bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability regions for synchronized τ-periodic orbits of coupled maps with coupling delay τ
Authors: Karabacak Özkan , Alikoç Baran , Atay Fatihcan M.
Published: September 2016

Motivated by the chaos suppression methods based on stabilizing an unstable periodic orbit, we study the stability of synchronized periodic orbits of coupled map systems when the period of the orbit is the same as the delay in the information transmission between coupled units. We show that the stability region of a synchronized periodic orbit is determined by the Floquet multiplier of the periodic orbit for the uncoupled map, the coupling constant, the smallest and the largest Laplacian eigenvalue of the adjacency matrix. We prove that the stabilization of an unstable τ-periodic orbit via coupling with delay τ is possible only when the Floquet multiplier of the orbit is negative and the connection structure is not bipartite. For a given coupling structure, it is possible to find the values of the coupling strength that stabilizes unstable periodic orbits. The most suitable connection topology for stabilization is found to be the all-to-all coupling. On the other hand, a negative coupling constant may lead to destabilization of τ-periodic orbits that are stable for the uncoupled map. We provide examples of coupled logistic maps demonstrating the stabilization and destabilization of synchronized τ-periodic orbits as well as chaos suppression via stabilization of a synchronized τ-periodic orbit.
Pressure-induced phase transition of calcite and aragonite: A first principles study
Authors: Ukita Masaya , Toyoura Kazuaki , Nakamura Atsutomo , Matsunaga Katsuyuki
Published: September 2016

The thermodynamic phase stabilities of calcite and aragonite have been investigated from lattice vibrational analyses based on first-principles calculations. Different pressure dependences in phonon feature were found between the two polymorphs, suggesting different physical origins of the pressure-induced phase transitions. In the most stable phase in calcite (calcite I), an imaginary phonon mode consisting of rotation of CO3 ions with slight displacement of Ca ions appears at the F point in the Brillouin zone above 0.8 GPa. Such a soft mode means that external pressure induces the lattice-dynamical instability of calcite I leading to the phase transition to calcite II. On the other hand, the origin of the phase transition in aragonite is not due to such a lattice-dynamical instability. The estimated thermodynamical properties indicate that a first-order phase transition occurs between aragonite and post-aragonite at 34.7 GPa, coinciding with the reported experimental value at room temperature (35 GPa).
Super-resolution for scanning light stimulation systems
Authors: Bitzer L. A. , Neumann K. , Benson N. , Schmechel R.
Published: September 2016

Super-resolution (SR) is a technique used in digital image processing to overcome the resolution limitation of imaging systems. In this process, a single high resolution image is reconstructed from multiple low resolution images. SR is commonly used for CCD and CMOS (Complementary Metal-Oxide-Semiconductor) sensor images, as well as for medical applications, e.g., magnetic resonance imaging. Here, we demonstrate that super-resolution can be applied with scanning light stimulation (LS) systems, which are common to obtain space-resolved electro-optical parameters of a sample. For our purposes, the Projection Onto Convex Sets (POCS) was chosen and modified to suit the needs of LS systems. To demonstrate the SR adaption, an Optical Beam Induced Current (OBIC) LS system was used. The POCS algorithm was optimized by means of OBIC short circuit current measurements on a multicrystalline solar cell, resulting in a mean square error reduction of up to 61% and improved image quality.
A generalized theoretical framework for the description of spin decoupling in solid-state MAS NMR: Offset effect on decoupling performance
Authors: Tan Kong Ooi , Agarwal Vipin , Meier Beat H. , Ernst Matthias
Published: September 2016

We present a generalized theoretical framework that allows the approximate but rapid analysis of residual couplings of arbitrary decoupling sequences in solid-state NMR under magic-angle spinning conditions. It is a generalization of the tri-modal Floquet analysis of TPPM decoupling [Scholz et al., J. Chem. Phys. 130, 114510 (2009)] where three characteristic frequencies are used to describe the pulse sequence. Such an approach can be used to describe arbitrary periodic decoupling sequences that differ only in the magnitude of the Fourier coefficients of the interaction-frame transformation. It allows a ∼100 times faster calculation of second-order residual couplings as a function of pulse sequence parameters than full spin-dynamics simulations. By comparing the theoretical calculations with full numerical simulations, we show the potential of the new approach to examine the performance of decoupling sequences. We exemplify the usefulness of this framework by analyzing the performance of commonly used high-power decoupling sequences and low-power decoupling sequences such as amplitude-modulated XiX (AM-XiX) and its super-cycled variant SC-AM-XiX. In addition, the effect of chemical-shift offset is examined for both high- and low-power decoupling sequences. The results show that the cross-terms between the dipolar couplings are the main contributions to the line broadening when offset is present. We also show that the SC-AM-XIX shows a better offset compensation.
Vacuum arc cathode spot motion in oblique magnetic fields: An interpretation of the Robson experiment
Authors: Beilis I. I.
Published: September 2016

A model was developed of vacuum arc cathode spot motion in a magnetic field that obliquely intercepts the cathode surface. The model takes into account a force under an electric field caused by retrograde spot motion across the normal component of the magnetic field, producing a drift velocity component in the direction of the acute angle between the magnetic field and the cathode surface. The relationship between velocity of the retrograde direction and drift velocity of the cathode spot motion to the acute angle was developed. The dependencies of the drift angle θ on the acute angle φ, magnetic field strength B, and arc current I were calculated. It was found that the calculated θ increased with φ, B, and I in accordance with Robson's measurements.
Effects of electron pressure anisotropy on current sheet configuration
Authors: Artemyev A. V. , Vasko I. Y. , Angelopoulos V. , Runov A.
Published: September 2016

Recent spacecraft observations in the Earth's magnetosphere have demonstrated that the magnetotail current sheet can be supported by currents of anisotropic electron population. Strong electron currents are responsible for the formation of very thin (intense) current sheets playing the crucial role in stability of the Earth's magnetotail. We explore the properties of such thin current sheets with hot isotropic ions and cold anisotropic electrons. Decoupling of the motions of ions and electrons results in the generation of a polarization electric field. The distribution of the corresponding scalar potential is derived from the electron pressure balance and the quasi-neutrality condition. We find that electron pressure anisotropy is partially balanced by a field-aligned component of this polarization electric field. We propose a 2D model that describes a thin current sheet supported by currents of anisotropic electrons embedded in an ion-dominated current sheet. Current density profiles in our model agree well with THEMIS observations in the Earth's magnetotail.
Electrocaloric cooler combining ceramic multi-layer capacitors and fluid
Authors: Sette Daniele , Asseman Alexis , Gérard Mathieu , Strozyk Hervé , Faye Romain , Defay Emmanuel
Published: September 2016

In this paper, an electrocaloric (EC) cooler prototype made of 150 ceramic-based Multi-Layer Capacitors (MLCs) has been detailed. This cooler involves a column of dielectric fluid where heat exchange with the MLCs takes place. The maximum variation of temperature in the fluid column due to the EC effect reaches 0.13 K whereas the heat exchanged during one stroke is 0.28 J. Although this prototype requires improvements with respect to heat exchange, the basic principle of creating a temperature gradient in a column of fluid has been validated.
Ferromagnetic bond of Li10 cluster: An alternative approach in terms of effective ferromagnetic sites
Authors: Donoso Roberto , Rössler Jaime , Llano-Gil Sandra , Fuentealba Patricio , Cárdenas Carlos
Published: September 2016

In this work, a model to explain the unusual stability of atomic lithium clusters in their highest spin multiplicity is presented and used to describe the ferromagnetic bonding of high-spin Li10 and Li8 clusters. The model associates the (lack of-)fitness of Heisenberg Hamiltonian with the degree of (de-)localization of the valence electrons in the cluster. It is shown that a regular Heisenberg Hamiltonian with four coupling constants cannot fully explain the energy of the different spin states. However, a more simple model in which electrons are located not at the position of the nuclei but at the position of the attractors of the electron localization function succeeds in explaining the energy spectrum and, at the same time, explains the ferromagnetic bond found by Shaik using arguments of valence bond theory. In this way, two different points of view, one more often used in physics, the Heisenberg model, and the other in chemistry, valence bond, come to the same answer to explain those atypical bonds.
Repetition rate multiplication of frequency comb using all-pass fiber resonator
Authors: Yang Lijun , Yang Honglei , Zhang Hongyuan , Wei Haoyun , Li Yan
Published: September 2016

We propose a stable method for repetition rate multiplication of a 250-MHz Er-fiber frequency comb by a phase-locked all-pass fiber ring resonator, whose phase-locking configuration is simple. The optical path length of the fiber ring resonator is automatically controlled to be accurately an odd multiple of half of the original cavity length using an electronical phase-locking unit with an optical delay line. As for shorter cavity length of the comb, high-order odd multiple is preferable. Because the power loss depends only on the net-attenuation of the fiber ring resonator, the energetic efficiency of the proposed method is high. The input and output optical spectrums show that the spectral width of the frequency comb is clearly preserved. Besides, experimental results show less pulse intensity fluctuation and 35 dB suppression ratio of side-modes while providing a good long-term and short-term frequency stability. Higher-order repetition rate multiplication to several GHz can be obtained by using several fiber ring resonators in cascade configuration.
Characterization of process-induced damage in Cu/low-k interconnect structure by microscopic infrared spectroscopy with polarized infrared light
Authors: Seki Hirofumi , Hashimoto Hideki , Ozaki Yukihiro
Published: September 2016

Microscopic Fourier-transform infrared (FT-IR) spectra are measured for a Cu/low-k interconnect structure using polarized IR light for different widths of low-k spaces and Cu lines, and for different heights of Cu lines, on Si substrates. Although the widths of the Cu line and the low-k space are 70 nm each, considerably smaller than the wavelength of the IR light, the FT-IR spectra of the low-k film were obtained for the Cu/low-k interconnect structure. A suitable method was established for measuring the process-induced damage in a low-k film that was not detected by the TEM-EELS (Transmission Electron Microscope-Electron Energy-Loss Spectroscopy) using microscopic IR polarized light. Based on the IR results, it was presumed that the FT-IR spectra mainly reflect the structural changes in the sidewalls of the low-k films for Cu/low-k interconnect structures, and the mechanism of generating process-induced damage involves the generation of Si-OH groups in the low-k film when the Si-CH3 bonds break during the fabrication processes. The Si-OH groups attract moisture and the OH peak intensity increases. It was concluded that the increase in the OH groups in the low-k film is a sensitive indicator of low-k damage. We achieved the characterization of the process-induced damage that was not detected by the TEM-EELS and speculated that the proposed method is applicable to interconnects with line and space widths of 70 nm/70 nm and on shorter scales of leading edge devices. The location of process-induced damage and its mechanism for the Cu/low-k interconnect structure were revealed via the measurement method.
An improved correlation method for amplitude estimation of gravitational background signal with time-varying frequency
Authors: Wu Wei-Huang , Tian Yuan , Luo Jie , Shao Cheng-Gang , Xu Jia-Hao , Wang Dian-Hong
Published: September 2016

In the measurement of the gravitational constant G with angular acceleration method, the accurate estimation of the amplitude of the useful angular acceleration generated by source masses depends on the effective subtraction of the spurious gravitational signal caused by room fixed background masses. The gravitational background signal is of time-varying frequency, and mainly consists of the prominent fundamental frequency and second harmonic components. We propose an improved correlation method to estimate the amplitudes of the prominent components of the gravitational background signal with high precision. The improved correlation method converts a sinusoidal signal with time-varying frequency into a standard sinusoidal signal by means of the stretch processing of time. Based on Gaussian white noise model, the theoretical result shows the uncertainty of the estimated amplitude is proportional to σNT, where σ and N are the standard deviation of noise and the number of the useful signal period T, respectively.
Comparison of polystyrene scintillator fiber array and monolithic polystyrene for neutron imaging and radiography
Authors: Simpson R. , Cutler T. E. , Danly C. R. , Espy M. A. , Goglio J. H. , Hunter J. F. , Madden A. C. , Mayo D. R. , Merrill F. E. , Nelson R. O. , Swift A. L. , Wilde C. H. , Zocco T. G.
Published: September 2016

The neutron imaging diagnostic at the National Ignition Facility has been operating since 2011 generating neutron images of deuterium-tritium (DT) implosions at peak compression. The current design features a scintillating fiber array, which allows for high imaging resolution to discern small-scale structure within the implosion. In recent years, it has become clear that additional neutron imaging systems need to be constructed in order to provide 3D reconstructions of the DT source and these additional views need to be on a shorter line of sight. As a result, there has been increased effort to identify new image collection techniques that improve upon imaging resolution for these next generation neutron imaging systems, such as monolithic deuterated scintillators. This work details measurements performed at the Weapons Neutron Research Facility at Los Alamos National Laboratory that compares the radiographic abilities of the fiber scintillator with a monolithic scintillator, which may be featured in a future short line of sight neutron imaging systems.
The fast reciprocating magnetic probe system on the J-TEXT tokamak
Authors: Li Fuming , Chen Zhipeng , Zhuang Ge , Liu Hai , Zhu Lizhi
Published: September 2016

The fast reciprocating magnetic probe (FRMP) system is newly developed on the Joint Texas Experimental Tokamak (J-TEXT) to measure the local magnetic fluctuations at the plasma edge. The magnetic probe array in the FRMP consists of four 2-dimensional magnetic probes arranged at different radial locations to detect local poloidal and radial magnetic fields. These probes are protected by a graphite and boron nitride casing to improve the frequency response of each probe; they are mounted on the head of a movable rod, which is oriented along radial direction at the top of the torus. In the experiments, multiple core diagnostics show that the insertion of the FRMP has little impact on the equilibrium of the plasma. Local magnetic fluctuations inside the last closed flux surface are successfully measured by the FRMP.
Quantitative Fermi level tuning in amorphous organic semiconductor by molecular doping: Toward full understanding of the doping mechanism
Authors: Yang Jin-Peng , Wang Wen-Qing , Bussolotti Fabio , Cheng Li-Wen , Li Yan-Qing , Kera Satoshi , Tang Jian-Xin , Zeng Xiang-Hua , Ueno Nobuo
Published: September 2016

The doping mechanism in organic-semiconductor films has been quantitatively studied via ultrahigh-sensitivity ultraviolet photoelectron spectroscopy of N,N-bis(1-naphthyl)-N,N-diphenyl-1,1-biphenyl-4,4-diamine (α-NPD) films doped with hexaazatriphenylene-hexacarbonitrile [HAT(CN)6]. We observed that HOMO of α-NPD shifts to the Fermi level (EF) in two different rates with the doping concentration of HAT(CN)6, but HOMO distributions of both pristine and doped amorphous α-NPD films are excellently approximated with a same Gaussian distribution without exponential tail states over ∼5 × 1018 cm−3 eV−1. From the theoretical simulation of the HAT(CN)6-concentration dependence of the HOMO in doped films, we show that the passivation of Gaussian-distributed hole traps, which peak at 1.1 eV above the HOMO onset, occurs at ultralow doping [HAT(CN)6 molecular ratio (MR) < 0.01], leading to a strong HOMO shift of ∼0.40 eV towards EF, and MR dependence of HOMO changes abruptly at MR ∼ 0.01 to a weaker dependence for MR > 0.01 due to future of the dopant acceptor level.
Measurement of high carrier mobility in graphene in an aqueous electrolyte environment
Authors: Brown Morgan A. , Crosser Michael S. , Leyden Matthew R. , Qi Yabing , Minot Ethan D.
Published: September 2016

Graphene is a promising material for applications in aqueous electrolyte environments. To explore the impact of such environments on graphene's electrical properties, we performed Hall bar measurements on electrolyte-gated graphene. Assuming a Drude model, we find that the room temperature carrier mobility in water-gated, SiO2-supported graphene reaches 7000 cm2/Vs, comparable to the best dry SiO2-supported graphene devices. Our results show that the electrical performance of graphene is robust, even in the presence of dissolved ions that introduce an additional mechanism for Coulomb scattering.
High efficiency bifacial Cu2ZnSnSe4 thin-film solar cells on transparent conducting oxide glass substrates
Authors: Kim Jung-Sik , Kang Jin-Kyu , Hwang Dae-Kue
Published: September 2016

In this work, transparent conducting oxides (TCOs) have been employed as a back contact instead of Mo on Cu2ZnSnSe4 (CZTSe) thin-film solar cells in order to examine the feasibility of bifacial Cu2ZnSn(S,Se)4 (CZTSSe) solar cells based on a vacuum process. It is found that the interfacial reaction between flourine doped tin oxide (FTO) or indium tin oxide (ITO) and the CZTSe precursor is at odds with the conventional CZTSe/Mo reaction. While there is no interfacial reaction on CZTSe/FTO, indium in CZTSe/ITO was significantly diffused into the CZTSe layers; consequently, a SnO2 layer was formed on the ITO substrate. Under bifacial illumination, we achieved a power efficiency of 6.05% and 4.31% for CZTSe/FTO and CZTSe/ITO, respectively.
Depth-resolved ballistic imaging in a low-depth-of-field optical Kerr gated imaging system
Authors: Zheng Yipeng , Tan Wenjiang , Si Jinhai , Ren YuHu , Xu Shichao , Tong Junyi , Hou Xun
Published: September 2016

We demonstrate depth-resolved imaging in a ballistic imaging system, in which a heterodyned femtosecond optical Kerr gate is introduced to extract useful imaging photons for detecting an object hidden in turbid media and a compound lens is proposed to ensure both the depth-resolved imaging capability and the long working distance. Two objects of about 15-μm widths hidden in a polystyrene-sphere suspension have been successfully imaged with approximately 600-μm depth resolution. Modulation-transfer-function curves with the object in and away from the object plane have also been measured to confirm the depth-resolved imaging capability of the low-depth-of-field (low-DOF) ballistic imaging system. This imaging approach shows potential for application in research of the internal structure of highly scattering fuel spray.
Magnetic field sensor based on cascaded microfiber coupler with magnetic fluid
Authors: Mao Lianmin , Pu Shengli , Su Delong , Wang Zhaofang , Zeng Xianglong , Lahoubi Mahieddine
Published: September 2016

A kind of magnetic field sensor based on cascaded microfiber coupler with magnetic fluid is proposed and experimentally demonstrated. The magnetic fluid is utilized as the cladding of the fused regions of the cascaded microfiber coupler. As the interference valley wavelength of the sensing structure is sensitive to the ambient variation, considering the magnetic-field-dependent refractive index of magnetic fluid, the proposed structure is employed for magnetic field sensing. The effective coupling length for each coupling region of the as-fabricated cascaded microfiber coupler is 6031 μm. The achieved sensitivity is 125 pm/Oe, which is about three times larger than that of the previously similar structure based on the single microfiber coupler. Experimental results indicate that the sensing sensitivity can be easily improved by increasing the effective coupling length or cascading more microfiber couplers. The proposed magnetic field sensor is attractive due to its low cost, immunity to electromagnetic interference, as well as high sensitivity, which also has the potentials in other tunable all-fiber photonic devices, such as filter.
Paleoclimate record connects Asian monsoons and ice-age cycles
Authors: Wilson R. Mark
Published: September 2016

A new analysis of cave stalagmites almost doubles the span of known variations in rainfall over East Asia.
Underwater microscope brings marine life into focus
Authors: Miller Johanna L.
Published: September 2016

Some of the ocean’s smallest organisms can now be observed in their natural habitat.
Models poised to boost grid efficiency
Authors: Kramer David
Published: September 2016

Improvements in nonlinear algorithms will harness the full benefits of renewable power.
Cold War computers, California supercars, and the pursuit of lithium-ion power
Authors: Eisler Matthew N.
Published: September 2016

The electric vehicle’s history offers a lesson to the wise: Harvesting the fruits of basic science requires industrial foresight, investment, and a healthy dose of realpolitik.
Two-dimensional van der Waals materials
Authors: Ajayan Pulickel , Kim Philip , Banerjee Kaustav
Published: September 2016

Graphene is not the only atomically thin material of technological importance. Diverse families of newly harnessed monolayers have far-reaching implications for basic physics, materials science, and engineering.
Is the Partners in Recovery program connecting with the intended population of people living with severe and persistent mental illness? What are their prioritised needs?
Authors: Hancock Nicola , Smith-Merry Jennifer , Gillespie James A. , Yen Ivy
Published: September 2016

Objective
The Partners in Recovery (PIR) program is an Australian government initiative designed to make the mental health and social care sectors work in more coordinated ways to meet the needs of those with severe and complex mental illness. Herein we reflect on demographic data collected during evaluation of PIR implementation in two Western Sydney sites. The aims of the present study were to: (1) explore whether two Sydney-based PIR programs had recruited their intended population, namely people living with severe and persistent mental illness; and (2) learn more about this relatively unknown population and their self-identified need priorities.

Methods
Routinely collected initial client assessment data were analysed descriptively.

Results
The data suggest that the two programs are engaging the intended population. The highest unmet needs identified included psychological distress, lack of daytime activities and company, poor physical health and inadequate accommodation. Some groups remain hard to connect, including people from Aboriginal and other culturally diverse communities.

Conclusions
The data confirm that the PIR program, at least in the two regions evaluated, is mostly reaching its intended audience. Some data were being collected inconsistently, limiting the usefulness of the data and the ability to build on PIR findings to develop ongoing support for this population.

What is known about the topic?
PIR is a unique national program funded to engage with and address the needs of Australians living with severe and persistent mental illness by facilitating service access.

What does this paper add?
This paper reports on recruitment of people living with severe and persistent mental illness, their need priorities and data collection. These are three central elements to successful roll-out of the much anticipated mental health component of the National Disability Insurance Scheme, as well as ongoing PIR operation.

What are the implications for practitioners?
Active recruitment, exploration of self-reported need priorities and routine outcome measurement are essential yet challenging work practices when working with people living with severe and persistent mental illness.
A review of whole farm-system analysis in evaluating greenhouse-gas mitigation strategies from livestock production systems
Authors: Rawnsley Richard , Dynes Robyn A. , Christie Karen M. , Harrison Matthew Tom , Doran-Browne Natalie A. , Vibart Ronaldo , Eckard Richard
Published: September 2016

Recognition is increasingly given to the need of improving agricultural production and efficiency to meet growing global food demand, while minimising environmental impacts. Livestock forms an important component of global food production and is a significant contributor to anthropogenic greenhouse-gas (GHG) emissions. As such, livestock production systems (LPS) are coming under increasing pressure to lower their emissions. In developed countries, LPS have been gradually reducing their emissions per unit of product (emissions intensity; EI) over time through improvements in production efficiency. However, the global challenge of reducing net emissions (NE) from livestock requires that the rate of decline in EI surpasses the productivity increases required to satisfy global food demand. Mechanistic and dynamic whole farm-system models can be used to estimate farm-gate GHG emissions and to quantify the likely changes in farm NE, EI, farm productivity and farm profitability as a result of applying various mitigation strategies. Such models are also used to understand the complex interactions at the farm-system level and to account for how component mitigation strategies perform within the complexity of these interactions, which is often overlooked when GHG mitigation research is performed only at the component level. The results of such analyses can be used in extension activities and to encourage adoption, increase awareness and in assisting policy makers. The present paper reviews how whole farm-system modelling has been used to assess GHG mitigation strategies, and the importance of understanding metrics and allocation approaches when assessing GHG emissions from LPS.
The biology and palaeontology of the Peramelemorphia: a review of current knowledge and future research directions
Authors: Warburton N. M. , Travouillon K. J.
Published: September 2016

Bandicoots and bilbies (Marsupialia : Peramelemorphia) represent the dominant omnivorous clade of Australasian marsupials and, as ground-dwelling, small- to medium-sized mammals, have not fared well in the 200 years since European settlement. Unlike large or charismatic marsupial species, the cryptic nature of bandicoots and bilbies tends to keep them out of the public eye, at a time when public interest plays a significant role in conservation efforts. The inconspicuous ‘rat-like’ appearance of many bandicoots and a generalist ecological strategy belie a complex biology of adaptive traits and evolutionary diversity. For a few species these biological traits have enabled them to make use of urban environments. In the main, however, peramelemorphians are facing ongoing pressure from introduced predators and human impacts. Basic biological information for many species, particularly those from New Guinea, is still lacking. In this review, we examine advances in the knowledge of the biology of this group over the past 25 years including anatomical, physiological and ecological studies. We also provide a comprehensive review of the fossil records of bandicoots in order to provide an up-to-date platform for future studies. From this work, it is clear that there is still much to be done regarding the taxonomy and biology of these animals before a more detailed understanding of the evolutionary history of this group can be elucidated.
RNA-binding protein DUS16 plays an essential role in primary miRNA processing in the unicellular alga
Chlamydomonas reinhardtii
Authors: Yamasaki Tomohito , Onishi Masayuki , Kim Eun-Jeong , Cerutti Heriberto , Ohama Takeshi
Published: September 2016

Significance

MicroRNAs are important regulators of gene expression in unicellular and multicellular eukaryotes. They are generally embedded in stem–loops of precursor transcripts and are excised by the dsRNA-specific nuclease DICER with the assistance of dsRNA-binding proteins. In animals and plants, proteins harboring two or three dsRNA-binding domains (dsRBDs) are involved in microRNA (miRNA) biogenesis. In contrast, we found that the Dull slicer-16 (DUS16) protein, which contains a single dsRBD and also an ssRNA-binding domain, is involved in miRNA biogenesis in the unicellular green alga
Chlamydomonas
. This finding sheds light on a molecular mechanism of miRNA biogenesis in unicellular organisms that may be similar to that in a common ancestor of animals and plants.
Oncometabolite
d
-2-hydroxyglutarate impairs α-ketoglutarate dehydrogenase and contractile function in rodent heart
Authors: Karlstaedt Anja , Zhang Xiaotian , Vitrac Heidi , Harmancey Romain , Vasquez Hernan , Wang Jing Han , Goodell Margaret A. , Taegtmeyer Heinrich
Published: September 2016

Significance

We show that the oncometabolite
d
-2-hydroxyglutarate (D2-HG) affects cardiac function in the isolated working heart by inhibiting α-KGDH, a key regulatory enzyme of cellular energy metabolism. Analyzing metabolic flux rates by using in vitro and ex vivo approaches in combination with integrative mathematical modeling enabled us to identify the mechanisms by which D2-HG perturbs metabolic flux and induces epigenetic modifications in the heart. The results provide knowledge about malignancy-related changes in enzymatic activity and posttranslational modifications in the context of cardiac remodeling.
Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC
Authors: Ilgü Hüseyin , Jeckelmann Jean-Marc , Gapsys Vytautas , Ucurum Zöhre , de Groot Bert L. , Fotiadis Dimitrios
Published: September 2016

Significance

Disease-causing bacteria are able to survive the strongly acidic environment of the stomach by activating extreme acid-resistance responses. One of these responses in gut bacteria consists of converting
l
-arginine into agmatine, which results in removal of one proton from the cytoplasm. In
Escherichia coli
, the transport protein AdiC assures the efflux of agmatine in exchange with
l
-arginine. We have solved the structures of wild-type AdiC in the presence and absence of the substrate agmatine at high resolution, allowing for the identification of crucial water molecules and of their functional roles in the substrate-binding pocket. Furthermore, structure-based site-directed mutagenesis combined with a radioligand binding assay improved our understanding of substrate binding and specificity of the
l
-arginine/agmatine antiporter AdiC.
School tracking, educational mobility and inequality in German secondary education: developments across cohorts
Authors: Schindler Steffen
Published: September 2016

Secondary education is associated with a comparatively high level of inequality in Germany. This has often been attributed to the early ability-based between-school tracking in the German school system. However, as yet there has been no empirical evaluation of the actual impact of initial track placement on social inequality in final school attainment. Since educational reforms in the 1960s increased educational mobility after track placement, it can be expected that initial track allocation has become less important for the process of secondary educational attainment and the inequalities therein. By drawing on longitudinal life-course data for different birth cohorts from the 1930s to the 1980s, this paper analyses temporal developments in the connections between track placement, educational mobility and social inequality in final school outcomes. The analyses reveal that the impact of track placement actually diminished for those cohorts exposed to the reformed school system. Instead, social inequalities in school attainment are increasingly influenced by processes of educational mobility after track allocation. Furthermore, the analyses show that developments in educational mobility have contributed more to declining inequalities in access to upper secondary education than changes of the selectivities in the transition to secondary education.
A characterization of 𝜇-equicontinuity for topological dynamical systems
Authors: García-Ramos Felipe
Published: September 2016

Two different notions of measure theoretical equicontinuity (

μ
−

\mu -

equicontinuity) for topological dynamical systems with respect to Borel probability measures appeared in works by Gilman (1987) and Huang, Lee and Ye (2011). We show that if the probability space satisfies Lebesgue’s density theorem and Vitali’s covering theorem (for example a Cantor set or a subset of

R

d

\mathbb {R}^{d}

), then both notions are equivalent. To show this we characterize Lusin measurable maps using

μ
−

\mu -

continuity points. As a corollary we also obtain a new characterization of

μ
−

\mu -

mean equicontinuity.
On tangent cones in Wasserstein space
Authors: Lott John
Published: September 2016

If

M
M

is a smooth compact Riemannian manifold, let

P
(
M
)

P(M)

denote the Wasserstein space of probability measures on

M
M

. If

S
S

is an embedded submanifold of

M
M

, and

μ
\mu

is an absolutely continuous measure on

S
S

, then we compute the tangent cone of

P
(
M
)

P(M)

at

μ
\mu

.
Presence of a carboxy-terminal pseudorepeat and disease-like pseudohyperphosphorylation critically influence tau’s interaction with microtubules in axon-like processes
Authors: Niewidok Benedikt , Igaev Maxim , Sündermann Frederik , Janning Dennis , Bakota Lidia , Brandt Roland
Published: September 2016

A current challenge of cell biology is to investigate molecular interactions in subcellular compartments of living cells to overcome the artificial character of in vitro studies. To dissect the interaction of the neuronal microtubule (MT)-associated protein tau with MTs in axon-like processes, we used a refined fluorescence decay after photoactivation approach and single-molecule tracking. We found that isoform variation had only a minor influence on the tau–MT interaction, whereas the presence of a C-terminal pseudorepeat region (PRR) greatly increased MT binding by a greater-than-sixfold reduction of the dissociation rate. Bioinformatic analysis revealed that the PRR contained a highly conserved motif of 18 amino acids. Disease-associated tau mutations in the PRR (K369I, G389R) did not influence apparent MT binding but increased its dynamicity. Simulation of disease-like tau hyperphosphorylation dramatically diminished the tau–MT interaction by a greater-than-fivefold decrease of the association rate with no major change in the dissociation rate. Apparent binding of tau to MTs was similar in axons and dendrites but more sensitive to increased phosphorylation in axons. Our data indicate that under the conditions of high MT density that prevail in the axon, tau’s MT binding and localization are crucially affected by the presence of the PRR and tau hyperphosphorylation.
A unified model based multifactor dimensionality reduction framework for detecting gene–gene interactions
Authors: Yu Wenbao , Lee Seungyeoun , Park Taesung
Published: September 2016

Motivation

Gene–gene interaction (GGI) is one of the most popular approaches for finding and explaining the missing heritability of common complex traits in genome-wide association studies. The multifactor dimensionality reduction (MDR) method has been widely studied for detecting GGI effects. However, there are several disadvantages of the existing MDR-based approaches, such as the lack of an efficient way of evaluating the significance of multi-locus models and the high computational burden due to intensive permutation. Furthermore, the MDR method does not distinguish marginal effects from pure interaction effects.

Methods

We propose a two-step unified model based MDR approach (UM-MDR), in which, the significance of a multi-locus model, even a high-order model, can be easily obtained through a regression framework with a semi-parametric correction procedure for controlling Type I error rates. In comparison to the conventional permutation approach, the proposed semi-parametric correction procedure avoids heavy computation in order to achieve the significance of a multi-locus model. The proposed UM-MDR approach is flexible in the sense that it is able to incorporate different types of traits and evaluate significances of the existing MDR extensions.

Results

The simulation studies and the analysis of a real example are provided to demonstrate the utility of the proposed method. UM-MDR can achieve at least the same power as MDR for most scenarios, and it outperforms MDR especially when there are some single nucleotide polymorphisms that only have marginal effects, which masks the detection of causal epistasis for the existing MDR approaches.

Conclusions

UM-MDR provides a very good supplement of existing MDR method due to its efficiency in achieving significance for every multi-locus model, its power and its flexibility of handling different types of traits.

Availability and implementation

A R package “umMDR” and other source codes are freely available at http://statgen.snu.ac.kr/software/umMDR/.

Contact

tspark@stats.snu.ac.kr

Supplementary information

Supplementary data are available at Bioinformatics online.
Gene-set association tests for next-generation sequencing data
Authors: Lee Jaehoon , Kim Young Jin , Lee Juyoung ,   T2D-Genes Consortium, Kim Bong-Jo , Lee Seungyeoun , Park Taesung
Published: September 2016

Motivation

Recently, many methods have been developed for conducting rare-variant association studies for sequencing data. These methods have primarily been based on gene-level associations but have not been proven to be as effective as expected. Gene-set-level tests have shown great advantages over gene-level tests in terms of power and robustness, because complex diseases are often caused by multiple genes that comprise of biological gene sets.

Results

Here, we propose several novel gene-set tests that employ rapid and efficient dimensionality reduction. The performance of these tests was investigated using extensive simulations and application to 1058 whole-exome sequences from a Korean population. We identified some known pathways and novel pathways whose rare or common variants are associated with elevated liver enzymes and replicated the results in an independent cohort.

Availability and Implementation

Source R code for our algorithm is freely available at http://statgen.snu.ac.kr/software/QTest.

Contact

tspark@stats.snu.ac.kr

Supplementary information

Supplementary data are available at Bioinformatics online.
Higher order methylation features for clustering and prediction in epigenomic studies
Authors: Kapourani Chantriolnt-Andreas , Sanguinetti Guido
Published: September 2016

Motivation

DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the well-understood methylation-switch at CpG islands.

Results

Here, we use probabilistic machine learning to extract higher order features associated with the methylation profile across a defined region. These features quantitate precisely notions of shape of a methylation profile, capturing spatial correlations in DNA methylation across genomic regions. Using these higher order features across promoter-proximal regions, we are able to construct a powerful machine learning predictor of gene expression, significantly improving upon the predictive power of average DNA methylation levels. Furthermore, we can use higher order features to cluster promoter-proximal regions, showing that five major patterns of methylation occur at promoters across different cell lines, and we provide evidence that methylation beyond CpG islands may be related to regulation of gene expression. Our results support previous reports of a functional role of spatial correlations in methylation patterns, and provide a mean to quantitate such features for downstream analyses.

Availability and Implementation

https://github.com/andreaskapou/BPRMeth

Contact

G.Sanguinetti@ed.ac.uk

Supplementary information

Supplementary data are available at Bioinformatics online.
Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization
Authors: Ammad-ud-din Muhammad , Khan Suleiman A. , Malani Disha , Murumägi Astrid , Kallioniemi Olli , Aittokallio Tero , Kaski Samuel
Published: September 2016

Motivation

A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially valuable in oncology, where molecular and genetic heterogeneity of the cells has a major impact on the response. However, the prediction task is extremely challenging, raising the need for methods that can effectively model and predict drug responses.

Results

In this study, we propose a novel formulation of multi-task matrix factorization that allows selective data integration for predicting drug responses. To solve the modeling task, we extend the state-of-the-art kernelized Bayesian matrix factorization (KBMF) method with component-wise multiple kernel learning. In addition, our approach exploits the known pathway information in a novel and biologically meaningful fashion to learn the drug response associations. Our method quantitatively outperforms the state of the art on predicting drug responses in two publicly available cancer datasets as well as on a synthetic dataset. In addition, we validated our model predictions with lab experiments using an in-house cancer cell line panel. We finally show the practical applicability of the proposed method by utilizing prior knowledge to infer pathway-drug response associations, opening up the opportunity for elucidating drug action mechanisms. We demonstrate that pathway-response associations can be learned by the proposed model for the well-known EGFR and MEK inhibitors.

Availability and implementation

The source code implementing the method is available at http://research.cs.aalto.fi/pml/software/cwkbmf/.

Contacts

muhammad.ammad-ud-din@aalto.fi or samuel.kaski@aalto.fi

Supplementary information

Supplementary data are available at Bioinformatics online.
Patterns of amino acid conservation in human and animal immunodeficiency viruses
Authors: Voitenko Olga S , Dhroso Andi , Feldmann Anna , Korkin Dmitry , Kalinina Olga V
Published: September 2016

Motivation

Due to their high genomic variability, RNA viruses and retroviruses present a unique opportunity for detailed study of molecular evolution. Lentiviruses, with HIV being a notable example, are one of the best studied viral groups: hundreds of thousands of sequences are available together with experimentally resolved three-dimensional structures for most viral proteins. In this work, we use these data to study specific patterns of evolution of the viral proteins, and their relationship to protein interactions and immunogenicity.

Results

We propose a method for identification of two types of surface residues clusters with abnormal conservation: extremely conserved and extremely variable clusters. We identify them on the surface of proteins from HIV and other animal immunodeficiency viruses. Both types of clusters are overrepresented on the interaction interfaces of viral proteins with other proteins, nucleic acids or low molecular-weight ligands, both in the viral particle and between the virus and its host. In the immunodeficiency viruses, the interaction interfaces are not more conserved than the corresponding proteins on an average, and we show that extremely conserved clusters coincide with protein–protein interaction hotspots, predicted as the residues with the largest energetic contribution to the interaction. Extremely variable clusters have been identified here for the first time. In the HIV-1 envelope protein gp120, they overlap with known antigenic sites. These antigenic sites also contain many residues from extremely conserved clusters, hence representing a unique interacting interface enriched both in extremely conserved and in extremely variable clusters of residues. This observation may have important implication for antiretroviral vaccine development.

Availability and Implementation

A Python package is available at https://bioinf.mpi-inf.mpg.de/publications/viral-ppi-pred/

Contact

voitenko@mpi-inf.mpg.de or kalinina@mpi-inf.mpg.de

Supplementary information

Supplementary data are available at Bioinformatics online.
A probabilistic model for detecting rigid domains in protein structures
Authors: Nguyen Thach , Habeck Michael
Published: September 2016

Motivation

Large-scale conformational changes in proteins are implicated in many important biological functions. These structural transitions can often be rationalized in terms of relative movements of rigid domains. There is a need for objective and automated methods that identify rigid domains in sets of protein structures showing alternative conformational states.

Results

We present a probabilistic model for detecting rigid-body movements in protein structures. Our model aims to approximate alternative conformational states by a few structural parts that are rigidly transformed under the action of a rotation and a translation. By using Bayesian inference and Markov chain Monte Carlo sampling, we estimate all parameters of the model, including a segmentation of the protein into rigid domains, the structures of the domains themselves, and the rigid transformations that generate the observed structures. We find that our Gibbs sampling algorithm can also estimate the optimal number of rigid domains with high efficiency and accuracy. We assess the power of our method on several thousand entries of the DynDom database and discuss applications to various complex biomolecular systems.

Availability and Implementation

The Python source code for protein ensemble analysis is available at: https://github.com/thachnguyen/motion_detection

Contact

mhabeck@gwdg.de