bluuebunny/crossref_metadata_2025 huggingface dataset:
Controlled synthesis of germanium nanoparticles by nonthermal plasmas
Authors: Ahadi Amir Mohammad , Hunter Katharine I. , Kramer Nicolaas J. , Strunskus Thomas , Kersten Holger , Faupel Franz , Kortshagen Uwe R.
Published: March 2016

The size, composition, and crystallinity of plasma produced nanoparticles are crucial factors for their physical and chemical properties. Here, we investigate the role of the process gas composition, particularly the hydrogen (H2) flow rate, on germanium (Ge) nanoparticles synthesized from a chlorinated precursor by nonthermal plasma. We demonstrate that the gas composition can significantly change the nanoparticle size and also adjust the surface chemistry by altering the dominant reaction mechanisms. A red shift of the Ge-Clx infrared absorptions with increasing H2 flow indicates a weakening of the Ge-Clx bonds at high H2 content. Furthermore, by changing the gas composition, the nanoparticles microstructure can be controlled from mostly amorphous at high hydrogen flow to diamond cubic crystalline at low hydrogen flow.
Communication: Enhanced dissociative chemisorption of CO2 via vibrational excitation
Authors: Jiang Bin , Guo Hua
Published: March 2016

A fully coupled global nine-dimensional potential energy surface for the dissociative chemisorption of CO2 on Ni(100) is constructed from ∼18 000 density functional points. It reveals a complex reaction pathway dominated by two near iso-energetic transition states. The dissociation probabilities obtained by quasi-classical trajectories on the potential energy surface reproduced experimental trends, and indicate that vibrational excitations of CO2 significantly promote the dissociation. Using the sudden vector projection model, the behavior of the reactivity is rationalized by couplings with the reaction coordinate at each transition state. These results offer plausible rationalization for the observed enhancement of CO2 dissociation in non-thermal plasmas by metal surfaces.
Locally enhanced surface plasmons and modulated “hot-spots” in nanoporous gold patterns on atomically thin MoS2 with a comparison to SiO2 substrate
Authors: Yan Aiming , Hua Yi , Dravid Vinayak P.
Published: March 2016

Plasmonic phenomena in metals have garnered significant scientific and technological interest in the past decade. Despite many promising applications based on plasmonics, one remaining challenge is to control the surface geometry or morphology of the metallic structures, which can significantly affect the plasmonic properties of nanostructures. Here, we report the morphological modulation of gold (Au) nanopatterns on atomically thin layered molybdenum disulfide (MoS2), compared to Au nanopatterns grown on SiO2/Si substrate. We have used electron energy loss spectroscopy in a scanning transmission electron microscope to probe the locally enhanced surface plasmons in nanoporous Au patterns grown on SiO2/Si substrate as well as on single- and few-layer MoS2 flakes. Thin flakes of MoS2 as substrates significantly influence the morphology of Au patterns, which locally alters the plasmonic behavior. Features such as nanoscale pores exhibit plasmon localization with strong near fields, akin to “hot spots.” Boundary element method simulations demonstrate that the dipolar and breathing modes can be excited at different positions of the nanopatterns.
Charge dynamics at heterojunctions for PbS/ZnO colloidal quantum dot solar cells probed with time-resolved surface photovoltage spectroscopy
Authors: Spencer B. F. , Leontiadou M. A. , Clark P. C. J. , Williamson A. I. , Silly M. G. , Sirotti F. , Fairclough S. M. , Tsang S. C. E. , Neo D. C. J. , Assender H. E. , Watt A. A. R. , Flavell W. R.
Published: March 2016

Time-resolved laser-pump X-ray-photoemission-probe spectroscopy of a ZnO (101¯0) substrate with and without PbS quantum dots (QDs) chemically linked to the surface is performed, using laser photon energies resonant with and below the band gap energy of the substrate (λ = 372 and 640 nm, hν = 3.33 and 1.94 eV). Charge injection from the photoexcited QDs to ZnO is demonstrated through the change in the surface photovoltage of the ZnO substrate observed when the heterojunction is illuminated with 1.94 eV radiation. The measured carrier dynamics are limited by the persistent photoconductivity of ZnO, giving dark carrier lifetimes of the order of 200 μs in a depletion layer at the interface. The chemical specificity of soft X-rays is used to separately measure the charge dynamics in the quantum dots and the substrate, yielding evidence that the depletion region at the interface extends into the PbS QD layer.
Direct measurement of kilo-tesla level magnetic field generated with laser-driven capacitor-coil target by proton deflectometry
Authors: Law K. F. F. , Bailly-Grandvaux M. , Morace A. , Sakata S. , Matsuo K. , Kojima S. , Lee S. , Vaisseau X. , Arikawa Y. , Yogo A. , Kondo K. , Zhang Z. , Bellei C. , Santos J. J. , Fujioka S. , Azechi H.
Published: March 2016

A kilo-tesla level, quasi-static magnetic field (B-field), which is generated with an intense laser-driven capacitor-coil target, was measured by proton deflectometry with a proper plasma shielding. Proton deflectometry is a direct and reliable method to diagnose strong, mm3-scale laser-produced B-field; however, this was not successful in the previous experiment. A target-normal-sheath-accelerated proton beam is deflected by Lorentz force in the laser-produced magnetic field with the resulting deflection pattern recorded on a radiochromic film stack. A 610 ± 30 T of B-field amplitude was inferred by comparing the experimental proton pattern with Monte-Carlo calculations. The amplitude and temporal evolutions of the laser-generated B-field were also measured by a differential magnetic probe, independently confirming the proton deflectometry measurement results.
Large anisotropic thermal transport properties observed in bulk single crystal black phosphorus
Authors: Wang Yue , Xu Guizhou , Hou Zhipeng , Yang Bingchao , Zhang Xiaoming , Liu Enke , Xi Xuekui , Liu Zhongyuan , Zeng Zhongming , Wang Wenhong , Wu Guangheng
Published: March 2016

The anisotropy of thermal transport properties for bulk black phosphorus (BP) single crystal, which might be of particular interest in the fabrication of thermoelectric/optoelectronic devices, was investigated by using angular dependent thermal conductivity and Seebeck coefficient measurements at various temperatures. We found that the maximum thermal conductivities in x (zigzag), y (armchair), and z (perpendicular to the puckered layers) directions are 34, 17, and 5 W m−1 K−1, respectively, exhibiting large anisotropy. At temperature around 200 K, a large Seebeck coefficient up to +487 ± 10 μV/K has been obtained in x direction, which is 1.5 times higher than that in z direction. The large anisotropy of thermal transport properties can be understood from the crystal structure and bonding characters of BP. In addition, the energy gap has been obtained from nuclear spin lattice relaxation measurements, which is consistent with the value derived from temperature-dependent Seebeck coefficient measurements.
Development of a fast electromagnetic beam blanker for compressed sensing in scanning transmission electron microscopy
Authors: Béché A. , Goris B. , Freitag B. , Verbeeck J.
Published: March 2016

The concept of compressed sensing was recently proposed to significantly reduce the electron dose in scanning transmission electron microscopy (STEM) while still maintaining the main features in the image. Here, an experimental setup based on an electromagnetic beam blanker placed in the condenser plane of a STEM is proposed. The beam blanker deflects the beam with a random pattern, while the scanning coils are moving the beam in the usual scan pattern. Experimental images at both the medium scale and high resolution are acquired and reconstructed based on a discrete cosine algorithm. The obtained results confirm that compressed sensing is highly attractive to limit beam damage in experimental STEM even though some remaining artifacts need to be resolved.
Adjoining of negative stiffness and negative density bands in an elastic metamaterial
Authors: Oh Joo Hwan , Seung Hong Min , Kim Yoon Young
Published: March 2016

In this paper, we explore an elastic metamaterial adjoining the frequency band of negative density and that of negative stiffness. If the band-adjoining occurs, a fully continuous widened stop band covering the entire ranges of the negative density and stiffness can form. The resulting stop band can be useful for various vibration applications such as vibration shielding. We show that the band-adjoining frequency is characterized by a standing wave with peculiar “unbalanced” motions. Experiments with the symmetric Lamb waves were conducted to validate the theoretical prediction and the effects of perturbed adjoining band on wave physics are also investigated.
Comparing superconducting and permanent magnets for magnetic refrigeration
Authors: Bjørk R. , Nielsen K. K. , Bahl C. R. H. , Smith A. , Wulff A. C.
Published: March 2016

We compare the cost of a high temperature superconducting (SC) tape-based solenoid with a permanent magnet (PM) Halbach cylinder for magnetic refrigeration. Assuming a five liter active magnetic regenerator volume, the price of each type of magnet is determined as a function of aspect ratio of the regenerator and desired internal magnetic field. It is shown that to produce a 1 T internal field in the regenerator a permanent magnet of hundreds of kilograms is needed or an area of superconducting tape of tens of square meters. The cost of cooling the SC solenoid is shown to be a small fraction of the cost of the SC tape. Assuming a cost of the SC tape of 6000 $/m2 and a price of the permanent magnet of 100 $/kg, the superconducting solenoid is shown to be a factor of 0.3-3 times more expensive than the permanent magnet, for a desired field from 0.5-1.75 T and the geometrical aspect ratio of the regenerator. This factor decreases for increasing field strength, indicating that the superconducting solenoid could be suitable for high field, large cooling power applications.
Magnetic properties and high frequency characteristics of FeCoN thin films
Authors: Hwang Tae-Jong , Lee Joonsik , Kim Ki Hyeon , Kim Dong Ho
Published: March 2016

(Fe65Co35)N soft magnetic thin films were prepared by reactive RF magnetron sputtering with the sputtering power of 100 W on thermally oxidized Si substrate in various nitrogen partial pressures (PN2). A strong uniaxial in-plane magnetic anisotropy with the easy-axis coercive field as low as 1∼2 Oe was observed in films grown at PN2 in the range from 3.3% to 5.5%. The saturation magnetizations for those films were about 20 KG. Outside this range, almost isotropic magnetization curves were observed. Vector network analyzer and grounded coplanar waveguide were used to measure the ferromagnetic resonance (FMR) signals up to 25 GHz. The FMR signals were detected only in anisotropic films and their FMR frequencies were well fit to the Kittel formula. The obtained g-values and damping parameters at magnetic fields >20 kOe for films grown at PN2 of 3.3%, 4.8% and 5.5% were 1.96, 1.86, 1.92 and 0.0055, 0.0047, 0.0046, respectively. This low damping factor qualifies FeCoN thin films for high-frequency applications.
Core losses of an inverter-fed permanent magnet synchronous motor with an amorphous stator core under no-load
Authors: Denis Nicolas , Kato Yoshiyuki , Ieki Masaharu , Fujisaki Keisuke
Published: March 2016

In this paper, an interior permanent magnet synchronous motor (IPMSM) with a stator core made of amorphous magnetic material (AMM) is presented. The IPMSM is driven by a voltage source three-phase inverter with classical pulse width modulation (PWM) control. The core losses under no-load condition are measured by experiment and compared to an equivalent IPMSM with a stator core made of NO steel. Under these conditions, the core losses are influenced by the stator, rotor and magnet shapes but also by the PWM carrier signal that implies a high frequency harmonic in the magnetic flux density. It is demonstrated that the AMM can reduce the core losses by about 56 %.
The most energetic supernova conceivable?
Authors: Blau Steven K.
Published: March 2016

Astrophysical theories strain to accommodate a cosmic explosion observed months ago.
A resonant circuit accelerates spontaneous spin-flip transitions
Authors: Miller Johanna L.
Published: March 2016

Reducing the radiative transition’s time constant from thousands of years to a fraction of a second could benefit quantum information schemes.
Economic value of pregnancy scanning and optimum nutritional management of dry, single- and twin-bearing Merino ewes
Authors: Young J. M. , Behrendt R. , Curnow M. , Oldham C. M. , Thompson A. N.
Published: March 2016

The nutritional requirements of twin-bearing ewes are ~25% greater than those of ewes with single fetuses during late pregnancy and nearly twice those of non-pregnant ewes. Underfeeding ewes, resulting in liveweight loss during late pregnancy, can have adverse effects on the production and survival of both the lamb and the ewe, and improving twin-lamb survival is critical to improving the overall reproductive performance of the National Merino flock. Scanning for pregnancy status and litter size allows for more precise management of the nutrition of the ewe flock according to the different nutritional needs of dry, single- and twin-bearing ewes. In the present paper, we tested the hypothesis that it is profitable to identify pregnancy status and litter size, and the optimum nutrition profiles are different for dry, single- and twin-bearing ewes. We tested this by examining a range of nutrition strategies for flocks where only the dry ewes were identified, or for flocks where the single- and twin-bearing ewes were identified. A MIDAS model set up for the Hamilton region in south-western Victoria was used for this analysis as it represents the whole flock and it includes a powerful feed-budgeting module that optimises animal and pasture management across the whole farm. The survival and production of the single- and twin-born progeny was adjusted on the basis of the liveweight profile of the single- and twin-bearing ewes. Our hypothesis was supported and profitability was increased by approximately AU$4630/farm or AU$0.80/ewe, by scanning ewes for pregnancy status and litter size, and the optimum liveweight profiles were different for dry, single- and twin-bearing ewes. The majority of the increase in profit was due to identifying litter size and being able to differentially manage the single- and twin-bearing ewes. When ewes are scanned for pregnancy status and litter size, the most profitable combination of profiles involves all ewes losing 4 kg in early pregnancy and single-bearing ewes regaining the 4 kg to lamb at their standard reference weight, twin-bearing ewes gaining 8 kg to lamb above their standard reference weight and dry ewes losing a further 4 kg to be 8 kg lighter than their standard reference weight at lambing time.
Roles of intracellular ice formation, vitrification of cell water, and recrystallisation of intracellular ice on the survival of mouse embryos and oocytes
Authors: Mazur Peter , Paredes Estefania
Published: March 2016

Mazur and collaborators began examining the validity of initial views regarding mouse oocyte and embryo vitrification and found that most are partially or fully wrong. First, the relative effects of warming and cooling rates on the survival of mouse oocytes subjected to a vitrification procedure were determined. The high sensitivity to warming rate strongly suggests that the lethality of slow warming is a consequence of either the crystallisation of intracellular glassy water during warming or the recrystallisation during slow warming of small intracellular crystals that had formed during cooling. Warming rates of 107°C min–1 were achieved in 0.1-µL drops of ethylene glycol–acetamide–Ficoll–sucrose (EAFS) solution plus a small amount of India ink on Cryotops warmed using an infrared laser pulse. Under these conditions, survival rates of 90% were obtained even when mouse oocytes were suspended in 0.3× EAFS, a concentration that falls in the range that many cells can tolerate. A second important finding was that the survival of oocytes is more dependent on the osmotic withdrawal of much of the intracellular water before vitrification than it is on the penetration of cryoprotective solutes into the cells. Herein we review the roles of internal ice formation, vitrification and recrystallisation. It remains to be seen how widely these findings will be applicable to other types of cells and tissues from other species.
Insights into global diatom distribution and diversity in the world’s ocean
Authors: Malviya Shruti , Scalco Eleonora , Audic Stéphane , Vincent Flora , Veluchamy Alaguraj , Poulain Julie , Wincker Patrick , Iudicone Daniele , de Vargas Colomban , Bittner Lucie , Zingone Adriana , Bowler Chris
Published: March 2016

Significance

Diatoms, considered one of the most diverse and ecologically important phytoplanktonic groups, contribute around 20% of global primary productivity. They are particularly abundant in nutrient-rich coastal ecosystems and at high latitudes. Here, we have explored the dataset generated by
Tara
Oceans from a wide range of oceanic regions to characterize diatom diversity patterns on a global scale. We confirm the dominance of diatoms as a major photosynthetic group and identify the most widespread and diverse genera. We also provide a new estimate of marine planktonic diatom diversity and a global view of their distribution in the world’s ocean.
Mushrooms use convectively created airflows to disperse their spores
Authors: Dressaire Emilie , Yamada Lisa , Song Boya , Roper Marcus
Published: March 2016

Significance

Mushroom spore dispersal is usually described as a two-phase process: active ejection of spores clear of the gill surface by surface tension catapults, followed by a passive phase in which the spores are carried by whatever winds are present beneath the mushroom cap. Here, we show that control extends into the second phase of dispersal: water vapor loss creates slow airflows that carry spores out from under the mushroom cap and potentially tens of centimeters into the air. In addition to clarifying why mushrooms have such high water needs, and providing a mechanism by which spore dispersal can occur even in a low-wind environment, our work shows that the physics of apparently passive dispersal may be under organismal control.
Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography
Authors: Fukuda Yohta , Tse Ka Man , Nakane Takanori , Nakatsu Toru , Suzuki Mamoru , Sugahara Michihiro , Inoue Shigeyuki , Masuda Tetsuya , Yumoto Fumiaki , Matsugaki Naohiro , Nango Eriko , Tono Kensuke , Joti Yasumasa , Kameshima Takashi , Song Changyong , Hatsui Takaki , Yabashi Makina , Nureki Osamu , Murphy Michael E. P. , Inoue Tsuyoshi , Iwata So , Mizohata Eiichi
Published: March 2016

Significance

Copper nitrite reductase (CuNiR) is involved in denitrification of the nitrogen cycle. Synchrotron X-rays rapidly reduce copper sites and decompose the substrate complex structure, which has made crystallographic studies of CuNiR difficult. Using femtosecond X-ray free electron lasers, we determined intact structures of CuNiR with and without nitrite. Based on the obtained structures, we proposed a redox-coupled proton switch model, which provides an explanation for proton-coupled electron transfer (PCET) in CuNiR. PCET is widely distributed through biogenic processes including respiratory and photosynthetic systems and is highly expected to be incorporated into bioinspired molecular devices. Our study also establishes the foundation for future studies on PCET in other systems.
Novel genomic island modifies DNA with 7-deazaguanine derivatives
Authors: Thiaville Jennifer J. , Kellner Stefanie M. , Yuan Yifeng , Hutinet Geoffrey , Thiaville Patrick C. , Jumpathong Watthanachai , Mohapatra Susovan , Brochier-Armanet Celine , Letarov Andrey V. , Hillebrand Roman , Malik Chanchal K. , Rizzo Carmelo J. , Dedon Peter C. , de Crécy-Lagard Valérie
Published: March 2016

Significance

The discovery of a novel modification system that inserts 7-deazaguanine derivatives in DNA, modifications thought until now to occur only in RNA, is an excellent illustration of the power of biological evolution to alter the ultimate function not only of the distinct proteins but also of entire metabolic pathways. The extensive lateral transfer of the gene cluster responsible for this modification highlights its significance as a previously unrecognized foreign DNA defense system that bacteria and phages use to protect their genomes. The characterization of these DNA modification pathways also opens the door to novel tools to manipulate nucleic acids.
Structural basis for DNA cleavage by the potent antiproliferative agent (–)-lomaiviticin A
Authors: Woo Christina M. , Li Zhenwu , Paulson Eric K. , Herzon Seth B.
Published: March 2016

Significance

DNA is a canonical target for chemotherapeutic intervention, and several DNA-reactive natural products are in clinical use. An understanding of the mode of DNA binding of these agents is an essential component of translational development. Here we show that (–)-lomaiviticin A (1), a naturally occurring DNA cleavage agent undergoing preclinical evaluation, binds DNA by an unusual mode of association involving insertion of two complex polycyclic arene fragments into the duplex, with concomitant disruption of base pairing. Additionally, our studies suggest that DNA binding activates the DNA cleavage activity of 1. This study provides a structural basis for the activity of 1 and for the development of synthetic DNA-damaging agents capable of recapitulating this mechanism of association and activation.
Long-ranged contributions to solvation free energies from theory and short-ranged models
Authors: Remsing Richard C. , Liu Shule , Weeks John D.
Published: March 2016

Significance

Many important biological and industrial processes, ranging from protein folding and ligand binding to self-assembly of materials at interfaces, take place in solution and are mediated by driving forces rooted in solvation. However, conceptual and computational difficulties arising from long-ranged Coulomb interactions still present a challenge to current approaches. Here we present a framework to determine very accurately the long-ranged contributions to solvation free energies in charged and polar systems from models with only short-ranged, local interactions. We examine a variety of ubiquitous solvation processes, including hydrophobic and ionic hydration, as well as colloidal overcharging. The theory additionally suggests ways to improve density functional theories of solvation by providing insights into commonly used approximations.
High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility
Authors: Pattenden Samantha G. , Simon Jeremy M. , Wali Aminah , Jayakody Chatura N. , Troutman Jacob , McFadden Andrew W. , Wooten Joshua , Wood Cameron C. , Frye Stephen V. , Janzen William P. , Davis Ian J.
Published: March 2016

Significance

Transcriptional regulators lacking enzymatic activity or binding pockets with targetable molecular features have typically been considered “undruggable,” and a reductionist approach based on identification of their molecular targets has largely failed. We have demonstrated that the Ewing sarcoma chimeric transcription factor, EWSR1-FLI1, maintains accessible chromatin at disease-specific regions. We adapted formaldehyde-assisted isolation of regulatory elements (FAIRE), an assay for accessible chromatin, to screen an epigenetically targeted small molecule library for compounds that reverse the disease-associated signature. This approach can be applied broadly for discovery of chromatin-based developmental therapeutics and offers significant advantages because it does not require the selection of a single molecular target. Using this approach, we identified a specific class of compounds with therapeutic potential.
Junctophilin-4, a component of the endoplasmic reticulum–plasma membrane junctions, regulates Ca
2+
dynamics in T cells
Authors: Woo Jin Seok , Srikanth Sonal , Nishi Miyuki , Ping Peipei , Takeshima Hiroshi , Gwack Yousang
Published: March 2016

Significance

Distinct membranes separate cellular organelles, and communication between organelles occurs primarily at the interorganelle membrane junctions, which are established by junctional proteins. The junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are essential for lipid transfer and Ca
2+
dynamics; however, little is known about the composition of these junctions in T cells. We identified a protein complex containing junctophilin-4 and junctate as components of the ER–PM junctions that regulate Ca
2+
dynamics in T cells by interacting with stromal interaction molecule 1 (STIM1), an essential activator of store-operated Ca
2+
channels. This study highlights an important role of junctional proteins in T cells and helps in uncovering the pathological mechanisms underlying human diseases due to mutations in these proteins.
Type VI secretion system sheaths as nanoparticles for antigen display
Authors: Del Tordello Elena , Danilchanka Olga , McCluskey Andrew J. , Mekalanos John J.
Published: March 2016

Significance

Critical aspects that limit use of nanoparticles as vaccine delivery systems include the technical difficulty of preparing particles under conditions that allow controlled protein loading and folding. Biologic nanoparticles offer advantages over chemically derived particles that require harsh organic solvents for preparation. Here, we demonstrate that the multimeric sheath structure of the bacterial type 6 secretion system (T6SS) can be exploited to generate particles that display on their surface many copies of specific proteins of interest. T6SS sheaths represent a functional vaccine delivery system with remarkable flexibility due to the ability to biochemically modify these structures to expand or enhance potential immunogenicity.
Tungsten isotopic constraints on the age and origin of chondrules
Authors: Budde Gerrit , Kleine Thorsten , Kruijer Thomas S. , Burkhardt Christoph , Metzler Knut
Published: March 2016

Significance

The origin of chondrules—millimeter-sized silicate-rich spherules that dominate the most primitive meteorites, the chondrites—is a long-standing puzzle in cosmochemistry. Here, we present isotopic evidence that chondrules and matrix from the Allende chondrite contain different and complementary proportions of presolar matter, indicating that chondrules and matrix formed together from a single reservoir of solar nebula dust. This finding rules out formation of chondrules in protoplanetary impacts and demonstrates that chondrules are the product of localized melting events in the solar protoplanetary disk. Moreover, the isotopic complementarity of chondrules and matrix requires that chondrules formed in a narrow time interval and were rapidly accreted to a parent body, implying that chondrule formation was a critical step toward forming planetesimals.
Measures with locally finite support and spectrum
Authors: Meyer Yves F.
Published: March 2016

Significance

An important problem in harmonic analysis is solved in this article: Is the Poisson summation formula unique or does it belong to a wider class? The latter is true. The method that is used to prove this statement is surprising. Our new Poisson’s formulas were hidden inside an old and almost forgotten paper published in 1959 by A. P. Guinand. The role of number theory in this issue is fascinating.
Pressure-induced superconductivity in a three-dimensional topological material ZrTe
5
Authors: Zhou Yonghui , Wu Juefei , Ning Wei , Li Nana , Du Yongping , Chen Xuliang , Zhang Ranran , Chi Zhenhua , Wang Xuefei , Zhu Xiangde , Lu Pengchao , Ji Cheng , Wan Xiangang , Yang Zhaorong , Sun Jian , Yang Wenge , Tian Mingliang , Zhang Yuheng , Mao Ho-kwang
Published: March 2016

Significance

Three-dimensional (3D) Dirac semimetals have attracted a lot of advanced research recently on many exotic properties and their association with crystalline and electronic structures under extreme conditions. As one of the fundamental state parameters, high pressure is an effective, clean way to tune lattice as well as electronic states, especially in quantum states, thus their electronic and magnetic properties. In this paper, by combining multiple experimental probes (synchrotron X-ray diffraction, low-temperature transport under magnetic field) and theoretical investigations, we discover the pressure-induced 3D Dirac semimetal to superconductor transition in ZrTe
5
.
Structure of an endogenous yeast 26S proteasome reveals two major conformational states
Authors: Luan Bai , Huang Xiuliang , Wu Jianping , Mei Ziqing , Wang Yiwei , Xue Xiaobin , Yan Chuangye , Wang Jiawei , Finley Daniel J. , Shi Yigong , Wang Feng
Published: March 2016

Significance

Mechanistic understanding of proteasome function requires elucidation of its three-dimensional structure. Previous investigations have revealed increasingly detailed information on the overall organization of the yeast 26S proteasome. In this study, we further improved the resolution of cryo-EM structures of endogenous proteasomes from
Saccharomyces cerevisiae
. These structures reveal two distinct conformational states, which appear to correspond to different states of ATP hydrolysis and substrate binding. This information may guide future functional analysis of the proteasome.
Functional requirements of AID’s higher order structures and their interaction with RNA-binding proteins
Authors: Mondal Samiran , Begum Nasim A. , Hu Wenjun , Honjo Tasuku
Published: March 2016

Significance

This paper demonstrates that activation-induced cytidine deaminase (AID), an essential enzyme in antigen-induced antibody diversification, forms distinct ribonucleoprotein complexes depending on its structural states: namely monomers or dimers. The identified RNA-binding proteins are required for the function of AID: namely DNA cleavage or recombination. In addition, the complex formation between AID and heterogeneous nuclear ribonucleoproteins (hnRNPs) is RNA-dependent.
Aspects of interrogative use in near-native French
Authors: Donaldson Bryan
Published: March 2016

This paper reports on interrogative (question) use in the informal spontaneous speech of near-native second-language French speakers. Interrogatives present considerable variation in French, and choices of interrogative form depend on semantics, communicative function, and register. Using a corpus of spontaneous conversations between near-native (NNSs) and native speakers (NSs), the inventory of interrogatives used is described; A detailed examination is then given of the question marker est-ce que (“is it that”), a candidate for overuse in L2 French (Zwanziger 2008, p. 91). The results, from 825 occurrences of interrogative structures, reveal that the NNSs possess extremely similar inventories of interrogative forms to their NS interlocutors and that their interrogative choices are both communicatively and socio-stylistically appropriate. What appears quantitatively as overuse of est-ce que by two NNSs is, from a communicative point of view, entirely felicitous: Like NSs, the NNSs reserve est-ce que for several marked interrogative contexts. The results suggest that the NNSs successfully integrate syntactic, semantic, communicative, and sociolinguistic information in spontaneous conversation.
Egalitarians, sufficientarians, and mathematicians: a critical notice of Harry Frankfurt’s On Inequality
Authors: Rondel David
Published: March 2016

This critical notice provides an overview of Harry Frankfurt’s On Inequality and assesses whether Frankfurt is right to argue that equality is merely formal and empty. I counter-argue that egalitarianism, properly tweaked and circumscribed, can be defended against Frankfurt’s repudiation. After surveying the main arguments in Frankfurt’s book, I argue that whatever plausibility the ‘doctrine of sufficiency’ defended by Frankfurt may have, it does not strike a fatal blow against egalitarianism. There is nothing in egalitarianism that forbids acceptance of the moral platitude expressed in sufficientarianism's positive thesis, (viz., it is morally important that everyone have enough). Nor is there anything in egalitarianism as such that makes it impossible to recognize the banal truth that there are many important things besides equality, and that many dimensions of human affairs are improperly appraised from a relational or comparative point of view. The fact that a relational or comparative point of view is sometimes out of place, however, surely does not mean that it always is. I conclude with the suggestion that egalitarianism is most compelling when it is understood as a normative conception of social relations (rather than, as Frankfurt seems to assume throughout his book, a thesis about the equal distribution of something) and thus presides over precisely those aspects of human affairs for which that relational or comparative point of view is germane.
Ypq3p-dependent histidine uptake by the vacuolar membrane vesicles of Saccharomyces cerevisiae
Authors: Manabe Kunio , Kawano-Kawada Miyuki , Ikeda Koichi , Sekito Takayuki , Kakinuma Yoshimi
Published: March 2016

The vacuolar membrane proteins Ypq1p, Ypq2p, and Ypq3p of Saccharomyces cerevisiae are known as the members of the PQ-loop protein family. We found that the ATP-dependent uptake activities of arginine and histidine by the vacuolar membrane vesicles were decreased by ypq2Δ and ypq3Δ mutations, respectively. YPQ1 and AVT1, which are involved in the vacuolar uptake of lysine/arginine and histidine, respectively, were deleted in addition to ypq2Δ and ypq3Δ. The vacuolar membrane vesicles isolated from the resulting quadruple deletion mutant ypq1Δypq2Δypq3Δavt1Δ completely lost the uptake activity of basic amino acids, and that of histidine, but not lysine and arginine, was evidently enhanced by overexpressing YPQ3 in the mutant. These results suggest that Ypq3p is specifically involved in the vacuolar uptake of histidine in S. cerevisiae. The cellular level of Ypq3p-HA3 was enhanced by depletion of histidine from culture medium, suggesting that it is regulated by the substrate.
Exchange relation planar algebras of small rank
Authors: Liu Zhengwei
Published: March 2016

The main purpose of this paper is to classify exchange relation planar algebras with 4 dimensional 2-boxes. Besides its skein theory, we emphasize the positivity of subfactor planar algebras based on the Schur product theorem. We will discuss the lattice of projections of 2-boxes, specifically the rank of the projections. From this point, several results about biprojections are obtained. The key break of the classification is to show the existence of a biprojection. By this method, we also classify another two families of subfactor planar algebras: subfactor planar algebras generated by 2-boxes with 4 dimensional 2-boxes and at most 23 dimensional 3-boxes; subfactor planar algebras generated by 2-boxes, such that the quotient of 3-boxes by the basic construction ideal is abelian. They extend the classification of singly generated planar algebras obtained by Bisch, Jones and the author.
Entry and Exit Patterns of “Toxic” Firms
Authors: De Silva Dakshina G. , Hubbard Timothy P. , Schiller Anita R.
Published: March 2016

We pair an establishment‐level dataset from Texas with public information available in the Toxics Release Inventory (TRI) to evaluate the standing of dirty industries in Texas census tracts with a focus on environmental justice concerns. The share of nonwhite residents in a tract is positively correlated with the number of TRI‐reporting firms, and an inverse‐U‐shaped relationship characterizes the number of TRI‐reporting firms and a tract's median income. Even after controlling for factor prices and other covariates that might drive firm location decisions, entrants that report to the TRI are more likely to locate in areas with a higher share of nonwhite residents. Firms that report to the TRI are also more likely to enter areas with a low share of college graduates. In contrast, the number of entrants from industries that do not have TRI reporters is negatively related to the percentage of nonwhite residents in a tract. Firms in these non‐reporting industries are also more likely to enter areas with a high share of college graduates. Polluters appear to agglomerate, raising concerns about both chemical releases being concentrated in certain tracts, and also affecting nonwhite‐dense areas disproportionately. The strength of these effects often depend on an urban/rural classification, with rural areas experiencing the most pronounced concerns. Moreover, TRI‐reporting firms are less likely to exit the market relative to their peers that operate in the same industry but do not need to file TRI reports, suggesting that releases may affect a region in the long run.
Direct calculation of minimal cut sets involving a specific reaction knock-out
Authors: Tobalina Luis , Pey Jon , Planes Francisco J.
Published: March 2016

Motivation: The concept of Minimal Cut Sets (MCSs) is used in metabolic network modeling to describe minimal groups of reactions or genes whose simultaneous deletion eliminates the capability of the network to perform a specific task. Previous work showed that MCSs where closely related to Elementary Flux Modes (EFMs) in a particular dual problem, opening up the possibility to use the tools developed for computing EFMs to compute MCSs. Until recently, however, there existed no method to compute an EFM with some specific characteristic, meaning that, in the case of MCSs, the only strategy to obtain them was to enumerate them using, for example, the standard K-shortest EFMs algorithm.

Results: In this work, we adapt the recently developed theory to compute EFMs satisfying several constraints to the calculation of MCSs involving a specific reaction knock-out. Importantly, we emphasize that not all the EFMs in the dual problem correspond to real MCSs, and propose a new formulation capable of correctly identifying the MCS wanted. Furthermore, this formulation brings interesting insights about the relationship between the primal and the dual problem of the MCS computation.

Availability and implementation: A Matlab-Cplex implementation of the proposed algorithm is available as a supplementary material.

Contact:  fplanes@ceit.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Lights, Camera … Income! Illuminating the National Accounts-Household Surveys Debate *
Authors: Pinkovskiy Maxim , Sala-i-Martin Xavier
Published: March 2016

GDP per capita and household survey means present conflicting pictures of the rate of economic development in emerging countries. One of the areas in which the national accounts–household surveys debate is key is the measurement of developing world poverty. We propose a data-driven method to assess the relative quality of GDP per capita and survey means by comparing them to the evolution of satellite-recorded nighttime lights. Our main assumption, which is robust to a variety of specification checks, is that the measurement error in nighttime lights is unrelated to the measurement errors in either national accounts or survey means. We obtain estimates of weights on national accounts and survey means in an optimal proxy for true income; these weights are very large for national accounts and very modest for survey means. We conclusively reject the null hypothesis that the optimal weight on surveys is greater than the optimal weight on national accounts, and we generally fail to reject the null hypothesis that the optimal weight on surveys is zero. Additionally, we provide evidence that national accounts are good indicators of desirable outcomes for the poor (such as longer life expectancy, better education and access to safe water), and we show that surveys appear to perform worse in developing countries that are richer and that are growing faster. Therefore, we interpret our results as providing support for estimates of world poverty that are based on national accounts.
Identification and Characterization of Plant Cell Death–Inducing Secreted Proteins From Ustilaginoidea virens
Authors: Fang Anfei , Han Yanqing , Zhang Nan , Zhang Min , Liu Lijuan , Li Shuai , Lu Fen , Sun Wenxian
Published: March 2016

Ustilaginoidea virens (Cooke) Takah (telemorph Villosiclava virens) is an ascomycetous fungus that causes rice false smut, one of the most important rice diseases. Fungal effectors often play essential roles in host-pathogen coevolutionary interactions. However, little is known about the functions of U. virens effectors. Here, we performed functional studies on putative effectors in U. virens and demonstrated that 13 of 119 putative effectors caused necrosis or necrosis-like phenotypes in Nicotiana benthamiana. Among them, 11 proteins were confirmed to be secreted, using a yeast secretion system, and the corresponding genes are all highly induced during infection, except UV_44 and UV_4753. Eight secreted proteins were proven to trigger cell death or defenses in rice protoplasts and the secretion signal of these proteins is essential for their cell death–inducing activity. The ability of UV_44 and UV_1423 to trigger cell death is dependent on the predicted serine peptidase and ribonuclease catalytic active sites, respectively. We demonstrated that UV_1423 and UV_6205 are N-glycosylated proteins, which glycosylation has different impacts on their abilities to induce cell death. Collectively, the study identified multiple secreted proteins in U. virens with specific structural motifs that induce cell death or defense machinery in nonhost and host plants.
The Potential for Cereal Rye Cover Crops to Host Corn Seedling Pathogens
Authors: Bakker Matthew G. , Acharya Jyotsna , Moorman Thomas B. , Robertson Alison E. , Kaspar Thomas C.
Published: March 2016

Cover cropping is a prevalent conservation practice that offers substantial benefits to soil and water quality. However, winter cereal cover crops preceding corn may diminish beneficial rotation effects because two grass species are grown in succession. Here, we show that rye cover crops host pathogens capable of causing corn seedling disease. We isolated Fusarium graminearum, F. oxysporum, Pythium sylvaticum, and P. torulosum from roots of rye and demonstrate their pathogenicity on corn seedlings. Over 2 years, we quantified the densities of these organisms in rye roots from several field experiments and at various intervals of time after rye cover crops were terminated. Pathogen load in rye roots differed among fields and among years for particular fields. Each of the four pathogen species increased in density over time on roots of herbicide-terminated rye in at least one field site, suggesting the broad potential for rye cover crops to elevate corn seedling pathogen densities. The radicles of corn seedlings planted following a rye cover crop had higher pathogen densities compared with seedlings following a winter fallow. Management practices that limit seedling disease may be required to allow corn yields to respond positively to improvements in soil quality brought about by cover cropping.
A Single-Dose, Open-Label Study of the Pharmacokinetics, Safety, and Tolerability of Lisdexamfetamine Dimesylate in Individuals With Normal and Impaired Renal Function
Authors: Ermer James , Corcoran Mary , Lasseter Kenneth , Marbury Thomas , Yan Brian , Martin Patrick T.
Published: March 2016

Background:

Lisdexamfetamine (LDX) and d-amphetamine pharmacokinetics were assessed in individuals with normal and impaired renal function after a single LDX dose; LDX and d-amphetamine dialyzability was also examined.

Methods:

Adults (N = 40; 8/group) were enrolled in 1 of 5 renal function groups [normal function, mild impairment, moderate impairment, severe impairment/end-stage renal disease (ESRD) not requiring hemodialysis, and ESRD requiring hemodialysis] as estimated by glomerular filtration rate (GFR). Participants with normal and mild to severe renal impairment received 30 mg LDX; blood samples were collected predose and serially for 96 hours. Participants with ESRD requiring hemodialysis received 30 mg LDX predialysis and postdialysis separated by a washout period of 7–14 days. Predialysis blood samples were collected predose, serially for 72 hours, and from the dialyzer during hemodialysis; postdialysis blood samples were collected predose and serially for 48 hours. Pharmacokinetic end points included maximum plasma concentration (Cmax) and area under the plasma concentration versus time curve from time 0 to infinity (AUC0–∞) or to last assessment (AUClast).

Results:

Mean LDX Cmax, AUClast, and AUC0–∞ in participants with mild to severe renal impairment did not differ from those with normal renal function; participants with ESRD had higher mean Cmax and AUClast than those with normal renal function. d-amphetamine exposure (AUClast and AUC0–∞) increased and Cmax decreased as renal impairment increased. Almost no LDX and little d-amphetamine were recovered in the dialyzate.

Conclusions:

There seems to be prolonged d-amphetamine exposure after 30 mg LDX as renal impairment increases. In individuals with severe renal impairment (GFR: 15 ≤ 30 mL·min−1·1.73 m−2), the maximum LDX dose is 50 mg/d; in patients with ESRD (GFR: <15 mL·min−1·1.73 m−2), the maximum LDX dose is 30 mg/d. Neither LDX nor d-amphetamine is dialyzable.
Prevalence and severity of vasomotor symptoms and joint pain in women at midlife in Bangladesh: a population-based survey
Authors: Islam Rakibul M. , Bell Robin J. , Billah Baki , Hossain Mohammad B. , Davis Susan R.
Published: March 2016

Objective:

The aim of the study was to document the prevalence of menopausal symptoms and the extent to which women are bothered by vasomotor symptoms (VMS) and joint pain in Bangladesh.

Methods:

A total of 1,590 women, aged 30 to 59 years, participated in a cross-sectional, questionnaire-based study between September 2013 and March 2014. The main outcome measures were moderate to severely bothersome VMS and joint pain, measured by the Menopause-Specific Quality of Life questionnaire.

Results:

Of participants, 59.4% were premenopausal, 8.4% perimenopausal, and 32.3% postmenopausal. Approximately all women reached menopause by the age of 50 years. The prevalence of moderate to severely bothersome VMS was 4.1% in premenopausal, 33.3% in perimenopausal, and 28.2% in postmenopausal women. Factors associated with moderate to severely bothersome VMS were being perimenopausal (odds ratio [OR] 46.34, 95% CI 13.29-161.56; P < 0.001) or postmenopausal (OR 19.15, 95% CI 5.63-65.11; P < 0.001) and obesity (OR 2.20, 95% CI 1.03-4.71; P = 0.042). The prevalence of moderate to severely bothersome joint pain was 40.3% in postmenopausal, 36.2% in perimenopausal, and 15.3% in premenopausal women. Moderate to severely bothersome joint pain was more likely both in perimenopausal (OR 2.64, 95% CI 1.63-4.29; P < 0.001) and postmenopausal women (OR 2.96, 95% CI 2.06-4.24; P < 0.001). Moderate to severely bothersome joint pain was also more likely in women with no education compared with women having education beyond secondary school (OR 2.38, 95% CI 1.02-2.32; P < 0.001). No women reported prescription therapy for menopausal symptoms.

Conclusions:

This study demonstrates that a high proportion of Bangladeshi women experience moderate to severely bothersome VMS and joint pain. Despite the considerable symptom prevalence, no women reported treatment, suggesting that menopause remains neglected in Bangladesh.