bluuebunny/crossref_metadata_2025 huggingface dataset:
Potentiality of delocalized states in indium-involved amorphous silicon oxide
Authors: Wan Y. Z. , Gao M. , Li Y. , Du H. W. , Li Y. H. , Guo H. B. , Xu F. , Ma Z. Q.
Published: May 2017

In this short report, the specific molecular coacervate and two kinds of quantum states in indium-involved amorphous silicon oxide [a-SiOx(In)] are studied. The a-SiOx(In) layer is prepared by the magnetron sputtering process for indium tin oxide (ITO) films deposited on n-type silicon substrates, which has been predicted by molecular dynamics simulation and density function theory calculation. The results have been applied to the interpretation of the electronic structure and hole tunneling transport in ITO-SiOx/n-Si photovoltaic (PV) devices. The most significant achievement is that there is either a transition level at 0.30 eV for p-type conductive conversion or an extra level at Ev + 4.60 eV induced by In-O-Si bonding, denoted as molecular orbital levels, within the dielectric amorphous oxide (a-SiOx). The cognizance is crucial for the concepts of passivation, tunneling, selective contact, inversion, and useful defects in modern PV devices.
Fabry-Pérot interferometer for sensing polar liquids at terahertz frequencies
Authors: Jahn David , Soltani Amin , Balzer Jan C. , Withayachumnankul Withawat , Koch Martin
Published: May 2017

We propose and validate a sensor for polar liquids that operates in conjunction with terahertz time-domain spectroscopy. The sensor is constructed from an optically thick silicon wafer and a ground plane, separated by a gap into which the liquid is injected. This arrangement represents a Fabry-Pérot interferometer that causes a sharp minimum in the reflection spectrum. Compared to resonance-based sensors, this sensor design can maintain its sharp spectral response when loaded with highly absorbing polar liquids. This overcomes an issue of damped resonance caused by material losses in resonance-based sensors. We report a reflection minimum shift of 8 GHz per percent ethanol in water. The sensor can be readily integrated with a microfluidic channel for real-time fluid monitoring.
Total internal reflection fluorescence based multiplane localization microscopy enables super-resolved volume imaging
Authors: Mondal Partha Pratim , Hess Samuel T.
Published: May 2017

Total internal reflection fluorescence (TIRF) based geometry is attractive for super-resolution localization microscopy. Although the traditional TIRF configuration enables near-surface 2D imaging, it is not capable of imaging multiple axial planes. We propose a simultaneous multiplane imaging based localization encoded (SMILE) technique in the TIRF configuration that utilizes point spread function (PSF) information (PSF size, corresponding to single molecules located at the focal plane and off-focal planes, and the detected photons per PSF) to reconstruct a near-surface volume stack. The natural spread of the detection PSFs (far from the specimen-coverslip interface) is used to fix the axial locations of single molecules, and the corresponding photon count determines their localization precision. The proposed SMILE microscopy technique enables super-resolved volume reconstruction based on 2D recorded data.
High power, higher order ultrafast hollow Gaussian beams
Authors: Apurv Chaitanya N. , Chaitanya Amrit , Banerji J. , Samanta G. K.
Published: May 2017

We report on linear and nonlinear generation of ultrafast hollow Gaussian beams (HGBs). Using only two spiral phase plates (SPPs) having phase variation corresponding to vortex orders, l = 1 and 2, and an experimental scheme, we have generated high power, ultrafast HGBs of orders up to 3 at 1064 nm. Based on single-pass, frequency doubling of the HGBs in a 5 mm long, MgO doped, periodically poled LiNbO3 (MgO:PPLN) crystal, we have produced HGBs of average output power in excess of 250 mW at 532 nm and order as high as 6. Experimentally, we verified that the frequency doubled HGBs have orders twice those of the pump HGBs. Like the Gaussian beams, the HGBs of all orders have an optimum focusing condition for the highest conversion efficiency. On the contrary to previous reports, we observed that the propagation of the vortex beam of order, l, through a SPP corresponding to the vortex order of, –l, results in HGBs of the same order, |l|.
Phonon conduction in silicon nanobeams
Authors: Park Woosung , Shin Dongsuk D. , Kim Soo Jin , Katz Joseph S. , Park Joonsuk , Ahn Chae Hyuck , Kodama Takashi , Asheghi Mehdi , Kenny Thomas W. , Goodson Kenneth E.
Published: May 2017

Despite extensive studies on thermal transport in thin silicon films, there has been little work studying the thermal conductivity of single-crystal rectangular, cross-sectional nanobeams that are commonly used in many applications such as nanoelectronics (FinFETs), nano-electromechanical systems, and nanophotonics. Here, we report experimental data on the thermal conductivity of silicon nanobeams of a thickness of ∼78 nm and widths of ∼65 nm, 170 nm, 270 nm, 470 nm, and 970 nm. The experimental data agree well (within ∼9%) with the predictions of a thermal conductivity model that uses a combination of bulk mean free paths obtained from ab initio calculations and a suppression function derived from the kinetic theory. This work quantifies the impact of nanobeam aspect ratios on thermal transport and establishes a criterion to differentiate between thin films and beams in studying thermal transport. The thermal conductivity of a 78 nm × 65 nm nanobeam is ∼32 W m−1 K−1, which is roughly a factor of two smaller than that of a 78 nm thick film.
Scalability and reliability issues of Ti/HfOx-based 1T1R bipolar RRAM: Occurrence, mitigation, and solution
Authors: Rahaman Sk. Ziaur , Lee Heng-Yuan , Chen Yu-Sheng , Lin Yu-De , Chen Pang-Shiu , Chen Wei-Su , Wang Pei-Hua
Published: May 2017

Scalability and reliability issues are the most dominant obstacle for the development of resistive switching memory (RRAM) technology. Owing to the excellent memory performance and process compatibility with current CMOS technology of Ti/HfOx-based filamentary type bipolar RRAM, its scalability and reliability issues have been investigated in this document. Towards this goal, we demonstrate that there exists a clear correlation between the transistor and memory cell, which ultimately limits the scaling in terms of operation current and size of the transistor as well and performance of the Ti/HfOx-based 1T1R bipolar RRAM. Due to the resemblance of switching behaviour between complementary resistive switching, i.e., CRS in a single memory stack, and bipolar resistive switching, the Ti/HfOx-based bipolar RRAM suffers from resistance pinning (RP) issues, whereas the minimum resistance during the 1st RESET operation always impeded below 20 kΩ; this occurs through the interaction between the transistor and memory cell during the FORMING process. However, a sufficiently lower FORMING voltage can mitigate the RP issue occurring in Ti/HfOx-based bipolar RRAM and an alternative Ta buffer layer over HfOx dielectrics is proposed to prevent the activation of self-CRS in the memory cell during the FORMING process.
Mixed protonic and electronic conductors hybrid oxide synaptic transistors
Authors: Fu Yang Ming , Zhu Li Qiang , Wen Juan , Xiao Hui , Liu Rui
Published: May 2017

Mixed ionic and electronic conductor hybrid devices have attracted widespread attention in the field of brain-inspired neuromorphic systems. Here, mixed protonic and electronic conductor (MPEC) hybrid indium-tungsten-oxide (IWO) synaptic transistors gated by nanogranular phosphorosilicate glass (PSG) based electrolytes were obtained. Unique field-configurable proton self-modulation behaviors were observed on the MPEC hybrid transistor with extremely strong interfacial electric-double-layer effects. Temporally coupled synaptic plasticities were demonstrated on the MPEC hybrid IWO synaptic transistor, including depolarization/hyperpolarization, synaptic facilitation and depression, facilitation-stead/depression-stead behaviors, spiking rate dependent plasticity, and high-pass/low-pass synaptic filtering behaviors. MPEC hybrid synaptic transistors may find potential applications in neuron-inspired platforms.
Optical properties of AlGaN nanowires synthesized via ion beam techniques
Authors: Parida Santanu , Magudapathy P. , Sivadasan A. K. , Pandian Ramanathaswamy , Dhara Sandip
Published: May 2017

AlGaN plays a vital role in hetero-structure high electron mobility transistors by employing a two-dimensional electron gas as an electron blocking layer in multi-quantum well light emitting diodes. Nevertheless, the incorporation of Al into GaN for the formation of the AlGaN alloy is limited by the diffusion barrier formed by instant nitridation of Al adatoms by reactive atomic N. The incorporation of Al above the miscibility limit, however, can be achieved by the ion beam technique. The well known ion beam mixing (IBM) technique was carried out with the help of Ar+ irradiation for different fluences. A novel approach was also adopted for the synthesis of AlGaN by the process of post-irradiation diffusion (PID) as a comparative study with the IBM technique. The optical investigations of AlGaN nanowires, synthesized via two different methods of ion beam processing, are reported. The effect of irradiation fluence and post-irradiation annealing temperature on the random alloy formation was studied by the vibrational and photoluminescence (PL) spectroscopic studies. Vibrational studies show one-mode phonon behavior corresponding to the longitudinal optical (LO) mode of A1 symmetry [A1(LO)] for the wurtzite phase of AlGaN nanowires in the random alloy model. A maximum Al atomic percentage of ∼6.3%–6.7% was calculated with the help of band bowing formalism from the Raman spectral analysis for samples synthesized in IBM and PID processes. PL studies show the extent of defects present in these samples.
Athermal synchronization of laser source with WDM filter in a silicon photonics platform
Authors: Li Nanxi , Su Zhan , Purnawirman  , Salih Magden E. , Poulton Christopher V. , Ruocco Alfonso , Singh Neetesh , Byrd Matthew J. , Bradley Jonathan D. B. , Leake Gerald , Watts Michael R.
Published: May 2017

In an optical interconnect circuit, microring resonators (MRRs) are commonly used in wavelength division multiplexing systems. To make the MRR and laser synchronized, the resonance wavelength of the MRR needs to be thermally controlled, and the power consumption becomes significant with a high-channel count. Here, we demonstrate an athermally synchronized rare-earth-doped laser and MRR. The laser comprises a Si3N4 based cavity covered with erbium-doped Al2O3 to provide gain. The low thermo-optic coefficient of Al2O3 and Si3N4 and the comparable thermal shift of the effective index in the laser and microring cross-sections enable lasing and resonance wavelength synchronization over a wide range of temperatures. The power difference between matched and unmatched channels remains greater than 15 dB from 20 to 50 °C due to a synchronized wavelength shift of 0.02 nm/°C. The athermal synchronization approach reported here is not limited to microring filters but can be applied to any Si3N4 filter with integrated lasers using rare earth ion doped Al2O3 as a gain medium to achieve system-level temperature control free operation.
Nitrogen-vacancy centers created by N+ ion implantation through screening SiO2 layers on diamond
Authors: Ito Kazuki , Saito Hiroshi , Sasaki Kento , Watanabe Hideyuki , Teraji Tokuyuki , Itoh Kohei M. , Abe Eisuke
Published: May 2017

We report on an ion implantation technique utilizing a screening mask made of SiO2 to control both the depth profile and the dose. By appropriately selecting the thickness of the screening layer, this method fully suppresses the ion channeling, brings the location of the highest nitrogen-vacancy (NV) density to the surface, and effectively reduces the dose by more than three orders of magnitude. With a standard ion implantation system operating at the energy of 10 keV and the dose of 1011 cm2 and without an additional etching process, we create single NV centers close to the surface with coherence times of a few tens of μs.
Dependence of transition width on current and critical current in transition-edge sensors
Authors: Morgan K. M. , Pappas C. G. , Bennett D. A. , Gard J. D. , Hays-Wehle J. P. , Hilton G. C. , Reintsema C. D. , Schmidt D. R. , Ullom J. N. , Swetz D. S.
Published: May 2017

In superconducting transition-edge sensor X-ray detectors, we observe that as the thermal conductance (G) to the heat bath increases, the resistive transition broadens. Consequently, the sensitivity of films to deposited energy worsens. Using a two-fluid model for the superconducting-to-normal transition in a thin film, we show that this broadening can be attributed to the larger current (I0) necessary for biasing the film at a given point in the transition for higher-G devices, resulting in a higher Ic0/I0 ratio (Ic0 is the film's critical current at zero temperature). To recover a sharper transition, we fabricated rectangular films with varying numbers of internal normal-metal structures while keeping G constant, allowing the independent variation of both I0 and Ic0. We show that it is possible to manipulate the transition width and G independently, thus enabling fast thermal sensors with an excellent energy resolution.
Pressure driven depolarization behavior of Bi0.5Na0.5TiO3 based lead-free ceramics
Authors: Liu Zhen , Ren Weijun , Nie Hengchang , Peng Ping , Liu Yun , Dong Xianlin , Cao Fei , Wang Genshui
Published: May 2017

Pressure driven depolarization behavior has been widely investigated for its scientific significance and practical applications. However, previous related studies were all based on lead-containing ferroelectric (FE) materials leading to detrimental environmental concerns. In the present work, we report the pressure driven depolarization behavior in Bi-based lead-free 0.97[(1-x)Bi0.5Na0.5TiO3-xBiAlO3)]-0.03K0.5Na0.5NbO3 (BNT-x) ceramics. Particularly, with increasing hydrostatic pressure from 0 MPa to 495 MPa, the remanent polarization of BNT-0.04 decreases from 30.7 μC/cm2 to 8.2 μC/cm2, reducing ∼73% of its initial value. The observed depolarization phenomenon is associated with the pressure induced polar FE-nonpolar relaxor phase transition. The results reveal BNT based ceramics as promising lead free candidates for mechanical-electrical energy conversion applications based on the pressure driven depolarization behavior.
Effect of the incident power on permittivity, losses and tunability of BaSrTiO3 thin films in the microwave frequency range
Authors: Nadaud Kevin , Borderon Caroline , Renoud Raphaël , Ghalem Areski , Crunteanu Aurelian , Huitema Laure , Dumas-Bouchiat Frédéric , Marchet Pascal , Champeaux Corinne , Gundel Hartmut W.
Published: May 2017

Domain wall motions in ferroelectrics participate to the material's complex permittivity and are responsible for their sensitivity of the dielectric properties to the driving electric field and thus to the incident power at microwave frequencies. In the present study, the dependence of the permittivity, the dielectric losses, and the tunability of Ba2∕3Sr1∕3TiO3 (BST) thin films on the incident power and on the bias fields is examined at a frequency of 500 MHz. While the domain wall motion participates only slightly to the permittivity (<5%), it strongly influences the losses due to its very dissipative behavior. As a consequence, the Figure of Merit (FoM, the ratio between tunability and dielectric losses) of the material depends on the applied microwave power. In the present study, a decrease in the FoM from 29 to 21 is observed for an incident power varying from –20 dBm to 5 dBm. When characterizing ferroelectric materials, the incident power has to be considered; moreover, domain wall motion effects should be limited in order to achieve a high FoM and less power sensitivity.
Cutting a Gordian Knot: Dispersion of plasmonic modes in Bi2Se3 topological insulator
Authors: Politano A. , Lamuta C. , Chiarello G.
Published: May 2017

Combining optical microscopy and high-resolution electron energy loss spectroscopy, we unraveled the puzzling controversy of plasmon dispersion in a Bi2Se3 topological insulator. We demonstrate that Bi2Se3 surfaces with superb flatness host dispersing plasmons. In contrast, cleaved Bi2Se3 surfaces exhibiting extensive large-scale faceting and shattering are characterized by an opposite behavior of the plasmon dispersion, i.e., the frequency does not change with the momentum. Moreover, we show that plasmonic modes are quenched in samples modified by the implantation of defects upon ion sputtering. These results indicate that the control of the morphology and the crystalline quality are mandatory in the prospect of low-loss plasmonics with topological insulators.
Counting near infrared photons with microwave kinetic inductance detectors
Authors: Guo W. , Liu X. , Wang Y. , Wei Q. , Wei L. F. , Hubmayr J. , Fowler J. , Ullom J. , Vale L. , Vissers M. R. , Gao J.
Published: May 2017

We demonstrate photon counting at 1550 nm wavelength using microwave kinetic inductance detectors (MKIDs) made from TiN/Ti/TiN trilayer films with superconducting transition temperature Tc≈ 1.4 K. The detectors have a lumped-element design with a large interdigitated capacitor covered by aluminum and inductive photon absorbers whose volume ranges from 0.4 μm3 to 20 μm3. The energy resolution improves as the absorber volume is reduced. We achieved an energy resolution of 0.22 eV and resolved up to 7 photons per optical pulse, both greatly improved from previously reported results at 1550 nm wavelength using MKIDs. Further improvements are possible by optimizing the optical coupling to maximize photon absorption into the inductive absorber.
Relaxation mechanisms in a gold thin film on a compliant substrate as revealed by X-ray diffraction
Authors: Godard Pierre , Renault Pierre-Olivier , Faurie Damien , Thiaudière Dominique
Published: May 2017

The fact that the polymeric substrate does not relax after a load jump allows realizing an original relaxation experiment of a metallic thin film. Thanks to the combination of two strain probes done at different scales, namely, X-ray synchrotron diffraction and digital image correlation techniques, the apparent activation volumes are monitored and their values help to capture leading deformation mechanisms in thin films. Such experiments have been performed on a nanocrystalline gold thin film, and deformation mechanisms involved during a biaxial straining have been distinguished between different texture components.
Interference-enhanced infrared-to-visible upconversion in solid-state thin films sensitized by colloidal nanocrystals
Authors: Wu Mengfei , Jean Joel , Bulović Vladimir , Baldo Marc A.
Published: May 2017

Infrared-to-visible photon upconversion has potential applications in photovoltaics, sensing, and bioimaging. We demonstrate a solid-state thin-film device that utilizes sensitized triplet-triplet exciton annihilation, converting infrared photons absorbed by colloidal lead sulfide nanocrystals (NCs) into visible photons emitted from a luminescent dopant in rubrene at low incident light intensities. A typical bilayer device consisting of a monolayer of NCs and a doped film of rubrene is limited by low infrared absorption in the thin NC film. Here, we augment the bilayer with an optical spacer layer and a silver-film back reflector, resulting in interference effects that enhance the optical field and thus the absorption in the NC film. The interference-enhanced device shows an order-of-magnitude increase in the upconverted emission at the wavelength of λ = 610 nm when excited at λ = 980 nm. At incident light intensities above 1.1 W/cm2, the device attains maximum efficiency, converting (1.6 ± 0.2)% of absorbed infrared photons into higher-energy singlet excitons in rubrene.
Dairy cattle industry and genetic improvement programs in Thailand
Authors: Pangmao Santi , Thomson Peter C. , Khatkar Mehar S.
Published: May 2017

The objective of the present study was to estimate genetic parameters and evaluate the genetic trends of 100-day milk yield (MY), fat percentage (FP) and protein percentage (PP) in three government dairy cattle farms in Thailand, located in the north and north-east of the country. The data consisted of records from 1745 first-lactation cows that calved between 1986 and 2015, which were the progeny of 287 sires and 1237 dams. Most of the animals were crossbred Holstein-Friesian with native or zebu animals. The total number of animals in the pedigree was 4753. Univariate and bivariate linear mixed models were used to estimate genetic parameters and breeding values by using ASReml-R. The fixed effects in the model were herd, year of calving, season of calving, breed group and the interaction between year and season of calving, and the random effects were animal and residual. All fixed effects had significant effects on the three traits, except breed group. The estimated heritabilities for MY, FP and PP were 0.242 ± 0.061, 0.066 ± 0.048 and 0.329 ± 0.072 respectively. The genetic correlation for MY and FP, MY and PP, and FP and PP were 0.219 ± 0.352, –0.271 ± 0.177 and 0.452 ± 0.255 respectively. The genetic trends based on estimated breeding values over year of birth did not show consistent improvement in all three traits, although there was a slight declining trend in MY in the later years.
Metal removal by pine bark compost using a permeable reactive barrier device at laboratory scale
Authors: Cancelo-González Javier , Martiñá-Prieto Diego , Hernández-Huerta Daniel , Barral María T.
Published: May 2017

Environmental contextPermeable reactive barriers are a developing technology to clean up contaminated groundwater. The contaminant plume moves through a reactive material placed below ground that retains or degrades the pollutants. This study shows that pine bark compost strongly adsorbs and retains metals, mostly by interaction with the organic matter of the compost, and thereby serves as a suitable reactive filler material to clean up contaminated groundwater.
AbstractPermeable reactive barriers (PRBs) are in situ systems for groundwater remediation, consisting of a screen perpendicular to the flow of contaminated groundwater filled with a material capable of retaining or degrading pollutants. The use of waste materials as reactive substrates in PRBs is of particular interest owing to the possibility of their reutilisation and their generally lower cost. With this aim, the sorption capacity for copper, nickel and zinc of pine bark compost (PBC) was evaluated in competitive batch experiments that showed that metal adsorption is a rapid process and that adsorption capacities followed the sequence Cu>Ni>Zn, with maximum adsorption capacities of 0.157mmolg–1 for Cu2+, 0.052mmolg–1 for Ni2+, 0.046mmolg–1 for Zn2+ and 0.259mmolg–1 for the sum of the three metals. Subsequently, a dynamic percolation experiment was carried out with a multi-metal solution prepared with 50mgL–1 of Cu, Ni and Zn in 0.01M KNO3 as saline background, using an experimental device that reproduced a PRB at laboratory scale. Metal retention ranged from 92 to 99% (Cu>Ni>Zn). The metals were strongly retained by the filling material because low desorption was detected by subsequent leaching with 0.01M KNO3 (0.3, 1.8 and 4.1% of the previously adsorbed metal for Cu, Ni and Zn respectively). The results show that PBC is a potential candidate as a filler material for the retention of cationic metals in permeable reactive barriers.
Prediction of cyanobacterial blooms in the Dau Tieng Reservoir using an artificial neural network
Authors: Bui Manh-Ha , Pham Thanh-Luu , Dao Thanh-Son
Published: May 2017

An artificial neural network (ANN) model was used to predict the cyanobacteria bloom in the Dau Tieng Reservoir, Vietnam. Eight environmental parameters (pH, dissolved oxygen, temperature, total dissolved solids, total nitrogen (TN), total phosphorus, biochemical oxygen demand and chemical oxygen demand) were introduced as inputs, whereas the cell density of three cyanobacteria genera (Anabaena, Microcystis and Oscillatoria) with microcystin concentrations were introduced as outputs of the three-layer feed-forward back-propagation ANN. Eighty networks covering all combinations of four learning algorithms (Bayesian regularisation (BR), gradient descent with momentum and adaptive learning rate, Levenberg–Mardquart, scaled conjugate gradient) with two transfer functions (tansig, logsig) and 10 numbers of hidden neurons (6–16) were trained and validated to find the best configuration fitting the observed data. The result is a network using the BR learning algorithm, tansig transfer function and nine neurons in the hidden layer, which shows satisfactory predictions with the low values of error (root mean square error=0.108) and high correlation coefficient values (R=0.904) between experimental and predicted values. Sensitivity analysis on the developed ANN indicated that TN and temperature had the most positive and negative effects respectively on microcystin concentrations. These results indicate that ANN modelling can effectively predict the behaviour of the cyanobacteria bloom process.
Mouse minipuberty coincides with gonocyte transformation into spermatogonial stem cells: a model for human minipuberty
Authors: Li Ruili , Vannitamby Amanda , Yue Sarah S. K. , Handelsman David , Hutson John
Published: May 2017

As the transient postnatal hormone surge in humans, known as ‘minipuberty’, occurs simultaneously with key steps in germ-cell development, we investigated whether similar changes occur in the hypothalamic–pituitary–testicular axis of neonatal mice at a time that would coincide with gonocyte transformation into spermatogonial stem cells (SSC). Serum and testes were collected from C57Bl/6 mice at embryonic Day 17 (E17), birth (postnatal Day 0; P0) and daily until P10. Serum FSH and testosterone levels in both serum and testes were analysed and gene expression of FSH receptor (Fshr), luteinising hormone receptor (Lhr), anti-Müllerian hormone (Amh), octamer-binding transcription factor 4 (Oct-4), membrane type 1 metalloprotease (Mt1-mmp), proto-oncogene C-kit and promyelocytic leukaemia zinc finger (Plzf ) was quantified by real-time polymerase chain reaction. We found a transient surge of serum and testicular testosterone levels between P1 and P3 and a gradual increase in FSH from P1 to P10. Testis Lhr expression remained low from P0 until P10 but Fshr expression peaked between P3 and P6 (P < 0.01). The same was found for Oct-4 expression (a gonocyte marker), which surged between P3 and P6 (P < 0.01). Mt1-mmp expression peaked at P3 (P < 0.05). The expression pattern of both C-kit and Plzf (SSC markers) was similar with a steady increase from P1 to P10. These results show a transient activation of the hypothalamic–pituitary–testicular axis postnatally with increases in serum and testicular testosterone at P1–P3 and testicular Fshr (but not Lhr) at P3–P6. These changes coincide with increases in gene expression of Oct4, Mt1-mmp, Plzf and C-kit, reflecting gonocyte activation, migration and transformation into SSC. In conclusion, these findings suggest that ‘minipuberty’ does occur in mice and that gonocyte transformation may be driven by a transient FSH signalling pathway.
The distribution of reflexive intensifiers in learner English
Authors: Rankin Tom
Published: May 2017

This study investigates the use of reflexive intensifiers by L1 German-speaking learners of L2 English against the background of previous research which has identified non-target-like distribution of such features which are sensitive to discourse constraints and/or register variation. Occurrences of intensified NPs are compared between theLouvain Corpus of Native English Essaysand the German component of theInternational Corpus of Learner English.In line with previous research, it is found that learners overuse this lexico-grammatical means of information highlighting. However, there is only significant overuse of a specific sub-type of intensifier, the inclusive adverbial intensifier. These results are discussed in terms of (i) general learnability considerations which may account for learners’ problems in mastering the use of register-sensitive information-structural patterns, and (ii) pedagogical issues which arise in connection with addressing residual non-target performance in written production beyond the stage at which target properties of lexico-grammar have generally been acquired.
Quantitative research methods and study quality in learner corpus research
Authors: Paquot Magali , Plonsky Luke
Published: May 2017

This study aims to provide the first empirical assessment of quantitative research methods and study quality in learner corpus research. We systematically review quantitative primary studies referenced in theLearner Corpus Bibliography(LCB), a representative bibliography of learner corpus research maintained by theLearner Corpus Associationwhich contained 1,276 references when the current study began. Each primary study in the LCB was coded for over fifty features representing six dimensions: (a) publication type (i.e. conference paper, book chapter, journal article), (b) research focus (e.g. lexis, grammar), (c) methodological features (e.g. keyword analysis, error analysis, use of reference corpus), (d) statistical analyses (e.g. X²,t-test, regression analysis), and (e) reporting practices (e.g. reliability coefficients, means). Results point to several systematic strengths as well as many flaws, such as the absence of research questions, incomplete and inconsistent reporting practices (e.g. means without standard deviations), and lack of statistical literacy (i.e. LCR studies generally overrely on tests of statistical significance, do not report effect sizes, rarely check or report whether statistical assumptions have been met, and rarely use multivariate analyses). Improvements over time, however, are clearly noted and there are signs that, like other related disciplines, learner corpus research is slowly undergoing methodological reform.
Minimal graphematic words in English and German
Authors: Evertz Martin
Published: May 2017

It has been frequently noted in the literature that content words need to consist of at least three letters; this observation is commonly dubbed “three letter rule.” However, a survey of the CELEX database (Baayen et al. 1995) shows that there are (nearly) no content words in English and German that begin with two or more consonant letters and end in a single vowel letter. Words such as [bruː] are not spelt * but  with an additional letter. These findings cannot be accounted for by the three letter rule but they are explicable within a supra-segmental theory of graphematics that includes graphematic feet and graphematic weight: a well-formed graphematic word consists of at least one graphematic foot that in turn consists of at least one heavy graphematic syllable. This paper offers a data-based survey in order to answer the question whether there is a suprasegmental minimality constraint for monosyllabic graphematic words in English and German.
Long-Term PM2.5 Exposure and Respiratory, Cancer, and Cardiovascular Mortality in Older US Adults
Authors: Pun Vivian C , Kazemiparkouhi Fatemeh , Manjourides Justin , Suh Helen H
Published: May 2017

The impact of chronic exposure to fine particulate matter (particulate matter with an aerodynamic diameter less than or equal to 2.5 μm (PM2.5)) on respiratory disease and lung cancer mortality is poorly understood. In a cohort of 18.9 million Medicare beneficiaries (4.2 million deaths) living across the conterminous United States between 2000 and 2008, we examined the association between chronic PM2.5 exposure and cause-specific mortality. We evaluated confounding through adjustment for neighborhood behavioral covariates and decomposition of PM2.5 into 2 spatiotemporal scales. We found significantly positive associations of 12-month moving average PM2.5 exposures (per 10-μg/m3 increase) with respiratory, chronic obstructive pulmonary disease, and pneumonia mortality, with risk ratios ranging from 1.10 to 1.24. We also found significant PM2.5-associated elevated risks for cardiovascular and lung cancer mortality. Risk ratios generally increased with longer moving averages; for example, an elevation in 60-month moving average PM2.5 exposures was linked to 1.33 times the lung cancer mortality risk (95% confidence interval: 1.24, 1.40), as compared with 1.13 (95% confidence interval: 1.11, 1.15) for 12-month moving average exposures. Observed associations were robust in multivariable models, although evidence of unmeasured confounding remained. In this large cohort of US elderly, we provide important new evidence that long-term PM2.5 exposure is significantly related to increased mortality from respiratory disease, lung cancer, and cardiovascular disease.
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive
Authors: Bernstein Matthew N , Doan AnHai , Dewey Colin N
Published: May 2017

Motivation

The NCBI’s Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants and references to outside sources of information. Furthermore, manual annotation of the data remains intractable due to the large number of samples in the archive. For these reasons, it has been difficult to perform large-scale analyses that study the relationships between biomolecular processes and phenotype across diverse diseases, tissues and cell types present in the SRA.

Results

We present MetaSRA, a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties. We automated these tasks via a novel computational pipeline.

Availability and implementation

The MetaSRA is available at metasra.biostat.wisc.edu via both a searchable web interface and bulk downloads. Software implementing our computational pipeline is available at http://github.com/deweylab/metasra-pipeline

Supplementary information

Supplementary data are available at Bioinformatics online.
Cholinergic Grb2-Associated-Binding Protein 1 Regulates Cognitive Function
Authors: Lu Nan-Nan , Tan Chao , Sun Ning-He , Shao Ling-Xiao , Liu Xiu-Xiu , Gao Yin-Ping , Tao Rong-Rong , Jiang Quan , Wang Cheng-Kun , Huang Ji-Yun , Zhao Kui , Wang Guang-Fa , Liu Zhi-Rong , Fukunaga Kohji , Lu Ying-Mei , Han Feng
Published: May 2017

Grb2-associated-binding protein 1 (Gab1) is a docking/scaffolding molecule known to play an important role in cell growth and survival. Here, we report that Gab1 is decreased in cholinergic neurons in Alzheimer’s disease (AD) patients and in a mouse model of AD. In mice, selective ablation of Gab1 in cholinergic neurons in the medial septum impaired learning and memory and hippocampal long-term potentiation. Gab1 ablation also inhibited SK channels, leading to an increase in firing in septal cholinergic neurons. Gab1 overexpression, on the other hand, improved cognitive function and restored hippocampal CaMKII autorphosphorylation in AD mice. These results suggest that Gab1 plays an important role in the pathophysiology of AD and may represent a novel therapeutic target for diseases involving cholinergic dysfunction.
A transcriptional serenAID: the role of noncoding RNAs in class switch recombination
Authors: Yewdell William T. , Chaudhuri Jayanta
Published: May 2017

During an immune response, activated B cells may undergo class switch recombination (CSR), a molecular rearrangement that allows B cells to switch from expressing IgM and IgD to a secondary antibody heavy chain isotype such as IgG, IgA or IgE. Secondary antibody isotypes provide the adaptive immune system with distinct effector functions to optimally combat various pathogens. CSR occurs between repetitive DNA elements within the immunoglobulin heavy chain (Igh) locus, termed switch (S) regions and requires the DNA-modifying enzyme activation-induced cytidine deaminase (AID). AID-mediated DNA deamination within S regions initiates the formation of DNA double-strand breaks, which serve as biochemical beacons for downstream DNA repair pathways that coordinate the ligation of DNA breaks. Myriad factors contribute to optimal AID targeting; however, many of these factors also localize to genomic regions outside of the Igh locus. Thus, a current challenge is to explain the specific targeting of AID to the Igh locus. Recent studies have implicated noncoding RNAs in CSR, suggesting a provocative mechanism that incorporates Igh-specific factors to enable precise AID targeting. Here, we chronologically recount the rich history of noncoding RNAs functioning in CSR to provide a comprehensive context for recent and future discoveries. We present a model for the RNA-guided targeting of AID that attempts to integrate historical and recent findings, and highlight potential caveats. Lastly, we discuss testable hypotheses ripe for current experimentation, and explore promising ideas for future investigations.
Activation of group 2 innate lymphoid cells exacerbates and confers corticosteroid resistance to mouse nasal type 2 inflammation
Authors: Morikawa Taiyo , Fukuoka Ayumi , Matsushita Kazufumi , Yasuda Koubun , Iwasaki Naruhito , Akasaki Shoko , Fujieda Shigeharu , Yoshimoto Tomohiro
Published: May 2017

Both Th2 cells and group 2 innate lymphoid cells (ILC2s) contribute to allergic diseases. However, their exact role and relationship in nasal allergic disorders are unclear. In this study, we investigated the cooperation of Th2 cells and ILC2s in a mouse model of nasal allergic disorder. To differentially activate Th2 cells and/or ILC2s in nasal mucosa, mice were intra-nasally administered ovalbumin (OVA) antigen, papain, an ILC2-activator, or both for 2 weeks. Epithelial thickness and number of eosinophils in the nasal mucosa were evaluated at 24 h after the final challenge. Intra-nasal administration of OVA and papain preferentially activated Th2 cells and ILC2s, respectively, in the nose. Both OVA and papain increased the nasal epithelial thickness and number of eosinophils, and their coadministration significantly enhanced the symptoms. Although T-/B-cell-deficient mice showed severely decreased nasal symptoms induced by OVA or OVA-plus-papain, the mice still showed slight papain-induced nasal symptoms. In ILC2-deficient mice, OVA-plus-papain-induced nasal symptoms were suppressed to the same level as OVA-alone. Similarly, IL-33- and ST2-deficient mice showed decreased OVA-plus-papain-induced nasal symptoms. IL-5 induced eosinophilia only, but IL-13 contributed to both nasal epithelial thickening and eosinophilia induced by OVA-plus-papain. Dexamethasone ameliorated OVA-alone-induced nasal epithelial thickening. However, OVA-plus-papain-induced nasal epithelial thickening was only partially controlled by dexamethasone. These results demonstrate that IL-33/ST2-pathway-mediated ILC2 activation exacerbated Th2-cell-induced nasal inflammation by producing IL-13. Although Th2-cell-alone-induced nasal inflammation was controlled by corticosteroid treatment, the activation of ILC2s conferred treatment resistance. Therefore, ILC2s and their activators could be therapeutic targets for treatment-refractory nasal allergic disorders.
On the level of cluster assembly bias in SDSS
Authors: Zu Ying , Mandelbaum Rachel , Simet Melanie , Rozo Eduardo , Rykoff Eli S.
Published: May 2017

Recently, several studies have discovered a strong discrepancy between the large-scale clustering biases of two subsamples of galaxy clusters at the same halo mass, split by their average projected membership distances 〈Rmem〉. The level of this discrepancy significantly exceeds the maximum halo assembly bias predicted by Λ cold dark matter (ΛCDM). We explore whether some of the large-scale bias differences could be caused by projection effects in 〈Rmem〉 due to other systems along the line of sight. We thoroughly investigate the assembly bias of the redMaPPer clusters in Sloan Digital Sky Survey (SDSS), by defining a new variant of the average membership distance estimator $\tilde{R}_{\mathrm{mem}}$ that is robust against projection effects in the cluster membership identification. Using the angular mark correlation functions, we show that the large-scale bias differences when splitting by 〈Rmem〉 can be mostly attributed to projection effects. After splitting by $\tilde{R}_{\mathrm{mem}}$, the anomalously large signal is reduced, giving a ratio of 1.02 ± 0.14 between the two clustering biases as measured from weak lensing. Using a realistic mock cluster catalogue, we predict that the bias ratio between two $\tilde{R}_{\mathrm{mem}}$-split subsamples should be ≃1.10, which is >60 per cent weaker than the maximum halo assembly bias (1.24) when split by halo concentration. Therefore, our results demonstrate that the level of halo assembly bias exhibited by clusters in SDSS is consistent with the ΛCDM prediction. With a 10-fold increase in cluster numbers, deeper ongoing surveys will enable a more robust detection of halo assembly bias. Our findings also have important implications for quantifying the impact of projection effects on cosmological constraints using photometrically selected clusters.
New hard X-ray sources discovered in the ongoing INTEGRAL Galactic plane survey after 14 yr of observations
Authors: Krivonos Roman A. , Tsygankov Sergey S. , Mereminskiy Ilya A. , Lutovinov Alexander A. , Sazonov Sergey Yu. , Sunyaev Rashid A.
Published: May 2017

The International Gamma-Ray Astrophysics Laboratory (INTEGRAL) continues to successfully work in orbit after its launch in 2002. The mission provides the deepest ever survey of hard X-ray sources throughout the Galaxy at energies above 20 keV. We report on a catalogue of new hard X-ray source candidates based on the latest sky maps comprising 14 yr of data acquired with the IBIS telescope onboard INTEGRAL in the Galactic Plane (|b| < 17.5°). The current catalogue includes in total 72 hard X-ray sources detected at S/N > 4.7σ and not known to previous INTEGRAL surveys. Among them, 31 objects have also been detected in the on-going all-sky survey by the BAT telescope of the Swift observatory. For 26 sources on the list, we suggest possible identifications: 21 active galactic nuclei, two cataclysmic variables, two isolated pulsars or pulsar wind nebulae and one supernova remnant; 46 sources from the catalogue remain unclassified.
The first eclipsing binary catalogue from the MOA-II data base
Authors: Li M. C. A. , Rattenbury N. J. , Bond I. A. , Sumi T. , Bennett D. P. , Koshimoto N. , Abe F. , Asakura Y. , Barry R. , Bhattacharya A. , Donachie M. , Evans P. , Freeman M. , Fukui A. , Hirao Y. , Itow Y. , Ling C. H. , Masuda  K. , Matsubara Y. , Muraki Y. , Nagakane M. , Ohnishi  K. , Saito To. , Sharan A. , Sullivan D. J. , Suzuki D. , Tristram P. J. , Yonehara A.
Published: May 2017

We present the first catalogue of eclipsing binaries in two MOA (Microlensing Observations in Astrophysics) fields towards the Galactic bulge, in which over 8000 candidates, mostly contact and semidetached binaries of periods <1 d, were identified. In this paper, the light curves of a small number of interesting candidates, including eccentric binaries, binaries with noteworthy phase modulations and eclipsing RS Canum Venaticorum type stars, are shown as examples. In addition, we identified three triple object candidates by detecting the light-travel-time effect in their eclipse time variation curves.
Cigarette Smoking Cessation Intervention for Buprenorphine Treatment Patients
Authors: Hall Sharon M , Humfleet Gary L , Gasper James J , Delucchi Kevin L , Hersh David F , Guydish Joseph R
Published: May 2017

Introduction

Patients receiving medication assisted therapy (MAT) for opioid use disorder have high cigarette smoking rates. Cigarette smoking interventions have had limited success. We evaluated an intervention to increase cigarette abstinence rates in patients receiving buprenorphine-assisted therapy.

Methods

Cigarette smokers (N = 175; 78% male; 69% Caucasian; 20% Hispanic), recruited from a buprenorphine clinic were randomly assigned to either an extended innovative system intervention (E-ISI) or to Standard Treatment Control (STC). The E-ISI combined motivational intervention with extended treatment (long-term nicotine replacement therapy , varenicline, and extended cognitive behavioral therapy). STC received written information about quit-lines, medication, and resources. Assessments were held at baseline and 3, 6, 12, and 18 months. Seven-day biochemically verified point-prevalence cigarette abstinence was the primary outcome measure.

Results

Fifty-four percent of E-ISI participants entered the extended treatment intervention; E-ISI and STC differed at 3 months on abstinence status but not at months 6, 12, and 18. E-ISI participants were more likely to attempt to quit, to have a goal of complete abstinence, and to be in a more advanced stage of change than STC participants. A higher number of cigarettes smoked and the use of cannabis in the previous 30 days predicted continued smoking

Conclusions

The E-ISI was successful in increasing motivation to quit smoking but did not result in long-term abstinence. The failure of treatments that have been efficacious in the general population to produce abstinence in patients receiving MAT of opioid use disorder suggests that harm reduction and other innovative interventions should be explored.

Implications

This study demonstrates that an intervention combining motivational interviewing with an extended treatment protocol can increase cigarette quit attempts, enhance cigarette abstinence goals, and further movement through stages of change about quitting smoking in patients receiving MAT for opioid use disorder who smoke cigarettes. The intervention did not increase abstinence rates over those observed in a standard treatment control, however. The latter finding supports those of earlier investigators who also failed to find efficacy for smoking cessation in this population and who also used interventions effective in the general population. This pattern of findings suggests that patients with opioid use disorder can be motivated to change smoking behavior, but alternative and innovative approaches to cigarette smoking treatment should be studied.