bluuebunny/crossref_metadata_2025 huggingface dataset:
Amplitude-phase cross talk as a deterioration factor of signal-to-noise ratio in phase-detection noise-cancellation technique for spectral pump/probe measurements and compensation of the amplitude-phase cross talk
Authors: Seto Keisuke , Tarumi Takashi , Tokunaga Eiji
Published: June 2018

Noise cancellation of the light source is an important method to enhance the signal-to-noise ratio (SNR) and facilitate high-speed detection in pump/probe measurements. We developed a method to eliminate the noise for the multichannel spectral pump/probe measurements with a spectral dispersion of a white probe pulse light. In this method, the sample-induced intensity modulation is converted to the phase modulation of the pulse repetition irrespective of the intensity noise of the light source. The SNR is enhanced through the phase detection of the observed signal with the signal synchronized to the pulse repetition serving as the phase reference (synchronized signal). However, the shot-noise limited performance is not achieved with an intense probe light. In this work, we demonstrate that the performance limitation below the shot noise limit is caused by the amplitude-phase cross talk. It converts the amplitude noise into the phase noise and is caused by the space-charge effect in the photodetector, the reverse bias voltage drop across the load impedance, and the phase detection circuit. The phase delay occurs with an intense light at a PIN photodiode, whereas the phase is advanced in an avalanche photodiode. Although the amplitude distortion characteristics also reduce the performance, the distortion effect is equivalent to the amplitude-phase cross talk. We also propose possible ways to compensate the cross talk effect by using the phase modulation of the synchronized signal for the phase detection based on the instantaneous amplitude.
Velocity- and pointing-error measurements of a 300 000-r/min self-bearing permanent-magnet motor for optical applications
Authors: Breitkopf Sven , Lilienfein Nikolai , Achtnich Timon , Zwyssig Christof , Tünnermann Andreas , Pupeza Ioachim , Limpert Jens
Published: June 2018

Compact, ultra-high-speed self-bearing permanent-magnet motors enable a wide scope of applications including an increasing number of optical ones. For implementation in an optical setup, the rotors have to satisfy high demands regarding their velocity and pointing errors. Only a restricted number of measurements of these parameters exist and only at relatively low velocities. This manuscript presents the measurement of the velocity and pointing errors at rotation frequencies up to 5 kHz. The acquired data allow us to identify the rotor drive as the main source of velocity variations with fast fluctuations of up to 3.4 ns (RMS) and slow drifts of 23 ns (RMS) over ∼120 revolutions at 5 kHz in vacuum. At the same rotation frequency, the pointing fluctuated by 12 μrad (RMS) and 33 μrad (peak-to-peak) over ∼10 000 round trips. To our best knowledge, this states the first measurement of velocity and pointing errors at multi-kHz rotation frequencies and will allow potential adopters to evaluate the feasibility of such rotor drives for their application.
Bistability in two simple symmetrically coupled oscillators with symmetry-broken amplitude- and phase-locking
Authors: Röhm André , Lüdge Kathy , Schneider Isabelle
Published: June 2018

In the model system of two instantaneously and symmetrically coupled identical Stuart-Landau oscillators, we demonstrate that there exist stable solutions with symmetry-broken amplitude- and phase-locking. These states are characterized by a non-trivial fixed phase or amplitude relationship between both oscillators, while simultaneously maintaining perfectly harmonic oscillations of the same frequency. While some of the surrounding bifurcations have been previously described, we present the first detailed analytical and numerical description of these states and present analytically and numerically how they are embedded in the bifurcation structure of the system, arising both from the in-phase and the anti-phase solutions, as well as through a saddle-node bifurcation. The dependence of both the amplitude and the phase on parameters can be expressed explicitly with analytic formulas. As opposed to the previous reports, we find that these symmetry-broken states are stable, which can even be shown analytically. As an example of symmetry-breaking solutions in a simple and symmetric system, these states have potential applications as bistable states for switches in a wide array of coupled oscillatory systems.
First-principles study of structural, electronic, and optical properties of surface defects in GaAs(001) - β2(2x4)
Authors: Bacuyag Dhonny , Escaño Mary Clare Sison , David Melanie , Tani Masahiko
Published: June 2018

We performed first-principles calculations based on density functional theory (DFT) to investigate the role of point defects in the structural, electronic, and optical properties of the GaAs(001)- β2(2x4). In terms of structural properties, AsGa is the most stable defect structure, consistent with experiments. With respect to the electronic structure, band structures revealed the existence of sub-band and midgap states for all defects. The induced sub-bands and midgap states originated from the redistributions of charges towards these defects and neighboring atoms. The presence of these point defects introduced deep energy levels characteristic of EB3 (0.97 eV), EL4 (0.52 eV), and EL2 (0.82 eV) for AsGa, GaAs, GaV, respectively. The optical properties are found to be strongly related to these induced gap states. The calculated onset values in the absorption spectra, corresponding to the energy gaps, confirmed the absorption below the known bulk band gap of 1.43 eV. These support the possible two-step photoabsorption mediated by midgap states as observed in experiments.
Simulation study of the nanoparticles nucleation in a pulse-modulated capacitively coupled rf acetylene discharge
Authors: Akhoundi A. , Foroutan G.
Published: June 2018

The multi-fluid plasma equations are combined with the hydrocarbon chemical kinetics to simulate the nucleation stage of the nanoparticle formation in a pulse-modulated capacitively coupled rf acetylene discharge. The simulation code is validated by comparing its results with the available experimental and simulation results, and the agreement is quite satisfactory. It is shown that, with pulsing of the rf power, periodic oscillations develop on the temporal profiles of all hydrocarbon species. The amplitude of the oscillations decreases with the increasing pulse repetition frequency and species mass. On the long time scale of several pulse periods, the average number density of neutral molecules grows linearly with time. However, due to strong wall losses, radicals are saturated after experiencing an initial linear growth. The average number density of large neutral molecules and radicals increases with the increasing pulse repetition frequency and duty ratio. Anions are strongly affected by the power modulation, and their amplitude of oscillations is much larger than that of the radicals. Cations oscillate almost simultaneously with the electrons, and as their average number density does not grow on the long time scale, they do not play a noticeable role in the nucleation process. All roots of the nanoparticle formation can be effectively suppressed when pulses of low repetition frequency and low duty ratio are applied.
Thermoresponsive light scattering device utilizing surface behavior effects between polyimide and an ionic liquid-water mixture exhibiting lower critical solution temperature (LCST)-type phase separation
Authors: Goda Kazuya , Takatoh Kohki , Funasako Yusuke , Inokuchi Makoto
Published: June 2018

We proposed a thermoresponsive light scattering device that utilizes the surface behavior between polyimide and an ionic liquid-water mixture exhibiting lower critical solution temperature (LCST)-type phase separation. The LCST behavior for an ionic liquid device utilizing the polyimide with and without alkyl side chains was investigated. In the here-reported ionic liquid device that utilized the polyimide with alkyl side chains, [nBu4P][CF3COO] droplets were generated by phase separation—they were predominantly formed at the alkyl surface by a surface pinning effect. A stable transmittance in the opaque state could be obtained with this device. In contrast, an ionic liquid device using polyimide without alkyl side chains deteriorated transmittance in the opaque state because there was no surface pinning effect. Additionally, the viewing angle, contrast ratio, and heat cycle testing of this ionic liquid device with polyimide with alkyl side chains were also investigated. The results indicated that no parallax was obtained and that the ionic liquid device has a stable transmittance (verified by heat cycle testing). This unique device is expected to find use in the smart window applications that are activated by temperature changes.
Observation of the standing wave effect in large-area, very-high-frequency capacitively coupled plasmas by using a fiber Bragg grating sensor
Authors: Han Dao-Man , Liu Yong-Xin , Gao Fei , Wang Xiang-Yu , Li Ang , Xu Jun , Jing Zhen-Guo , Wang You-Nian
Published: June 2018

The large-area capacitive discharges driven at very high frequencies have been attracting much attention due to their wide applications in material etching and thin film deposition. However, in the regime, the standing wave effect (SWE) becomes a major limitation for plasma material processing uniformity. In this work, a fiber Bragg grating sensor was utilized for the observation of the SWE in a large-area capacitive discharge reactor by measuring the radial distribution of the neutral gas temperature Tg. The influences of the RF power and the working pressure on the radial profiles of Tg were studied. At a higher frequency (100 MHz) and a lower pressure (5 Pa), Tg presents a center-peaked radial distribution, indicating a significant SWE. As the RF power increases, the central peak of Tg becomes more evident due to the enhanced SWE. By contrast, at 100 MHz and a higher pressure (40 Pa), the radial distribution of Tg shows an evident peak at the electrode edge and Tg decays dramatically towards the discharge center because the electromagnetic waves are strongly damped as they are propagating from the edge to the center. At a lower frequency (27 MHz), only edge-high profiles of Tg are observed for various pressures. For the sake of a comparison, a hairpin resonance probe was used to measure the radial distributions of the plasma density np under the same condition. The radial profiles of Tg are found to generally resemble those of np under various conditions. Based on the experimental results, the neutral gas heating mechanism was analyzed.
Ignition sensitivity study of an energetic train configuration using experiments and simulation
Authors: Kim Bohoon , Yu Hyeonju , Yoh Jack J.
Published: June 2018

A full scale hydrodynamic simulation intended for the accurate description of shock-induced detonation transition was conducted as a part of an ignition sensitivity analysis of an energetic component system. The system is composed of an exploding foil initiator (EFI), a donor explosive unit, a stainless steel gap, and an acceptor explosive. A series of velocity interferometer system for any reflector measurements were used to validate the hydrodynamic simulations based on the reactive flow model that describes the initiation of energetic materials arranged in a train configuration. A numerical methodology with ignition and growth mechanisms for tracking multi-material boundary interactions as well as severely transient fluid-structure coupling between high explosive charges and metal gap is described. The free surface velocity measurement is used to evaluate the sensitivity of energetic components that are subjected to strong pressure waves. Then, the full scale hydrodynamic simulation is performed on the flyer impacted initiation of an EFI driven pyrotechnical system.
Predicting vapor liquid equilibria using density functional theory: A case study of argon
Authors: Goel Himanshu , Ling Sanliang , Ellis Breanna Nicole , Taconi Anna , Slater Ben , Rai Neeraj
Published: June 2018

Predicting vapor liquid equilibria (VLE) of molecules governed by weak van der Waals (vdW) interactions using the first principles approach is a significant challenge. Due to the poor scaling of the post Hartree-Fock wave function theory with system size/basis functions, the Kohn-Sham density functional theory (DFT) is preferred for systems with a large number of molecules. However, traditional DFT cannot adequately account for medium to long range correlations which are necessary for modeling vdW interactions. Recent developments in DFT such as dispersion corrected models and nonlocal van der Waals functionals have attempted to address this weakness with a varying degree of success. In this work, we predict the VLE of argon and assess the performance of several density functionals and the second order Møller-Plesset perturbation theory (MP2) by determining critical and structural properties via first principles Monte Carlo simulations. PBE-D3, BLYP-D3, and rVV10 functionals were used to compute vapor liquid coexistence curves, while PBE0-D3, M06-2X-D3, and MP2 were used for computing liquid density at a single state point. The performance of the PBE-D3 functional for VLE is superior to other functionals (BLYP-D3 and rVV10). At T = 85 K and P = 1 bar, MP2 performs well for the density and structural features of the first solvation shell in the liquid phase.
Fabrication method of two-photon luminescent organic nano-architectures using electron-beam irradiation
Authors: Kamura Yoshio , Imura Kohei
Published: June 2018

Optical recording on organic thin films with a high spatial resolution is promising for high-density optical memories, optical computing, and security systems. The spatial resolution of the optical recording is limited by the diffraction of light. Electrons can be focused to a nanometer-sized spot, providing the potential for achieving better resolution. In conventional electron-beam lithography, however, optical tuning of the fabricated structures is limited mostly to metals and semiconductors rather than organic materials. In this article, we report a fabrication method of luminescent organic architectures using a focused electron beam. We optimized the fabrication conditions of the electron beam to generate chemical species showing visible photoluminescence via two-photon near-infrared excitations. We utilized this fabrication method to draw nanoscale optical architectures on a polystyrene thin film.
Direct measurements of anode/cathode gap plasma in cylindrically imploding loads on the Z machine
Authors: Porwitzky A. , Dolan D. H. , Martin M. R. , Laity G. , Lemke R. W. , Mattsson T. R.
Published: June 2018

By deploying a photon Doppler velocimetry based plasma diagnostic, we have directly observed low density plasma in the load anode/cathode gap of cylindrically converging pulsed power targets. The arrival of this plasma is temporally correlated with gross current loss and subtle power flow differences between the anode and the cathode. The density is in the range where Hall terms in the electromagnetic equations are relevant, but this physics is lacking in the magnetohydrodynamics codes commonly used to design, analyze, and optimize pulsed power experiments. The present work presents evidence of the importance of physics beyond traditional resistive magnetohydrodynamics for the design of pulsed power targets and drivers.
On pairs of interacting electrons in a quantum wire
Authors: Kerner Joachim
Published: June 2018

In this paper, we consider pairs of interacting electrons moving in a simple quantum wire, namely, the half-line R+. In particular, we extend recently obtained results by allowing for contact interactions of the Lieb-Liniger type between the two electrons constituting the pair. We construct the associated Hamiltonian rigorously and study its spectral properties. We then investigate Bose-Einstein condensation of pairs and prove, as a main result, the existence of condensation whenever the Hamiltonian has a non-trivial discrete spectrum. Most importantly, condensation is proved for very weak and very strong contact interactions.
Laser-driven shock compression of gold foam in the terapascal pressure range
Authors: Liu Wei , Duan Xiaoxi , Jiang Shaoen , Wang Zhebin , Sun Liang , Liu Hao , Yang Weiming , Zhang Huan , Ye Qing , Wang Peng , Li Yulong , Yi Lin , Dong Suo
Published: June 2018

Shock compression experiments are carried out on gold foam with an initial density of 3.2 g/cm3 through indirectly laser-driven shock waves at the SG-III prototype laser facility. The impedance-matching technique is applied to determine the equation-of-state (EOS) data of the shocked gold foam. A passive shock breakout diagnostic system is employed to obtain the shock velocities in both the standard material and gold foam. The gold foams are compressed to a maximum density of 20 g/cm3 under a shock pressure of about 2 TPa. The effects of the unsteadiness of shock waves on the EOS measurement are quantitatively analyzed and corrected. The correction of unsteady waves, as well as the good planarity of the shock waves and the low preheating of the gold foam, contributes high-confidence EOS data for the gold foam. The corrected experimental data are compared with the Hugoniot states from the SESAME library. The comparison suggests that the database is suitable for describing the states of gold foam with an initial density of 3.2 g/cm3 under a pressure of about 2 TPa.
Tunneling anisotropic magnetoresistance in fully epitaxial magnetic tunnel junctions with different barriers
Authors: Tao B. S. , Jiang L. N. , Kong W. J. , Chen W. Z. , Yang B. S. , Wang X. , Wan C. H. , Wei H. X. , Hehn M. , Lacour D. , Lu Y. , Han X. F.
Published: June 2018

We report the tunneling anisotropic magnetoresistance (TAMR) in fully epitaxial Fe/Barrier/Fe (001) magnetic tunnel junctions (MTJs) where the Barrier is annealed MgO, MgAlOx, MgO-MgAlOx, or as-grown MgO/MgAlOx. The TAMR was measured as the magnetization of Fe electrodes rotated from in-plane to out-of-plane. The angular dependence of TAMR for all samples exhibited superposed behavior of twofold and fourfold symmetries. The proportion of fourfold symmetry is larger in MTJs with MgO and MgO-MgAlOx than that in MTJs with MgAlOx and MgO/MgAlOx barriers. By characterizing inelastic electron tunneling spectroscopy in the antiparallel state and parallel conductance of the MTJs, we revealed diverse minority interfacial resonant states (IRSs) and different contributions from Δ1 and Δ5 symmetry states to the conductance in the MTJs. Our results illustrate that the minority IRS dominated by Δ5 symmetry can mix with majority Δ1 states and give rise to the enhanced fourfold symmetric angular dependence in MTJs with MgO and MgO-MgAlOx barriers.
Electrical nanopatterning of TiO2 single crystal surfaces
in situ via local resistance and potential switching
Authors: Rodenbücher C. , Wrana D. , Meuffels P. , Rogala M. , Krok F. , Szot K.
Published: June 2018

The resistive switching effect in transition metal oxides allows for a dedicated manipulation of the oxide resistance via electrical stimuli. Here, we perform local-conductivity atomic force microscopy simultaneously with the Kelvin probe force microscopy under ultra-high vacuum conditions using the very same tip investigating the very same sample area to monitor the surface conductivity and surface potential of thermally reduced TiO2 single crystals. We show that the resistance of confined surface areas can be switched by applying a voltage of several volts to the tip during scanning in the contact mode. By conducting in situ oxidation experiments, we present that this surface switching is related to a local redox reaction, which can be controlled electrically allowing for surface nanopatterning and illustrates the capability of transition metal oxides for multilevel resistive switching being a prerequisite for neuromorphic computing. We discuss that the features of the electrically engraved nanopattern can be scaled down to a lower boundary at several tens of nanometers. The observed limit around 25 nm is determined by the presence of intrinsic local variations in electrical surface properties appearing as a common phenomenon of slightly reduced metal oxide surfaces.
Gas-pressure chemical vapor transport growth of millimeter-sized c-BAs single crystals with moderate thermal conductivity
Authors: Xing Jie , Glaser Evan R. , Song Bai , Culbertson James C. , Freitas Jaime A. , Duncan Ryan A. , Nelson Keith A. , Chen Gang , Ni Ni
Published: June 2018

We have grown c-BAs single crystals up to 1000 μm size by the chemical vapor transport (CVT) technique using combined As and I2 transport agents with the As:I ratio of 1:3 under gas pressures of up to 35 atm. Raman spectroscopy revealed a very sharp (∼2.4 cm−1) P1 phonon mode and an interesting splitting behavior of P1 from detailed polarization studies. Electron paramagnetic resonance (EPR) experiments revealed no evidence for EPR active growth-related defects under the experimental resolution. Finally, a moderate thermal conductivity value of ∼132 W/m-K was obtained using a transient thermal grating technique. These results suggest that although the high As gas vapor pressure environment in CVT growth can increase the transport rate of c-BAs significantly, it may not be efficient in reducing the defects and enhancing the thermal conductivity in c-BAs significantly.
Nature conservation in a brave new (post-truth) world: arguments for and against public advocacy by conservation biologists
Authors: Boon Paul I.
Published: June 2018

Conservation biologists are obliged to function in a ‘post-truth’ environment in which ‘alternative facts’ are used by those who oppose meaningful action to conserve the natural world. Objections to public advocacy by scientists are usually based on the inter-related assumptions that (1) advocacy calls into question the objectivity of scientific advice and its special place in policy formulation; (2) conservation biologists are no better qualified to advise on conservation topics than anyone else in the community; (3) advocacy leads to conservation science being politicised; and (4) the conflation of advocacy with individual self-promotion. These objections are shown to fall short in the face of two obvious conservation failures: (1) the manifest inability of current approaches to generate globally sustainable fisheries; and (2) the lack of success in convincing the wider public about anthropogenic climate change. Instead of refraining from public advocacy, conservation biologists should acknowledge their primary responsibility in a civil society as informed citizens possessing specialised knowledge and experience that most other citizens lack. They should aim to influence conservation policy and on-ground works through a multitude of channels: (1) traditionally, through peer-reviewed articles in the scientific literature; (2) through formal input into professional advisory panels to inform government; and (3) through public advocacy. The positions adopted with regard to contentious issues by practitioners in other branches of scientific enquiry can provide useful guidance as to how conservation biologists can contribute meaningfully to discourse in the public interest without compromising their professional standing.
Caspase-1 inhibition prevents glial inflammasome activation and pyroptosis in models of multiple sclerosis
Authors: McKenzie Brienne A. , Mamik Manmeet K. , Saito Leina B. , Boghozian Roobina , Monaco Maria Chiara , Major Eugene O. , Lu Jian-Qiang , Branton William G. , Power Christopher
Published: June 2018

Significance

The pore-forming protein gasdermin D (GSDMD) was recently identified as the principal executioner of pyroptosis (“fiery death”), a type of proinflammatory programmed cell death driven by inflammasomes. Caspase-1 cleaves GSDMD, but whether this process contributes to neuroinflammation is unknown. Here, we report evidence of GSDMD-mediated pyroptosis as a primary mechanism of inflammatory demyelination in the central nervous system during multiple sclerosis (MS), a debilitating and incurable demyelinating disease that causes profound loss of myelin-forming oligodendrocytes. By identifying GSDMD induction and pyroptosis in oligodendrocytes and microglia, we discovered a previously unrecognized mechanism driving neuroinflammation and demyelination. Pharmacologically inhibiting caspase-1 prevented pyroptosis in experimental models of MS, reducing demyelination and neurodegeneration. These findings highlight therapeutic approaches for understanding and treating inflammatory demyelination.
Unique function words characterize genomic proteins
Authors: Scaiewicz Andrea , Levitt Michael
Published: June 2018

Significance

The vast, mostly unknown protein universe can be explored by analyzing protein sequences as a string of domains. A broader coverage can be achieved when these domains, the essential blocks in protein evolution, are detected using sequence profiles. Using clustering to collapse redundant profiles into unique function words (UFWs), we find that over the years 2009–2016, the number of UFWs saturates while the number of sequences matched by a combination of two or more UFWs grows exponentially.
Species coexistence through simultaneous fluctuation-dependent mechanisms
Authors: Letten Andrew D. , Dhami Manpreet K. , Ke Po-Ju , Fukami Tadashi
Published: June 2018

Significance

Fluctuating environmental conditions are thought to be important for the maintenance of species diversity, and yet our understanding of the relative contribution of different fluctuation-dependent coexistence mechanisms (the temporal storage effect and relative nonlinearity of competition) in real systems is limited. Using experiments and simulations, we show that both mechanisms consistently affect coexistence and that, contrary to long-held assumptions, the effect of relative nonlinearity can be larger in magnitude. These results may be general in that the simultaneous emergence of both mechanisms rests on two factors common to nearly all ecological systems, from the human gut to the soil microbiome: variable environmental conditions and saturating population growth rates.
Cancer-mutation network and the number and specificity of driver mutations
Authors: Iranzo Jaime , Martincorena Iñigo , Koonin Eugene V.
Published: June 2018

Significance

Cancer genomics yields a wealth of information on cancer-associated mutations in various cancer types, but current understanding of the number and tissue specificity of the driver mutations remains limited. We applied mathematical methods for network analysis to identify distinct modules linking tumors to driver mutations. About 27% of the tumors belong to such modules, whereas the rest form a diffuse component of the gene–tumor network. The cancers from the diffuse component show an onset later in life than those in the modules and have fewer associated known drivers, implying the existence of multiple unidentified and/or interchangeable drivers in the former.
Microfluidic chambers using fluid walls for cell biology
Authors: Soitu Cristian , Feuerborn Alexander , Tan Ann Na , Walker Henry , Walsh Pat A. , Castrejón-Pita Alfonso A. , Cook Peter R. , Walsh Edmond J.
Published: June 2018

Significance

Despite improvements in our ability to manipulate ever-smaller volumes, most workflows in cell biology still use volumes of many microliters. We describe a method for creating microfluidic arrangements containing submicroliter volumes. It exploits interfacial forces dominant at the microscale to confine liquids with fluid (not solid) walls. We demonstrate many basic manipulations required for cell culture and some widely used downstream workflows. The method eliminates many problems associated with the fabrication of conventional microfluidic devices, thereby providing a simple on-demand approach for fabrication of microfluidic devices using materials familiar to biologists.
Efficient encapsulation of proteins with random copolymers
Authors: Nguyen Trung Dac , Qiao Baofu , Olvera de la Cruz Monica
Published: June 2018

Significance

Inside cells of living organisms, aggregates rich in disordered proteins organize the local environment to promote cellular functions. These membraneless organelles are able to concentrate enzymes and biomolecules to regulate interactions via the multiple conformations and compositions of disordered proteins. The interior of these organelles seems to behave akin to organic solvents. This opens the possibility of assembling synthetic organelles using random copolymers that mimic disordered proteins to disperse and stabilize enzymatic proteins in different environments, including organic solvents. Here, we demonstrate that random copolymers with solvophobic and solvophilic groups can encapsulate numerous proteins, including
Candida antarctica
lipase B, subtilisin, cutinase, and pseudolysin, in basically any solvent. These aggregates are promising constituents of synthetic membraneless organelles.
Considerations to improve the quality of cochlear implant surgery using measurements on postoperatively measured changes in the vestibular system
Authors: Alzhrani Farid
Published: June 2018

Introduction:

The vestibular system is at risk of damage during cochlear implantation, especially during electrode insertion. It is important to choose the best CI electrode according to the patient´s condition considering the preoperative status of the vestibular system.

Objectives:

To monitor the quality of the cochlear implant surgeries by evaluating:

(1) possibility of vestibular damage following cochlear implantation surgery using two different types of implant electrode arrays (straight and perimodiolar) and formulate a recommendation on choosing the most appropriate type of array design;

(2) provide guidance on how experienced surgeons can assist in improving the skills of more junior surgeons to minimize loss of vestibular function.

Study design:

Retrospective study.

Method:

Review of our cochlear-implant databank yielded 997 surgeries between January 2012 and December 2013. Postoperative videonystagmography records were analysed for patients who received either a Nucleus Contour Advance or Nucleus Slim Straight with preoperative and postoperative results at 4–6 weeks. Self-report records were available where patients had postoperative symptoms of vertigo. The degree of loss of vestibular function when surgery was performed by a senior or junior surgeon evaluated.

Results:

Of the 550 patients who had received a Nucleus implant, 85 recipients fulfilled the inclusion criteria. This study showed a significant difference in the value indicating vestibular changes for the implanted ear. There was a trend for slightly poorer postoperative vestibular function in patients with contour advance electrode compared to slim straight electrode. The junior group had more cases of diminished postoperative vestibular function than the senior group.

Conclusion:

Our study indicates that the design of the cochlear implant electrodes used, may affect function of the vestibular organ. We recommend using slim and lateral wall electrode in case of only functioning vestibular organ. Senior surgeons should assist junior surgeons while performing the cochlear implant surgery.
Mixed Wooden-Concrete Piles: A Solution for Structures Located Near Saltwater Lakes
Authors: Tataru I , Corbu O , Bucur I
Published: June 2018

This paper aims to present an ecological solution for creating a long-living structure using wood and eco-friendly concrete. Nowadays, it is an imminent need to reduce the use of non-renewable natural resources and, at the same time, to minimize the negative impacts of waste production from the construction sector. As a result, the option of reusing and reintroducing materials in production cycles in order to form totally different products becomes more common day by day. Even if wood is a hugely capable civil engineering material, the area of untreated pile situated above ground water level is vulnerable. This problem can be found in salty water resorts, as in the case of Oglinzi Baths located in Neamţ County. A proper solution for solving this problem could consist of using an already patented concrete that has in composition recycled glass aggregates and, moreover, has outstanding durability properties. This mixed piles structure can be a sustainable alternative benefiting from two commonly used materials and local resources.
Long-Term Outcomes in Breast Augmentation in Trans-Women: A 20-Year Experience
Authors: Fakin Richard M , Zimmermann Simon , Kaye Kai , Lunger Lukas , Weinforth Geraldine , Giovanoli Pietro
Published: June 2018

Background

Breast augmentation in trans-women requires special consideration and thorough preoperative planning.

Objectives

This study aimed to present our long-term outcome and experience gained over the past 21 years.

Methods

Trans-women who have undergone breast augmentation since 1995 were reviewed for primary surgery, type of incision, implant site, implant size and shape, and revisions.

Results

A total of 138 patients with a follow-up of 4.6 years (range, 2.0-13.3) were included. In 112 patients (82.4%), the inframammary incision was chosen. Subpectoral implantation was performed in 70 patients (51.5%). Round breast implants (91 patients, 66.9%, P = 0.010) with low projection (103 patients, 75.7%, P < 0.001) were favored. The implant size used during 2011-2016 of 363.3 ± 97.3 cc was significantly increased as compared to the implant size reported during 1995-1999 (mean difference, +142.1 cc, P < 0.001) and 2000-2004 (mean difference, +113.5 cc, P < 0.001). Simultaneously, revision rates dropped significantly over time (52.9% during 1995-1999 as compared to 6.9% during 2011-2016, P < 0.001). Overall, request for larger implants was the most common indication for revision (13 patients, 9.4%) after 6 months (range, 4.0-18.7). At revision, implant volume was 355.4 ± 132.8 cc, showing significant increase of 107.0 ± 48.1 cc as compared to primary implants (+30.0%, P = 0.048).

Conclusions

Request for larger breast implants was the most common reason for revision. Depending on the various degrees of breast tissue growth due to hormonal therapy, whenever applicable, we recommend round, low projection implants with a mean size of 360 cc in the prepectoral pocket.

Level of Evidence: 4
dbCID: a manually curated resource for exploring the driver indels in human cancer
Authors: Yue Zhenyu , Zhao Le , Cheng Na , Yan Hua , Xia Junfeng
Published: June 2018

While recent advances in next-generation sequencing technologies have enabled the creation of a multitude of databases in cancer genomic research, there is no comprehensive database focusing on the annotation of driver indels (insertions and deletions) yet. Therefore, we have developed the database of Cancer driver InDels (dbCID), which is a collection of known coding indels that likely to be engaged in cancer development, progression or therapy. dbCID contains experimentally supported and putative driver indels derived from manual curation of literature and is freely available online at http://bioinfo.ahu.edu.cn:8080/dbCID. Using the data deposited in dbCID, we summarized features of driver indels in four levels (gene, DNA, transcript and protein) through comparing with putative neutral indels. We found that most of the genes containing driver indels in dbCID are known cancer genes playing a role in tumorigenesis. Contrary to the expectation, the sequences affected by driver frameshift indels are not larger than those by neutral ones. In addition, the frameshift and inframe driver indels prefer to disrupt high-conservative regions both in DNA sequences and protein domains. Finally, we developed a computational method for discriminating cancer driver from neutral frameshift indels based on the deposited data in dbCID. The proposed method outperformed other widely used non-cancer-specific predictors on an external test set, which demonstrated the usefulness of the data deposited in dbCID. We hope dbCID will be a benchmark for improving and evaluating prediction algorithms, and the characteristics summarized here may assist with investigating the mechanism of indel–cancer association.
Predicting clone genotypes from tumor bulk sequencing of multiple samples
Authors: Miura Sayaka , Gomez Karen , Murillo Oscar , Huuki Louise A , Vu Tracy , Buturla Tiffany , Kumar Sudhir
Published: June 2018

Motivation

Analyses of data generated from bulk sequencing of tumors have revealed extensive genomic heterogeneity within patients. Many computational methods have been developed to enable the inference of genotypes of tumor cell populations (clones) from bulk sequencing data. However, the relative and absolute accuracy of available computational methods in estimating clone counts and clone genotypes is not yet known.

Results

We have assessed the performance of nine methods, including eight previously-published and one new method (CloneFinder), by analyzing computer simulated datasets. CloneFinder, LICHeE, CITUP and cloneHD inferred clone genotypes with low error (<5% per clone) for a majority of datasets in which the tumor samples contained evolutionarily-related clones. Computational methods did not perform well for datasets in which tumor samples contained mixtures of clones from different clonal lineages. Generally, the number of clones was underestimated by cloneHD and overestimated by PhyloWGS, and BayClone2, Canopy and Clomial required prior information regarding the number of clones. AncesTree and Canopy did not produce results for a large number of datasets. Overall, the deconvolution of clone genotypes from single nucleotide variant (SNV) frequency differences among tumor samples remains challenging, so there is a need to develop more accurate computational methods and robust software for clone genotype inference.

Availability and implementation

CloneFinder is implemented in Python and is available from https://github.com/gstecher/CloneFinderAPI.

Supplementary information

Supplementary data are available at Bioinformatics online.
gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations
Authors: Irrgang M Eric , Hays Jennifer M , Kasson Peter M
Published: June 2018

Molecular dynamics simulations have found use in a wide variety of biomolecular applications, from protein folding kinetics to computational drug design to refinement of molecular structures. Two areas where users and developers frequently need to extend the built-in capabilities of most software packages are implementing custom interactions, for instance biases derived from experimental data, and running ensembles of simulations. We present a Python high-level interface for the popular simulation package GROMACS that i) allows custom potential functions without modifying the simulation package code, ii) maintains the optimized performance of GROMACS and iii) presents an abstract interface to building and executing computational graphs that allows transparent low-level optimization of data flow and task placement. Minimal dependencies make this integrated API for the GROMACS simulation engine simple, portable and maintainable. We demonstrate this API for experimentally-driven refinement of protein conformational ensembles.

Availability and implementation

LGPLv2.1 source and instructions are available at https://github.com/kassonlab/gmxapi.

Supplementary information

Supplementary data are available at Bioinformatics online.
MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data
Authors: Simon L M , Karg S , Westermann A J , Engel M , Elbehery A H A , Hense B , Heinig M , Deng L , Theis F J
Published: June 2018

Background

With the advent of the age of big data in bioinformatics, large volumes of data and high-performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts; however, its generic nature also enables the detection of microbial and viral transcripts.

Findings

We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from six independent, controlled infection experiments of cell line models and compared them with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from more than 17,000 samples from more than 400 studies relevant to human disease using state-of-the-art high-performance computing systems. The resulting data from this large-scale re-analysis are made available in the presented MetaMap resource.

Conclusions

Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation toward the role of the microbiome in human disease. Additionally, codes to process new datasets and perform statistical analyses are made available.
Kelch-like protein 14 promotes B-1a but suppresses B-1b cell development
Authors: Li Shuyin , Liu Jun , Min Qing , Ikawa Tomokatsu , Yasuda Shoya , Yang Yang , Wang Yan-Qing , Tsubata Takeshi , Zhao Yaofeng , Wang Ji-Yang
Published: June 2018

B-1 cells are innate-like B-cell population and produce natural antibodies that contribute to the first line of host defense. There are two subsets of B-1 cells: B-1a and B-1b. B-1a cells are the main producer of poly-reactive and autoreactive natural IgM antibodies, whereas B-1b cells can respond specifically to T-cell-independent antigens. Despite the functional significance of B-1a and B-1b cells, little information is available about what regulates the development of these two subsets. We found that Kelch-like protein 14 (KLHL14) was expressed at high levels in B cells but only at low levels in a few non-lymphoid tissues. Although mice lacking KLHL14 died right after birth, the heterozygotes developed normally with no gross abnormalities by appearance. B-cell development in the bone marrow and maturation and activation in the spleen were not affected in the heterozygous mice. However, the number of peritoneal B-1a cells was significantly reduced while B-1b cells were increased in Klhl14 heterozygous mice compared with wild-type (WT) mice. Consistently, Rag1−/− mice reconstituted with Klhl14−/− fetal liver cells had a more severe reduction of B-1a and an increase of B-1b cells in the peritoneal cavity. KLHL14 did not affect the turnover or apoptosis of B-1a and B-1b cells in vivo. Moreover, Klhl14−/− fetal liver contained a similar proportion and absolute numbers of the B-1 progenitor cells as did WT fetal liver. These results suggest that KLHL14 promotes B-1a development in mice.
Trial by Statistics: Is a High Probability of Guilt Enough to Convict?
Authors: Di Bello Marcello
Published: June 2018

Suppose one hundred prisoners are in a yard under the supervision of a guard, and at some point, ninety-nine of them collectively kill the guard. If, after the fact, a prisoner is picked at random and tried, the probability of his guilt is 99%. But despite the high probability, the statistical chances, by themselves, seem insufficient to justify a conviction. The question is why. Two arguments are offered. The first, decision-theoretic argument shows that a conviction solely based on the statistics in the prisoner scenario is unacceptable so long as the goal of expected utility maximization is combined with fairness constraints. The second, risk-based argument shows that a conviction solely based on the statistics in the prisoner scenario lets the risk of mistaken conviction surge potentially too high. The same, by contrast, cannot be said of convictions solely based on DNA evidence or eyewitness testimony. A noteworthy feature of the two arguments in the paper is that they are not confined to criminal trials and can in fact be extended to civil trials.
Diagnostic Approach for Classic Compared With Localized Whipple Disease
Authors: Crews Nicholas R , Cawcutt Kelly A , Pritt Bobbi S , Patel Robin , Virk Abinash
Published: June 2018

Background

Whipple disease (WD), a rare systemic infection caused by Tropheryma whipplei, can be a diagnostic challenge due to its variable presentation. The role of T. whipplei polymerase chain reaction (PCR) is unclear as small bowel biopsy with Periodic acid-Schiff (PAS) staining remains the diagnostic gold standard. Individualized diagnostic approaches based on variable clinical manifestations are underutilized. We investigated the methodologies employed at our institution to diagnose WD.

Methods

We retrospectively collected all cases of WD diagnosed from 1994 to 2016. Microbiology laboratory and anatomic pathology databases were queried. Case characteristics and disease clinical phenotypes (classical, localized WD arthritis, and localized central nervous system [CNS] disease) were described. The diagnostic approach and testing yield were analyzed and reported.

Results

Thirty-three cases of WD were diagnosed (18 classic WD [CWD], 9 localized WD arthritis [LWD], 6 CNS WD). Misdiagnosis and delay in diagnosis were frequent. Diagnostic approach and test yield differed by classical vs localized WD involvement. Small bowel tissue biopsy PAS stain/PCR was overwhelmingly positive (86%/92%) in CWD, yet seldom positive (12%/42%) in LWD (P < .001). Affected joint synovial fluid PCR was frequently positive in both CWD (100%, 3/3) and LWD (85%, 6/7).

Conclusions

These results support the role of small bowel biopsy PAS stain/PCR in the diagnosis of CW, though this approach may be of limited utility in LWD or CNS WD without gastrointestinal symptoms. Affected joint synovial fluid or cerebrospinal fluid PCR was frequently positive in both CWD and LWD, supporting its diagnostic usefulness.
Abundance of C‐terminal binding protein isoform is a prerequisite for exit from pluripotency in mouse embryonic stem cells
Authors: Suh Min Young , Kim Tae Wan , Lee Han‐Teo , Shin Jihoon , Kim Jae‐Hwan , Jang Hyonchol , Kim Hye Ji , Kim Seong‐Tae , Cho Eun‐Jung , Youn Hong‐Duk
Published: June 2018

Unlike lower organisms, mammals have 2 C‐terminal binding protein (Ctbp) isoforms, Ctbp1 and Ctbp2. Ctbp2 is revealed as a key factor involved in determining cell fate decisions by regulating the epigenetic state in active embryonic stem cell (ESC) genes. However, the molecular mechanism underlying how Ctbp1 and Ctbp2 have different roles remains elusive. Here we demonstrate that Ctbp isoform abundance is important for mouse embryonic ESCs (mESCs) to exit from pluripotency. Temporal expression patterns of Ctbp isoforms were quite different; Ctbp2 is more highly expressed in mESCs and decreases during differentiation, while Ctbp1 is constantly expressed at a lower level. Ctbp2 knockdown, but not Ctbpl knockdown, in mESCs resulted in impaired exit from pluripotency. Interestingly, Ctbp1 and Ctbp2 overexpression in Ctbp2‐knockdown mESCs leads to exiting from pluripotency in a manner similar to that of wild‐type mESCs. Quantification of Ctbp1 and Ctbp2 revealed that differentiation ability correlates with abundance of Ctbp isoform in undifferentiated mESCs, suggesting that a sufficient amount of Ctbp isoform is a prerequisite for exiting from pluripotency. The results support the contention that 2 redundant Ctbp isoforms regulate elaborate differentiation via temporally distinctive regulatory patterns in mESCs.—Suh, M. Y., Kim, T. W., Lee, H.‐T., Shin, J., Kim, J.‐H., Jang, H., Kim, H. J., Kim, S.‐T., Cho, E.‐J., Youn, H.‐D. Abundance of C‐terminal binding protein isoformis a prerequisite for exit from pluripotency in mouse embryonic stem cells. FASEB J. 32, 6423–6435 (2018). www.fasebj.org