bluuebunny/crossref_metadata_2025 huggingface dataset:
Large spectral weight transfer in optical conductivity of SrTiO3 induced by intrinsic vacancies
Authors: Asmara T. C. , Wang X. , Santoso I. , Zhang Q. , Shirakawa T. , Qi D. , Kotlov A. , Motapothula M. , Breese M. H. , Venkatesan T. , Yunoki S. , Rübhausen M. , Ariando  , Rusydi A.
Published: June 2014

The optical conductivity (σ1) of SrTiO3 for various vacancies has been systematically studied using a combination of ultraviolet-vacuum ultraviolet reflectivity and spectroscopic ellipsometry. For cation (Ti) vacancies, σ1 shows large spectral weight transfer over a wide range of energy from as high as 35 eV to as low as 0.5 eV and the presence of mid-gap states, suggesting that strong correlations play an important role. Meanwhile, for anion (O) vacancies, σ1 shows changes from 7.4 eV up to 35 eV.
Fluctuation-induced transport of two coupled particles: Effect of the interparticle interaction
Authors: Makhnovskii Yurii A. , Rozenbaum Viktor M. , Sheu Sheh-Yi , Yang Dah-Yen , Trakhtenberg Leonid I. , Lin Sheng Hsien
Published: June 2014

We consider a system of two coupled particles fluctuating between two states, with different interparticle interaction potentials and particle friction coefficients. An external action drives the interstate transitions that induces reciprocating motion along the internal coordinate x (the interparticle distance). The system moves unidirectionally due to rectification of the internal motion by asymmetric friction fluctuations and thus operates as a dimeric motor that converts input energy into net movement. We focus on how the law of interaction between the particles affects the dimer transport and, in particular, the role of thermal noise in the motion inducing mechanism. It is argued that if the interaction potential behaves at large distances as xα, depending on the value of the exponent α, the thermal noise plays a constructive (α > 2), neutral (α = 2), or destructive (α < 2) role. In the case of α = 1, corresponding piecewise linear potential profiles, an exact solution is obtained and discussed in detail.
Spectroscopy of Mn atoms isolated in solid 4He
Authors: Moroshkin P. , Lebedev V. , Weis A.
Published: June 2014

We present an experimental study of the laser-induced luminescence spectra of Mn atoms in solid helium matrices. We observe transitions of the valence electron and of inner-shell electrons. We find that the Mn-He interaction perturbs the inner-shell transitions to a lesser extent than the valence-electron transitions. The observed lineshapes of the inner-shell transitions of Mn are similar to those of an inner-shell transition in Ba studied earlier. At the same time, they are more strongly perturbed than the corresponding transitions in Au and Cu under the same conditions. We suggest a qualitative explanation of these observations based on the atomic bubble model. Our results also suggest that the inner-shell transitions of Mn in solid He are more strongly perturbed than the same lines of Mn isolated in solid Ar or Kr matrices.
Quasiparticle electronic structure and optical absorption of diamond nanoparticles from ab initio many-body perturbation theory
Authors: Yin Huabing , Ma Yuchen , Hao Xiaotao , Mu Jinglin , Liu Chengbu , Yi Zhijun
Published: June 2014

The excited states of small-diameter diamond nanoparticles in the gas phase are studied using the GW method and Bethe-Salpeter equation (BSE) within the ab initio many-body perturbation theory. The calculated ionization potentials and optical gaps are in agreement with experimental results, with the average error about 0.2 eV. The electron affinity is negative and the lowest unoccupied molecular orbital is rather delocalized. Precise determination of the electron affinity requires one to take the off-diagonal matrix elements of the self-energy operator into account in the GW calculation. BSE calculations predict a large exciton binding energy which is an order of magnitude larger than that in the bulk diamond.
Exact axisymmetric Taylor states for shaped plasmas
Authors: Cerfon Antoine J. , O'Neil Michael
Published: June 2014

We present a general construction for exact analytic Taylor states in axisymmetric toroidal geometries. In this construction, the Taylor equilibria are fully determined by specifying the aspect ratio, elongation, and triangularity of the desired plasma geometry. For equilibria with a magnetic X-point, the location of the X-point must also be specified. The flexibility and simplicity of these solutions make them useful for verifying the accuracy of numerical solvers and for theoretical studies of Taylor states in laboratory experiments.
Reduction of metal contact resistance of graphene devices via CO2 cluster cleaning
Authors: Gahng Sarang , Ho Ra Chang , Jin Cho Yu , Ah Kim Jang , Kim Taesung , Jong Yoo Won
Published: June 2014

We report on a cleaning technique using CO2 clusters for large-scale mono-layer graphene fabricated via chemical vapor deposition (CVD) and its application to reduce contact resistance of the CVD graphene device. We found that polymeric residues, i.e., polymethyl methacrylate and photoresist which are generated during transfer and patterning of graphene, can be effectively removed via rapid shrinkage, induced by thermal energy transfer to low temperature CO2 clusters. By applying the CO2 clusters to the cleaning of the interface between metal and graphene, the metal contact resistance of the fabricated graphene field effect transistor was lowered to 26.6% of pristine graphene. The contact resistance shows the best result at an optimized CO2 cluster cleaning condition with a flow rate of 20 l/min, and the resistance was further lowered to 270 Ω μm when a gate bias of −40 V was applied. We expect that the proposed CO2 cluster cleaning to be a very promising technique for future device application using 2-dimensional materials, as it can enable low-energy, large-area, high-throughput, and mass-production-compatible process.
Properties of (Ga,Mn)As codoped with Li
Authors: Miyakozawa Shohei , Chen Lin , Matsukura Fumihiro , Ohno Hideo
Published: June 2014

We grow Li codoped (Ga,Mn)As layers with nominal Mn composition up to 0.15 by molecular beam epitaxy. The layers before and after annealing are characterized by x-ray diffraction, transport, magnetization, and ferromagnetic resonance measurements. The codoping with Li reduces the lattice constant and electrical resistivity of (Ga,Mn)As after annealing. We find that (Ga,Mn)As:Li takes similar Curie temperature to that of (Ga,Mn)As, but with pronounced magnetic moments and in-plane magnetic anisotropy, indicating that the Li codoping has nontrivial effects on the magnetic properties of (Ga,Mn)As.
O-vacancies mediated room temperature ferromagnetism in Cu-implanted In2O3:Cu nanowires
Authors: Zou C. W. , Wu H. Z. , Liang F. , Xue S. W. , Shao L. X.
Published: June 2014

The correlation between the ferromagnetism and oxygen vacancy (VO) of Cu-implanted In2O3 nanowires was investigated. When annealed in vacuum, the saturation magnetization first increased to 0.71 Cu/μB for In2O3:Cu nanowires annealed at 800 °C, after which it rapidly decreased to 0.55 Cu/μB when annealed at 900 °C. However, the saturation magnetization showed a monotonously decreased trend when annealed in O2. The In2O3:Cu nanowires showed a direct relationship between the oxygen vacancy concentration and the degree of magnetization. The oxygen vacancies orbitals mediated indirect double-exchange model has been used to explain the ferromagnetism properties in Cu-doped In2O3 and a sufficient amount of both oxygen vacancies and Cu impurities is essential to the observed ferromagnetism.
Pinning effects of dislocations on vortex domain structure in ferroelectric nanodots
Authors: Chen W. J. , Zheng Yue , Wang Biao
Published: June 2014

Effects of interfacial and internal dislocations on formation of vortex domain structure in ferroelectric nanodots have been investigated. Due to the highly inhomogeneous strain field near the dislocation core, dislocations are found to play important roles in vortex nucleation stage and can significantly affect vortex formation temperature. More importantly, the vortex core may be pinned by the dislocations, leading to a possible control of vortex domain pattern (e.g., vortices number and orientation) in the nanodots. This study should be very instructive for practical applications of ferroelectric vortex domain structure in systems where dislocations exist.
In-plane emission of indistinguishable photons generated by an integrated quantum emitter
Authors: Kalliakos Sokratis , Brody Yarden , Schwagmann Andre , Bennett Anthony J. , Ward Martin B. , Ellis David J. P. , Skiba-Szymanska Joanna , Farrer Ian , Griffiths Jonathan P. , Jones Geb A. C. , Ritchie David A. , Shields Andrew J.
Published: June 2014

We demonstrate the emission of indistinguishable photons along a semiconductor chip originating from carrier recombination in an InAs quantum dot. The emitter is integrated in the waveguiding region of a photonic crystal structure, allowing for on-chip light propagation. We perform a Hong-Ou-Mandel-type of experiment with photons collected from the exit of the waveguide, and we observe two-photon interference under continuous wave excitation. Our results pave the way for the integration of quantum emitters in advanced photonic quantum circuits.
Wideband radar cross section reduction using two-dimensional phase gradient metasurfaces
Authors: Li Yongfeng , Zhang Jieqiu , Qu Shaobo , Wang Jiafu , Chen Hongya , Xu Zhuo , Zhang Anxue
Published: June 2014

Phase gradient metasurface (PGMs) are artificial surfaces that can provide pre-defined in-plane wave-vectors to manipulate the directions of refracted/reflected waves. In this Letter, we propose to achieve wideband radar cross section (RCS) reduction using two-dimensional (2D) PGMs. A 2D PGM was designed using a square combination of 49 split-ring sub-unit cells. The PGM can provide additional wave-vectors along the two in-plane directions simultaneously, leading to either surface wave conversion, deflected reflection, or diffuse reflection. Both the simulation and experiment results verified the wide-band, polarization-independent, high-efficiency RCS reduction induced by the 2D PGM.
High sensitivity optomechanical reference accelerometer over 10 kHz
Authors: Guzmán Cervantes Felipe , Kumanchik Lee , Pratt Jon , Taylor Jacob M.
Published: June 2014

We present an optically detected mechanical accelerometer that achieves a sensitivity of 100 ngn/Hz over a bandwidth of 10 kHz and is traceable. We have incorporated a Fabry-Pérot fiber-optic micro-cavity that is currently capable of measuring the test-mass displacement with sensitivities of 200 am/Hz, and whose length determination enables traceability to the International System of Units. The compact size and high mQ-product achieved combined with the high sensitivity and simplicity of the implemented optical detection scheme highlight our device and this category of accelerometers, outlining a path for high sensitivity reference acceleration measurements and observations in seismology and gravimetry.
Spontaneous radial liquid crystals alignment on curved polymeric surfaces
Authors: De Sio Luciano , Tabiryan Nelson , Bunning Timothy
Published: June 2014

We report on the fabrication and characterization of curved periodic microstructures formed through the controlled phase separation of a liquid crystal and a polymerizing matrix comprising self-aligned liquid crystal. Imaging through a “Fresnel like” structure imparts an intensity profile onto a photosensitive mixture which subsequently forms periodic alternating curved polymeric and liquid crystal slices. The phase separated concentric rings of nematic liquid crystal self-align in a radial alignment in between the polymer walls as indicated by polarizing optical microscopy analysis (Maltese cross). Electro-optical experiments confirm the possibility to control this alignment and the optical properties of the macroscopic structure by means of a quite low external voltage. The system exhibits high-quality and self-alignment of an ordered (liquid crystal) fluid without the need of surface chemistry or functionalization.
Relativistic effects in the photoionization of hydrogen-like ions with screened Coulomb interaction
Authors: Xie L. Y. , Wang J. G. , Janev R. K.
Published: June 2014

The relativistic effects in the photoionization of hydrogen-like ion with screened Coulomb interaction of Yukawa type are studied for a broad range of screening lengths and photoelectron energies. The bound and continuum wave functions have been determined by solving the Dirac equation. The study is focused on the relativistic effects manifested in the characteristic features of photoionization cross section for electric dipole nl→ε,l±1 transitions: shape resonances, Cooper minima and cross section enhancements due to near-zero-energy states. It is shown that the main source of relativistic effects in these cross section features is the fine-structure splitting of bound state energy levels. The relativistic effects are studied in the photoionization of Fe25+ ion, as an example.
Dawson-type Polyoxometalate Covalently Linked to Naphthalene: Synthesis, Characterisation and Material Properties
Authors: Ni Jing , Zhou Zhou , Liu Li , Liu Shi-Zhong , Li Fa-Bao , Li Guang-Hua , Du Zu-Liang
Published: June 2014

A novel covalently linked organic–polyoxometalate (POM) hybrid compound [N(C4H9)4]6[α2-P2W17O61{P(O)C6H4C≡CC10H7}2] (NOD) was prepared by Sonogashira coupling reaction of 1-iodonaphthalene with (NBu4)6[α2-P2W17O61{P(O)C6H4C≡CH}2] (OD), and characterised by NMR, infrared spectroscopy, UV–vis spectroscopy, fluorescence spectroscopy, and cyclic voltammetry. The UV–vis and luminescence spectra of NOD showed delocalisation and electron transfer in the hybrid system. The redox potential of the polyanion could be tuned by grafting organic composites on it. NOD displayed interesting electrical conductivity behaviours, photovoltage response, and photocatalytic activity.
Do repeated references result in sign reduction?
Authors: Hoetjes Marieke , Krahmer Emiel , Swerts Marc
Published: June 2014

Previous research on speech and gesture has found that repeated references are often linguistically reduced in terms of, for example, the number of words and the acoustic realization of these words, compared to initial references. The present study looks at the production of repeated references by 14 signers of Sign Language of the Netherlands (NGT). Participants had to describe figures to an addressee, who had to pick the correct figure from a large group of figures. Several figures had to be described several times. The question was whether there would be reduction in the repeated references. We found systematic effects of repetition in that repeated references were shorter, contained fewer signs, and shorter signs than initial references. Moreover, in order to measure sign precision, a perception test was used where participants had to judge, in a forced choice task, which sign they considered to be the most precise, looking at 40 pairs of video clips with signs produced in either initial or repeated references to the same object by the same signer. We found that, non-signing participants (but not signing participants) consider signs produced during repeated references to be less precise than the signs produced during initial references. Taking together these results suggest that a similar reduction process in repeated references occurs in NGT as has been found previously for speech and gesture.
A quantitative analysis of sign lengthening in American Sign Language
Authors: Stewart Jesse
Published: June 2014

In spoken languages, disfluent speech, narrative effects, discourse information, and phrase position may influence the lengthening of segments beyond their typical duration. In sign languages, however, the primary use of the visual-gestural modality results in articulatory differences not expressed in spoken languages. This paper looks at sign lengthening in American Sign Language (ASL). Comparing two retellings of the Pear Story narrative from five signers, three primary lengthening mechanisms were identified: elongation, repetition, and deceleration. These mechanisms allow signers to incorporate lengthening into signs which may benefit from decelerated language production due to high information load or complex articulatory processes. Using a mixed effects model, significant differences in duration were found between (i) non-conventionalized forms vs. lexical signs, (ii) signs produced during role shift vs. non-role shift, (iii) signs in phrase-final/initial vs. phrase-medial position, (iv) new vs. given information, and (v) (non-disordered) disfluent signing vs. non-disfluent signing. These results provide insights into duration effects caused by information load and articulatory processes in ASL.
Factors Affecting Partial Migration in Puget Sound Coho Salmon
Authors: Rohde Jessica , Fresh Kurt L. , Quinn Thomas P.
Published: June 2014

Partial migration, the behavior pattern in which a portion of a population migrates while others do not, is a widespread phenomenon with ecological and evolutionary consequences. Most Coho Salmon Oncorhynchus kisutch from Puget Sound, Washington, migrate to feed over the continental shelf or offshore in the North Pacific Ocean, but some remain in the semiestuarine waters of Puget Sound and are termed residents. The objective of this study was to determine which of several factors influenced residency in Puget Sound Coho Salmon. Coded wire tag recovery data showed that resident Coho Salmon were smaller than their migratory counterparts, and we used this size difference and the relative catch patterns along the coast and in Puget Sound to classify Coho Salmon caught in Puget Sound between November and August as residents. We then analyzed the effects of location of origin, day of release, weight at release, hatchery or wild rearing, and year on the proportion of fish caught as residents. Based on 268 release groups between 1975 and 1992, we classified 3.4% of fish recovered as residents, 61.3% as migrants, and 35.3% as ambiguous because they were recovered in Puget Sound in September and October, when residents and migrants were mixed. The proportion of residents varied as a function of year, basin, and day of the year. Releases into south Puget Sound produced the highest proportion of residents, and resident fish tended to be recovered in the basin where they entered Puget Sound. While other factors may influence residency in Coho Salmon, the effects of day of release and location of origin may be useful for management of these populations, as the tendency to remain in Puget Sound or migrate to the coast affects the fisheries in which the fish are taken and their growth rate, their uptake of contaminants, and their role in food webs.

Received August 15, 2013; accepted February 3, 2014
Performance of a Surface Bypass Structure to Enhance Juvenile Steelhead Passage and Survival at Lower Granite Dam, Washington
Authors: Adams Noah S. , Plumb John M. , Perry Russell W. , Rondorf Dennis W.
Published: June 2014

An integral part of efforts to recover stocks of Pacific salmon Oncorhynchus spp. and steelhead O. mykiss in Pacific Northwest rivers is to increase passage efficacy and survival of juveniles past hydroelectric dams. As part of this effort, we evaluated the efficacy of a prototype surface bypass structure, the removable spillway weir (RSW), installed in a spillbay at Lower Granite Dam, Washington, on the Snake River during 2002, 2003, 2005, and 2006. Radio-tagged juvenile steelhead were released upstream from the dam and their route of passage through the turbines, juvenile bypass, spillway, or RSW was recorded. The RSW was operated in an on-or-off condition and passed 3–13% of the total discharge at the dam when it was on. Poisson rate models were fit to the passage counts of hatchery- and natural-origin juvenile steelhead to predict the probability of fish passing the dam. Main-effect predictor variables were RSW operation, diel period, day of the year, proportion of flow passed by the spillway, and total discharge at the dam. The combined fish passage through the RSW and spillway was 55–85% during the day and 37–61% during the night. The proportion of steelhead passing through nonturbine routes was <88% when the RSW was off during the day and increased to >95% when the RSW was on during the day. The ratio of the proportion of steelhead passed to the proportion of water passing the RSW was from 6.3:1 to 10.0:1 during the day and from 2.7:1 to 5.2:1 during the night. Steelhead passing through the RSW exited the tailrace about 15 min faster than fish passing through the spillway. Mark–recapture single-release survival estimates for steelhead passing the RSW ranged from 0.95 to 1.00. The RSW appeared to be an effective bypass structure compared with other routes of fish passage at the dam.

Received June 13, 2013; accepted February 2, 2014
Genetic Identification of Chinook Salmon in the Columbia River Estuary: Stock-Specific Distributions of Juveniles in Shallow Tidal Freshwater Habitats
Authors: Teel David J. , Bottom Daniel L. , Hinton Susan A. , Kuligowski David R. , McCabe George T. , McNatt Regan , Roegner G. Curtis , Stamatiou Lia A. , Simenstad Charles A.
Published: June 2014

Extensive efforts are underway to restore and conserve nearshore shallow water habitats in the Columbia River estuary with the intent of increasing the estuary's capacity to provide food, refuge, and other crucial ecosystem functions for juvenile salmon. Juvenile Chinook Salmon Oncorhynchus tshawytscha, including those from the five Evolutionarily Significant Units listed as threatened or endangered under the U.S. Endangered Species Act, are particularly expected to benefit from the habitat improvements. However, information on the temporal and spatial estuarine distributions of juveniles from specific populations or stocks is lacking and impedes restoration planning for at-risk salmon. We conducted a series of surveys to sample juvenile Chinook Salmon occupying shallow-water habitats with sandy beaches in six hydrogeomorphic reaches across the tidal freshwater portion of the estuary and also at one long-term reference site near the estuary mouth. Sites were sampled bimonthly over 26 months during 2010–2012 to capture seasonal patterns of stock-specific habitat use. Genetic stock identification analyses were conducted on the samples using microsatellite DNA loci and genotypic data representing spawning populations from throughout the Columbia River basin. We identified three tidal freshwater areas that could be distinguished by genetic stock composition. Lower tidal freshwater reaches were dominated by fall-run juveniles from West Cascade tributaries (>70%), upper reaches had a large proportion of fish from the upper Columbia River summer–fall stock (>60%), and middle reaches were characterized by greater stock diversity with no single stock contributing more than 30% in each reach. Stock-specific juvenile habitat use differed by season, life history type, and between natural and hatchery-produced fish. Data from this study provide improved descriptions of the near-shore estuary habitat use of several Columbia River genetic stocks of Chinook Salmon that can assist managers in the design and selection of estuary restoration projects.

Received November 11, 2013; accepted February 18, 2014
Quantifying the Effectiveness of Conservation Measures to Control the Spread of Anthropogenic Hybridization in Stream Salmonids: a Climate Adaptation Case Study
Authors: Al-Chokhachy Robert , Muhlfeld Clint C. , Boyer Matthew C. , Jones Leslie A. , Steed Amber , Kershner Jeffrey L.
Published: June 2014

Quantifying the effectiveness of management actions to mitigate the effects of changing climatic conditions (i.e., climate adaptation) can be difficult, yet critical for conservation. We used population genetic data from 1984 to 2011 to assess the degree to which ambient climatic conditions and targeted suppression of sources of nonnative Rainbow Trout Oncorhynchus mykiss have influenced the spread of introgressive hybridization in native populations of Westslope Cutthroat Trout O. clarkii lewisi. We found rapid expansion in the spatial distribution and proportion of nonnative genetic admixture in hybridized populations from 1984 to 2004, but minimal change since 2004. The spread of hybridization was negatively correlated with the number of streamflow events in May that exceeded the 75th percentile of historic flows (r = −0.98) and positively correlated with August stream temperatures (r = 0.89). Concomitantly, suppression data showed a 60% decline in catch per unit effort for fish with a high proportion of Rainbow Trout admixture, rendering some uncertainty as to the relative strength of factors controlling the spread of hybridization. Our results illustrate the importance of initiating management actions to mitigate the potential effects of climate change, even where data describing the effectiveness of such actions are initially limited but the risks are severe.

Received November 22, 2013; accepted March 1, 2014
Size Selective Feeding in Captive and Free Ranging Atlantic Bluefin Tuna
Authors: Butler Christopher M. , Hanrahan Brian , Buckel Jeffrey A. , Rudershausen Paul J. , Juanes Francis , Smith Joseph W.
Published: June 2014

We examined size selective feeding in captive and free ranging Atlantic Bluefin Tuna Thunnus thynnus. For the captive study, Bluefin Tuna were maintained in a cylindrical net pen enclosure (30.5 m in diameter; 15.2 m deep) located 32.2 km offshore of Virginia. Tests of prey size selectivity by captive Bluefin Tuna were observed using underwater video. In free ranging Bluefin Tuna, size selection was examined by comparing the sizes of Atlantic Menhaden Brevoortia tyrannus found in stomach contents with the sizes of those collected during the fall purse seine fishery for Atlantic Menhaden off the North Carolina coast. Captive Bluefin Tuna selected larger prey when prey length : predator length ratios (PPRs) were less than 10%; however, size selectivity was not observed when the PPRs exceeded 10%. For free ranging Bluefin Tuna, PPRs were mostly greater than 10% (12.98 ± 0.06% [mean ± SE]), and there were no significant differences in length between Atlantic Menhaden from stomach contents and those from purse seine collections. The minimum and median sizes of Atlantic Menhaden prey increased with increasing predator size; however, the maximum size of Atlantic Menhaden prey did not change, indicating that the smallest Bluefin Tuna sampled could consume the largest Atlantic Menhaden. We conclude that the relatively small size of forage fishes commonly observed in Bluefin Tuna stomachs was likely due to the high abundance of these fishes in the environment rather than to active selection for small prey.

Received August 29, 2013; accepted January 14, 2014
Small Scale Vertical Movements of Summer Flounder Relative to Diurnal, Tidal, and Temperature Changes
Authors: Henderson Mark J. , Fabrizio Mary C.
Published: June 2014

Observation of animal movements on small spatial scales provides a means to understand how large scale species distributions are established from individual behavioral decisions. Small scale vertical movements of 14 Summer Flounder Paralichthys dentatus residing in Chesapeake Bay were observed by using depth data collected with archival tags. A generalized linear mixed model was employed to examine the relationship between these vertical movements and environmental covariates such as tidal state, time of day, lunar phase, and temperature. Vertical movements increased with warming water temperatures, and this pattern was most apparent at night and during rising and falling tides. Fish generally exhibited greater vertical movements at night, but the difference between vertical movements in the day and those at night decreased as fish increased in size. Results from this study fill a void in understanding the small scale movements of Summer Flounder and could be incorporated into individual based models to investigate how species distributions develop in response to environmental conditions.

Received October 28, 2013; accepted January 28, 2014
Central Lyapunov exponent of partially hyperbolic diffeomorphisms of 𝕋³
Authors: Ponce G. , Tahzibi A.
Published: June 2014

In this paper we construct some “pathological” volume preserving partially hyperbolic diffeomorphisms on

T

3

\mathbb T^{3}

such that their behavior in small scales in the central direction (Lyapunov exponent) is opposite to the behavior of their linearization. These examples are isotopic to Anosov. We also get partially hyperbolic diffeomorphisms isotopic to Anosov (consequently with non-compact central leaves) with zero central Lyapunov exponent at almost every point.
The Effect of Chronic Illness on Participation in the Supplemental Nutrition Assistance and Medicaid Programs
Authors: Meyerhoefer Chad D. , Pylypchuk Yuriy
Published: June 2014

We examine enrollment in the U.S. Medicaid and Supplemental Nutrition Assistance Programs (SNAP) and find that while SNAP‐eligible adults in poor physical health and with multiple chronic conditions are more likely to jointly enroll in SNAP and Medicaid, they are less likely to enroll in SNAP alone. We also find that the conditional probability of SNAP enrollment given Medicaid participation is higher for individuals with multiple chronic conditions. As a result, the expansion of Medicaid and state policies that promote enrollment coordination between SNAP and Medicaid are expected to increase the number of individuals in SNAP with chronic medical conditions.
Re‐examining the Reported Rates of Return to Food and Agricultural Research and Development
Authors: Hurley Terrance M. , Rao Xudong , Pardey Philip G.
Published: June 2014

At odds with a vast body of economic evidence reporting exceptionally high rates of return to investments in agricultural research and development (R&D), growth in public R&D spending for food and agriculture has slowed in numerous, especially rich, countries worldwide. The observed R&D spending behavior is consistent with a determination that the reported rates of return are perceived as implausible by policy makers. We examine this notion by scrutinizing 2,242 investment evaluations reported in 372 separate studies from 1958 to 2011. We find that the internal rate of return (IRR) is the predominant summary measure of investment performance used in the literature despite methodological criticisms dating back more than a half century. The reported IRRs imply rates of return that are implausibly high. We investigate the reasons for these implausibly high estimates by analytically comparing the IRR to the modified internal rate of return (MIRR). The MIRR addresses several methodological concerns with using the IRR, has the intuitive interpretation as the annual compounding interest rate paid by an investment, and is directly related to the benefit–cost ratio. To obtain more credible rate of return estimates, we then develop a novel method for recalibrating previously reported IRR estimates using the MIRR when there is limited information on an investment's stream of benefits and costs. Our recalibrated estimates of the rate of return are more modest (median of 9.8% versus 39% per year); however, they are still substantial enough to question the current scaling back of public agricultural R&D spending in many countries.
EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes
Authors: Sallet Erika , Gouzy Jérôme , Schiex Thomas
Published: June 2014

Summary: It is now easy and increasingly usual to produce oriented RNA-Seq data as a prokaryotic genome is being sequenced. However, this information is usually just used for expression quantification. EuGene-PP is a fully automated pipeline for structural annotation of prokaryotic genomes integrating protein similarities, statistical information and any oriented expression information (RNA-Seq or tiling arrays) through a variety of file formats to produce a qualitatively enriched annotation including coding regions but also (possibly antisense) non-coding genes and transcription start sites.

Availability and implementation: EuGene-PP is an open-source software based on EuGene-P integrating a Galaxy configuration. EuGene-PP can be downloaded at eugene.toulouse.inra.fr.

Contact:  erika.sallet@toulouse.inra.fr

Supplementary information: Supplementary data are available at Bioinformatics online.
Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
Authors: Phanstiel Douglas H. , Boyle Alan P. , Araya Carlos L. , Snyder Michael P.
Published: June 2014

Motivation: Interpretation and communication of genomic data require flexible and quantitative tools to analyze and visualize diverse data types, and yet, a comprehensive tool to display all common genomic data types in publication quality figures does not exist to date. To address this shortcoming, we present Sushi.R, an R/Bioconductor package that allows flexible integration of genomic visualizations into highly customizable, publication-ready, multi-panel figures from common genomic data formats including Browser Extensible Data (BED), bedGraph and Browser Extensible Data Paired-End (BEDPE). Sushi.R is open source and made publicly available through GitHub ( https://github.com/dphansti/Sushi ) and Bioconductor ( http://bioconductor.org/packages/release/bioc/html/Sushi.html ).

Contact:  mpsnyder@stanford.edu or dphansti@stanford.edu
Linking tagging technology and molecular genetics to gain insight in the spatial dynamics of two stocks of cod in Northeast Atlantic waters
Authors: Michalsen Kathrine , Johansen Torild , Subbey Sam , Beck Alexander
Published: June 2014

The Northeast Arctic cod (Gadus morhua L.: NEAC) remains the most abundant cod stock in the North Atlantic, while the catches of the partially co-occurring Norwegian coastal cod (NCC) stocks have dramatically decreased in recent years. To ensure effective management of the two stocks, it is necessary to know if the population genetic structure is associated with any pattern in the spatial dynamics or whether it is affected by any distinct environmental factors. By combining information from electronic data storage tags (DST) and molecular genetics methods with statistical tools, we have been able to associate spatial dynamics and distinct environmental factors to the two cod stocks. In general, adult NEAC migrate between deep, warm overwintering grounds and shallow summer feeding grounds where water temperatures maybe low. In contrast, NCC do not undertake large-scale seasonal migrations, show little seasonal variation in depth distribution, and experience the opposite seasonal change in temperature compared with NEAC. However, within the NCC group, some individuals did conduct longer horizontal movements than others. Even though the distances calculated in this study represent the shortest distance between release and recapture positions, they are far higher than previously reported by NCC. Distinctive depth profiles indicate that this migrant NCC have moved out of the area, passing the deep trenches outside Lofoten while more stationary NCC occupies shallower depths throughout the year. The temperature profiles also indicate that migrant and stationary NCC has occupied different areas during the year. We demonstrate that the combination of information from DSTs and molecular genetics offers a deeper understanding of individual cod behaviour, provides an insight in the spatial dynamics of the species, and ultimately, improves the scientific basis for management of a complex mixed fishery of Atlantic cod.
Occurrence and Development of the Cereal Cyst Nematode (Heterodera avenae) in Shandong, China
Authors: Wu Hai Yan , He Qiong , Liu Jing , Luo Jian , Peng De Liang
Published: June 2014

The cereal cyst nematode (CCN), Heterodera aveane, has been found in 16 provinces of China, including the Shandong winter-wheat-growing region. This study investigated the population dynamics of H. avenae in the winter wheat ‘Jimai 22’ and ‘Tainong 18’ for two consecutive years in the field. Soil and root samples were collected during the winter-wheat-growing season and H. avenae population densities and life-stages determined. H. avenae population dynamics in roots and soil of the two winter wheat cultivars were similar over the 2-year period. Second-stage juvenile (J2) population densities in wheat roots were greatest during booting stage (April), when mean soil temperature was between 11.8 and 14.4°C. Cysts in rhizosphere soil increased significantly when new cysts were formed after Zadoks (Z) 47 (booting stage). There was a peak in J2 population densities in soil during Z23 and Z30 (tillering and stem elongation, respectively) whereas J2 population densities were the lowest at Z13 (seedling stage). This research provides important information indicating that J2 populations in roots and soil increased after the wheat winter dormancy period. Knowledge of when different life stages of H. avenae occur in winter wheat in Shandong will provide valuable insights to enable the development of an integrated approach to manage this plant-parasitic nematode.
Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., isolated from human faeces, and emended description of the genus Butyricimonas
Authors: Sakamoto Mitsuo , Tanaka Yoshiki , Benno Yoshimi , Ohkuma Moriya
Published: June 2014

Two bacterial strains, designated 180-3T and 214-4T, isolated from human faeces were characterized by using a polyphasic taxonomic approach that included analysis of their phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that these strains represented members of the genus

Butyricimonas

. These strains shared 97.9 % 16S rRNA gene sequence similarity with each other and were related to

Butyricimonas virosa

JCM 15149T (97 % sequence similarity) and

Butyricimonas synergistica

JCM 15148T (94–95 %). Although strain 180-3T was related to (but distinct from)

B. virosa

JCM 15149T and

B. synergistica

JCM 15148T, with hsp60 gene sequence similarities of 89.4 and 84.6 %, respectively, strain 214-4T exhibited high hsp60 gene sequence similarity (100 %) with

B. virosa

JCM 15149T and was different from

B. synergistica

JCM 15148T (83.5 %). DNA–DNA hybridization experiments demonstrated a genomic distinction of strains 180-3T and 214-4T from

B. virosa

JCM 15149T and

B. synergistica

JCM 15148T. The strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. Growth of the strains was inhibited on medium containing 20 % bile. The two strains produced butyric and isobutyric acids as the end products from glucose, as has been observed in the other two species of the genus
Butyricimonas
. The major cellular fatty acid of strains 180-3T and 214-4T was iso-C15 : 0. The major menaquinone of the isolates was MK-10 (>50 %). Strains 180-3T and 214-4T have DNA G+C contents of 45 mol%. On the basis of these data, strains 180-3T and 214-4T represent two novel species of the genus

Butyricimonas

, for which the names Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., respectively, are proposed. The type strains of B. faecihominis and B. paravirosa are 180-3T ( = JCM 18676T = CCUG 65562T) and 214-4T ( = JCM 18677T = CCUG 65563T), respectively.
Antibody detection in tear samples as a surrogate to monitor host immunity against papillomavirus infections in vaccinated and naturally infected hosts
Authors: Hu Jiafen , Brendle Sarah , Balogh Karla , Bywaters Stephanie , Christensen Neil
Published: June 2014

Monitoring serum antibodies against natural infections or after immunizations has been a standard clinical diagnostic procedure. However, collecting blood samples requires trained personnel, and may cause discomfort and increase the risk of complications. In this study, we investigated whether tear samples could serve as a surrogate for serum samples to measure specific antibodies. A widely used preclinical cottontail rabbit papillomavirus (CRPV)/rabbit model has been a surrogate model for high-risk human papillomavirus (HPV) infections. New Zealand white rabbits, either naturally infected with CRPV or immunized with two clinically available HPV vaccines (Gardasil and Cervarix), were examined for antibody generation in both tear and serum samples. We demonstrated that antibodies were detectable in tears from both naturally infected as well as vaccinated animals. Overall, the antibody levels in tears were ~10-fold lower than those from the corresponding serum samples, but background noise was lower in tear samples. The isotypes of antibodies in tears were predominantly IgA and IgG. These findings showed clearly that tears could be a surrogate for serum samples for monitoring antibody responses. As collecting tears causes no discomfort and poses no risk to patients, it represents a novel and promising method for monitoring future HPV epidemiological studies as well as for use in clinical practice.
The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20
Authors: Price Morgan N. , Ray Jayashree , Wetmore Kelly M. , Kuehl Jennifer V. , Bauer Stefan , Deutschbauer Adam M. , Arkin Adam P.
Published: June 2014

Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants ofDesulfovibrio alaskensisG20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly, during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. During hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions.
High-throughput functional annotation of influenza A virus genome at single-nucleotide resolution
Authors: Wu Nicholas C. , Young Arthur P. , Al-Mawsawi Laith Q. , Olson Anders C. , Feng Jun , Qi Hangfei , Chen Shu-Hwa , Lu I-Hsuan , Lin Chung-Yen , Chin Robert G. , Luan Harding H. , Nguyen Nguyen , Nelson Stanley F. , Li Xinmin , Wu Ting-Ting , Sun Ren
Published: June 2014

A novel genome-wide genetics platform is presented in this study, which permits functional interrogation of all point mutations across a viral genome in parallel. Here we generated the first fitness profile of individual point mutations across the influenza virus genome. Critical residues on the viral genome were systematically identified, which provided a collection of subdomain data informative for structure-function studies and for effective rational drug and vaccine design. Our data was consistent with known, well-characterized structural features. In addition, we have achieved a validation rate of 68% for severely attenuated mutations and 94% for neutral mutations. The approach described in this study is applicable to other viral or microbial genomes where a means of genetic manipulation is available.
Phylogenetic Identification and Functional Characterization of Orthologs and Paralogs across Human, Mouse, Fly, and Worm
Authors: Wu Yi-Chieh , Bansal Mukul S. , Rasmussen Matthew D. , Herrero Javier , Kellis Manolis
Published: June 2014

Model organisms can serve the biological and medical community by enabling the study of conserved gene families and pathways in experimentally-tractable systems. Their use, however, hinges on the ability to reliably identify evolutionary orthologs and paralogs with high accuracy, which can be a great challenge at both small and large evolutionary distances. Here, we present a phylogenomics-based approach for the identification of orthologous and paralogous genes in human, mouse, fly, and worm, which forms the foundation of the comparative analyses of the modENCODE and mouse ENCODE projects. We study a median of 16,101 genes across 2 mammalian genomes (human, mouse), 12Drosophilagenomes, 5Caenorhabditisgenomes, and an outgroup yeast genome, and demonstrate that accurate inference of evolutionary relationships and events across these species must account for frequent gene-tree topology errors due to both incomplete lineage sorting and insufficient phylogenetic signal. Furthermore, we show that integration of two separate phylogenomic pipelines yields increased accuracy, suggesting that their sources of error are independent, and finally, we leverage the resulting annotation of homologous genes to study the functional impact of gene duplication and loss in the context of rich gene expression and functional genomic datasets of the modENCODE, mouse ENCODE, and human ENCODE projects.
Genomic evidence for adaptation by gene duplication
Authors: Qian Wenfeng , Zhang Jianzhi
Published: June 2014

Gene duplication is widely believed to facilitate adaptation, but unambiguous evidence for this hypothesis has been found in only a small number of cases. Although gene duplication may increase the fitness of the involved organisms by doubling gene dosage or neofunctionalization, it may also result in a simple division of ancestral functions into daughter genes, which need not promote adaptation. Hence, the general validity of the adaptation by gene duplication hypothesis remains uncertain. Indeed, a genome-scale experiment found similar fitness effects of deleting pairs of duplicate genes and deleting individual singleton genes from the yeast genome, leading to the conclusion that duplication rarely results in adaptation. Here we contend that the above comparison is unfair because of a known duplication bias among genes with different fitness contributions. To rectify this problem, we compare homologous genes from the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. We discover that simultaneously deleting a duplicate gene pair in S. cerevisiae reduces fitness significantly more than deleting their singleton counterpart in S. pombe, revealing post-duplication adaptation. The duplicates–singleton difference in fitness effect is not attributable to a potential increase in gene dose after duplication, suggesting that the adaptation is owing to neofunctionalization, which we find to be explicable by acquisitions of binary protein–protein interactions rather than gene expression changes. These results provide genomic evidence for the role of gene duplication in organismal adaptation and are important for understanding the genetic mechanisms of evolutionary innovation.