bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-oscillation up to 9 MHz based on voltage triggered switching in VO2/TiN point contact junctions
Authors: Mian Md. Suruz , Okimura Kunio , Sakai Joe
Published: June 2015

We demonstrate self-sustaining electrical oscillations with frequency of MHz range based on out-of-plane voltage-triggered switching in VO2 thin films grown on conductive layers. VO2 films deposited by a reactive sputtering method at a low temperature of 250 °C on conductive TiN layers showed thermally induced out-of-plane insulator-metal transition with two orders of change in resistance. By applying dc voltage to the layered device in a point contact configuration, self-sustaining electrical oscillations were triggered and the highest frequency of 9 MHz was achieved. Dependence of the frequency on the film thickness, as well as on the source voltage and on the series resistance, was examined in order to clarify the oscillation mechanism and the factors that affect the frequency. The oscillation frequency, which is dominated by recovering time from metallic to insulating state, decreased with increasing film thickness, indicating that the resistance of VO2 film determines the time constant for the recovery path. Self-sustaining oscillation phenomena achieved in point contact devices has great potential for applications in MHz band generators and micro-inverters.
Magnetoelectric sensor excitations in hexaferrite slabs
Authors: Zare Saba , Izadkhah Hessam , Somu Sivasubramanian , Vittoria Carmine
Published: June 2015

We developed techniques for H- and E-field sensors utilizing single phase magnetoelectric (ME) hexaferrite slabs in the frequency range of 100 Hz to 10 MHz. Novel circuit designs incorporating both spiral and solenoid coils and single and multi-capacitor banks were developed to probe the physics and properties of ME hexaferrites and explore ME effects for sensor detections. Fundamental measurements of the anisotropic tensor elements of the magneto-electric coupling parameter were performed using these novel techniques. In addition, for H-field sensing experiments we measured sensitivity of about 3000 Vm−1/G using solenoid coils and 8000 Vm−1/G using spiral coils. For E-field, sensing the sensitivity was 10−4 G/Vm−1 and using single capacitor detector. Sensitivity for multi-capacitor detectors was measured to be in the order of 10−3 G/Vm−1 and frequency dependent exhibiting a maximum value at ∼1 MHz. Tunability of 0.1%–90% was achieved for tunable inductor applications using both single and multi-capacitors excitation. We believe that significant (∼106) improvements in sensitivity and tunability are feasible with simple modifications of the fabrication process.
Efficient charge transfer and field-induced tunneling transport in hybrid composite device of organic semiconductor and cadmium telluride quantum dots
Authors: Varade Vaibhav , Jagtap Amardeep M. , Anjaneyulu P. , Koteswara Rao K. S. R. , Ramesh K. P. , Menon R.
Published: June 2015

Temperature and photo-dependent current–voltage characteristics are investigated in thin film devices of a hybrid-composite comprising of organic semiconductor poly(3,4-ethylenedioxythiophene):polystyrenesulfonate (PEDOT:PSS) and cadmium telluride quantum dots (CdTe QDs). A detailed study of the charge injection mechanism in ITO/PEDOT:PSS-CdTe QDs/Al device exhibits a transition from direct tunneling to Fowler–Nordheim tunneling with increasing electric field due to formation of high barrier at the QD interface. In addition, the hybrid-composite exhibits a huge photoluminescence quenching compared to aboriginal CdTe QDs and high increment in photoconductivity (∼ 400%), which is attributed to the charge transfer phenomena. The effective barrier height (ΦB ≈ 0.68 eV) is estimated from the transition voltage and the possible origin of its variation with temperature and photo-illumination is discussed.
Contribution of mixed dislocations to the acoustic nonlinearity in plastically deformed materials
Authors: Xiang Yanxun , Deng Mingxi , Liu Chang-Jun , Xuan Fu-Zhen
Published: June 2015

An analytical model is proposed based on dislocation line energy and variable line tension to describe the influence of mixed dislocations on acoustic nonlinearity in plastically deformed materials. Numerical results indicate that the acoustic nonlinearity parameter β is strongly dependent on the Poisson's ratio, and the fraction and type of the dislocation. For edge dislocations, β is found to increase with increasing Poisson's ratio, which is different from the behavior predicted by existing models. Moreover, this result indicates that β should be more sensitive to edge dislocations in materials with large Poisson's ratios. The proposed model is validated by experimental measurements of cold-rolled 304 stainless steel plates and plastically deformed 30Cr2Ni4MoV martensite stainless steels.
Relationship between martensitic plate size and austenitic grain size in martensitic transformations
Authors: La Roca P. , Isola L. , Vermaut Ph. , Malarría J.
Published: June 2015

A systematic experimental analysis based on an assessment of the mean martensite plate size (hplate) in sub-grain domains was implemented to characterize the martensite morphology in polycrystalline Cu-based shape memory alloys. In the grain size range below 100 μm, a linear relationship between the average width of the martensite plates and the mean grain size was obtained for a thermal-induced martensitic transformation. This evaluation allows us to perform an analysis of how microstructural length scales affect the martensitic transformation.
Factorized molecular wave functions: Analysis of the nuclear factor
Authors: Lefebvre R.
Published: June 2015

The exact factorization of molecular wave functions leads to nuclear factors which should be nodeless functions. We reconsider the case of vibrational perturbations in a diatomic species, a situation usually treated by combining Born-Oppenheimer products. It was shown [R. Lefebvre, J. Chem. Phys. 142, 074106 (2015)] that it is possible to derive, from the solutions of coupled equations, the form of the factorized function. By increasing artificially the interstate coupling in the usual approach, the adiabatic regime can be reached, whereby the wave function can be reduced to a single product. The nuclear factor of this product is determined by the lowest of the two potentials obtained by diagonalization of the potential matrix. By comparison with the nuclear wave function of the factorized scheme, it is shown that by a simple rectification, an agreement is obtained between the modified nodeless function and that of the adiabatic scheme.
Deep ultraviolet distributed Bragg reflectors based on graded composition AlGaN alloys
Authors: Brummer Gordie , Nothern Denis , Nikiforov A. Yu. , Moustakas T. D.
Published: June 2015

Distributed Bragg reflectors (DBRs) with peak reflectivity at approximately 280 nm, based on compositionally graded AlxGa1−xN alloys, were grown on 6H-SiC substrates by plasma-assisted molecular beam epitaxy. DBRs with square, sinusoidal, triangular, and sawtooth composition profiles were designed with the transfer matrix method. The crystal structure of these DBRs was studied with high-resolution x-ray diffraction of the (1¯015) reciprocal lattice point. The periodicity of the DBR profiles was confirmed with cross-sectional Z-contrast scanning transmission electron microscopy. The peak reflectance of these DBRs with 15.5 periods varies from 77% to 56% with corresponding full width at half maximum of 17–14 nm. Coupled mode analysis was used to explain the dependence of the reflectivity characteristics on the profile of the graded composition.
Transformation of surface plasmon polaritons to radiation in graphene in terahertz regime
Authors: Gong Sen , Zhao Tao , Sanderson Matthew , Hu Min , Zhong Renbin , Chen Xiaoxing , Zhang Ping , Zhang Chao , Liu Shenggang
Published: June 2015

We demonstrate a concept that allows direct excitation of surface plasmon polaritons (SPPs) by a moving electron bunch above a single layer graphene sheet deposited on a dielectric substrate without any additional coupling requirements. We show that if the two-dimensional current in the graphene is dominated by the third order nonlinear effect when the surface electric field exceeds a moderate strength of ∼5 kV/cm, the SPP mode can cross the light line although the group velocity remains much smaller than the speed of light. This effect gives rise to direct transformation of SPPs into radiation. The underlying mechanism of the crossing of the SPP dispersion into the light line is the energy shift of charged particles in the nonlinear regime and the finite transport scattering time in graphene. Both the energy and lifetime of the SPPs increase with the field intensity. The radiation intensity and frequency can be tuned with an AC bias.
A note on the accuracy of a computable approximation for the period of a pendulum
Authors: Oden Eric , Richards Kendall
Published: June 2015

We discuss the accuracy of a previously proposed computable approximation for the period of the simple pendulum. In particular, we apply known inequalities for the Gaussian hypergeometric function to prove that the associated error is a monotonic function of the maximum angular displacement, α. For any given range of α, this provides an analytical verification of a precise bound for the associated error.
Multi-stacked InAs/GaAs quantum dots grown with different growth modes for quantum dot solar cells
Authors: Kim Yeongho , Ban Keun-Yong , Honsberg Christiana B.
Published: June 2015

We have studied the material properties and device performance of InAs/GaAs quantum dot solar cells (QDSCs) made using three different QD growth modes: Stranski-Krastanov (S-K), quasi-monolayer (QML), and sub-monolayer (SML) growth modes. All QDSCs show an extended external quantum efficiency (EQE) at near infrared wavelengths of 950–1070 nm from the QD absorption. Compared to the S-K and SML QDSCs, the QML QDSC with a higher strain exhibits a poor EQE response in the wavelength region of 300–880 nm due to increased non-radiative recombination. The conversion efficiency of the S-K and SML QDSCs exceeds that of the reference cell (13.4%) without QDs due to an enhanced photocurrent (>16% increase) produced by the silicon doped QD stacks. However, as expected from the EQE of the QML QDSC, the increase of strain-induced crystalline defects greatly degrades the photocurrent and open-circuit voltage, leading to the lowest conversion efficiency (8.9%).
Physical activity and sedentary behaviour among Asian and Anglo‐Australian adolescents
Authors: Strugnell Claudia , Renzaho Andre M. N. , Ridley Kate , Burns Cate
Published: June 2015

Issue addressed

Evidence suggests that physical activity (PA) and sedentary behaviour (SB) participation varies among culturally and linguistically diverse (CALD) adolescents. The present study examined differences in PA and SB among a CALD sample of Chinese Australian, South‐east Asian and Anglo‐Australian adolescents.

Methods

Data from 286 adolescents aged 12–16 years involved in the Chinese and Australian Adolescent Health Survey in metropolitan Melbourne, Australia, were analysed. Accelerometry outcomes included median activity counts per minute (counts.min‐1) and minutes per day (min.day‐1) spent in light‐intensity PA (LPA), moderate‐to‐vigorous‐intensity PA (MVPA) and sedentary time (ST). Kruskal‐Wallis one‐way analysis of variance and sequential multiple hierarchical linear regressions were used to examine CALD differences in PA and ST.

Results

Multivariate analyses of accelerometry data found Chinese Australian and South‐east Asian adolescents engaged in significantly less daily MVPA (5–8 min.day‐1) and LPA (50–58 min.day‐1; P < 0.05), but greater daily ST (40–41 min.day‐1), than Anglo‐Australian adolescents, after adjusting for age, gender and socioeconomic category.

Conclusion

The results demonstrate lower engagement in daily MVPA and LPA and greater engagement in ST using accelerometry among Chinese Australian and South‐east Asian adolescents compared with Anglo‐Australian adolescents. These findings have important public health implications in furthering our understanding of CALD differences in PA and SB.
Effect of fire prevention programs on accidental and incendiary wildfires on tribal lands in the United States
Authors: Abt Karen L. , Butry David T. , Prestemon Jeffrey P. , Scranton Samuel
Published: June 2015

Humans cause more than 55% of wildfires on lands managed by the USDA Forest Service and US Department of the Interior, contributing to both suppression expenditures and damages. One means to reduce the expenditures and damages associated with these wildfires is through fire prevention activities, which can include burn permits, public service programs or announcements, outreach efforts to schools, youth groups and equipment operators, and law enforcement. Using data from 17 US Bureau of Indian Affairs tribal units, we modelled the effect of prevention programs and law enforcement on the number of human-caused ignitions. We also included weather and lagged burned area in our estimation of fixed-effects count models. The results show that prevention activities led to significant reductions in wildfires caused by escaped campfires, juveniles, fire-use (e.g. escaped debris burns) and equipment. Increased law enforcement resulted in fewer incendiary- and equipment-caused wildfires. Using average suppression expenditures by wildfire and our estimate of avoided wildfires per additional year of prevention, we estimate partial benefit–cost ratios of greater than 4.5 for all Bureau of Indian Affairs regions for the continuation of the prevention program.
Dormant season grazing may decrease wildfire probability by increasing fuel moisture and reducing fuel amount and continuity
Authors: Davies Kirk W. , Boyd Chad S. , Bates Jon D. , Hulet April
Published: June 2015

Mega-fires and unprecedented expenditures on fire suppression over the past decade have resulted in a renewed focus on presuppression management. Dormant season grazing may be a treatment to reduce fuels in rangeland, but its effects have not been evaluated. In the present study, we evaluated the effect of dormant season grazing (winter grazing in this ecosystem) by cattle on fuel characteristics in sagebrush (Artemisia L.) communities at five sites in south-eastern Oregon. Winter grazing reduced herbaceous fuel cover, continuity, height and biomass without increasing exotic annual grass biomass or reducing bunchgrass basal area or production. Fuel moisture in winter-grazed areas was high enough that burning was unlikely until late August; in contrast, fuels in ungrazed areas were dry enough to burn in late June. Fuel biomass on perennial bunchgrasses was decreased by 60% with winter grazing, which may reduce the potential for fire-induced mortality. The cumulative effect of winter grazing from altering multiple fuel characteristics may reduce the likelihood of fire and the potential severity in sagebrush communities with an understorey dominated by herbaceous perennials. Dormant season grazing has the potential to reduce wildfire suppression expenditures in many rangelands where herbaceous fuels are an issue; however, increasing woody vegetation and extreme fire weather may limit its influence.
Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism
Authors: Werner Gijsbert D. A. , Cornwell William K. , Cornelissen Johannes H. C. , Kiers E. Toby
Published: June 2015

Understanding the origins and evolutionary trajectories of symbiotic partnerships remains a major challenge. Why are some symbioses lost over evolutionary time whereas others become crucial for survival? Here, we use a quantitative trait reconstruction method to characterize different evolutionary stages in the ancient symbiosis between legumes (
Fabaceae
) and nitrogen-fixing bacteria, asking how labile is symbiosis across different host clades. We find that more than half of the 1,195 extant nodulating legumes analyzed have a high likelihood (>95%) of being in a state of high symbiotic persistence, meaning that they show a continued capacity to form the symbiosis over evolutionary time, even though the partnership has remained facultative and is not obligate. To explore patterns associated with the likelihood of loss and retention of the N
2
-fixing symbiosis, we tested for correlations between symbiotic persistence and legume distribution, climate, soil and trait data. We found a strong latitudinal effect and demonstrated that low mean annual temperatures are associated with high symbiotic persistence in legumes. Although no significant correlations between soil variables and symbiotic persistence were found, nitrogen and phosphorus leaf contents were positively correlated with legumes in a state of high symbiotic persistence. This pattern suggests that highly demanding nutrient lifestyles are associated with more stable partnerships, potentially because they “lock” the hosts into symbiotic dependency. Quantitative reconstruction methods are emerging as a powerful comparative tool to study broad patterns of symbiont loss and retention across diverse partnerships.
The Science Framework for Implementing the Fisheries Protection Provisions of Canada's Fisheries Act
Authors: Rice Jake , Bradford Michael J. , Clarke Keith D. , Koops Marten A. , Randall Robert G. , Wysocki Roger
Published: June 2015

In 2012, Canada's Fisheries Act was amended. New fisheries protection provisions provide for the sustainability and ongoing productivity of commercial, recreational, and Aboriginal fisheries. These provisions replace previous provisions that focused on fish habitats, and concerns have been expressed that the amended Act has lowered aquatic habitat protection. The science framework developed for implementation of the new provisions is based on the relationships between fisheries productivity and the response of habitats or populations to pressures, with pressures linked to specific classes of activities through pathways of effects models. The framework includes guidance on quantifying productivity, scales and types of impacts, establishing equivalence in offsetting, and managing risk. Risk of failing to achieve the intent of the fisheries protection provisions is only managed when impacts of activities have a net neutral or positive effect on fisheries productivity. This standard applies whether the evaluation of an activity is by self- or assisted assessment or a more comprehensive project evaluation.

En el año 2012, el Acta Pesquera de Canadá fue enmendada. Las nuevas provisiones para la protección de pesquerías tienen como objetivo proveer sustentabilidad y productividad a las pesquerías comerciales, recreativas y nativas. Estas provisiones reemplazan varias de las anteriores que se enfocaban en el hábitat de los peces, y ahora se han suscitado ciertas preocupaciones en cuanto a que el acta enmendada reduce la protección de hábitats acuáticos. El contexto científico que se ha desarrollado para implementar las nuevas provisiones se basa en la relación entre la productividad pesquera y la respuesta de los hábitats o de las poblaciones a las presiones; presiones que a su vez se relacionan con tipos específicos de actividades mediante modelos de “rutas de efectos”. El contexto incluye guías de cómo cuantificar la productividad, tipos y escala de los impactos, establecimiento de equivalencias compensatorias y manejo del riesgo. El riesgo de que no se logren cumplir los objetivos de las provisiones de protección de las pesquerías, comienza a ser controlado sólo cuando el impacto de las actividades tiene un efecto neto neutral o positivo en la productividad pesquera. Este estándar aplica ya sea cuando la evaluación de la actividad es asistida o bien auto evaluación, o cuando se hace mediante un proyecto de evaluación más exhaustivo.
Development of an efficient soymilk cream production method by papain digestion, heat treatment, and low-speed centrifugation
Authors: Abe Naoki , Wu Chang-Yu , Kim Yoon-Kyung , Fujii Tomoyuki , Abe Keietsu
Published: June 2015

We developed the simple method of soymilk cream production from the high-fat soymilk, which was prepared by papain digestion and heat treatment. As a result of the treatment, high-fat soymilk was aggregated and it became possible to separate soymilk cream as the surface fraction by low-speed centrifugation (6000 × g, 10 min).
Inhibitory phonetic priming: Where does the effect come from?
Authors: Dufour Sophie , Frauenfelder Ulrich Hans
Published: June 2015

Both phonological and phonetic priming studies reveal inhibitory effects that have been interpreted as resulting from lexical competition between the prime and the target. We present a series of phonetic priming experiments that contrasted this lexical locus explanation with that of a prelexical locus by manipulating the lexical status of the prime and the target and the task used. In the related condition of all experiments, spoken targets were preceded by spoken primes that were phonetically similar but shared no phonemes with the target (/bak/–/d∊t/). In Experiments 1 and 2, word and nonword primes produced an inhibitory effect of equal size in shadowing and same–different tasks respectively. Experiments 3 and 4 showed robust inhibitory phonetic priming on both word and nonword targets in the shadowing task, but no effect at all in a lexical decision task. Together, these findings show that the inhibitory phonetic priming effect occurs independently of the lexical status of both the prime and the target, and only in tasks that do not necessarily require the activation of lexical representations. Our study thus argues in favour of a prelexical locus for this effect.
Reading Galileo’sDiscorsiin the Early Modern University*
Authors: Raphael Renée J.
Published: June 2015

This article examines the scholarly practices with which readers at three universities read select passages from Galileo’s 1638Discorsi,a work depicted by Galileo as one that eschewed the goals and methods of Aristotelian natural philosophy in favor of the quantitative and experimental ones characteristic of modern science. The article reveals that a group of readers — diverse in terms of institutional affiliation, disciplinary identity, geography, and attitude toward Galileo — approached Galileo’s text using the tools of what Ann Blair has termed “bookish” natural philosophy. It argues that, contrary to Galileo’s rhetoric, these readers saw old and new methods as interchangeable.
Operator Lipschitz estimates in the unitary setting
Authors: Ayre P. , Cowling M. , Sukochev F.
Published: June 2015

We develop a Lipschitz estimate for unitary operators. More specifically, we show that for each

p
∈
(
1
,
∞
)

p\in (1,\infty )

there exists a constant

d
p

d_p

such that
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="double-vertical-bar f left-parenthesis upper U right-parenthesis minus f left-parenthesis upper V right-parenthesis double-vertical-bar Subscript p Baseline less-than-or-equal-to d Subscript p Baseline double-vertical-bar upper U minus upper V double-vertical-bar Subscript p">

‖
f
(
U
)
−
f
(
V
)
‖

p

≤

d
p

‖
U
−
V
‖

p

\left \Vert f(U) - f(V)\right \Vert _p \leq d_p \left \Vert U - V\right \Vert _p

for all Lipschitz functions

f
:

T

→

C

f: \mathbb {T} \to \mathbb {C}

and unitary operators

U
U

and

V
V

.
Myristoylated CIL-7 regulates ciliary extracellular vesicle biogenesis
Authors: Maguire Julie E. , Silva Malan , Nguyen Ken C.Q. , Hellen Elizabeth , Kern Andrew D. , Hall David H. , Barr Maureen M.
Published: June 2015

The cilium both releases and binds to extracellular vesicles (EVs). EVs may be used by cells as a form of intercellular communication and mediate a broad range of physiological and pathological processes. The mammalian polycystins (PCs) localize to cilia, as well as to urinary EVs released from renal epithelial cells. PC ciliary trafficking defects may be an underlying cause of autosomal dominant polycystic kidney disease (PKD), and ciliary–EV interactions have been proposed to play a central role in the biology of PKD. In Caenorhabditis elegans and mammals, PC1 and PC2 act in the same genetic pathway, act in a sensory capacity, localize to cilia, and are contained in secreted EVs, suggesting ancient conservation. However, the relationship between cilia and EVs and the mechanisms generating PC-containing EVs remain an enigma. In a forward genetic screen for regulators of C. elegans PKD-2 ciliary localization, we identified CIL-7, a myristoylated protein that regulates EV biogenesis. Loss of CIL-7 results in male mating behavioral defects, excessive accumulation of EVs in the lumen of the cephalic sensory organ, and failure to release PKD-2::GFP-containing EVs to the environment. Fatty acylation, such as myristoylation and palmitoylation, targets proteins to cilia and flagella. The CIL-7 myristoylation motif is essential for CIL-7 function and for targeting CIL-7 to EVs. C. elegans is a powerful model with which to study ciliary EV biogenesis in vivo and identify cis-targeting motifs such as myristoylation that are necessary for EV–cargo association and function.
FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads
Authors: Lam Ka-Kit , LaButti Kurt , Khalak Asif , Tse David
Published: June 2015

We introduce FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.

Availability and implementation: The tool and data are available and will be maintained at http://kakitone.github.io/finishingTool/

Contact: dntse@stanford.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Modelling the effect of antimicrobial treatment on carriage of hospital pathogens with application to MRSA
Authors: Verykouki E. , Kypraios T. , O'neill P.D.
Published: June 2015

Numerous studies have sought to assess the effectiveness of control measures aimed at reducing the spread of pathogens such as Methicillin-resistant Staphylococcus aureus (MRSA) in hospital settings. Far less is known about possible short-term effects of antibiotics and other antimicrobial treatments on pathogen carriage in patients. This paper is concerned with developing and applying methods for the analysis of detailed data on hospital patients which include information on patient treatments and screening tests for the pathogen in question. The carriage status (colonized, or not) of each patient is modelled as a Markov chain, and models for both perfect and imperfect test sensitivity are developed. Goodness-of-fit procedures based on simulation are also proposed. The methods are illustrated using both simulated data and data on MRSA.
Birth month affects lifetime disease risk: a phenome-wide method
Authors: Boland Mary Regina , Shahn Zachary , Madigan David , Hripcsak George , Tatonetti Nicholas P
Published: June 2015

Objective An individual’s birth month has a significant impact on the diseases they develop during their lifetime. Previous studies reveal relationships between birth month and several diseases including atherothrombosis, asthma, attention deficit hyperactivity disorder, and myopia, leaving most diseases completely unexplored. This retrospective population study systematically explores the relationship between seasonal affects at birth and lifetime disease risk for 1688 conditions.

Methods We developed a hypothesis-free method that minimizes publication and disease selection biases by systematically investigating disease-birth month patterns across all conditions. Our dataset includes 1 749 400 individuals with records at New York-Presbyterian/Columbia University Medical Center born between 1900 and 2000 inclusive. We modeled associations between birth month and 1688 diseases using logistic regression. Significance was tested using a chi-squared test with multiplicity correction.

Results We found 55 diseases that were significantly dependent on birth month. Of these 19 were previously reported in the literature (P < .001), 20 were for conditions with close relationships to those reported, and 16 were previously unreported. We found distinct incidence patterns across disease categories.

Conclusions Lifetime disease risk is affected by birth month. Seasonally dependent early developmental mechanisms may play a role in increasing lifetime risk of disease.
Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host
Authors: Aguiar Eric Roberto Guimarães Rocha , Olmo Roenick Proveti , Paro Simona , Ferreira Flavia Viana , de Faria Isaque João da Silva , Todjro Yaovi Mathias Honore , Lobo Francisco Pereira , Kroon Erna Geessien , Meignin Carine , Gatherer Derek , Imler Jean-Luc , Marques João Trindade
Published: June 2015

Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects.
Use of Oropharyngeal Washes to Diagnose and Genotype Pneumocystis jirovecii
Authors: Juliano Jonathan J. , Barnett Eric , Parobek Christian M. , Taylor Steve M. , Meshnick Steven R. , Stone Stephen , Chang Emily , Fong Serena , Huang Laurence
Published: June 2015

Pneumocystis jirovecii is a symbiotic respiratory fungus that presents in 2 clinical forms: pneumonia in immunocompromised patients or colonization, defined by the presence of the organism without associated clinical symptoms. Currently, diagnosis requires invasive bronchoscopy, which may not be available in some settings and is inappropriate for detecting colonization in healthy individuals. Noninvasive diagnostic techniques and molecular strain typing tools that can be used on these samples are critical for conducting studies to better understand transmission. We evaluated 2 real-time polymerase chain reaction (PCR) assays targeting dihydropteroate synthase and the major surface glycoprotein for detection in 77 oropharyngeal washes (OPWs) from 43 symptomatic human immunodeficiency virus-infected patients who underwent bronchoscopy. We also evaluated the ability of a new microsatellite (MS) genotyping panel to strain type infections from these samples. Each PCR used individually provided a high sensitivity (>80%) for detection of pneumonia but a modest specificity (<70%). When used in combination, specificity was increased to 100% with a drop in sensitivity (74%). Concentration of organisms by PCR in the OPW tended to be lower in colonized individuals compared with those with pneumonia, but differences in concentration could not clearly define colonization in symptomatic individuals. Oropharyngeal wash samples were genotyped using 6 MSs with ≥4 alleles successfully genotyped in the majority of colonized patients and ≥5 alleles in patients with pneumonia. The MS profile was consistent over time within patients with serial OPWs analyzed. Microsatellite genotyping on noninvasive samples may aid in studying the molecular epidemiology of this pathogen without requiring invasive diagnostic techniques.
The AKARI far-infrared all-sky survey maps
Authors: Doi Yasuo , Takita Satoshi , Ootsubo Takafumi , Arimatsu Ko , Tanaka Masahiro , Kitamura Yoshimi , Kawada Mitsunobu , Matsuura Shuji , Nakagawa Takao , Morishima Takahiro , Hattori Makoto , Komugi Shinya , White Glenn J. , Ikeda Norio , Kato Daisuke , Chinone Yuji , Etxaluze Mireya , Cypriano Elysandra F.
Published: June 2015

We present a far-infrared all-sky atlas from a sensitive all-sky survey using the Japanese AKARI satellite. The survey covers > 99% of the sky in four photometric bands centred at 65 μm, 90 μm, 140 μm, and 160 μm, with spatial resolutions ranging from 1′ to 1${^{\prime\prime}_{.}}$5. These data provide crucial information on the investigation and characterisation of the properties of dusty material in the interstellar medium (ISM), since a significant portion of its energy is emitted between ∼ 50 and 200 μm. The large-scale distribution of interstellar clouds, their thermal dust temperatures, and their column densities can be investigated with the improved spatial resolution compared to earlier all-sky survey observations. In addition to the point source distribution, the large-scale distribution of ISM cirrus emission, and its filamentary structure, are well traced. We have made the first public release of the full-sky data to provide a legacy data set for use in the astronomical community.
Revealing progenitors of type Ia supernovae from their light curves and spectra
Authors: Kutsuna Masamichi , Shigeyama Toshikazu
Published: June 2015

In the single degenerate (SD) scenario of type Ia supernovae (SNe Ia), the collision of the ejecta with its companion results in stripping hydrogen-rich matter from the companion star. This hydrogen-rich matter might leave its trace in the light curves and/or spectra. In this paper, we perform radiation hydrodynamical simulations of this collision for three binary systems. As a result, we find that the emission from the shock-heated region is not as strong as in previous studies. This weak emission, however, may be a result of our underestimation of the coupling between the gas and radiation in the shock interaction. Therefore, though our results suggest that the observed early light curves of SNe Ia cannot rule out a binary system with a short separation as the progenitor system, more elaborate numerical studies will be needed to reach a fair conclusion. Alternatively, our results indicate that the feature observed in the early phase of a recent type Ia SN 2014J might result from interaction of the ejecta with a red giant companion star. We also discuss the dependence of spectral features of Hα and Si ii absorption lines on viewing angles and investigate whether they can constrain the event rate of the SD progenitor.
Eddington limit for a gaseous stratus with finite optical depth
Authors: Fukue Jun
Published: June 2015

The Eddington luminosity of a spherical source is usually defined for a uniformly extending normal plasma. We usually suppose that the gas can accrete to the central object at the sub-Eddington luminosity, while it would be blown off from the central luminous source in the super-Eddington case. We reconsider this central dogma of the Eddington limit under the radiative transfer effect for the purely scattering case, using analytical and numerical methods. For the translucent isolated gas cloud (stratus) with finite optical depth, the concept of the Eddington luminosity is drastically changed. In an heuristic way, we find that the critical condition is approximately expressed as Γ = (1 + μ* + τc)/2, where Γ (=L/LE) is the central luminosity L normalized by the Eddington luminosity LE, τc is the optical depth of the stratus, and μ* ($=\sqrt{1-R_*^2/R^2}$) is the direction cosine of the central object, R* being the radius of the central object, and R the distance from the central object. When the optical depth of the stratus is around unity, the classical Eddington limit roughly holds for the stratus; Γ ∼ 1. However, when the optical depth is greater than unity, the critical condition becomes roughly Γ ∼ τc/2, and the stratus would infall on to the central source even at the highly super-Eddington luminosity. When the optical depth is less than unity, on the other hand, the critical condition reduces to Γ ≳ (1 + μ*)/2, and the stratus could be blown off in some limited ranges, depending on μ*. This new concept of the Eddington limit for the isolated stratus could drastically change the accretion and outflow physics of highly inhomegeneous plasmas, with relevance for astrophysical jets and winds and supermassive black hole formation.
Attitudes towards HIV testing via home-sampling kits ordered online (RUClear pilots 2011–12)
Authors: Ahmed-Little Y. , Bothra V. , Cordwell D. , Freeman Powell D. , Ellis D. , Klapper P. , Scanlon S. , Higgins S. , Vivancos R.
Published: June 2015

Background

The burden of disease relating to undiagnosed HIV infection is significant in the UK. BHIVA (British HIV Association) recommends population screening in high prevalence areas, expanding outside traditional antenatal/GUM settings.

Methods

RUClear 2011–12 piloted expanding HIV testing outside traditional settings using home-sampling kits (dry-blood-spot testing) ordered online. Greater Manchester residents (≥age 16) could request testing via an established, online chlamydia testing service (www.ruclear.co.uk). Participant attitudes towards this new service were assessed. Qualitative methods (thematic analysis) were used to analyse free-text data submitted by participants via hard copy questionnaires issued in all testing kits.

Results

79.9% (2447/3062) participants completed questionnaires, of which 30.9% (756/2447) provided free-text data. Participants overwhelmingly supported the service, valuing particularly accessibility and convenience, allowing individuals to order tests any time of day and self-sample comfortably at home; avoiding the invasive nature of venipuncture and avoiding the need for face-to-face interaction with health services. The pilot was also clinically and cost-effective.

Conclusion

Testing via home-sampling kits ordered online (dry-blood-spot testing) was felt to be an acceptable and convenient method for accessing a HIV test. Many individuals undertook HIV testing where they would otherwise not have been tested at all. Expansion of similar services may increase the uptake of HIV testing.
Biological Impact of Transpulmonary Driving Pressure in Experimental Acute Respiratory Distress Syndrome
Authors: Samary Cynthia S. , Santos Raquel S. , Santos Cíntia L. , Felix Nathane S. , Bentes Maira , Barboza Thiago , Capelozzi Vera L. , Morales Marcelo M. , Garcia Cristiane S. N. B. , Souza Sergio A. L. , Marini John J. , Gama de Abreu Marcelo , Silva Pedro L. , Pelosi Paolo , Rocco Patricia R. M.
Published: June 2015

AbstractAbstract

Different combinations of tidal volume and positive end-expiratory pressure (PEEP) were used to create a range of driving pressures in a rat model of acute respiratory distress syndrome due to tracheal instillation of endotoxin for 24 h. Low transpulmonary driving pressure was associated with alveolar collapse and high driving pressure was associated with hyperinflation. The combination of a tidal volume of 6 ml/kg predicted body weight and the lowest PEEP and driving pressure to maintain oxygenation in a normal range minimized ventilator-induced lung injury even in the presence of alveolar collapse.

Supplemental Digital Content is available in the text.

Background:

Ventilator-induced lung injury has been attributed to the interaction of several factors: tidal volume (VT), positive end-expiratory pressure (PEEP), transpulmonary driving pressure (difference between transpulmonary pressure at end-inspiration and end-expiration, ΔP,L), and respiratory system plateau pressure (Pplat,rs).

Methods:

Forty-eight Wistar rats received Escherichia coli lipopolysaccharide intratracheally. After 24 h, animals were randomized into combinations of VT and PEEP, yielding three different ΔP,L levels: ΔP,LLOW (VT = 6 ml/kg, PEEP = 3 cm H2O); ΔP,LMEAN (VT = 13 ml/kg, PEEP = 3 cm H2O or VT = 6 ml/kg, PEEP = 9.5 cm H2O); and ΔP,LHIGH (VT = 22 ml/kg, PEEP = 3 cm H2O or VT = 6 ml/kg, PEEP = 11 cm H2O). In other groups, at low VT, PEEP was adjusted to obtain a Pplat,rs similar to that achieved with ΔP,LMEAN and ΔP,LHIGH at high VT.

Results:

At ΔP,LLOW, expressions of interleukin (IL)-6, receptor for advanced glycation end products (RAGE), and amphiregulin were reduced, despite morphometric evidence of alveolar collapse. At ΔP,LHIGH (VT = 6 ml/kg and PEEP = 11 cm H2O), lungs were fully open and IL-6 and RAGE were reduced compared with ΔP,LMEAN (27.4 ± 12.9 vs. 41.6 ± 14.1 and 0.6 ± 0.2 vs. 1.4 ± 0.3, respectively), despite increased hyperinflation and amphiregulin expression. At ΔP,LMEAN (VT = 6 ml/kg and PEEP = 9.5 cm H2O), when PEEP was not high enough to keep lungs open, IL-6, RAGE, and amphiregulin expression increased compared with ΔP,LLOW (41.6 ± 14.1 vs. 9.0 ± 9.8, 1.4 ± 0.3 vs. 0.6 ± 0.2, and 6.7 ± 0.8 vs. 2.2 ± 1.0, respectively). At Pplat,rs similar to that achieved with ΔP,LMEAN and ΔP,LHIGH, higher VT and lower PEEP reduced IL-6 and RAGE expression.

Conclusion:

In the acute respiratory distress syndrome model used in this experiment, two strategies minimized ventilator-induced lung injury: (1) low VT and PEEP, yielding low ΔP,L and Pplat,rs; and (2) low VT associated with a PEEP level sufficient to keep the lungs open.
Aminocaproic Acid and Tranexamic Acid Fail to Reverse Dabigatran-Induced Coagulopathy
Authors: Levine Michael , Huang Margaret , Henderson Sean O. , Carmelli Guy , Thomas Stephen H.
Published: June 2015

In recent years, dabigatran has emerged as a popular alternative to warfarin for treatment of atrial fibrillation. If rapid reversal is required, however, no reversal agent has clearly been established. The primary purpose of this manuscript was to evaluate the efficacy of tranexamic acid and aminocaproic acid as agents to reverse dabigatran-induced coagulopathy. Rats were randomly assigned to 6 groups. Each rat received either dabigatran or oral placebo, followed by saline, tranexamic acid, or aminocaproic acid. An activated clotting test was used to measure the coagulopathy. Neither tranexamic acid nor aminocaproic acid successfully reversed dabigatran-induced coagulopathy. In this rodent model of dabigatran-induced coagulopathy, neither tranexamic acid nor aminocaproic acid were able to reverse the coagulopathy.
Potential Clinical and Economic Impact of Switching Branded Medications to Generics
Authors: Straka Robert J. , Keohane Denis J. , Liu Larry Z.
Published: June 2015

Switching branded to generic medications has become a common cost-containment measure. Although this is an important objective for health care systems worldwide, the impact of this practice on patient outcomes needs to be carefully considered. We reviewed the literature summarizing the potential clinical and economic consequences of switching from branded to generic medications on patient outcomes. A literature search of peer-reviewed articles published 2003–2013 using key words of “generic switching” or “substitution” was conducted using PubMed, OvidSP, and ScienceDirect. Of 30 articles identified and reviewed, most were related to the diseases of the central nervous system, especially epilepsy. Based on our review, potential impacts of switching fell into 3 broad categories: patient attitudes and adherence, clinical and safety outcomes, and cost and resource utilization. Although in many cases generics may represent an appropriate alternative to branded products, this may not always be the case. Specifically, several studies suggested that switching may negatively impact medication adherence, whereas other studies found that generic switching was associated with poorer clinical outcomes and more adverse events. In some instances, switching accomplished cost savings but did so at increased total cost of care because of increased physician visits or hospitalizations. Although in many cases generics may represent an appropriate alternative, mandatory generic switching may lead to unintended consequences, especially in certain therapeutic areas. Although further study is warranted, based on our review, it may be medically justifiable for physicians and patients to retain the right to request the branded product in certain cases.
Human Milk Fortification Increases Bnip3 Expression Associated With Intestinal Cell Death In Vitro
Authors: Diehl‐Jones William , Archibald Alyssa , Gordon Joseph W. , Mughal Wajihah , Hossain Zakir , Friel James K.
Published: June 2015

Objectives:

The aim of the present study was to determine the in vitro effect(s) of a bovine‐based human breast milk fortifier (HMF) on human intestinal cells. HMF increases the expression of BCL2/adenovirus E1B 19 kDa protein‐interacting protein (Bnip3) and cell death; the prostaglandin analogue misoprostol will rescue this effect.

Methods:

Cultured intestinal cells were exposed to in vitro–digested human breast milk (BM) ± HMF. Intracellular oxidation, cell damage/cell death, and BNIP3 expression were measured after exposure.

Results:

In vitro–digested BM + HMF significantly increased intracellular oxidation, cell damage, and cell death in enterocyte cell cultures compared with either saline or BM controls, an effect that was rescued by the prostaglandin analogue, misoprostol. Bnip3 transcript and Bnip3 protein levels were significantly increased in vitro after treatment with BM + HMF. We also provide evidence that transfection of enterocytes with Bnip3 increases cell death, an effect that is rescued by a nonfunctional Bnip3 splice variant.

Conclusions:

Our data support the hypothesis that HMF increases intestinal Bnip3 in vitro, and that the gene product triggers cell death. We suggest that misoprostol is a promising therapy, which may reduce intestinal cell death.
First indications that northern bottlenose whales are sensitive to behavioural disturbance from anthropogenic noise
Authors: Miller P. J. O. , Kvadsheim P. H. , Lam F. P. A. , Tyack P. L. , Curé C. , DeRuiter S. L. , Kleivane L. , Sivle L. D. , van IJsselmuide S. P. , Visser F. , Wensveen P. J. , von Benda-Beckmann A. M. , Martín López L. M. , Narazaki T. , Hooker S. K.
Published: June 2015

Although northern bottlenose whales were the most heavily hunted beaked whale, we have little information about this species in its remote habitat of the North Atlantic Ocean. Underwater anthropogenic noise and disruption of their natural habitat may be major threats, given the sensitivity of other beaked whales to such noise disturbance. We attached dataloggers to 13 northern bottlenose whales and compared their natural sounds and movements to those of one individual exposed to escalating levels of 1–2 kHz upsweep naval sonar signals. At a received sound pressure level (SPL) of 98 dB re 1 μPa, the whale turned to approach the sound source, but at a received SPL of 107 dB re 1 μPa, the whale began moving in an unusually straight course and then made a near 180° turn away from the source, and performed the longest and deepest dive (94 min, 2339 m) recorded for this species. Animal movement parameters differed significantly from baseline for more than 7 h until the tag fell off 33–36 km away. No clicks were emitted during the response period, indicating cessation of normal echolocation-based foraging. A sharp decline in both acoustic and visual detections of conspecifics after exposure suggests other whales in the area responded similarly. Though more data are needed, our results indicate high sensitivity of this species to acoustic disturbance, with consequent risk from marine industrialization and naval activity.