charges initially residing at the other electrode. We derive an analytical expression for the first component and illustrate that it agrees reasonably with its numerical counterpart at early times. Exploiting the unitary evolution of a wavefunction, we construct a more general Landauer style formula and illustrate the emergence of Landauer transport from our simulations without the assumption of time-independent charge flow. Our generalized Landauer formula is valid at all times for models beyond the wide-band limit, non-uniform electrode density of states and for time and energy-dependent electronic coupling between the subsystems. Subsequently, we investigate the ingredients in our model that regulate the onset time scale of this steady state. We compare the performance of our general current expression with the Landauer current for time-dependent electronic coupling. Finally, we comment on the applicability of the Landauer formula to compute hot-electron current arising upon plasmon decoherence.
Existence regimes for shocks in inhomogeneous magneto-plasmas having entropy
Authors: Iqbal Javed , Yaqub Khan M.
Published: April 2018

The finding of connection of plasma density and temperature with entropy gives an incitement to study different plasma models with respect to entropy. Nonlinear dissipative one- and two-dimensional structures (shocks) are investigated in nonuniform magnetized plasma with respect to entropy. The dissipation comes in the medium through ion-neutral collisions. The linear dispersion relation is derived. The Korteweg–deVries-Burgers and Kadomtsev-Petviashvili-Burgers equations are derived for nonlinear drift waves in 1-D and 2-D by employing the drift approximation. It is found that vd/u (vd is the diamagnetic drift velocity and u is the velocity of nonlinear structure) plays a significant role in the shock formation. It is also found that entropy has a significant effect on the strength of shocks. It is noticed that  vd/u  determines the rarefactive and compressive nature of the shocks. It is observed that upper and lower bounds exist for the shock velocity. It is also observed that the existing regimes for both one- and two-dimensional shocks for kappa distributed electrons are different from shocks with Cairns distributed electrons. Both rarefactive and compressive shocks are found for the 1-D drift waves with kappa distributed electrons. Interestingly, it is noticed that entropy enhances the strength of one- and two-dimensional shocks.
Spatially resolved proton momentum distributions in KDP from first-principles
Authors: Engel Edgar A.
Published: April 2018

The ferroelectric to paraelectric (PE) phase transition of KH2PO4 (KDP) is investigated as a stringent test of the first-principles, normal modes framework proposed for calculating anharmonic quantum nuclear motion. Accurate spatially resolved momentum distribution functions (MDFs) are directly calculated from the nuclear wavefunction, overcoming the limitations of path-integral molecular dynamics methods. They indicate coherent, correlated tunneling of protons across hydrogen bonds in the PE phase in agreement with neutron Compton scattering data and reproduces the key features of the experimental MDF. It further highlights the role of Slater’s lateral configurations in the PE phase. The analysis in terms of normal modes demonstrates the importance of collective, correlated proton motion and underlines the value of the employed framework in interpreting experimental data. This also makes the framework very attractive for application to deuterated KDP to further elucidate the nature of the PE transition and to systems exhibiting strong quantum nuclear effects in general.
Polarization imprint effects on the photovoltaic effect in Pb(Zr,Ti)O3 thin films
Authors: Tan Zhengwei , Tian Junjiang , Fan Zhen , Lu Zengxing , Zhang Luyong , Zheng Dongfeng , Wang Yadong , Chen Deyang , Qin Minghui , Zeng Min , Lu Xubing , Gao Xingsen , Liu Jun-Ming
Published: April 2018

The polarization imprint along with the photovoltaic (PV) effect has been studied in Pt/Pb(Zr0.3Ti0.7)O3/SrRuO3 ferroelectric capacitors. It is shown that the positive DC poling induces the imprint with a downward direction whereas the negative DC poling suppresses the imprint (i.e., rejuvenation). In the polarization up state, the imprinted capacitor exhibits degraded PV properties compared with the rejuvenated one. This may be because the imprint reduces the number of upward domains, thus lowering the driving force for the PV effect. In the polarization down state, however, the rejuvenated capacitor enters the imprinted state spontaneously. This rejuvenation-to-imprint transition can be further aggravated by applying positive voltages and ultraviolet illumination. It is proposed that the domain pinning/depinning, which are associated with the oxygen vacancies and trapped electrons modulated by polarization, voltage, and illumination, may be responsible for the polarization imprint and rejuvenation. Our study therefore sheds light on the correlation between the polarization imprint and the PV effect in the ferroelectrics and also provides some viable suggestions to address the imprint-induced degradation of PV performance.
Effect of toroidal rotation on resistive magnetohydrodynamic instability with a nonmonotonic q profile in cylindrical geometry
Authors: Xu J. Q. , Peng X. D.
Published: April 2018

The effect of plasma rotation on the linear stability of the resistive magnetohydrodynamic (MHD) instabilities with a nonmonotonic q profile is investigated numerically in the cylindrical geometry. The results have shown that the plasma rotation has a stabilization effect on the double tearing modes (DTMs) depending on the magnitude of the velocity, while the velocity shear has a relatively weak effect. The effect of rotation on DTMs is determined by the velocity at each rational surface. A toroidal velocity imposed on the innermost rational surface has a weak effect on m > 1 DTMs. When the velocity is imposed on the outboard resonant surface, the growth rates of the DTMs are reduced for m > 1 modes; however, it has an obvious destabilizing effect on both m = 1 (with m the poloidal mode number) DTM and single tearing mode branches if the distance between the two rational surfaces is sufficiently small. It is shown that the effect of plasma rotation on the growth rates of the MHD instabilities is in phase with the integrated value of the coupling between potential fluctuation and magnetic flux perturbation.
Electric-field driven insulator-metal transition and tunable magnetoresistance in ZnO thin film
Authors: Zhang Le , Chen Shanshan , Chen Xiangyang , Ye Zhizhen , Zhu Liping
Published: April 2018

Electrical control of the multistate phase in semiconductors offers the promise of nonvolatile functionality in the future semiconductor spintronics. Here, by applying an external electric field, we have observed a gate-induced insulator-metal transition (MIT) with the temperature dependence of resistivity in ZnO thin films. Due to a high-density carrier accumulation, we have shown the ability to inverse change magnetoresistance in ZnO by ionic liquid gating from 10% to –2.5%. The evolution of photoluminescence under gate voltage was also consistent with the MIT, which is due to the reduction of dislocation. Our in-situ gate-controlled photoluminescence, insulator-metal transition, and the conversion of magnetoresistance open up opportunities in searching for quantum materials and ZnO based photoelectric devices.
Forward-biased nanophotonic detector for ultralow-energy dissipation receiver
Authors: Nozaki Kengo , Matsuo Shinji , Fujii Takuro , Takeda Koji , Shinya Akihiko , Kuramochi Eiichi , Notomi Masaya
Published: April 2018

Generally, reverse-biased photodetectors (PDs) are used for high-speed optical receivers. The forward voltage region is only utilized in solar-cells, and this photovoltaic operation would not be concurrently obtained with high efficiency and high speed operation. Here we report that photonic-crystal waveguide PDs enable forward-biased high-speed operation at 40 Gbit/s with keeping high responsivity (0.88 A/W). Within our knowledge, this is the first demonstration of the forward-biased PDs with high responsivity. This achievement is attributed to the ultracompactness of our PD and the strong light confinement within the absorber and depleted regions, thereby enabling efficient photo-carrier generation and fast extraction. This result indicates that it is possible to construct a high-speed and ultracompact photo-receiver without an electrical amplifier nor an external bias circuit. Since there is no electrical energy required, our estimation shows that the consumption energy is just the optical energy of the injected signal pulse which is about 1 fJ/bit. Hence, it will lead to an ultimately efficient and highly integrable optical-to-electrical converter in a chip, which will be a key ingredient for dense nanophotonic communication and processors.
Visualization of anomalous Ettingshausen effect in a ferromagnetic film: Direct evidence of different symmetry from spin Peltier effect
Authors: Seki T. , Iguchi R. , Takanashi K. , Uchida K.
Published: April 2018

Spatial distribution of temperature modulation due to the anomalous Ettingshausen effect (AEE) is visualized in a ferromagnetic FePt thin film with in-plane and out-of-plane magnetizations using the lock-in thermography technique. Comparing the AEE of FePt with the spin Peltier effect (SPE) of a Pt/yttrium iron garnet junction provides direct evidence of different symmetries of AEE and SPE. Our experiments and numerical calculations reveal that the distribution of heat sources induced by AEE strongly depends on the direction of magnetization, leading to the remarkable different temperature profiles in the FePt thin film between the in-plane and perpendicularly magnetized configurations.
Collisionless coupling of a high-β expansion to an ambient, magnetized plasma. I. Rayleigh model and scaling
Authors: Bonde Jeffrey
Published: April 2018

The dynamics of a magnetized, expanding plasma with a high ratio of kinetic energy density to ambient magnetic field energy density, or β, are examined by adapting a model of gaseous bubbles expanding in liquids as developed by Lord Rayleigh. New features include scale magnitudes and evolution of the electric fields in the system. The collisionless coupling between the expanding and ambient plasma due to these fields is described as well as the relevant scaling relations. Several different responses of the ambient plasma to the expansion are identified in this model, and for most laboratory experiments, ambient ions should be pulled inward, against the expansion due to the dominance of the electrostatic field.
Blowup phenomenon for the initial-boundary value problem of the non-isentropic compressible Euler equations
Authors: Cheung Ka Luen , Wong Sen , Yuen Manwai
Published: April 2018

The blowup phenomenon for the initial-boundary value problem of the non-isentropic compressible Euler equations is investigated. More precisely, we consider a functional F(t) associated with the momentum and weighted by a general test function f and show that if F(0) is sufficiently large, then the finite time blowup of the solutions of the non-isentropic compressible Euler equations occurs. As the test function f is a general function with only mild conditions imposed, a class of blowup conditions is established.
Recovery of ovulation rate in ewes following their removal from an oestrogenic lucerne forage
Authors: Fields R. L. , Moot D. J. , Sedcole J. R. , Barrell G. K.
Published: April 2018

Grazing ewes on lucerne crops that contain elevated coumestrol concentrations before and during their mating period can decrease ovulation rate, which results in fewer multiple birth lambs. In this experiment, the ovulation rate of ewes grazing a moderately oestrogenic (29.1 ± 2.88 mg coumestrol/kg DM) lucerne crop for 6 weeks was compared with those transferred to grass pasture for 1 or 3 weeks, and a Control group on grass throughout. Ordinal regression predicted an exponential relationship with a sharp initial increase in ovulation rate from 0 to 14 days on grass that levelled off when ewes were on grass for durations greater than 3 weeks. Of importance, moderate coumestrol levels in lucerne remained throughout the experiment, and liveweight was unaffected by grazing treatment. This experiment quantified the decrease in risk of impaired lambing performance due to moderately oestrogenic lucerne consumption in relation to time on grass before ovulation. Specifically, removal of ewes from lucerne 2 weeks before ovulation mitigated the risk of decreased lambing performance.
Effects of concentrates rich in by-products on growth performance, carcass characteristics and meat quality traits of light lambs
Authors: Ramírez C. Avilés , Blanco F. Peña , Ibáñez A. Horcada , Sánchez N. Núñez , Domenech F. Requena , Medina P. Guzmán , Martínez Marín A. L.
Published: April 2018

The effects of feeding concentrates with alternative ingredients to cereal and soybean meal on growth performance, carcass characteristics and meat quality traits of feedlot lambs were studied. A total of 105 non-castrated male lambs were randomly assigned to one of three treatments (5 replicates per treatment): Control (CON, similar to commercial concentrates), Camelina (CAM, where camelina meal replaced 50% of the crude protein from the soybean meal in the CON concentrate), and Fibrous (FIB, concentrate without cereals and soybean meal, with camelina meal in addition to several by-products, and 20% less energy). The CAM treatment performed as well as the CON one. The FIB treatment increased feed conversion rate and tended to improve the redness and the oxidative stability. The CAM and FIB were economically more favourable. We found that a concentrate for feedlot lambs based on alternative ingredients, including several by-products, could be a feasible alternative to typical cereal-soybean meal-based concentrates.
Shoot morphology and alkaloid content of Epichloë endophyte–Festuca sinensis associations
Authors: Pei Tian , Yu Kuang , Weihu Lin , Jianjun Wang , Zhibiao Nan
Published: April 2018

The Chinese native cool-season perennial grass species Festuca sinensis Keng ex E.B.Alexeev exhibits frequent asymptomatic infections with an asexual Epichloë fungal endophyte. Six Festuca sinensis ecotypes were collected in different geographical locations. Endophyte-positive (E+) plants and corresponding endophyte-free (E–) plants of these six ecotypes were identified and then measured for shoot morphological characteristics including plant height, tiller number and biomass. Significant difference due to different host ecotype was observed in both E+ and E– plants. However, significant difference due to endophyte was observed in only one or two ecotypes. Concentration of endophyte-derived alkaloids and semi-quantitative endophyte colonisation in E+ plants were also evaluated. All E+ plants produced both lolitrem B and peramine alkaloids, and significant variation in alkaloid concentration due to host ecotype or endophyte genotype was observed. Analysis of semi-quantitative endophyte colonisation by using qPCR revealed significant differences between ecotypes. This suggested that host ecotype had large impacts whereas the endophyte had only a minor effect. The results showed that endophyte, host ecotype and their complex interaction affected performance of Festuca sinensis ecotypes.
Energy-crises in well-aerated and anoxic tissue: does tolerance require the same specific proteins and energy-efficient transport?
Authors: Greenway Hank , Armstrong William
Published: April 2018

Many of the profound changes in metabolism that are caused by O2 deficiency also occur in well-aerated tissues when oxidative phosphorylation is partially or wholly inhibited. For these well-aerated tissues, reduction in energy formation occurs during exposure to inhibitors of oxidative phosphorylation, cold/chilling and wounding, so we prefer the term ‘energy crisis’ metabolism over ‘anaerobic’ metabolism. In this review, we note that the overwhelming body of data on energy crises has been obtained by exposure to hypoxia-anoxia, which we will indicate when discussing the particular experiments. We suggest that even transient survival of an energy crisis requires a network of changes common to a large number of conditions, ranging from changes in development to various adverse conditions such as high salinity, drought and nutrient deficiency, all of which reduce growth. During an energy crisis this general network needs to be complemented by energy specific proteins, including the so called ‘anaerobic proteins’ and the group of ERFVII transcription factors, which induces the synthesis of these proteins. Crucially, the difference between anoxia-intolerant and -tolerant tissues in the event of a severe energy crisis would mainly depend on changes in some ‘key’ energy crisis proteins: we suggest these proteins would include phytoglobin, the V-H+PPiase and pyruvate decarboxylase. A second characteristic of a high tolerance to an energy crisis is engagement of energy efficient transport. This feature includes a sharp reduction in rates of solute transport and use of energy-efficient modifications of transport systems by primary H+ transport and secondary H+-solute transport systems. Here we also discuss the best choice of species to study an energy crisis. Further, we consider confounding of the acclimative response by responses to injury, be it due to the use of tissues intolerant to an energy crisis, or to faulty techniques.
Quantitative trait locus analysis of adventitious and lateral root morphology of barley grown at low and high P
Authors: Guo Jingyi , Chen Guangdeng , Zhang Xizhou , Li Tingxuan , Yu Haiying , Liu Chunji
Published: April 2018

Barley (Hordeum vulgare L) may alter its root morphology to improve P acquisition efficiency under low-P (LP) stress. This research studied the variations in adventitious and lateral root morphological traits of barley and mapped their quantitative trait loci (QTLs) under LP and high P (HP). The recombinant inbred lines were derived from the F1 population of a cross between CN4027 and Baudin. Two experiments aimed to identify QTLs related to adventitious and lateral root morphological traits under LP and HP. The length, surface area and volume of adventitious and lateral roots were measured. Under HP, Baudin had larger root morphology, especially lateral root morphology, than CN4027. LP stress induced lateral root growth but inhibited adventitious root growth. Nineteen QTLs for root morphological traits were detected. These QTLs clustered within four regions (Cl−2H, Cl−3H, Cl−4H and Cl−7H) on chromosomes 2H, 3H, 4H and 7H, with corresponding contributions of 12.0–42.9%. Some QTLs are linked with the QTLs for P efficiency detected previously, demonstrating the role of root morphological traits in P efficiency. The Cl−2H region was identified in the interval bPb3927665–bPb3265744 on chromosome 2H and had major effects on lateral root growth, especially under LP. Lateral root length and surface area increased when alleles from Baudin were present at the QTLs in Cl−2H. This study demonstrated the patterns of growth among root types and the role of lateral roots in barley’s adaption to LP stress. The QTL clusters, especially Cl−2H, may offer clues for fine mapping and map-based cloning.
The impact of affectivity on the behaviour of Portuguese adolescents / El impacto de la afectividad en la conducta de los adolescentes portugueses
Authors: Santos-Lopes-Santos Ana-Cristina dos , García del Castillo José , Marzo Juan-Carlos
Published: April 2018

The theoretical literature about affectivity shows its influence over positive and negative behaviour. This study analyses the impact of affectivity on the behaviour of Portuguese adolescents, as this knowledge is considered relevant to promoting skills and decreasing risky behaviours in adolescents. A total of 696 students ( M = 15.22 years old; SD = 1.4) participated in this study by responding to the PANAS-N (Positive and Negative Affect Schedule) and SDQ (Strengths and Difficulties Questionnaire). The former measures the level of affect while the latter measures prosocial behaviours, emotional symptoms and behavioural problems. The results showed that positive affect positively influences prosocial behaviour. Emotional symptoms and behaviour problems are negatively affected by positive affect, and positive symptoms and behaviours by negative affect. Moreover, boys had higher scores on behaviour problems, while girls had higher scores in prosocial behaviour and emotional symptoms. For these reasons, affectivity should be considered in programmes to reduce behaviour problems and emotional symptoms.
Lymphatic exosomes promote dendritic cell migration along guidance cues
Authors: Brown Markus , Johnson Louise A. , Leone Dario A. , Majek Peter , Vaahtomeri Kari , Senfter Daniel , Bukosza Nora , Schachner Helga , Asfour Gabriele , Langer Brigitte , Hauschild Robert , Parapatics Katja , Hong Young-Kwon , Bennett Keiryn L. , Kain Renate , Detmar Michael , Sixt Michael , Jackson David G. , Kerjaschki Dontscho
Published: April 2018

Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified >1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments.
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis
Authors: Stapor Paul , Fröhlich Fabian , Hasenauer Jan
Published: April 2018

Motivation

Parameter estimation methods for ordinary differential equation (ODE) models of biological processes can exploit gradients and Hessians of objective functions to achieve convergence and computational efficiency. However, the computational complexity of established methods to evaluate the Hessian scales linearly with the number of state variables and quadratically with the number of parameters. This limits their application to low-dimensional problems.

Results

We introduce second order adjoint sensitivity analysis for the computation of Hessians and a hybrid optimization-integration-based approach for profile likelihood computation. Second order adjoint sensitivity analysis scales linearly with the number of parameters and state variables. The Hessians are effectively exploited by the proposed profile likelihood computation approach. We evaluate our approaches on published biological models with real measurement data. Our study reveals an improved computational efficiency and robustness of optimization compared to established approaches, when using Hessians computed with adjoint sensitivity analysis. The hybrid computation method was more than 2-fold faster than the best competitor. Thus, the proposed methods and implemented algorithms allow for the improvement of parameter estimation for medium and large scale ODE models.

Availability and implementation

The algorithms for second order adjoint sensitivity analysis are implemented in the Advanced MATLAB Interface to CVODES and IDAS (AMICI, https://github.com/ICB-DCM/AMICI/). The algorithm for hybrid profile likelihood computation is implemented in the parameter estimation toolbox (PESTO, https://github.com/ICB-DCM/PESTO/). Both toolboxes are freely available under the BSD license.

Supplementary information

Supplementary data are available at Bioinformatics online.
Predicting CTCF-mediated chromatin loops using CTCF-MP
Authors: Zhang Ruochi , Wang Yuchuan , Yang Yang , Zhang Yang , Ma Jian
Published: April 2018

Motivation

The three dimensional organization of chromosomes within the cell nucleus is highly regulated. It is known that CCCTC-binding factor (CTCF) is an important architectural protein to mediate long-range chromatin loops. Recent studies have shown that the majority of CTCF binding motif pairs at chromatin loop anchor regions are in convergent orientation. However, it remains unknown whether the genomic context at the sequence level can determine if a convergent CTCF motif pair is able to form a chromatin loop.

Results

In this article, we directly ask whether and what sequence-based features (other than the motif itself) may be important to establish CTCF-mediated chromatin loops. We found that motif conservation measured by ‘branch-of-origin’ that accounts for motif turn-over in evolution is an important feature. We developed a new machine learning algorithm called CTCF-MP based on word2vec to demonstrate that sequence-based features alone have the capability to predict if a pair of convergent CTCF motifs would form a loop. Together with functional genomic signals from CTCF ChIP-seq and DNase-seq, CTCF-MP is able to make highly accurate predictions on whether a convergent CTCF motif pair would form a loop in a single cell type and also across different cell types. Our work represents an important step further to understand the sequence determinants that may guide the formation of complex chromatin architectures.

Availability and implementation

The source code of CTCF-MP can be accessed at: https://github.com/ma-compbio/CTCF-MP

Supplementary information

Supplementary data are available at Bioinformatics online.
Novo&Stitch: accurate reconciliation of genome assemblies via optical maps
Authors: Pan Weihua , Wanamaker Steve I , Ah-Fong Audrey M V , Judelson Howard S , Lonardi Stefano
Published: April 2018

Motivation

De novo genome assembly is a challenging computational problem due to the high repetitive content of eukaryotic genomes and the imperfections of sequencing technologies (i.e. sequencing errors, uneven sequencing coverage and chimeric reads). Several assembly tools are currently available, each of which has strengths and weaknesses in dealing with the trade-off between maximizing contiguity and minimizing assembly errors (e.g. mis-joins). To obtain the best possible assembly, it is common practice to generate multiple assemblies from several assemblers and/or parameter settings and try to identify the highest quality assembly. Unfortunately, often there is no assembly that both maximizes contiguity and minimizes assembly errors, so one has to compromise one for the other.

Results

The concept of assembly reconciliation has been proposed as a way to obtain a higher quality assembly by merging or reconciling all the available assemblies. While several reconciliation methods have been introduced in the literature, we have shown in one of our recent papers that none of them can consistently produce assemblies that are better than the assemblies provided in input. Here we introduce Novo&Stitch, a novel method that takes advantage of optical maps to accurately carry out assembly reconciliation (assuming that the assembled contigs are sufficiently long to be reliably aligned to the optical maps, e.g. 50 Kbp or longer). Experimental results demonstrate that Novo&Stitch can double the contiguity (N50) of the input assemblies without introducing mis-joins or reducing genome completeness.

Availability and implementation

Novo&Stitch can be obtained from https://github.com/ucrbioinfo/Novo_Stitch.