bluuebunny/crossref_metadata_2025 huggingface dataset:
A generalized electron energy probability function for inductively coupled plasmas under conditions of nonlocal electron kinetics
Authors: Mouchtouris S. , Kokkoris G.
Published: January 2018

A generalized equation for the electron energy probability function (EEPF) of inductively coupled Ar plasmas is proposed under conditions of nonlocal electron kinetics and diffusive cooling. The proposed equation describes the local EEPF in a discharge and the independent variable is the kinetic energy of electrons. The EEPF consists of a bulk and a depleted tail part and incorporates the effect of the plasma potential, Vp, and pressure. Due to diffusive cooling, the break point of the EEPF is eVp. The pressure alters the shape of the bulk and the slope of the tail part. The parameters of the proposed EEPF are extracted by fitting to measure EEPFs (at one point in the reactor) at different pressures. By coupling the proposed EEPF with a hybrid plasma model, measurements in the gaseous electronics conference reference reactor concerning (a) the electron density and temperature and the plasma potential, either spatially resolved or at different pressure (10–50 mTorr) and power, and (b) the ion current density of the electrode, are well reproduced. The effect of the choice of the EEPF on the results is investigated by a comparison to an EEPF coming from the Boltzmann equation (local electron kinetics approach) and to a Maxwellian EEPF. The accuracy of the results and the fact that the proposed EEPF is predefined renders its use a reliable alternative with a low computational cost compared to stochastic electron kinetic models at low pressure conditions, which can be extended to other gases and/or different electron heating mechanisms.
Optical nutation in acetylene-filled hollow-core photonic crystal fiber
Authors: Ocegueda Manuel , Stepanov Serguei , Casillas Nayelli , Hernández Eliseo
Published: January 2018

We report detailed experimental results on the optical nutation effect in acetylene-filled hollow-core photonic crystal fibers (HC-PCFs). This coherent quantum optical effect is manifested by the appearance of attenuated oscillations in the profiles of transmitted step-like coherent optical pulses. The experiments used 15 ns optical pulses with peak powers up to ∼4 W and centered at 1530.37 nm, which corresponds to the acetylene (12C2H2) vibration-rotation resonance absorption line P9. The all-fiber cell made from a HC-PCF with internal diameter ∼10.3 μm contained a gas pressure of about 0.12 Torr. The Maxwell-Bloch equations are used to analyze the influence of the homogeneous relaxation, the inhomogeneous Doppler broadening of the absorption line, and the random orientation of the acetylene molecules. By comparing the experimental results with numerical simulations, we obtain the longitudinal and the transverse relaxation times to be close to 10 ns and find that the transition dipole moment of the acetylene P9 absorption line is ∼1.36×10−32 Cm.
Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways of Nicotiana tabacum Rubisco activase
Authors: Wang Quan , Serban Andrew J. , Wachter Rebekka M. , Moerner W. E.
Published: January 2018

Oligomerization plays an important role in the function of many proteins, but a quantitative picture of the oligomer distribution has been difficult to obtain using existing techniques. Here we describe a method that combines sub-stoichiometric labeling and recently developed single-molecule diffusometry to measure the size distribution of oligomers under equilibrium conditions in solution, one molecule at a time. We use this technique to characterize the oligomerization behavior of Nicotiana tabacum (Nt) Rubisco activase (Nt-Rca), a chaperone-like AAA-plus ATPase essential in regulating carbon fixation during photosynthesis. We directly observed monomers, dimers, and a tetramer/hexamer mixture and extracted their fractional abundance as a function of protein concentration. We show that the oligomerization pathway of Nt-Rca is nucleotide dependent: ATPγS binding strongly promotes tetramer/hexamer formation from dimers and results in a preferred tetramer/hexamer population for concentrations in the 1-10 μM range. Furthermore, we directly observed dynamic assembly and disassembly processes of single complexes in real time and from there estimated the rate of subunit exchange to be ∼0.1 s−1 with ATPγS. On the other hand, ADP binding destabilizes Rca complexes by enhancing the rate of subunit exchange by >2 fold. These observations provide a quantitative starting point to elucidate the structure-function relations of Nt-Rca complexes. We envision the method to fill a critical gap in defining and quantifying protein assembly pathways in the small-oligomer regime.
Phonon transmission at Si/Ge and polytypic Ge interfaces using full-band mismatch based models
Authors: Larroque Jérôme , Dollfus Philippe , Saint-Martin Jérôme
Published: January 2018

This paper presents theoretical investigations on the interfacial thermal conductance (Kapitza conductance) in both monotype Si/Ge (cubic 3C) and polytype (cubic 3C/hexagonal 2H) Ge interfaces by using full band extensions of diffusive and acoustic mismatch models. In that aims, phonon dispersions in the full 3D Brillouin zone have been computed via an atomistic adiabatic bond charge model. The effects of crystal orientation are investigated, and the main phonon modes involved in heat transfer are highlighted. According to our calculations, polytype interfaces without any mass mismatch but with a crystallographic phase mismatch exhibit a thermal conductance very close to that of Si/Ge interfaces with a mass mismatch but without any phase mismatch. Besides, the orientations of Ge polytype interface that have been observed experimentally in nanowires, i.e., along [115]/[505¯1], exhibit the lowest interfacial conductance and thus may offer new opportunities for nanoscale thermoelectric applications.
Efficient evaluation of atom tunneling combined with electronic structure calculations
Authors: Ásgeirsson Vilhjálmur , Arnaldsson Andri , Jónsson Hannes
Published: January 2018

Methodology for finding optimal tunneling paths and evaluating tunneling rates for atomic rearrangements is described. First, an optimal JWKB tunneling path for a system with fixed energy is obtained using a line integral extension of the nudged elastic band method. Then, a calculation of the dynamics along the path is used to determine the temperature at which it corresponds to an optimal Feynman path for thermally activated tunneling (instanton) and a harmonic approximation is used to estimate the transition rate. The method is illustrated with calculations for a modified two-dimensional Müller-Brown surface but is efficient enough to be used in combination with electronic structure calculations of the energy and atomic forces in systems containing many atoms. An example is presented where tunneling is the dominant mechanism well above room temperature as an H3BNH3 molecule dissociates to form H2. Also, a solid-state example is presented where density functional theory calculations of H atom tunneling in a Ta crystal give close agreement with experimental measurements on hydrogen diffusion over a wide range in temperature.
Continuous profile flexural GRIN lens: Focusing and harvesting flexural waves
Authors: Zareei Ahmad , Darabi Amir , Leamy Michael J. , Alam Mohammad-Reza
Published: January 2018

A significant challenge in flexural wave energy harvesting is the design of an aberration-free lens capable of finely focusing waves over a broad frequency range. To date, flexural lenses have been created using discrete inclusions, voids, or stubs, often in a periodic arrangement, to focus waves via scattering. These structures are narrowband either because scattering is efficient over a small frequency range or the arrangements exploit Bragg scattering bandgaps, which themselves are narrowband. In addition, current lens designs are based on a single frequency and approximate the necessary refractive index profile discretely, introducing aberrations and frequency-dependent focal points. Here, we design a flexural GRIN lens in a thin plate by smoothly varying the plate's rigidity and thus its refractive index. Our lens (i) is broadband since the design does not depend on frequency and does not require bandgaps, (ii) has a fixed focal point over a wide range of frequencies, and (iii) is theoretically capable of zero-aberration focusing. We numerically explore our Continuous Profile GRIN lens (CP-GRIN lens) and then experimentally validate an implemented design. Furthermore, we use a piezoelectric energy harvester disk, located at the first focus of the CP-GRIN, to document improvements in power gain.
Single molecule force spectroscopy at high data acquisition: A Bayesian nonparametric analysis
Authors: Sgouralis Ioannis , Whitmore Miles , Lapidus Lisa , Comstock Matthew J. , Pressé Steve
Published: January 2018

Bayesian nonparametrics (BNPs) are poised to have a deep impact in the analysis of single molecule data as they provide posterior probabilities over entire models consistent with the supplied data, not just model parameters of one preferred model. Thus they provide an elegant and rigorous solution to the difficult problem encountered when selecting an appropriate candidate model. Nevertheless, BNPs’ flexibility to learn models and their associated parameters from experimental data is a double-edged sword. Most importantly, BNPs are prone to increasing the complexity of the estimated models due to artifactual features present in time traces. Thus, because of experimental challenges unique to single molecule methods, naive application of available BNP tools is not possible. Here we consider traces with time correlations and, as a specific example, we deal with force spectroscopy traces collected at high acquisition rates. While high acquisition rates are required in order to capture dwells in short-lived molecular states, in this setup, a slow response of the optical trap instrumentation (i.e., trapped beads, ambient fluid, and tethering handles) distorts the molecular signals introducing time correlations into the data that may be misinterpreted as true states by naive BNPs. Our adaptation of BNP tools explicitly takes into consideration these response dynamics, in addition to drift and noise, and makes unsupervised time series analysis of correlated single molecule force spectroscopy measurements possible, even at acquisition rates similar to or below the trap’s response times.
Compositional and strain analysis of In(Ga)N/GaN short period superlattices
Authors: Dimitrakopulos G. P. , Vasileiadis I. G. , Bazioti C. , Smalc-Koziorowska J. , Kret S. , Dimakis E. , Florini N. , Kehagias Th. , Suski T. , Karakostas Th. , Moustakas T. D. , Komninou Ph.
Published: January 2018

Extensive high resolution transmission and scanning transmission electron microscopy observations were performed in In(Ga)N/GaN multi-quantum well short period superlattices comprising two-dimensional quantum wells (QWs) of nominal thicknesses 1, 2, and 4 monolayers (MLs) in order to obtain a correlation between their average composition, geometry, and strain. The high angle annular dark field Z-contrast observations were quantified for such layers, regarding the indium content of the QWs, and were correlated to their strain state using peak finding and geometrical phase analysis. Image simulations taking into thorough account the experimental imaging conditions were employed in order to associate the observed Z-contrast to the indium content. Energetically relaxed supercells calculated with a Tersoff empirical interatomic potential were used as the input for such simulations. We found a deviation from the tetragonal distortion prescribed by continuum elasticity for thin films, i.e., the strain in the relaxed cells was lower than expected for the case of 1 ML QWs. In all samples, the QW thickness and strain were confined in up to 2 ML with possible indium enrichment of the immediately abutting MLs. The average composition of the QWs was quantified in the form of alloy content.
Impacts of energy relaxation process on quasi-ballistic hole transport capability in germanium and silicon nanowires
Authors: Tanaka H. , Suda J. , Kimoto T.
Published: January 2018

The quasi-ballistic hole transport in germanium and silicon nanowires was theoretically investigated by solving the Boltzmann transport equation taking account of phonon scattering in an atomistic framework. Comparison of quasi-ballistic hole transport capabilities between germanium and silicon nanowires showed that the transmission coefficients for the two materials are similar. Then, the behavior of forward and backward current fluxes was analyzed focusing on the impact of energy relaxation process. The slower energy relaxation of holes in germanium nanowires leads to a longer distance where backscattering enables holes to return to the source. This cancels the benefit of the longer mean free path of holes in germanium nanowires, resulting in similar transmission coefficients in germanium and silicon nanowires.
The effect of stoichiometry on Cu-Zn ordering kinetics in Cu2ZnSnS4 thin films
Authors: Rudisch Katharina , Davydova Alexandra , Platzer-Björkman Charlotte , Scragg Jonathan
Published: January 2018

Cu-Zn disorder in Cu2ZnSnS4 (CZTS) may be responsible for the large open circuit voltage deficit in CZTS based solar cells. In this study, it was investigated how composition-dependent defect complexes influence the order-disorder transition. A combinatorial CZTS thin film sample was produced with a cation composition gradient across the sample area. The graded sample was exposed to various temperature treatments and the degree of order was analyzed with resonant Raman spectroscopy for various compositions ranging from E- and A-type to B-, F-, and C-type CZTS. We observe that the composition has no influence on the critical temperature of the order-disorder transition, but strongly affects the activation energy. Reduced activation energy is achieved with compositions with Cu/Sn > 2 or Cu/Sn < 1.8 suggesting an acceleration of the cation ordering in the presence of vacancies or interstitials. This is rationalized with reference to the effect of point defects on exchange mechanisms. The implications for reducing disorder in CZTS thin films are discussed in light of the new findings.
Effect of rattling motion without cage structure on lattice thermal conductivity in LaOBiS2−xSex
Authors: Lee C. H. , Nishida A. , Hasegawa T. , Nishiate H. , Kunioka H. , Ohira-Kawamura S. , Nakamura M. , Nakajima K. , Mizuguchi Y.
Published: January 2018

Low energy phonons in LaOBiS2−xSex are studied using inelastic neutron scattering. Dispersionless flat phonon branches that are mainly associated with a large vibration of Bi atoms are observed at a relatively low energy of E = 6–6.7 meV. The phonon energy softens upon Se doping presumably owing to its heavier atomic mass than the S atom and the expansion of the lattice constant. Simultaneously, the lattice thermal conductivity lowered upon Se doping as the same manner of the phonon softening. These suggest that despite the lack of an oversized cage in LaOBiS2−xSex, rattling motions of Bi atoms can scatter phonon like rattling in cage compounds, contributing to enhance the thermoelectric property.
Microwave irradiation-assisted deposition of Ga2O3 on III-nitrides for deep-UV opto-electronics
Authors: Jaiswal Piyush , Ul Muazzam Usman , Pratiyush Anamika Singh , Mohan Nagaboopathy , Raghavan Srinivasan , Muralidharan R. , Shivashankar S. A. , Nath Digbijoy N.
Published: January 2018

We report on the deposition of Ga2O3 on III-nitride epi-layers using the microwave irradiation technique. We also report on the demonstration of a Ga2O3 device: a visible-blind, deep-UV detector, with a GaN-based heterostructure as the substrate. The film deposited in the solution medium, at <200 °C, using a metalorganic precursor, was nanocrystalline. XRD confirms that the as-deposited film, when annealed at high temperature, turns to polycrystalline β−Ga2O3. SEM shows the as-deposited film to be uniform, with a surface roughness of 4–5 nm, as revealed by AFM. Interdigitated metal-semiconductor-metal devices with Ni/Au contact exhibited a peak spectral response at 230 nm and a good visible rejection ratio. This demonstration of a deep-UV detector on the β−Ga2O3/III-nitride stack is expected to open up possibilities of functional and physical integration of β−Ga2O3 and GaN material families towards enabling next-generation high-performance devices by exciting band and heterostructure engineering.
Detection and characterization of the tin dihydride (SnH2 and SnD2) molecule in the gas phase
Authors: Smith Tony C. , Clouthier Dennis J.
Published: January 2018

The SnH2 and SnD2 molecules have been detected for the first time in the gas phase by laser-induced fluorescence (LIF) and emission spectroscopic techniques through the Ã1B1–X̃1A1 electronic transition. These reactive species were prepared in a pulsed electric discharge jet using (CH3)4Sn or SnH4/SnD4 precursors diluted in high pressure argon. Transitions to the electronic excited state of the jet-cooled molecules were probed with LIF, and the ground state energy levels were measured from single rovibronic level emission spectra. The LIF spectrum of SnD2 afforded sufficient rotational structure to determine the ground and excited state geometries: r0″ = 1.768 Å, θ0″ = 91.0°, r0′ = 1.729 Å, θ0′ = 122.9°. All of the observed LIF bands show evidence of a rotational-level-dependent predissociation process which rapidly decreases the fluorescence yield and lifetime with increasing rotational angular momentum in each excited vibronic level. This behavior is analogous to that observed in SiH2 and GeH2 and is suggested to lead to the formation of ground state tin atoms and hydrogen molecules.
Intrinsic defect processes and elastic properties of Ti3AC2 (A = Al, Si, Ga, Ge, In, Sn) MAX phases
Authors: Christopoulos S.-R. G. , Filippatos P. P. , Hadi M. A. , Kelaidis N. , Fitzpatrick M. E. , Chroneos A.
Published: January 2018

Mn+1AXn phases (M = early transition metal; A = group 13–16 element and X = C or N) have a combination of advantageous metallic and ceramic properties, and are being considered for structural applications particularly where high thermal conductivity and operating temperature are the primary drivers: for example in nuclear fuel cladding. Here, we employ density functional theory calculations to investigate the intrinsic defect processes and mechanical behaviour of a range of Ti3AC2 phases (A = Al, Si, Ga, Ge, In, Sn). Based on the intrinsic defect reaction, it is calculated that Ti3SnC2 is the more radiation-tolerant 312 MAX phase considered herein. In this material, the C Frenkel reaction is the lowest energy intrinsic defect mechanism with 5.50 eV. When considering the elastic properties of the aforementioned MAX phases, Ti3SiC2 is the hardest and Ti3SnC2 is the softest. All the MAX phases considered here are non-central force solids and brittle in nature. Ti3SiC2 is elastically more anisotropic and Ti3AlC2 is nearly isotropic.
The dynamics and Lorentz transformation of magnetic nulls
Authors: Yang Shu-Di , Wang Xiao-Gang
Published: January 2018

Having previously treated the problem of the Lorentz transformation properties of static field lines around magnetic neutral points, it is time to explore the properties of dynamic nulls. We discuss the relativistic motion of magnetic nulls accounting for both the linear and the second order structure of the magnetic field. It is found that the dynamics of a magnetic null is given by a world line trajectory of the null point and the changing fieldline structure. The dynamics of magnetic null structure is also explored, showing the significance of both the null structure and the flow pattern. We describe relativistic transformation properties of the appearance and annihilation of magnetic nulls, where the previously proposed null region is used as an invariant identification of topological transition and bifurcation processes.
Pseudo-diode based on protonic/electronic hybrid oxide transistor
Authors: Fu Yang Ming , Liu Yang Hui , Zhu Li Qiang , Xiao Hui , Song An Ran
Published: January 2018

Current rectification behavior has been proved to be essential in modern electronics. Here, a pseudo-diode is proposed based on protonic/electronic hybrid indium-gallium-zinc oxide electric-double-layer (EDL) transistor. The oxide EDL transistors are fabricated by using phosphorous silicate glass (PSG) based proton conducting electrolyte as gate dielectric. A diode operation mode is established on the transistor, originating from field configurable proton fluxes within the PSG electrolyte. Current rectification ratios have been modulated to values ranged between ∼4 and ∼50 000 with gate electrode biased at voltages ranged between −0.7 V and 0.1 V. Interestingly, the proposed pseudo-diode also exhibits field reconfigurable threshold voltages. When the gate is biased at −0.5 V and 0.3 V, threshold voltages are set to ∼−1.3 V and −0.55 V, respectively. The proposed pseudo-diode may find potential applications in brain-inspired platforms and low-power portable systems.
Investigating non-equilibrium carrier lifetimes in nitrogen-doped and boron-doped single crystal HPHT diamonds with an optical method
Authors: Song Y. , Peng B. D. , Song G. Z. , Yue Z. Q. , Li B. K. , Ma J. M. , Sheng L. , Duan B. J. , Wang H. X.
Published: January 2018

Non-equilibrium carrier lifetimes in nitrogen-doped and boron-doped single crystal HPHT diamonds have been investigated using a non-destructive optical method. In this method, a fiber was used to send a probe beam into the double-side polished sample and collect the interference beams reflected from the front and rear surfaces for directly measuring the refractive index change with a spatial resolution of about 10 μm. Carrier lifetimes at several points in each sample have been investigated, whose relationships with the impurity concentrations have been analyzed. The nitrogen impurity can effectively reduce the carrier lifetime. Fast and slow carrier recombination components have been found in the boron-doped sample, which are caused by the deep traps and the compensated boron impurity, respectively. This investigation method can also provide a scheme for estimating the impurity concentration in diamond with a high spatial resolution.
Microgravity modulation effects on free convection problems LBM simulation
Authors: Javadi Khodayar , Kazemi Koorosh
Published: January 2018

In this paper, microgravity modulation effects on free convection in a cavity are investigated using the lattice Boltzmann method. In order to create microgravity modulation, a sinusoidal time-dependent function is considered. Parameters of the flow are chosen such that the maximum Rayleigh number approaches 106. The natural frequency of the system is obtained at first. Afterwards, effects of different frequencies on the flow and heat transfer fields are investigated in detail. Results are presented in four different frequency ratios categorized as (1) ω*=1200, 1100, 120, and 110; (2) ω*=18, 15, 13, and 12; (3) ω* = 0.75, 0.85, and 0.95; and (4) the last one is considered for natural frequency as a special case of ω* = 1. Furthermore, the fast Fourier transformation is used to describe the cavity flow behavior. The results indicated that at low frequency, the system has enough time to adapt itself with the gravity modulation while historical effects do not disappear. Increasing the frequency changes the behavior of the system and different flow patterns appear. Finally, at the natural frequency (ω* = 1), all system modes are stimulated and a strange flow pattern is formed.
Monte Carlo simulations identify cI16 as mechanically metastable for classical hard spheres
Authors: Yiu Yuen
Published: January 2018

Monte Carlo results confirm the body-centered cubic structure as an unstable phase for hard spheres and identify a mechanically stable amorphous crystalline structure.
Effects of applying lactic acid bacteria and propionic acid on fermentation quality, aerobic stability and in vitro gas production of forage-based total mixed ration silage in Tibet
Authors: Chen L. , Yuan X. J. , Li J. F. , Dong Z. H. , Wang S. R. , Guo G. , Shao T.
Published: January 2018

Total mixed ration (TMR) silage technology has been practically used to feed ruminants in Tibet. This study was conducted on forage-based TMR to evaluate the effects of supplementing lactic acid bacteria and propionic acid on its fermentation characteristics, aerobic stability and in vitro gas production kinetics and digestibility. Experimental treatments included four variants: (1) TMR supplemented with 10 mL deionised water per kilogram fresh matter (Control); (2) TMR supplemented with 1 × 106 cfu/g Lactobacillus plantarum (L); (3) TMR supplemented with 0.3% propionic acid (P); (4) TMR supplemented with a combination of 1 × 106 cfu/g Lactobacillus plantarum and 0.3% propionic acid (LP). The latter three additives were first dissolved in deionised water and then applied as a water solution (10 mL/kg fresh matter). All treatments were ensiled in laboratory-scale silos for 45 days, and then exposed to air for 12 days to evaluate the aerobic stability of TMR silage. Further, the four experimental treatments were fermented with buffered rumen fluid to measure in vitro gas production and nutrients’ digestibility. The results indicated that all TMR silages possessed good fermentation characteristics with low pH values (<4.18) and ammonia nitrogen (NH3-N) contents (<100 g/kg total nitrogen), and high lactic acid contents (>66 g/kg DM) and Flieg points (>80). The addition of L and LP stimulated a more efficient homofermentation of TMR silage than in the variant without L, as evidenced by higher ratios of lactic:acetic acid. The addition of P had no effect (P > 0.05) on lactic acid production of TMR silage compared with the Control, whereas it decreased NH3-N content (P < 0.05). Under aerobic conditions, L silage showed less aerobic stability compared with the Control silage, whereas P and LP silages were more (P < 0.05) aerobically stable. Compared with the Control, all additives elevated (P < 0.05) the total gas production and in vitro dry matter digestibility of TMR silages. L silage had a higher (P < 0.05) in vitro neutral detergent fibre digestibility than the Control silage. Data obtained from this study suggested that TMR silage based on oat and common vetch can be well conserved with or without additives. Lactic acid bacteria were compatible with propionic acid, and addition of lactic acid bacteria together with propionic acid can improve the fermentation quality, aerobic stability and in vitro dry matter digestibility of TMR silage.
Growth is required for perception of water availability to pattern root branches in plants
Authors: Robbins Neil E. , Dinneny José R.
Published: January 2018

Significance

Plant roots activate lateral branching in response to contact with available water, but the mechanism by which this environmental signal is perceived is poorly understood. Through a combination of empirical and mathematical-modeling approaches we discovered a central role of tissue growth in this process. Growth causes water uptake, and the biophysical changes that occur during this process are interpreted by the organism to position new lateral branches. This observation is a significant advancement in our understanding of how the environment shapes plant development and demonstrates that perception of water is intimately tied to a core biological function of the root.
Dual evolutionary origin of insect wings supported by an investigation of the abdominal wing serial homologs in
Tribolium
Authors: Linz David M. , Tomoyasu Yoshinori
Published: January 2018

Significance

Acquisition of morphologically novel structures can facilitate successful radiation during evolution. The emergence of wings in hexapods represents a profound moment in eukaryotic evolution, making insects one of the most successful groups. However, the tissue that gave rise to this novel and evolutionarily crucial structure, and the mechanism that facilitated its evolution, are still under intense debate. By studying various wing-related tissues in beetles, we demonstrated that two distinct lineages of wing-related tissues are present even outside the appendage-bearing segments. This outcome supports a dual evolutionary origin of insect wings, and shows that novelty can emerge through two previously unassociated tissues collaborating to form a new structure.
The social genome of friends and schoolmates in the National Longitudinal Study of Adolescent to Adult Health
Authors: Domingue Benjamin W. , Belsky Daniel W. , Fletcher Jason M. , Conley Dalton , Boardman Jason D. , Harris Kathleen Mullan
Published: January 2018

Significance

Our study reported significant findings of a “social genome” that can be quantified and studied to understand human health and behavior. In a national sample of more than 5,000 American adolescents, we found evidence of social forces that act to make friends and schoolmates more genetically similar to one another compared with random pairs of unrelated individuals. This subtle genetic similarity was observed across the entire genome and at sets of genomic locations linked with specific traits—educational attainment and body mass index—a phenomenon we term “social–genetic correlation.” We also find evidence of a “social–genetic effect” such that the genetics of a person’s friends and schoolmates influenced their own education, even after accounting for the person’s own genetics.
Golgi stress response reprograms cysteine metabolism to confer cytoprotection in Huntington’s disease
Authors: Sbodio Juan I. , Snyder Solomon H. , Paul Bindu D.
Published: January 2018

Significance

Golgi stress response is emerging as a major stress response pathway although molecular players in the process have not been identified. We show that Golgi stress response induced by the ionophore monensin is mediated by the PERK-ATF4 pathway. We further show that subtoxic levels of monensin precondition cells to respond to future damaging insults. Monensin stimulates the reverse transsulfuration pathway via cystathionine γ-lyase, the biosynthetic enzyme for cysteine, important for redox homeostasis. We have harnessed this pathway to mitigate toxicity associated with cysteine deprivation in Huntington’s disease (HD). These findings are relevant to not only HD, but also other diseases involving redox imbalance. Targeting the molecular controls for restoration of cysteine balance may offer more robust therapeutic avenues for disease management.
Key comparison BIPM.RI(I)-K1 of the air-kerma standards of the IST-LPSR, Portugal and the BIPM in 60Co gamma radiation
Authors: Kessler C , Burns D , Cardoso J
Published: January 2018

A comparison of the standards for air kerma of the Instituto Superior Técnico, Laboratório de Proteção e Segurança Radiológica (IST-LPSR), Portugal and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 60Co radiation beam of the BIPM in December 2015. The comparison result, evaluated as a ratio of the IST-LPSR and the BIPM standards for air kerma, is 1.0026 with a combined standard uncertainty of 1.7 × 10−3. The results for an indirect comparison made at the same time are consistent with the direct results at the level of 1.1 parts in 103. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Enrichment analysis with EpiAnnotator
Authors: Pageaud Yoann , Plass Christoph , Assenov Yassen
Published: January 2018

Motivation

Deciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations require time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user-friendly way.

Results

EpiAnnotator is an R Package accompanied by a web interface. It contains regularly updated annotations from 4 public databases: Blueprint, RoadMap, GENCODE and the UCSC Genome Browser. Annotations are hosted locally or in a server environment and automatically updated by scripts of our own design. Thousands of tracks are available, reflecting data on a variety of tissues, cell types and cell lines from the human and mouse genomes. Users need to upload sets of selected and background regions. Results are displayed in customizable and easily interpretable figures.

Availability and implementation

The R package and Shiny app are open source and available under the GPL v3 license. EpiAnnotator’s web interface is accessible at http://computational-epigenomics.com/en/epiannotator.
Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms
Authors: Ferraro Petrillo Umberto , Roscigno Gianluca , Cattaneo Giuseppe , Giancarlo Raffaele
Published: January 2018

Motivation

Information theoretic and compositional/linguistic analysis of genomes have a central role in bioinformatics, even more so since the associated methodologies are becoming very valuable also for epigenomic and meta-genomic studies. The kernel of those methods is based on the collection of k-mer statistics, i.e. how many times each k-mer in {A,C,G,T}k occurs in a DNA sequence. Although this problem is computationally very simple and efficiently solvable on a conventional computer, the sheer amount of data available now in applications demands to resort to parallel and distributed computing. Indeed, those type of algorithms have been developed to collect k-mer statistics in the realm of genome assembly. However, they are so specialized to this domain that they do not extend easily to the computation of informational and linguistic indices, concurrently on sets of genomes.

Results

Following the well-established approach in many disciplines, and with a growing success also in bioinformatics, to resort to MapReduce and Hadoop to deal with ‘Big Data’ problems, we present KCH, the first set of MapReduce algorithms able to perform concurrently informational and linguistic analysis of large collections of genomic sequences on a Hadoop cluster. The benchmarking of KCH that we provide indicates that it is quite effective and versatile. It is also competitive with respect to the parallel and distributed algorithms highly specialized to k-mer statistics collection for genome assembly problems. In conclusion, KCH is a much needed addition to the growing number of algorithms and tools that use MapReduce for bioinformatics core applications.

Availability and implementation

The software, including instructions for running it over Amazon AWS, as well as the datasets are available at http://www.di-srv.unisa.it/KCH.

Supplementary information

Supplementary data are available at Bioinformatics online.
Frontoparietal Activity Interacts With Task-Evoked Changes in Functional Connectivity
Authors: Hwang Kai , Shine James M , D’Esposito Mark
Published: January 2018

Flexible interactions between brain regions enable neural systems to adaptively transfer and process information. However, the neural substrates that regulate adaptive communications between brain regions are understudied. In this human fMRI study, we investigated this issue by tracking time-varying, task-evoked changes in functional connectivity between localized occipitotemporal regions while participants performed different tasks on the same visually presented stimuli. We found that functional connectivity between ventral temporal and the primary visual regions selectively increased during the processing of task-relevant information. Further, additional task demands selectively strengthen these targeted connectivity patterns. To identify candidate regions that contribute to this increase in inter-regional coupling, we regressed the task-specific time-varying connectivity strength between primary visual and occipitotemporal regions against voxel-wise activity patterns elsewhere in the brain. This allowed us to identify a set of frontal and parietal regions whose activity increased as a function of task-evoked functional connectivity. These results suggest that frontoparietal regions may provide top-down biasing signals to influence task-specific interactions between brain regions.
Exploring the economic viability of a mesopelagic fishery in the Bay of Biscay
Authors: Prellezo Raúl
Published: January 2018

The study analyses the economic viability of the mesopelagic fish exploitation. Operating characteristics of the selected bottom-trawl fleet operating in the Bay of Biscay were analysed on a trip basis, from the technical, financial and market perspectives. The results show that, while this activity is technically possible, it cannot be considered a viable financial alternative to the existing commercial fisheries. However, the landing obligation of the European Union Common Fisheries Policy, to become fully operational in 2019, provides an economic incentive in the form of alternative trips. The fishing effort is to be limited by this regulation. Thus, the discouraging opportunity costs of fishing mesopelagic species might be alleviated by the effort limitation. Additionally, the existing markets might expand, and new opportunities for commercial fisheries of mesopelagic species might be created. The sustainability of exploitation and its impact on the ecosystem services associated with these species should be considered in their management.
Vaginal health of postmenopausal women on nutraceutical containing equol
Authors: Caruso Salvatore , Cianci Stefano , Fava Valentina , Rapisarda Agnese M. C. , Cutello Silvia , Cianci Antonio
Published: January 2018

Objective:

The aim of the study was to evaluate the effects of nutraceuticals containing equol on vaginal health of postmenopausal women with vulvovaginal symptoms and dyspareunia.

Methods:

One hundred twenty-six natural postmenopausal women on +1b +1c (2 and 3-6 y after the final menstrual period, respectively) of the Stages of Reproductive Aging Workshop were enrolled in a nonrandomized trial. Of these, 72 women accepted to use nutraceutical (group A). The remaining 54 women refused the treatment and participated as the control group (group B). Group A was prescribed one tablet daily to take orally, for 8 months. All assessments were made at baseline and at 4 and 8 months. Determination of vaginal maturation index (VMI), evaluation of vaginal pH, and assessment of vaginal atrophy symptoms by the vaginal health index (VHI) were carried out. Dyspareunia score was also measured.

Results:

Group A had a significant increase in VMI (68 ± 5 vs 58 ± 8) and improvement of vaginal pH (4.1 ± 1.3 vs 5.1 ± 1.7) compared with baseline, mainly after 8 months of treatment (P < 0.001). Group A had an improvement of VHI after 4 (13 ± 3, P < 0.01) and 8 (16 ± 2, P < 0.001) months of nutraceutical intake. Dyspareunia reduced after 8 months (5.1 ± 1.3 vs 3.8 ± 1.2, P < 0.001) but not after 4 months (4.7 ± 1.1, P = 0.06) of treatment. Group B showed no changes from baseline evaluation (P = 0.22).

Conclusions:

Nutraceuticals containing equol could be effective in modulating postmenopausal symptoms, particularly vaginal symptoms, and could be well accepted by the women who usually do not wish to use hormone therapy or cannot use it for medical reasons.
Safety of Reiki Therapy for Newborns at Risk for Neonatal Abstinence Syndrome
Authors: Radziewicz Rosanne Marie , Wright-Esber Sandra , Zupancic Julie , Gargiulo Deb , Woodall Patricia
Published: January 2018

The incidence of opioid abuse and subsequent drug withdrawal is exponentially on the rise in the United States for many populations including newborns who are born to drug-addicted mothers. These newborns often exhibit symptoms of neonatal abstinence syndrome (NAS) within 24 to 72 hours of birth. Treatment of NAS includes monitoring of withdrawal symptoms, managing physiological parameters, and the use of supportive and pharmacologic treatments. Although a few randomized controlled trials exist, studies on supportive intervention are generally limited by small sample sizes, case study reports, expert opinions, and descriptive design. Few studies address the safety of Reiki for newborns at risk for NAS using neonatal parameters. This pilot study addresses feasibility and demonstrates that Reiki is safe when administered to this high-risk population. Considerations for future studies are discussed.
Prevalence of Hearing Loss and Hearing Care Use Among Asian Americans: A Nationally Representative Sample
Authors: Choi Janet S. , Kari Elina , Friedman Rick A. , Fisher Laurel M.
Published: January 2018

Objective:

To assess the prevalence of hearing loss and factors affecting hearing care use among Asian Americans, using the first nationally representative sample of Asian Americans.

Study Design:

National cross-sectional survey.

Setting:

Ambulatory examination centers.

Patients:

Three thousand six hundred twelve adults (522 Asian American) aged 20 to 69 in the 2011 to 2012 National Health and Examination Survey with pure-tone audiometry.

Main Outcome Measure(s):

Percentage with hearing loss, undertaking a hearing test before the study, and hearing aid use. Hearing loss was defined as better hearing ear speech frequency pure-tone average ≥25 dBHL. Analyses incorporated sampling weights to account for complex sampling design.

Results:

The prevalence of hearing loss was 6.0% [95% CI 3.1–8.9%] among Asian Americans, comparable to White, Black, and Hispanic groups, and increased substantially with age (OR: 2.25 [95% CI: 1.6–3.2]). After adjusting for age and pure-tone average, Asian Americans with hearing loss were less likely to have received a hearing test compared with White (OR: 0.27 [95% CI: 0.20–0.36, p = <0.001]) and Black groups (OR: 0.26 [95% CI: 0.16–0.38, p<0.001]), less likely to use hearing aids compared with Whites (OR: 0.06 [95% CI: 0.01–0.64], p = 0.02), and less likely to self-report poor hearing compared with Whites (OR: 0.30 [95% CI: 0.10–0.90], p = 0.03). Among Asian Americans, using more non-English than English, being foreign-born, less education, being married, and not having insurance were associated with lower levels of receiving a hearing test.

Conclusion:

The nationally representative sample of Asian Americans with hearing data suggests that hearing loss prevalence is similar to other races/ethnicities. However, hearing aid adoption by Asian Americans tends to be less frequent.
The Application of Sigmoid Sinus Tunnel-packing or Push-packing of the Inferior Petrous Sinus in the Microsurgical Management of Jugular Paragangliomas
Authors: Jang Mi , Liu Hongyan , Dai Chunfu
Published: January 2018

Objective:

To analyze the outcomes of microsurgically treated jugular paragangliomas with control of bleeding from the inferior petrous sinus.

Study Design:

Retrospective patient review.

Setting:

A single university hospital.

Patients:

Forty-three patients with jugular paragangliomas were diagnosed in the past 7 years in our clinic.

Main Outcome Measures:

Surgical tumor control, intraoperative blood loss, intraoperative management of the facial nerve, and the preoperative and postoperative function of the lower central nerves.

Results:

Twenty-six patients underwent microsurgical treatment. Eighteen tumors were class C2 (69.2%), six were class C3 (23.1%), and two were class CDe1 (7.7%). Gross total tumor resection was achieved in 92.3% of the patients. The mean blood loss during surgery was 438.5 ml. The recurrence rate was 3.8% over a mean follow-up of 29.2 months. New facial palsy and lower cranial nerve deficit occurred in 42.3 and 11.5% of the patients, respectively.

Conclusion:

The infratemporal fossa approach type A with sigmoid sinus tunnel-packing or push-packing technique facilitated the control of bleeding from the inferior petrous sinus and improved the outcomes of microsurgical treatment for jugular paragangliomas.
Kinetic transition in the order–disorder transformation at a solid/liquid interface
Authors: Galenko P. K. , Nizovtseva I. G. , Reuther K. , Rettenmayr M.
Published: January 2018

Phase-field analysis for the kinetic transition in an ordered crystal structure growing from an undercooled liquid is carried out. The results are interpreted on the basis of analytical and numerical solutions of equations describing the dynamics of the phase field, the long-range order parameter as well as the atomic diffusion within the crystal/liquid interface and in the bulk crystal. As an example, the growth of a binary A
50
B
50
crystal is described, and critical undercoolings at characteristic changes of growth velocity and the long-range order parameter are defined. For rapidly growing crystals, analogies and qualitative differences are found in comparison with known non-equilibrium effects, particularly solute trapping and disorder trapping. The results and model predictions are compared qualitatively with results of the theory of kinetic phase transitions (Chernov 1968
Sov. Phys. JETP
26
, 1182–1190) and with experimental data obtained for rapid dendritic solidification of congruently melting alloy with order–disorder transition (Hartmann
et al.
2009
Europhys. Lett.
87
, 40007 (
doi:10.1209/0295-5075/87/40007
)).

This article is part of the theme issue ‘From atomistic interfaces to dendritic patterns’.
A compromised gsdf signaling leads to gamatogenesis confusion and subfertility in medaka
Authors: Guan Guijun , Xu Shumei , Guo Anning , Zhao Xiaomiao , Zhang Yingqing , Sun Kaiqing , Kang Yi , Chang Yuyang , Wu Xiaowen , Chen Liangbiao
Published: January 2018

Summary statement

Gsdf signals trigger the gamatogenesis, alter the somatic expression of Fsh/Lh receptors and brain type aromatase in medaka brain and gonad.

Gonadal soma-derived factor (gsdf) and anti-Mullerian hormone (amh) are somatic male determinants in several species of teleosts, although the mechanisms by which they trigger the indifferent germ cells into the male pathway remain unknown. This study aimed to decipher the roles of gsdf/amh in directing the sexual fate of germ cells using medaka as a model. Transgenic lines (TgcryG) that restrictively and persistently express a Gsdf-Gfp fusion protein in the lens and the hypothalamus-pituitary-gonad (HPG) axis, were generated under the control of a mouse γF-crystallin promoter. A high frequency (44.4%) of XX male sex reversals was obtained in TgcryG lines, indicating that signals of gsdf-expressing cells in HPG were enough for the spermatogenesis activation in the genetic females. Furthermore, all TgcryG XY individuals with endogenous gsdf depletion (named Sissy) displayed intersex (100%) with enlarged ovotestis in contrast to a giant ovary developed in XY gsdf deficiency. The heterogeneous expression of gsdf led to the confusion of gamatogenesis and ovotestis development, similar to some hotei (amhr2) mutants, suggests that the signaling balance of gsdf/amh is essential for proper gamatogenesis, maintaining sex steroid production and gonadotropin secretion, which are evolutionarily conserved across phyla.