bluuebunny/crossref_metadata_2025 huggingface dataset:
A double-stream Xe:He jet plasma emission in the vicinity of 6.7 nm
Authors: Chkhalo N. I. , Garakhin S. A. , Golubev S. V. , Lopatin A. Ya. , Nechay A. N. , Pestov A. E. , Salashchenko N. N. , Toropov M. N. , Tsybin N. N. , Vodopyanov A. V. , Yulin S.
Published: May 2018

We present the results of investigations of extreme ultraviolet (EUV) light emission in the range from 5 to 10 nm. The light source was a pulsed “double-stream” Xe:He gas jet target irradiated by a laser beam with a power density of ∼1011 W/cm2. The radiation spectra were measured with a Czerny-Turner monochromator with a plane diffraction grating. The conversion efficiency of the laser energy into EUV radiation caused by Xe+14…+16 ion emission in the range of 6–8 nm was measured using a calibrated power meter. The conversion efficiency of the laser radiation into EUV in the vicinity of 6.7 nm was (2.17 ± 0.13)% in a 1 nm spectral band. In the spectral band of the real optical system (0.7% for La/B multilayer mirrors) emitted into the half-space, it was (0.1 ± 0.006)%. The results of this study provide an impetus for further research on laser plasma sources for maskless EUV lithography at a wavelength of 6.7 nm.
Advanced readout methods for superheated emulsion detectors
Authors: d’Errico F. , Di Fulvio A.
Published: May 2018

Superheated emulsions develop visible vapor bubbles when exposed to ionizing radiation. They consist in droplets of a metastable liquid, emulsified in an inert matrix. The formation of a bubble cavity is accompanied by sound waves. Evaporated bubbles also exhibit a lower refractive index, compared to the inert gel matrix. These two physical phenomena have been exploited to count the number of evaporated bubbles and thus measure the interacting radiation flux. Systems based on piezoelectric transducers have been traditionally used to acquire the acoustic (pressure) signals generated by bubble evaporation. Such systems can operate at ambient noise levels exceeding 100 dB; however, they are affected by a significant dead time (>10 ms). An optical readout technique relying on the scattering of light by neutron-induced bubbles has been recently improved in order to minimize measurement dead time and ambient noise sensitivity. Beams of infra-red light from light-emitting diode (LED) sources cross the active area of the detector and are deflected by evaporated bubbles. The scattered light correlates with bubble density. Planar photodiodes are affixed along the detector length in optimized positions, allowing the detection of scattered light from the bubbles and minimizing the detection of direct light from the LEDs. A low-noise signal-conditioning stage has been designed and realized to amplify the current induced in the photodiodes by scattered light and to subtract the background signal due to intrinsic scattering within the detector matrix. The proposed amplification architecture maximizes the measurement signal-to-noise ratio, yielding a readout uncertainty of 6% (±1 SD), with 1000 evaporated bubbles in a detector active volume of 150 ml (6 cm detector diameter). In this work, we prove that the intensity of scattered light also relates to the bubble size, which can be controlled by applying an external pressure to the detector emulsion. This effect can be exploited during the readout procedure to minimize shadowing effects between bubbles, which become severe when the latter are several thousands. The detector we used in this work is based on superheated C-318 (octafluorocyclobutane), emulsified in 100 μm ± 10% (1 SD) diameter drops in an inert matrix of approximately 150 ml. The detector was operated at room temperature and ambient pressure.
Fractal diffusion in high temperature polymer electrolyte fuel cell membranes
Authors: Hopfenmüller Bernhard , Zorn Reiner , Holderer Olaf , Ivanova Oxana , Lehnert Werner , Lüke Wiebke , Ehlers Georg , Jalarvo Niina , Schneider Gerald J. , Monkenbusch Michael , Richter Dieter
Published: May 2018

The performance of fuel cells depends largely on the proton diffusion in the proton conducting membrane, the core of a fuel cell. High temperature polymer electrolyte fuel cells are based on a polymer membrane swollen with phosphoric acid as the electrolyte, where proton conduction takes place. We studied the proton diffusion in such membranes with neutron scattering techniques which are especially sensitive to the proton contribution. Time of flight spectroscopy and backscattering spectroscopy have been combined to cover a broad dynamic range. In order to selectively observe the diffusion of protons potentially contributing to the ion conductivity, two samples were prepared, where in one of the samples the phosphoric acid was used with hydrogen replaced by deuterium. The scattering data from the two samples were subtracted in a suitable way after measurement. Thereby subdiffusive behavior of the proton diffusion has been observed and interpreted in terms of a model of fractal diffusion. For this purpose, a scattering function for fractal diffusion has been developed. The fractal diffusion dimension dw and the Hausdorff dimension df have been determined on the length scales covered in the neutron scattering experiments.
Spontaneous motion of localized structures induced by parity symmetry breaking transition
Authors: Alvarez-Socorro A. J. , Clerc M. G. , Tlidi M.
Published: May 2018

We consider a paradigmatic nonvariational scalar Swift-Hohenberg equation that describes short wavenumber or large wavelength pattern forming systems. This work unveils evidence of the transition from stable stationary to moving localized structures in one spatial dimension as a result of a parity breaking instability. This behavior is attributed to the nonvariational character of the model. We show that the nature of this transition is supercritical. We characterize analytically and numerically this bifurcation scenario from which emerges asymmetric moving localized structures. A generalization for two-dimensional settings is discussed.
Transmission through surface-corrugated unidirectional waveguides
Authors: Méndez-Bermúdez J. A. , Alcázar-López A.
Published: May 2018

We study wave transmission G through quasi-one-dimensional waveguides with constant cross section. Constant cross section means that an infinite set of lines of the same length (that do not intersect each other) which are perpendicular to one boundary of the waveguide are also perpendicular to the other boundary. This makes the sign of the tangential velocity for all collision points of an arbitrary particle trajectory to stay constant, so that the classical or ray dynamics in the waveguide is unidirectional. In particular, we report the systematic enhancement of transmission in unidirectional corrugated waveguides when contrasting their transmission properties with those for equivalent constant-width waveguides (for which the classical dynamics is not unidirectional since particles moving in one direction along the waveguide can change its direction of motion). Also, we verify the universality of the distribution of transmissions P(G) in the diffusive (⟨G⟩>1) and localized (⟨G⟩≪1) regimes of transport. Moreover, we show that in the transition regime, ⟨G⟩∼1, P(G) is well described by the DMPK approach (the Fokker-Planck approach of Dorokhov, Mello, Pereyra, and Kumar) to bulk-disordered wires.
Critical behavior in Ni2MnGa and Ni2Mn0.85Cu0.15Ga
Authors: Us Saleheen Ahmad , Chen Jing-Han , Young David P. , Dubenko Igor , Ali Naushad , Stadler Shane
Published: May 2018

The critical behaviors of polycrystalline Ni2MnGa and Ni2Mn0.85Cu0.15Ga have been examined through high-resolution bulk magnetization measurements. The critical exponents, β and γ, were derived from modified Arrott plots using the Kouvel-Fisher method. The values of the extracted critical exponents satisfied the scaling equation of state and associated exponent relations, indicating self-consistency of the extracted values. In Ni2MnGa, the critical exponents (β = 0.401 ± 0.003, γ = 1.27 ± 0.02) indicate a deviation from the 3D-Heisenberg values toward the mean-field values, likely due to the presence of long-range Ruderman-Kittel-Kasuya-Yosida interactions. However, the critical exponents of Ni2Mn0.85Cu0.15Ga (β = 0.389 ± 0.004, γ = 1.39 ± 0.02) are closer to the 3D-Heisenberg values. This indicates a weakening of the long-range exchange interactions due to the substitution of Cu in the Mn site.
Effect of the ionization wave velocity on the current and voltage of a gas-filled diode
Authors: Belomyttsev S. Ya. , Grishkov A. A. , Shklyaev V. A. , Ryzhov V. V.
Published: May 2018

Here, continuing our research in the breakdown of a gas diode with a highly inhomogeneous electric field, we present an analytical model which relates the diode current and voltage to the ionization wave velocity from cathode to anode in an axisymmetric statement. The model shows that the voltages cross- and lengthwise the diode can differ greatly and that the difference increases as the wave moves faster. This effect should be taken into account when analyzing subnanosecond pulsed breakdowns in a highly inhomogeneous electric field, otherwise a large discrepancy is possible between measured and actual diode voltages. The analytical model is based on charge conservation laws and Lorentz transforms for electric field strengths and coordinates, and it has been verified using the KARAT particle-in-cell (PIC) and X-Object Oriented Particle-in-cell PIC/Monte Carlo codes. The simulation results agree well with the analytical model developed.
Seesaw-like polarized transmission behavior of silver nanowire arrays aligned by off-center spin-coating
Authors: Kang Lu , Chen Hui , Yang Zhong-Jian , Yuan Yongbo , Huang Han , Yang Bingchu , Gao Yongli , Zhou Conghua
Published: May 2018

Straight silver nanowires were synthesized by accelerated oxidization and then aligned into ordered arrays by off-center spin-coating. Seesaw-like behavior was observed in the polarized transmission spectra of the arrays. With the increment of polarization angle (θP, defined as the angle between axis of nanowires and direction of electric field of light), transmission changed repeatedly with a period of 180°, but it moved to opposite directions between the two regions separated by supporting points locating at 494 nm. The behavior is ascribed to the competition between the extinction behaviors of the two modes of surface plasma polaritons on silver nanowires. One is the longitudinal mode which is excited by long wavelengths and tuned by function of cos2(θp) and the other is the transverse mode that is excited by short wavelengths and tuned by function of sin2(θp). Simulation was performed based on the finite-difference time domain method. The effect of the nanowire diameter and length (aspect ratio) on the position of the supporting point was studied. As nanowire width increased from 20 nm to 350 nm, the supporting point moved from 400 to 500 nm. While it changed slightly when the nanowire length increased from 3 μm to infinitely long (width fixed at 260 nm). In current study, the position of the supporting point is mainly determined by the nanowire width.
Optical design of GaN nanowire arrays for photocatalytic applications
Authors: Winnerl Julia , Hudeczek Richard , Stutzmann Martin
Published: May 2018

GaN nanowire (NW) arrays are interesting candidates for photocatalytic applications due to their high surface-to-volume ratio and their waveguide character. The integration of GaN NW arrays on GaN-based light emitting diodes (LEDs), serving as a platform for electrically driven NW-based photocatalytic devices, enables an efficient coupling of the light from the planar LED to the GaN NWs. Here, we present a numerical study of the influence of the NW geometries, i.e., the NW diameter, length, and period, and the illumination wavelength on the transmission of GaN NW arrays on transparent substrates. A detailed numerical analysis reveals that the transmission characteristics for large periods are determined by the waveguide character of the single NW, whereas for dense GaN NW arrays inter-wire coupling and diffraction effects originating from the periodic arrangement of the GaN NWs dominate the transmission. The numerically simulated results are confirmed by experimental transmission measurements. We also investigate the influence of a dielectric NW shell and of the surrounding medium on the transmission characteristics of a GaN NW array.
Diffusion-driven fluid dynamics in ideal gases and plasmas
Authors: Vold E. L. , Yin L. , Taitano W. , Molvig K. , Albright B. J.
Published: May 2018

The classical transport theory based on Chapman-Enskog methods provides self-consistent approximations for the kinetic flux of mass, heat, and momentum in a fluid limit characterized with a small Knudsen number. The species mass fluxes relative to the center of mass, or “diffusive fluxes,” are expressed as functions of known gradient quantities with kinetic coefficients evaluated using similar analyses for mixtures of gases or plasma components. The sum over species of the diffusive mass fluxes is constrained to be zero in the Lagrange frame, and thus results in a non-zero molar flux leading to a pressure perturbation. At an interface between two species initially in pressure equilibrium, the pressure perturbation driven by the diffusive molar flux induces a center of mass velocity directed from the species of greater atomic mass towards the lighter atomic mass species. As the ratio of the species particle masses increases, this center of mass velocity carries an increasingly greater portion of the mass across the interface and for a particle mass ratio greater than about two, the center of mass velocity carries more mass than the gradient driven diffusion flux. Early time transients across an interface between two species in a 1D plasma regime and initially in equilibrium are compared using three methods; a fluid code with closure in a classical transport approximation, a particle in cell simulation, and an implicit Fokker-Planck solver for the particle distribution functions. The early time transient phenomenology is shown to be similar in each of the computational simulation methods, including a pressure perturbation associated with the stationary “induced” component of the center of mass velocity which decays to pressure equilibrium during diffusion. At early times, the diffusive process generates pressure and velocity waves which propagate outward from the interface and are required to maintain momentum conservation. The energy in the outgoing waves dissipates as heat in viscous regions, and it is hypothesized that these diffusion driven waves may sustain fluctuations in less viscid finite domains after reflections from the boundaries. These fluid dynamic phenomena are similar in gases or plasmas and occur in flow transients with a moderate Knudsen number. The analysis and simulation results show how the kinetic flux, represented in the fluid transport closure, directly modifies the mass averaged flow described with the Euler equations.
Synergistic effects on microstructural evolution and hardening of the Hastelloy N alloy under subsequent He and Xe ion irradiation
Authors: Gao Jie , Huang Hefei , Liu Jizhao , Liu Renduo , Lei Qiantao , Li Yan
Published: May 2018

Synergistic effects in the evolution of He bubbles and dislocation loops in Hastelloy N alloy were investigated using transmission electron microscopy and nanoindentation. Results show that the sizes of both He bubbles and dislocation loops induced by the He and Xe irradiation were larger than those in the individual irradiation cases. The corresponding hardening degree of irradiated sample was also measured to be higher than the combined hardening value of two individual irradiation cases. The underlying physics controlling the synergistic effects have revealed that the vacancies are preferentially captured by pre-existed He bubbles as compared to their annihilation with the interstitial atoms during the subsequent Xe irradiation.
Influence of excitation frequency on the metastable atoms and electron energy distribution function in a capacitively coupled argon discharge
Authors: Sharma S. , Sirse N. , Turner M. M. , Ellingboe A. R.
Published: May 2018

One-dimensional particle-in-cell simulation is used to simulate the capacitively coupled argon plasma for a range of excitation frequency from 13.56 MHz to 100 MHz. The argon chemistry set can, selectively, include two metastable levels enabling multi-step ionization and metastable pooling. The results show that the plasma density decreases when metastable atoms are included with higher discrepancy at a higher excitation frequency. The contribution of multistep ionization to the overall density increases with the excitation frequency. The electron temperature increases with the inclusion of metastable atoms and decreases with the excitation frequency. At a lower excitation frequency, the density of Ar** (3p5 4p, 13.1 eV) is higher than that of Ar* (3p5 4s, 11.6 eV), whereas at higher excitation frequencies, the Ar* (3p5 4s, 11.6 eV) is the dominant metastable atom. The metastable and electron temperature profile evolve from a parabolic profile at a lower excitation frequency to a saddle type profile at a higher excitation frequency. With metastable, the electron energy distribution function (EEDF) changes its shape from Druyvesteyn type, at a low excitation frequency, to bi-Maxwellian, at a high frequency plasma excitation; however, a three-temperature EEDF is observed without metastable atoms.
Ultrahigh refractive index sensitivity via lattice-induced meta-dipole modes in flat metallic nanoantenna arrays
Authors: Gutha Rithvik R. , Sadeghi Seyed M. , Hatef Ali , Sharp Christina , Lin Yongbin
Published: May 2018

We investigate control of plasmonic-photonic coupling in flat metallic nanoantenna arrays. We demonstrate that when the nanoantennas are packed together along their short axis (transverse lattice constant) and the incident light polarization is along their long axis, they can support lattice-induced plasmonic resonance coupled to a super-photonic mode that densely fills the superstrate volume. Our results show that at a certain wavelength, this resonance joins the plasmonic tip modes of the nanoantennas, forming meta-dipole modes. These modes have field profiles similar to those of the natural plasmonic dipole modes of individual nanoantennas, but they occur at much shorter wavelengths and offer a very high bulk refractive index sensitivity (925 ± 12 nm/RIU). We show that with an increase in the transverse lattice constant, such a sensitivity decreases as the meta-dipole modes disappear. Under this condition, the refractive index sensitivity supported by natural modes of the nanoantennas increases, as the plasmonic edge mode suppression caused by charge rearrangement decreases.
Rigorous close-coupling quantum dynamics calculation of thermal rate constants for the water formation reaction of H2 + OH on a high-level PES
Authors: Welsch Ralph
Published: May 2018

Thermal rate constants for the prototypical H2 + OH → H + H2O reaction are calculated using quantum dynamics simulations including all degrees of freedom and accurately accounting for overall rotation via close-coupling. Results are reported for a recent, highly accurate neural network potential [J. Chen et al., J. Chem. Phys. 138, 154301 (2013)] and compared to results obtained on a previous, semi-empirical potential. Thermal rate constants between 300 K and 1000 K are reported and very good agreement with experimental work is found. Additionally, reasonable agreement for the close-coupling simulations on both potentials is found. In contrast to previous work, we find that the J-shifting approximation works well for the title reaction given that a high-level PES is used for the dynamics calculation. Moreover, the importance of treating the spin-orbit coupling in the reactant partition function is discussed. The highly accurate results reported here will provide a benchmark for the development of approximate methods.
1 eV Ga(NAsSb) grown by MOVPE using di-tertiary-butyl-arsano-amine (DTBAA)
Authors: Sterzer E. , Maßmeyer O. , Nattermann L. , Jandieri K. , Gupta S. , Beyer A. , Ringler B. , von Hänisch C. , Stolz W. , Volz K.
Published: May 2018

N containing lattice matched 1 eV materials, such as Ga(NAsSb) and (GaIn)(NAs), are discussed as potential solar subcells in a four junction solar cell alongside Ge, GaAs, and (GaIn)P, reaching theoretically conversion efficiencies of around 50 %. The solar subcell with the highest conversion efficiency, consisting of (GaIn)(NAsSb), was grown with molecular beam epitaxy (MBE). The growth of Sb/N containing materials have always been a challenge to metalorganic vapor phase epitaxy (MOVPE), as N incorporation is hindered drastically by even small amounts of Sb if 1,1-dimethylhydrazine is used. This strong N/Sb interaction was not observed by MBE, therefore gas phase reactions in MOVPE are held responsible for the N incorporation drop. In this work we will present a systematic study of Ga(NAsSb) on GaAs grown in MOVPE with the novel N/As precursor di-tertiary-butyl-arsano-amine, as well as triethylgallium and triethylantimony. The achieved 1 eV Ga(NAsSb) material opens up new possibilities for using MOVPE to grow further solar subcells like (GaIn)(NAsSb) or Ga(NAsSb) in the band gap range of 1.0 – 1.1 eV.
On the nature of dissolved copper ligands in the early buoyant plume of hydrothermal vents
Authors: Cotte Laura , Omanović Dario , Waeles Matthieu , Laës Agathe , Cathalot Cécile , Sarradin Pierre-Marie , Riso Ricardo D.
Published: May 2018

Environmental contextCopper released by deep-sea hydrothermal vents has been recognised to be partly stabilised against precipitation by its complexation with strong Cu binding ligands. Yet, the sources and nature of these compounds in such environments are still not fully understood. This study shows that the Cu ligands detected are hydrothermally sourced and could be mainly inorganic sulfur species.
AbstractThe apparent speciation of Cu in the early buoyant plume of two black smokers (Aisics and Y3) from the hydrothermal vent field Lucky Strike (Mid-Atlantic Ridge) was investigated using competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE–AdCSV). We have assessed the apparent Cu-binding ligand concentration ([L]) and the corresponding conditional stability constant (log K′) for 24 samples. At the smoker Aisics, [L] ranged from 18.2 to 2970 nM. Log K′CuL ranged from 12.4 to 13.4. At Y3, the binding capacity of natural ligands was from 32.5 to 1020 nM, with Log K′CuL ranging from 12.5 to 13.1. Total dissolved Cu ranged from 7.0 to 770 nM and from 12.7 to 409 nM at Aisics and Y3, respectively. Our results show that the amount of ligand L increases with dissolved Mn (dMn) concentrations, suggesting a hydrothermal origin of the Cu-binding ligands detected. In addition, such high concentrations of Cu-binding ligands can only be explained by an additional abiotic source differing from organic processes. Based on the massive in situ concentrations of free sulfides (up to 300 µM) and on the striking similarities between our log K′CuL and the log K′Cu(HS) previously published, we infer that the Cu-binding ligands could be predominantly inorganic sulfur species in the early buoyant plume of the two vent sites studied.
Implications of Zika virus and congenital Zika syndrome for the number of live births in Brazil
Authors: Castro Marcia C. , Han Qiuyi C. , Carvalho Lucas R. , Victora Cesar G. , França Giovanny V. A.
Published: May 2018

Significance

Zika virus (ZIKV) was discovered 70 years ago, and since then small isolated outbreaks occurred without major complications being reported. When ZIKV hit Brazil, however, a public health emergency was declared, given its link with microcephaly. Knowledge on ZIKV has advanced, but demographic impacts remain poorly understood. This study uses data from Brazil to assess whether a decline in births occurred after the onset of ZIKV. Forecasts show significant birth declines, particularly after April 2016. No significant changes in fetal death rates and no pattern of increase in hospitalizations due to abortion complications were observed, although hospitalizations occurred later in some states. We argue that postponement of pregnancy and abortions, primarily, likely affected fertility, with implications for women’s reproductive health.
TAp73 contributes to the oxidative stress response by regulating protein synthesis
Authors: Marini Alberto , Rotblat Barak , Sbarrato Thomas , Niklison-Chirou Maria Victoria , Knight John R. P. , Dudek Kate , Jones Carolyn , Bushell Martin , Knight Richard A. , Amelio Ivano , Willis Anne E. , Melino Gerry
Published: May 2018

Significance

Oxidative stress is a critical contributor to aging-associated diseases, including neurodegeneration, cancer, and cardiovascular disease. Here, we demonstrate that the p53 family transcription factor TAp73 contributes to the oxidative stress response by participating in the control of protein synthesis. Regulation of mRNA translation ensures a prompt and efficient method to overcome stress, and TAp73 depletion results in aberrant ribosomal biogenesis and impaired protein synthesis. In particular, TAp73 is important for maintaining active translation of mitochondrial transcripts in response to oxidative stress, thus promoting mitochondrial activity that contributes to adaptation to stress conditions. Our data therefore reveal an unexpected role for TAp73 in regulating protein synthesis responsible for its homeostatic ability.
Limiting global-mean temperature increase to 1.5–2 °C could reduce the incidence and spatial spread of dengue fever in Latin America
Authors: Colón-González Felipe J. , Harris Ian , Osborn Timothy J. , Steiner São Bernardo Christine , Peres Carlos A. , Hunter Paul R. , Warren Rachel , van Vuurene Detlef , Lake Iain R.
Published: May 2018

Significance

This study is a multigeneral circulation model, multiscenario modeling exercise developed to quantify the dengue-related health benefits of limiting global warming to 1.5–2.0 °C above preindustrial levels in Latin America and the Caribbean. We estimate the impact of future climate change and population growth on the additional number of dengue cases and provide insights about the regions and periods most likely affected by changes in the length of the transmission season. Here, we show that future climate change may amplify dengue transmission and that significant impacts could be avoided by constraining global warming to 1.5 °C above preindustrial levels. Our work could be a starting point for future risk assessments incorporating other important drivers of disease such as urbanization and international traveling.
Fluctuating radiocarbon offsets observed in the southern Levant and implications for archaeological chronology debates
Authors: Manning Sturt W. , Griggs Carol , Lorentzen Brita , Bronk Ramsey Christopher , Chivall David , Jull A. J. Timothy , Lange Todd E.
Published: May 2018

Significance

We observe a substantive and fluctuating offset in measured radiocarbon ages between plant material growing in the southern Levant versus the standard Northern Hemisphere radiocarbon calibration dataset derived from trees growing in central and northern Europe and North America. This likely relates to differences in growing seasons with a climate imprint. This finding is significant for, and affects, any radiocarbon application in the southern Levant region and especially for high-resolution archaeological dating—the focus of much recent work and scholarly debate, especially surrounding the timeframe of the earlier Iron Age (earlier Biblical period). Our findings change the basis of this debate; our data point to lower (more recent) ages by variously a few years to several decades.
Potent and selective antitumor activity of a T cell-engaging bispecific antibody targeting a membrane-proximal epitope of ROR1
Authors: Qi Junpeng , Li Xiuling , Peng Haiyong , Cook Erika M. , Dadashian Eman L. , Wiestner Adrian , Park HaJeung , Rader Christoph
Published: May 2018

Significance

Harnessing and enhancing the innate and adaptive immune system to fight cancer represents one of the most promising strategies in contemporary cancer therapy. Although bispecific antibodies (biAbs) that combine a T cell-engaging arm with a tumor cell-binding arm are particularly potent cancer immunotherapeutic agents, they rely on the identification of tumor antigens with highly restricted expression. The receptor tyrosine kinase ROR1 is expressed by numerous cancers and is largely absent from postnatal healthy cells and tissues. Here we show that T cell-engaging biAbs that target ROR1 are highly potent in in vitro, in vivo, and ex vivo models of cancer, in particular when targeting a conserved site on ROR1 close to the tumor cell membrane we precisely mapped by X-ray crystallography.
Quantitative assessment of prefrontal cortex in humans relative to nonhuman primates
Authors: Donahue Chad J. , Glasser Matthew F. , Preuss Todd M. , Rilling James K. , Van Essen David C.
Published: May 2018

Significance

A longstanding controversy in neuroscience pertains to differences in human prefrontal cortex (PFC) compared with other primate species; specifically, is human PFC disproportionately large? Distinctively human behavioral capacities related to higher cognition and affect presumably arose from evolutionary modifications since humans and great apes diverged from a common ancestor about 6–8 Mya. Accurate determination of regional differences in the amount of cortical gray and subcortical white matter content in humans, great apes, and Old World monkeys can further our understanding of the link between structure and function of the human brain. Using tissue volume analyses, we show a disproportionately large amount of gray and white matter corresponding to PFC in humans compared with nonhuman primates.
Doc2-mediated superpriming supports synaptic augmentation
Authors: Xue Renhao , Ruhl David A. , Briguglio Joseph S. , Figueroa Alexander G. , Pearce Robert A. , Chapman Edwin R.
Published: May 2018

Significance

Plastic changes in synaptic connections constitute the basis of learning and memory. Different forms of synaptic plasticity are generally distinguished experimentally by their timescales, but it is unclear whether each form of plasticity corresponds to a distinct biological process with a dedicated molecular mechanism. In the present study, we show that the Ca
2+
-binding protein, Doc2, “superprimes” a subset of already primed synaptic vesicles to make them more likely to release, and this process selectively contributes to augmentation (on the scale of seconds). The underlying molecular mechanism does not mediate other forms of short-term enhancement (that occur on the timescale of milliseconds or minutes). This work establishes a function of Doc2 in maintaining synaptic plasticity within a narrow time window.
CFH
and
VIPR2
as susceptibility loci in choroidal thickness and pachychoroid disease central serous chorioretinopathy
Authors: Hosoda Yoshikatsu , Yoshikawa Munemitsu , Miyake Masahiro , Tabara Yasuharu , Ahn Jeeyun , Woo Se Joon , Honda Shigeru , Sakurada Yoichi , Shiragami Chieko , Nakanishi Hideo , Oishi Akio , Ooto Sotaro , Miki Akiko ,   Nagahama Study Group, Iida Tomohiro , Iijima Hiroyuki , Nakamura Makoto , Khor Chiea Chuen , Wong Tien Yin , Song Kyuyoung , Park Kyu Hyung , Yamada Ryo , Matsuda Fumihiko , Tsujikawa Akitaka , Yamashiro Kenji , Yasuharu Tabara , Takahisa Kawaguchi , Kazuya Setoh , Yoshimitsu Takahashi , Shinji Kosugi , Takeo Nakayama , Fumihiko Matsuda
Published: May 2018

Significance

Although central serous chorioretinopathy (CSC) presumptively shares pathophysiological basis with age-related macular degeneration (AMD), the
CFH
risk alleles for AMD are reportedly protective against CSC development. Our finding, that the
CFH
risk allele for AMD is protective against choroidal thickening in a Japanese cohort, indicates that
CFH
affects CSC development through its choroid-thickening effects rather than its association with AMD, highlighting the need for a new AMD classification, with CSC/pachychoroid-associated choroidal neovascularization as a distinct disease. Furthermore, our genome-wide association study (GWAS) addressing choroidal thickness successfully discovered a susceptibility gene for CSC:
VIPR2
. Future GWASs on choroidal thickness will likely discover additional CSC susceptibility genes and provide key molecules to elucidate the pathophysiological difference between CSC and AMD.
Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors
Authors: Shi Hui , Lyu Mohan , Luo Yiwen , Liu Shoucheng , Li Yue , He Hang , Wei Ning , Deng Xing Wang , Zhong Shangwei
Published: May 2018

Significance

Seedlings of terrestrial flowering plants such as
Arabidopsis
display dramatically different morphologies depending on growing in the dark or light. Dark-grown seedlings exhibit long hypocotyls, apical hook formation, and closed small cotyledons with etioplast. In contrast, light represses hypocotyl elongation, unfolds apical hook, and promotes cotyledon development. How light-controlled seedling morphogenesis is regulated at the transcriptional level remains elusive. To date, three families of transcription factors—PIFs, EIN3/EIL1, and HY5/HYH—have been shown to mediate light responses in seedlings. This study systemically investigates their roles in regulating specific morphological aspects and provides both transcriptomic and genetic evidence that PIFs, EIN3/EIL1, and HY5 are master transcription factors for the proper establishment of seedling skotomorphogenesis and photomorphogenesis.
Selection of
Plasmodium falciparum
cytochrome B mutants by putative PfNDH2 inhibitors
Authors: Lane Kristin D. , Mu Jianbing , Lu Jinghua , Windle Sean T. , Liu Anna , Sun Peter D. , Wellems Thomas E.
Published: May 2018

Significance

The mitochondrial electron transport chain (ETC) of
Plasmodium falciparum
malaria parasites contains targets for antimalarial drug development including cytochrome B (PfCytB) and NADH dehydrogenase 2 (PfNDH2). Atovaquone (ATQ), a widely used antimalarial drug, is a hydroxynaphthoquinone inhibitor of PfCytB; substituted quinolone compounds (CK-2-68 and RYL-552) have also been developed as putative inhibitors of PfNDH2. Unexpectedly, our experiments yielded mutations of PfCytB, not PfNDH2, in parasites selected with these quinolones. ATQ selections yielded different PfCytB mutants that showed little change or slightly increased sensitivity to CK-2-68 or RYL-552. Differential patterns of drug response in various PfCytB mutants suggest that combinations of ETC inhibitors may help counter drug-resistant malaria.
NT3-chitosan enables de novo regeneration and functional recovery in monkeys after spinal cord injury
Authors: Rao Jia-Sheng , Zhao Can , Zhang Aifeng , Duan Hongmei , Hao Peng , Wei Rui-Han , Shang Junkui , Zhao Wen , Liu Zuxiang , Yu Juehua , Fan Kevin S. , Tian Zhaolong , He Qihua , Song Wei , Yang Zhaoyang , Sun Yi Eve , Li Xiaoguang
Published: May 2018

Significance

Spinal cord injury (SCI) is a severe medical condition often leading to permanent loss of sensory, motor, and autonomic functions, currently with no cure. This study provides evidence that in monkeys with severe SCI, a bioactive and biodegradable material, NT3-chitosan, elicited robust de novo neural regeneration including, for example, long-distance axonal growth of cortical motor neurons in the cortical spinal tract, as well as sensory and motor functional recovery. In this study, we utilized a battery of minimally invasive outcome measures including fMRI, magnetic resonance diffusion tensor imaging, and kinematics walking analyses, which are all clinical trial-compatible. Essentially, success in this approach in nonhuman primate SCI models provides a solid foundation for its potential therapeutic application.
Amelioration of surface cracking during hot rolling of AISI D2 tool steel
Authors: Bombač David , Terčelj Milan , Kugler Goran , Peruš Iztok
Published: May 2018

Reported is a relationship between a profile edge cracking during hot rolling of AISI D2 tool steel and material and processing parameters. Several months of observation of industrial hot rolling was done for neural network analysis and complemented with equilibrium thermodynamics calculations and laboratory hot deformation tests. Industrial results, in general, show that for the same chemical composition, hot rolling yield decreases with an increased profile aspect ratio. Cr content is significant for the soaking and strongly correlated with a hot workability at upper and lower limits of the hot working temperature range. Laboratory hot compression tests were employed to determine the optimal soaking temperature and to study hot workability to expand safe hot working temperature window.
Clear in its core, blurred in the outer contours: culturally normative conceptions of the family in Germany
Authors: Lück Detlev , Ruckdeschel Kerstin
Published: May 2018

This paper investigates which conceptions of the family exist in Germany and how widespread they are. It uses a multi-method design. The ‘Family Leitbild’ survey, conducted in Germany in 2012 with 5000 participants, provides quantitative data. Qualitative data are taken from the study ‘Family in Pictures’, in which 101 participants each drew a picture of what constitutes a ‘proper’ family in their subjective view, and thereafter were interviewed about the conception underlying their drawing. Findings suggest that conceptions of the family are diverse. They share a common well-established core that family in its prototypical form consists of a heterosexual couple with their own children, in conjunction with certain functions, relationship qualities and settings. Conceptions mostly are very generous extensions of this core understanding that also include a large number of other living arrangements, and forgo some of the family’s ‘traditional’ functions. However, which living arrangements are included varies. The contemporary cultural conception of the family is very clear in its core and blurred in its outer contours. For young people drafting their life plans, it leaves a lot of freedom. However, for those without firm personal preferences, it still proposes the nuclear family as a safe beaten track.
Modern dietary guidelines for healthy pregnancy; maximising maternal and foetal outcomes and limiting excessive gestational weight gain
Authors: Elliott‐Sale Kirsty Jayne , Graham Ashley , Hanley Stephanie Jane , Blumenthal Sherry , Sale Craig
Published: May 2018

Maternal dietary habits influence maternal and foetal health, representing a pathway for intervention to maximise pregnancy outcomes. Advice on energy intake is provided on a trimester basis, with no additional calories required in the first trimester and an additional 340 kcal d−1 and 452 kcal d−1 needed for the second and third trimesters. Energy intake depends on pre‐gravid body mass index (BMI); underweight women are recommended an increase of 150, 200 and 300 kcal d−1 during the first, second and third trimester, normal weight women an increase of 0, 350 and 500 kcal d−1 and obese women an increase of 0, 450 and 350 kcal day−1. The recommendations for carbohydrate and protein intake are 175 g d−1 and 0.88–1.1 g kgBM d−1, with no change to fat intake. The number of pre‐gravid obese women is rising; therefore, we need to regulate weight in women of childbearing age and limit gestational weight gain to within the recommended ranges [overweight women 6.8–11.3 kg and obese women 5.0–9.1 kg]. This can be achieved using nutritional interventions, as dietary changes have been shown to help with gestational weight management. As pregnancy has been identified as a risk factor for the development of obesity, normal weight women should gain 11.5–16.0 kg during pregnancy. While some research has shown that dietary interventions help to regulate gestational weight gain and promote postpartum weight loss to some extent, future research is needed to provide safe and effective guidelines to maximise these effects, while benefitting maternal and foetal health.
Accuracy and precision of loadsol® insole force‐sensors for the quantification of ground reaction force‐based biomechanical running parameters
Authors: Seiberl Wolfgang , Jensen Elisabeth , Merker Josephine , Leitel Marco , Schwirtz Ansgar
Published: May 2018

Force plates represent the “gold standard” in measuring running kinetics to predict performance or to identify the sources of running‐related injuries. As these measurements are generally limited to laboratory analyses, wireless high‐quality sensors for measuring in the field are needed. This work analysed the accuracy and precision of a new wireless insole forcesensor for quantifying running‐related kinetic parameters. Vertical ground reaction force (GRF) was simultaneously measured with pit‐mounted force plates (1 kHz) and loadsol® sensors (100 Hz) under unshod forefoot and rearfoot running‐step conditions. GRF data collections were repeated four times, each separated by 30 min treadmill running, to test influence of extended use. A repeated‐measures ANOVA was used to identify differences between measurement devices. Additionally, mean bias and Bland–Altman limits of agreement (LoA) were calculated. We found a significant difference (p < .05) in ground contact time, peak force, and force rate, while there was no difference in parameters impulse, time to peak, and negative force rate. There was no influence of time point of measurement. The mean bias of ground contact time, impulse, peak force, and time to peak ranged between 0.6% and 3.4%, demonstrating high accuracy of loadsol® devices for these parameters. For these same parameters, the LoA analysis showed that 95% of all measurement differences between insole and force plate measurements were less than 12%, demonstrating high precision of the sensors. However, highly dynamic behaviour of GRF, such as force rate, is not yet sufficiently resolved by the insole devices, which is likely explained by the low sampling rate.
An automated method for detecting alternatively spliced protein domains
Authors: Coelho Vitor , Sammeth Michael
Published: May 2018

Motivation

Alternative splicing (AS) has been demonstrated to play a role in shaping eukaryotic gene diversity at the transcriptional level. However, the impact of AS on the proteome is still controversial. Studies that seek to explore the effect of AS at the proteomic level are hampered by technical difficulties in the cumbersome process of casting forth and back between genome, transcriptome and proteome space coordinates, and the naïve prediction of protein domains in the presence of AS suffers many redundant sequence scans that emerge from constitutively spliced regions that are shared between alternative products of a gene.

Results

We developed the AstaFunk pipeline that computes for every generic transcriptome all domains that are altered by AS events in a systematic and efficient manner. In a nutshell, our method employs Viterbi dynamic programming, which guarantees to find all score-optimal hits of the domains under consideration, while complementary optimizations at different levels avoid redundant and other irrelevant computations. We evaluate AstaFunk qualitatively and quantitatively using RNAseq in well-studied genes with AS, and on large-scale employing entire transcriptomes. Our study confirms complementary reports that the effect of most AS events on the proteome seems to be rather limited, but our results also pinpoint several cases where AS could have a major impact on the function of a protein domain.

Availability and implementation

The JAVA implementation of AstaFunk is available as an open source project on http://astafunk.sammeth.net.

Supplementary information

Supplementary data are available at Bioinformatics online.
Comparing complex variants in family trios
Authors: Toptaş Berke Ç , Rakocevic Goran , Kómár Péter , Kural Deniz
Published: May 2018

Motivation

Several tools exist to count Mendelian violations in family trios by comparing variants at the same genomic positions. This naive variant comparison, however, fails to assess regions where multiple variants need to be examined together, resulting in reduced accuracy of existing Mendelian violation checking tools.

Results

We introduce VBT, a trio concordance analysis tool, which identifies Mendelian violations by approximately solving the 3-way variant matching problem to resolve variant representation differences in family trios. We show that VBT outperforms previous trio comparison methods by accuracy.

Availability and implementation

VBT is implemented in C++ and source code is available under GNU GPLv3 license at the following URL: https://github.com/sbg/VBT-TrioAnalysis.git.

Supplementary information

Supplementary data are available at Bioinformatics online.
Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints
Authors: Chan Siu H J , Wang Lin , Dash Satyakam , Maranas Costas D
Published: May 2018

Background

Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and directionality constraints but violate the second law of thermodynamics. Current practices involve implementing additional constraints to ensure not only optimal but also loopless flux distributions. However, the mixed integer linear programming problems required to solve become computationally intractable for genome-scale metabolic models.

Results

We aimed to identify the fewest needed constraints sufficient for optimality under the loopless requirement. We found that loopless constraints are required only for the reactions that share elementary flux modes representing TICs with reactions that are part of the objective function. We put forth the concept of localized loopless constraints (LLCs) to enforce this minimal required set of loopless constraints. By combining with a novel procedure for minimal null-space calculation, the computational time for loopless flux variability analysis (ll-FVA) is reduced by a factor of 10–150 compared to the original loopless constraints and by 4–20 times compared to the current fastest method Fast-SNP with the percent improvement increasing with model size. Importantly, LLCs offer a scalable strategy for loopless flux calculations for multi-compartment/multi-organism models of large sizes, for example, shortening the CPU time for ll-FVA from 35 h to less than 2 h for a model with more than104 reactions.

Availability and implementation

Matlab functions are available in the Supplementary Material or at https://github.com/maranasgroup/lll-FVA

Supplementary information

Supplementary data are available at Bioinformatics online.
Misdiagnosis of Bordetella bronchiseptica Respiratory Infection as Bordetella pertussis by Multiplex Molecular Assay
Authors: McNulty Moira C , Shibib Dena R , Steinbeck Jennifer L , Mullane Kathleen , Pisano Jennifer , Matushek Scott , Beavis Kathleen G , Tesic Vera , Pitrak David
Published: May 2018

Multiplex polymerase chain reaction (PCR) tests are useful for the rapid detection of pathogens, though diagnostic challenges may arise. We report 2 immunocompromised patients with Bordetella bronchiseptica respiratory infection misdiagnosed as Bordetella pertussis using PCR, including discussion of transmission, diagnostic testing, clinical implications, and infection control considerations.