bluuebunny/crossref_metadata_2025 huggingface dataset:
A noncoding RNA transcribed from the AGAMOUS (AG) second intron binds to CURLY LEAF and represses AG expression in leaves
Authors: Wu Hui‐Wen , Deng Shulin , Xu Haiying , Mao Hui‐Zhu , Liu Jun , Niu Qi‐Wen , Wang Huan , Chua Nam‐Hai
Published: June 2018

Dispersed H3K27 trimethylation (H3K27me3) of the AGAMOUS (AG) genomic locus is mediated by CURLY LEAF (CLF), a component of the Polycomb Repressive Complex (PRC) 2. Previous reports have shown that the AG second intron, which confers AG tissue‐specific expression, harbors sequences targeted by several positive and negative regulators.

Using RACE reverse transcription polymerase chain reaction, we found that the AG intron 2 encodes several noncoding RNAs. RNAi experiment showed that incRNA4 is needed for CLF repressive activity. AG‐incRNA4RNAi lines showed increased leaf AG mRNA levels associated with a decrease of H3K27me3 levels; these plants displayed AG overexpression phenotypes.

Genetic and biochemical analyses demonstrated that the AG‐incRNA4 can associate with CLF to repress AG expression in leaf tissues through H3K27me3‐mediated repression and to autoregulate its own expression level.

The mechanism of AG‐incRNA4‐mediated repression may be relevant to investigations on tissue‐specific expression of Arabidopsis MADS‐box genes.
Quantification of uncertainties in conifer sap flow measured with the thermal dissipation method
Authors: Peters Richard L. , Fonti Patrick , Frank David C. , Poyatos Rafael , Pappas Christoforos , Kahmen Ansgar , Carraro Vinicio , Prendin Angela Luisa , Schneider Loïc , Baltzer Jennifer L. , Baron‐Gafford Greg A. , Dietrich Lars , Heinrich Ingo , Minor Rebecca L. , Sonnentag Oliver , Matheny Ashley M. , Wightman Maxwell G. , Steppe Kathy
Published: June 2018

Trees play a key role in the global hydrological cycle and measurements performed with the thermal dissipation method (TDM) have been crucial in providing whole‐tree water‐use estimates. Yet, different data processing to calculate whole‐tree water use encapsulates uncertainties that have not been systematically assessed.

We quantified uncertainties in conifer sap flux density (Fd) and stand water use caused by commonly applied methods for deriving zero‐flow conditions, dampening and sensor calibration. Their contribution has been assessed using a stem segment calibration experiment and 4 yr of TDM measurements in Picea abies and Larix decidua growing in contrasting environments. Uncertainties were then projected on TDM data from different conifers across the northern hemisphere.

Commonly applied methods mostly underestimated absolute Fd. Lacking a site‐ and species‐specific calibrations reduced our stand water‐use measurements by 37% and induced uncertainty in northern hemisphere Fd. Additionally, although the interdaily variability was maintained, disregarding dampening and/or applying zero‐flow conditions that ignored night‐time water use reduced the correlation between environment and Fd.

The presented ensemble of calibration curves and proposed dampening correction, together with the systematic quantification of data‐processing uncertainties, provide crucial steps in improving whole‐tree water‐use estimates across spatial and temporal scales.
Modeling the productivity of commercialLactariusmushrooms: A case study in the Kizilcasu planning unit, Turkey
Authors: Mumcu Kucuker Derya , Baskent Emin Zeki
Published: June 2018

Empirical models for mushroom productivity are essential tools for analyzing trade‐offs among multiple objectives when developing and implementing integrated forest management plans. In this study, data measured in 30 permanent plots from a 4‐year period of mushroom production were used to predict mushroom productivity. The fresh weights ofLactarius deliciosusandL. salmonicolormushrooms were recorded in each sample plot. Owing to the hierarchical structure of the data obtained, equations were developed to produce mixed models using stand and topographic variables. The results showed that increasing slopes increased annual yield in northerly aspects, yet decreased the annual yield in southerly aspects. Besides, the productivity was negatively influenced by height, age and crown closure, and positively influenced by mean stand diameter, growing stock and elevation alone. However, the combined effects of age and diameter and the combined effects of growing stock and height separately showed a negative trend on mushroom yield.

Recommendation for Resource Managers

Productivity models were developed as important tools in developing nonwood forest products integrated forest management plans.

The models show that annual yield ofLactariusmushroom is significantly influenced by certain stand and topographic variables.

Use of these models is critical for analyzing trade‐offs among various forest values such as wood and nonwood forest products.

The models could lead to optimization of the production and conservation of fungal resources and allow forest managers and field foresters to forecast mushroom production and manage forest interventions affecting mushroom production.
Individualization of music‐based rhythmic auditory cueing in Parkinson's disease
Authors: Bella Simone Dalla , Dotov Dobromir , Bardy Benoît , de Cock Valérie Cochen
Published: June 2018

Gait dysfunctions in Parkinson's disease can be partly relieved by rhythmic auditory cueing. This consists in asking patients to walk with a rhythmic auditory stimulus such as a metronome or music. The effect on gait is visible immediately in terms of increased speed and stride length. Moreover, training programs based on rhythmic cueing can have long‐term benefits. The effect of rhythmic cueing, however, varies from one patient to the other. Patients’ response to the stimulation may depend on rhythmic abilities, often deteriorating with the disease. Relatively spared abilities to track the beat favor a positive response to rhythmic cueing. On the other hand, most patients with poor rhythmic abilities either do not respond to the cues or experience gait worsening when walking with cues. An individualized approach to rhythmic auditory cueing with music is proposed to cope with this variability in patients’ response. This approach calls for using assistive mobile technologies capable of delivering cues that adapt in real time to patients’ gait kinematics, thus affording step synchronization to the beat. Individualized rhythmic cueing can provide a safe and cost‐effective alternative to standard cueing that patients may want to use in their everyday lives.
Neuroimaging, neuromodulation, and population health: the neuroscience of chronic disease prevention
Authors: Hall Peter A. , Bickel Warren K. , Erickson Kirk I. , Wagner Dylan D.
Published: June 2018

Preventable chronic diseases are the leading cause of death in the majority of countries throughout the world, and this trend will continue for the foreseeable future. The potential to offset the social, economic, and personal burdens associated with such conditions depends on our ability to influence people's thought processes, decisions, and behaviors, all of which can be understood with reference to the brain itself. Within the health neuroscience framework, the brain can be viewed as a predictor, mediator, moderator, or outcome in relation to health‐related phenomena. This review explores examples of each of these, with specific reference to the primary prevention (i.e., prevention of initial onset) of chronic diseases. Within the topic of primary prevention, we touch on several cross‐cutting themes (persuasive communications, delay discounting of rewards, and self‐control), and place a special focus on obesity as a disorder influenced by both eating behavior and exercise habits.
Post‐weaning xenohormone intake affects adult rat submandibular gland in a sex‐dependent manner
Authors: Kouidhi Wided , Bergès Raymond , Drouin Gaêtan , Desmetz Catherine , Auger Jacques , El May Michèle , Canivenc‐Lavier Marie‐Chantal
Published: June 2018

Objectives

We previously reported that maternal exposure to genistein and vinclozolin, ingested alone or in combination, affects submandibular salivary glands of rat offspring. Here, we investigated the responsiveness of submandibular gland when such xenohormone exposure occurs later in life.

Materials and Methods

Chemicals were given orally to male and female Wistar rats (1 mg/kg body weight per day), from weaning to adulthood. Submandibular glands and plasma were collected at postnatal day 100 for histologic and molecular analysis.

Results

Whereas no effect was observed in females, increases in granular convoluted tubules area coupled with a modification of salivary secretions were found in male submandibular glands. Genistein and vinclozolin similarly increased the mRNA expression of Cystatin C, Mucin 10, Growth factors, and plasmatic EGF. Negative correlations were found between the expressions of androgen receptor and EGF (−0.34; p < 0.05), TGFα (−0.52; p < 0.01), Mucin 10 (−0.43; p < 0.05), and Cystatin C (−0.42; p < 0.05) as well as between progesterone receptor and EGF (−0.56; p < 0.01). The Spearman correlation test revealed also a positive correlation between salivary EGF‐mRNA expression and EGF in plasma (+0.32; p < 0.05).

Conclusion

Our findings confirm the sex‐dependent sensitivity of submandibular salivary glands to dietary xenohormones and underline the influence of the exposure period.
Causality from palaeontological time series
Authors: Hannisdal Bjarte , Liow Lee Hsiang
Published: June 2018

As custodians of deep time, palaeontologists have an obligation to seek the causes and consequences of long‐term evolutionary trajectories and the processes of ecosystem assembly and collapse. Building explicit process models on the relevant scales can be fraught with difficulties, and causal inference is typically limited to patterns of association. In this review, we discuss some of the ways in which causal connections can be extracted from palaeontological time series and provide an overview of three recently developed analytical frameworks that have been applied to palaeontological questions, namely linear stochastic differential equations, convergent cross mapping and transfer entropy. We outline how these methods differ conceptually, and in practice, and point to available software and worked examples. We end by discussing why a paradigm of dynamical causality is needed to decipher the messages encrypted in palaeontological patterns.
Independent selection for seed free tryptophan content and vernalization response in chickpea domestication
Authors: van‐Oss Ruth P. , Gopher Avi , Kerem Zohar , Peleg Zvi , Lev‐Yadun Simcha , Sherman Amir , Zhang Hong‐Bin , Vandemark George , Coyne Clare J. , Reany Ofer , Abbo Shahal
Published: June 2018

Chickpea shows a distinct domestication trajectory vis‐a‐vis pod dehiscence and growth cycle mediated by vernalization insensitivity compared with its companion Near Eastern legumes. Our objectives were: (i) to map the quantitative trait loci (QTLs) associated with vernalization response and seed free tryptophan in domesticated × wild chickpea progeny and (ii) estimate the genetic correlation between vernalization response and free tryptophan content. A domesticated × wild chickpea cross was used to document phenotypic segregation in both traits and to construct a skeletal genetic map for QTL detection. A number of vernalization response and seed free tryptophan content QTLs were documented in both F2 and F3 generations. No significant genetic correlation between these two traits was observed. Epistatic relationship between two free tryptophan loci was documented. It is evident that selection for high seed tryptophan is easier to accomplish relative to selection for vernalization insensitivity. This suggests that the two traits were selected independently in antiquity, thereby corroborating earlier claims for conscious selection processes associated with chickpea domestication.
Quasi Indexicals
Authors: Khoo Justin
Published: June 2018

I argue that not all context dependent expressions are alike. Pure (or ordinary) indexicals behave more or less as Kaplan thought. But quasi indexicals behave in some ways like indexicals and in other ways not like indexicals. A quasi indexical sentenceϕallows for cases in which one party uttersϕand the other its negation, and neither party's claim has to be false. In this sense, quasi indexicals are like pure indexicals (think: “I am a doctor”/“I am not a doctor” as uttered by different individuals). In such cases involving a pure indexical sentence, it is not appropriate for the two parties to reject each other's claims by saying, “No.” However, in such cases involving a quasi indexical sentence, itisappropriate for the parties to reject each other's claims. In this sense, quasi indexicals arenotlike pure indexicals. Drawing on experimental evidence, I argue that gradable adjectives like “rich” are quasi indexicals in this sense. The existence of quasi indexicals raises trouble for many existing theories of context dependence, including standard contextualist and relativist theories. I propose an alternative semantic and pragmatic theory of quasi indexicals, negotiated contextualism, that combines insights from Kaplan 1989 and Lewis 1979. On my theory, rejection is licensed with quasi indexicals (even when neither of the claims involved has to be false) because the two utterances involve conflicting proposals about how to update the conversational score. I also adduce evidence that conflicting truth value assessments of a single quasi indexical utterance exhibit the same behavior. I argue that negotiated contextualism can account for this puzzling property of quasi indexicals as well.
Formalizing the Precautionary Principle Accounting for Strategic Interaction, Natural Factors, and Technological Factors
Authors: Hausken Kjell
Published: June 2018

Four dimensions of the precautionary principle (PP), involving threat, uncertainty, action, and command, are formalized at the level of set theory and the level of individual players and natural and technological factors. Flow and decision diagrams with a feedback loop are developed to open up a new research agenda. The role of strategic interaction and games in the PP is underdeveloped or nonexistent in today's literature. To rectify this deficiency, six kinds of games are identified in the four PP dimensions. The games can be interlinked since player sets can overlap. Characteristics are illustrated. Accounting for strategic interaction, the article illustrates uncertainty in the PP regarding which game is played, which players participate in which game, strategy sets, payoffs, incomplete information, risk attitudes, and bounded rationality. The insurance and lottery games analyzed earlier for the safe minimum standard (SMS) for species extinction are revisited and placed into a broader context illustrating strategic interaction. Uncertainty about payoffs illustrates transformations back and forth between the chicken game, battle of the sexes, assurance game, and prisoner's dilemma.
Hybrid Quantile Regression Estimation for Time Series Models with Conditional Heteroscedasticity
Authors: Zheng Yao , Zhu Qianqian , Li Guodong , Xiao Zhijie
Published: June 2018

Estimating conditional quantiles of financial time series is essential for risk management and many other financial applications. For time series models with conditional heteroscedasticity, although it is the generalized auto-regressive conditional heteroscedastic (GARCH) model that has the greatest popularity, quantile regression for this model usually gives rise to non-smooth non-convex optimization which may hinder its practical feasibility. The paper proposes an easy-to-implement hybrid quantile regression estimation procedure for the GARCH model, where we overcome the intractability due to the square-root form of the conditional quantile function by a simple transformation. The method takes advantage of the efficiency of the GARCH model in modelling the volatility globally as well as the flexibility of quantile regression in fitting quantiles at a specific level. The asymptotic distribution of the estimator is derived and is approximated by a novel mixed bootstrapping procedure. A portmanteau test is further constructed to check the adequacy of fitted conditional quantiles. The finite sample performance of the method is examined by simulation studies, and its advantages over existing methods are illustrated by an empirical application to value-at-risk forecasting.
Validation of GPSkin Barrier® for assessing epidermal permeability barrier function and stratum corneum hydration in humans
Authors: Ye L. , Wang Z. , Li Z. , Lv C. , Man M.‐Q.
Published: June 2018

Background

Measurements of transepidermal water loss (TEWL) and stratum corneum (SC) hydration are important for assessing epidermal functions. However, the availability of reliable and user‐friendly devices, which can simultaneously measure both TEWL and SC hydration and can allow health providers to remotely access data in time, is limited.

Materials and Methods

GPSkin Barrier® was compared with MPA5 system in the measurements of TEWL and SC hydration on the cheek, the dorsal hand, and the forearm in 200 normal volunteers, including 126 females and 74 males, aged 1‐78 years with an average age of 45.24 ± 1.04 years. Correlation of data measured with MPA5 system and GPSkin Barrier® was determined.

Results

Levels of both TEWL and SC hydration measured with the Barrie GPSkin Barrier® were lower than that with MPA5 system on all 3 body sites except for hydration on the cheek. The levels of both TEWL and SC hydration measured with GpSkin Barrier® were correlated well with that measured with MPA5 system on all 3 body sites

Conclusions

GPSkin Barrier® is a reliable, affordable, and versatile device for assessing epidermal permeability barrier function and SC hydration.
Mechanical spectroscopy and imaging of skin components in vivo: Assignment of the observed moduli
Authors: Silver F. H. , Shah R. G.
Published: June 2018

Background

The need to quantitatively identify the composition and organization of the macromolecular components of skin, skin lesions, scars, tumors, extracellular matrices (ECMs), and wound tissue has been a goal of researchers for many decades. A variety of studies have been recently reported applying optical coherence tomography (OCT) to image skin and cutaneous lesions.

Materials and Methods

This article describes the use of vibrational OCT to image and noninvasively characterize the macromolecular components of the ECM of skin.

Results

We report that the major macromolecular components of skin and scar can be identified noninvasively by their characteristic moduli calculated from measurements of the resonant frequency and tissue thickness. Moduli for fat (0.03 MPa), elastic tissue (0.8 MPa), skin (2 MPa), and scar (7 MPa) can be differentiated using images and measurements of the resonant frequency and the sample thickness obtained from OCT.

Conclusions

Using vibrational OCT, it is possible to identify and map the location of the macromolecular components in skin and skin lesions.
Donor‐derived multiorgan transmission of mixed P. malariae and P. ovale infection: Impact of globalization on post‐transplant infections
Authors: Martín‐Dávila Pilar , Norman Francesca , Fortún‐Abete Jesus , Píris Miguel , Lovatti Ruben , Rubio Jose Miguel , Martinez‐Pérez Adolfo , Graus Javier , Ta Gema , Villarubia Jesus , Mahillo Beatriz , López‐Vélez Rogelio
Published: June 2018

A 57‐year‐old man was admitted with fever and thrombocytopenia 1 month after renal transplantation. He had never received a blood transfusion or travelled outside Spain. A peripheral blood smear revealed Plasmodium malariae and P. ovale parasites, diagnosis confirmed later by malaria PCR. The donor, from Equatorial Guinea, had negative thick and thin blood smears and rapid malaria antigen test prior to organ donation. Peripheral blood malaria PCR was not performed during donor screening. The second renal recipient and the liver recipient were evaluated and were found to be asymptomatic. Thick and thin films and rapid malaria diagnostic tests were negative for both patients and blood for malaria PCR was sent to the referral laboratory. The index patient was treated with oral chloroquine diphosphate, with a favorable outcome and was considered cured. Malaria PCR was negative for the other renal recipient and positive for P. malariae and P. ovale curtisi for the liver transplant patient. Both were treated with oral chloroquine and the liver recipient also completed treatment with primaquine phosphate. This reported case of multiorgan transmission of mixed malaria infection highlights the importance of PCR‐based tests for Plasmodium in the screening of donors from endemic areas.
Macroeconomic Drivers of Remittances and the Implication for Economic Growth in Nigeria
Authors: Atan Johnson A. , Esu Godwin Essang
Published: June 2018

Remittances have been one of the officially recorded sources of international flows, especially, to developing economies like Nigeria, hence the need to encourage its consistent flow as well as defining ways and means of redeploying it for an improved economy. Following this line of reasoning, an attempt was made in this study, to see whether the macroeconomic environment in the domestic economy can actually play a role in stimulating international remittance inflows. To achieve this, average remittance data were tested against that of per capita income, real exchange rate, trade openness, government expenditure, inflation rate and the demographic variable (population density), and the data were all from secondary sources (WDI and CBN Bulletin, 20170/2018). Drawing of the type of gravity model suggested by Greenwood (1975) and Borjas (1987, 1989) – as modified - for analyzing international migration, and exploring the two approaches to international remittances analysis – altruistic and investment approaches, the data were modelled and estimated. Error Correction Mechanism (ECM) was employed in estimating the model. The results indicated that the macroeconomic environment of Nigeria, plays a significant role in stimulating international remittance flows. Based on the outcome of this study, it is suggested that for consistent flow of remittances into Nigeria, especially for investment purposes, a conducive macroeconomic environment should be created and maintained, as this will not only stimulate inflows, but will aid effective redeployment of same for output growth.
VEGF‐A inhibits agonist‐mediated Ca2+ responses and activation of IKCa channels in mouse resistance artery endothelial cells
Authors: Ye Xi , Beckett Taylor , Bagher Pooneh , Garland Christopher J. , Dora Kim A.
Published: June 2018

Key points

Prolonged exposure to vascular endothelial growth factor A (VEGF‐A) inhibits agonist‐mediated endothelial cell Ca2+ release and subsequent activation of intermediate conductance Ca2+‐activated K+ (IKCa) channels, which underpins vasodilatation as a result of endothelium‐dependent hyperpolarization (EDH) in mouse resistance arteries.

Signalling via mitogen‐activated protein/extracellular signal‐regulated kinase kinase (MEK) downstream of VEGF‐A was required to attenuate endothelial cell Ca2+ responses and the EDH‐vasodilatation mediated by IKCa activation.

VEGF‐A exposure did not modify vasodilatation as a result of the direct activation of IKCa channels, nor the pattern of expression of inositol 1,4,5‐trisphosphate receptor 1 within endothelial cells of resistance arteries.

These results indicate a novel role for VEGF‐A in resistance arteries and suggest a new avenue for investigation into the role of VEGF‐A in cardiovascular diseases.

Vascular endothelial growth factor A (VEGF‐A) is a potent permeability and angiogenic factor that is also associated with the remodelling of the microvasculature. Elevated VEGF‐A levels are linked to a significant increase in the risk of cardiovascular dysfunction, although it is unclear how VEGF‐A has a detrimental, disease‐related effect. Small resistance arteries are central determinants of peripheral resistance and endothelium‐dependent hyperpolarization (EDH) is the predominant mechanism by which these arteries vasodilate. Using isolated, pressurized resistance arteries, we demonstrate that VEGF‐A acts via VEGF receptor‐2 (R2) to inhibit both endothelial cell (EC) Ca2+ release and the associated EDH vasodilatation mediated by intermediate conductance Ca2+‐activated K+ (IKCa) channels. Importantly, VEGF‐A had no direct effect against IKCa channels. Instead, the inhibition was crucially reliant on the downstream activation of the mitogen‐activated protein/extracellular signal‐regulated kinase kinase 1/2 (MEK1/2). The distribution of EC inositol 1,4,5‐trisphosphate (IP3) receptor‐1 (R1) was not affected by exposure to VEGF‐A and we propose an inhibition of IP3R1 through the MEK pathway, probably via ERK1/2. Inhibition of EC Ca2+ via VEGFR2 has profound implications for EDH‐mediated dilatation of resistance arteries and could provide a mechanism by which elevated VEGF‐A contributes towards cardiovascular dysfunction.
Delta Performance Models for Selection in Decision-Based Design
Authors: Gao Xinbao , Farritor Shane
Published: June 2018

The paper presents a modeling framework for rational selection between similar designs. Designers often make decisions between similar candidate designs such as deciding which off-the-shelf component should be used or whether to design that component from scratch. Such relative decisions between similar designs are common and important. A theoretical formulation of Delta Performance Models (DPM) is presented. DPM is an engineering design model that represents only the changes in performance that result from the small changes in competing designs. This method explicitly considers uncertainty and utilizes the fact that some uncertainty and modeling error is common to both candidate designs. DPM are intended to exploit the full resolution of engineering design models even if the models do not have high accuracy. The procedure is demonstrated on a simple design task using Monte Carlo simulations and a comparison is made with a traditional model.
Going Back in Time to Improve Design: The Elemental Function-Failure Design Method
Authors: Stock Michael E. , Stone Robert B. , Tumer Irem Y.
Published: June 2018

In today’s world it is more important than ever to quickly and accurately satisfy customer needs when launching a new product. It is equally important to design products that adequately accomplish their desired functions with a minimum amount of failures. When failure analysis and prevention are coupled with a product design from its conception, shorter design times and fewer redesigns are necessary to arrive at a final product design. In this article, we explore the potential of a novel design methodology to guide designers toward new designs or redesigns that avoid failures. The Elemental Function-Failure Design Method (EFDM) is based on functional similarity of the product being designed to failed products within a knowledge base. The idea of using component functionality to explore the failure space in design was first introduced as a function-failure analysis approach by Tumer and Stone (2003). The overall approach offers potential improvement over current failure analysis methods (FMEA, etc.), because it can be implemented hand in hand with other conceptual design steps and carried throughout a product’s design cycle. In this paper, this idea is formalized into a systematic methodology that is specifically tailored for use at the conceptual design stage before any physical design choices have been made, hence moving failure analysis earlier in the design cycle. In the following, formalized guidelines for using the EFDM will be outlined for use in new designs and for redesign in existing products. A function-failure knowledge base, derived from actual failure occurrences for Bell 206 rotorcraft will be introduced and used to derive potential failure modes in a comparison of the EFDM and traditional FMEA for two design examples. This comparison will demonstrate the EFDM’s potential in conceptual design failure analysis.
Comparative analyses of salivary proteins from the facultative symbiont-infected and uninfected Tetranychus truncatus
Authors: Zhu Yu-Xi , Song Yue-Ling , Huang Hai-Jian , Zhao Dian-Shu , Xia Xue , Yang Kun , Lu Yi-Jia , Hong Xiao-Yue
Published: June 2018

Salivary proteins of herbivorous insects play a central role in plant-insect interactions. Spider mite Tetranychus truncatus is a polyphagous agricultural pest harboring various bacterial symbionts. However, whether endosymbionts infection in spider mite alters the host saliva protein remains largely unknown. Here, by using shotgun LC-MS/MS analysis, we identified and characterized the components of saliva in Wolbachia-Spiroplasma infected and uninfected T. truncatus. In total, 177 putative salivary proteins were identified. The function of many proteins remains unknown, while in numerous cases belong to catalytic activity and binding proteins. The saliva enzymes included oxidoreductase, hydratase, isomerase, transferase, protease, esterase, ribonuclease, kinase, lyase and phosphorylase. Other proteins, such as ATP-binding, actin, heat shock proteins and vitellogenin were also detected in the T. truncatus saliva. In addition, we found some of the saliva proteins are mite strain-specific salivary proteins—14 proteins were only found in Wolbachia-Spiroplasma infected spider mite, and 6 proteins were only found in Wolbachia-Spiroplasma uninfected spider mite. Overall, this is the first research to identify and characterize the proteins in saliva of facultative symbionts-infected and uninfected spider mites, T. truncatus. Our novel findings revealed that the presence of bacterial symbionts affected the saliva components of spider mites, opening the path for future studies.
Microstructure design of lightweight fibrous material acting as a layered damper for a vibrating stiff panel
Authors: Xue Yutong , Bolton J. Stuart
Published: June 2018

Based on the idea that a layer of properly designed and manufactured fibrous material can serve as both a sound absorber and a structural damper, an approach is introduced in this article to design the microstructure of a fibrous layer for it to provide optimal damping performance. To begin with, previous work related to structural damping by fibrous layers was reviewed. Then the most appropriate models from the literature were adapted for use in the current study. A system comprising an aluminum panel and a limp fibrous layer was driven by a line force, and both the spatial velocity response of the panel and the power distribution within the system were calculated to quantify the degree of damping provided by the fibrous layer, which helped identify the airflow resistivity that provides optimal damping for any frequency and panel of interest. Given the optimal airflow resistivity, a model relating fiber microstructure to airflow resistivity was used to infer the optimal microstructure required to achieve the optimal damping performance. One finding of the current work, for example, was that as the target frequency was reduced, the fiber size required to achieve the optimal damping performance increased.
Application of a forward model of axisymmetric shear wave propagation in viscoelastic media to shear wave elastography
Authors: Yengul Sanjay S. , Barbone Paul E. , Madore Bruno
Published: June 2018

A simple but general solution of Navier's equation for axisymmetric shear wave propagation in a homogeneous isotropic viscoelastic medium is presented. It is well-suited for use as a forward model for some acoustic radiation force impulse based shear wave elastography applications because it does not require precise knowledge of the strength of the source, nor its spatial or temporal distribution. Instead, it depends on two assumptions: (1) the source distribution is axisymmetric and confined to a small region near the axis of symmetry, and (2) the propagation medium is isotropic and homogeneous. The model accounts for the vector polarization of shear waves and exactly represents geometric spreading of the shear wavefield, whether spherical, cylindrical, or neither. It makes no assumption about the frequency dependence of material parameters, i.e., it is material-model independent. Validation using measured shear wavefields excited by acoustic radiation force in a homogeneous gelatin sample show that the model accounts for well over 90% of the measured wavefield “energy.” An optimal fit of the model to simulated shear wavefields with noise in a homogeneous viscoelastic medium enables estimation of both the shear storage modulus and shear wave attenuation to within 1%.
The nutrient environment affects therapy
Authors: Muir Alexander , Vander Heiden Matthew G.
Published: June 2018

Nutrient availability affects cancer cell metabolism and therapeutic responses
A radical approach to the copper oxidative addition problem: Trifluoromethylation of bromoarenes
Authors: Le Chip , Chen Tiffany Q. , Liang Tao , Zhang Patricia , MacMillan David W. C.
Published: June 2018

Arenes get a light boost onto copper

Insertion of palladium into an aryl halide bond is the first step in numerous variants of cross-coupling chemistry used to make carbon-carbon bonds. Copper is an appealing alternative catalyst for such reactions because of its abundance and downstream reactivity profile. However, this preliminary step, termed oxidative addition, is often prohibitively slow for the cheaper metal. Le
et al.
report a photocatalytic way around this problem. A photoredox catalyst paired with a silane can activate aryl bromides to react with copper, likely via aryl radicals. The copper in this case then catalyzes trifluoromethylation of the arenes.

Science
, this issue p.
1010
The accessible predator
Orca: How We Came to Know and Love the Ocean's Greatest Predator
Jason M. Colby
Oxford University Press, 2018. 404 pp.
Authors: Baird Robin W.
Published: June 2018

Bloodthirsty murderers no more, captive killer whales helped to transform the species's reputation
Probing the microbial
Fundamentals of Microbiome Science: How Microbes Shape Animal Biology
Angela E. Douglas
Princeton University Press, 2018. 246 pp.
Authors: Vega Fernando E.
Published: June 2018

A wide-ranging text synthesizes what we know (and don't know) about the microbiome
Isolation of Toxigenic Clostridium difficile from Animal Manure and Composts Being Used as Biological Soil Amendments
Authors: Dharmasena Muthu , Jiang Xiuping
Published: June 2018

Clostridium difficile
infection (CDI) is a leading cause of antibiotic-associated diarrhea in health care facilities in developed countries. Extended hospital stays and recurrences severely increase the cost of treatments and the high mortality rate that is observed among the elderly. Community-associated CDI cases that occur without any recent contact with the hospital environment are increasing. Studies have reported the isolation of virulent
C. difficile
strains from water, soil, meat, vegetables, pets, livestock animals, and animal manure. The objective of this study was to isolate and characterize
C. difficile
strains from animal manure and commercially available compost products. Our results demonstrate that not only unprocessed animal manure but also finished composts made of different feedstocks can serve as a reservoir for
C. difficile
as well. Most importantly, our study revealed that properly processed compost is a potential source of toxigenic and clindamycin-resistant
C. difficile
isolates.
Insights into Circovirus Host Range from the Genomic Fossil Record
Authors: Dennis Tristan P. W. , Flynn Peter J. , de Souza William Marciel , Singer Joshua B. , Moreau Corrie S. , Wilson Sam J. , Gifford Robert J.
Published: June 2018

Advances in DNA sequencing have dramatically increased the rate at which new viruses are being identified. However, the host species associations of most virus sequences identified in metagenomic samples are difficult to determine. Our analysis indicates that viruses proposed to infect vertebrates (in some cases being linked to human disease) may in fact be restricted to arthropod hosts. The detection of these sequences in vertebrate samples may reflect their widespread presence in the environment as viruses of parasitic arthropods.
Persistent Replication of a Chikungunya Virus Replicon in Human Cells Is Associated with Presence of Stable Cytoplasmic Granules Containing Nonstructural Protein 3
Authors: Remenyi Roland , Gao Yanni , Hughes Ruth E. , Curd Alistair , Zothner Carsten , Peckham Michelle , Merits Andres , Harris Mark
Published: June 2018

Chikungunya virus (CHIKV) is a reemerging alphavirus transmitted by mosquitos and causes transient sickness but also chronic disease affecting muscles and joints. No approved vaccines or antivirals are available. Thus, a better understanding of the viral life cycle and the role of viral proteins can aid in identifying new therapeutic targets. Advances in microscopy and development of noncytotoxic replicons (A. Utt, P. K. Das, M. Varjak, V. Lulla, A. Lulla, A. Merits, J Virol 89:3145–3162, 2015,
https://doi.org/10.1128/JVI.03213-14
) have allowed researchers to study viral proteins within controlled laboratory environments over extended durations. Here we established human cells that stably replicate replicon RNA and express tagged nonstructural protein 3 (nsP3). The ability to track nsP3 within the host cell and during persistent replication can benefit fundamental research efforts to better understand long-term consequences of the persistence of viral protein complexes and thereby provide the foundation for new therapeutic targets to control CHIKV infection and treat chronic disease symptoms.
HIV-1 Protease Evolvability Is Affected by Synonymous Nucleotide Recoding
Authors: Nevot Maria , Jordan-Paiz Ana , Martrus Glòria , Andrés Cristina , García-Cehic Damir , Gregori Josep , Franco Sandra , Quer Josep , Martinez Miguel Angel
Published: June 2018

Large-scale synonymous recoding of virus genomes is a new tool for exploring various aspects of virus biology. Synonymous virus genome recoding can be used to investigate how a virus's position in sequence space defines its mutant spectrum, evolutionary trajectory, and pathogenesis. In this study, we evaluated how synonymous recoding of the human immunodeficiency virus type 1 (HIV-1) protease affects the development of protease inhibitor (PI) resistance. HIV-1 protease is a main target of current antiretroviral therapies. Our present results demonstrate that the wild-type (WT) virus and a virus with recoded protease exhibited different patterns of resistance mutations after PI treatment. Nevertheless, the developed PI resistance phenotypes were indistinguishable between the recoded virus and the WT virus, suggesting that the HIV-1 strain with synonymously recoded protease and the WT virus are equally robust and evolvable.
AupA and AupB Are Outer and Inner Membrane Proteins Involved in Alkane Uptake in Marinobacter hydrocarbonoclasticus SP17
Authors: Mounier Julie , Hakil Florence , Branchu Priscilla , Naïtali Muriel , Goulas Philippe , Sivadon Pierre , Grimaud Régis
Published: June 2018

This study describes the functional characterization of two proteins, AupA and AupB, which are required for growth on alkanes in the marine hydrocarbonoclastic bacterium
Marinobacter hydrocarbonoclasticus
. The
aupA
and
aupB
genes form an operon whose expression was increased upon adhesion to and biofilm formation on
n-
hexadecane. AupA and AupB are outer and inner membrane proteins, respectively, which are able to interact physically. Mutations in
aupA
or/and
aupB
reduced growth on solid paraffin and liquid
n-
hexadecane, while growth on nonalkane substrates was not affected. In contrast, growth of
aup
mutants on
n-
hexadecane solubilized in Brij 58 micelles was completely abolished. Mutant cells had also lost the ability to bind to
n
-hexadecane solubilized in Brij 58 micelles. These results support the involvement of AupA and AupB in the uptake of micelle-solubilized alkanes and provide the first evidence for a cellular process involved in the micellar uptake pathway. The phylogenetic distribution of the
aupAB
operon revealed that it is widespread in marine hydrocarbonoclastic bacteria of the orders
Oceanospirillales
and
Alteromonadales
and that it is present in high copy number (up to six) in some
Alcanivorax
strains. These features suggest that Aup proteins probably confer a selective advantage in alkane-contaminated seawater.

IMPORTANCE
Bacteria are the main actors of the biological removal of hydrocarbons in seawater, and so, it is important to understand how they degrade hydrocarbons and thereby mitigate marine environmental damage. Despite a considerable amount of literature about the dynamic of microbial communities subjected to hydrocarbon exposure and the isolation of strains that degrade hydrocarbons, most of the genetic determinants and molecular mechanisms of bacterial hydrocarbon uptake remain unknown. This study identifies two genes,
aupA
and
aupB
, in the hydrocarbonoclastic bacterium
Marinobacter hydrocarbonoclasticus
that are present frequently in multiple copies in most of the marine hydrocarbon-degrading bacteria for which the genomic sequence is available. AupA and AupB are two novel membrane proteins interacting together that are involved in the uptake of alkanes dissolved in surfactant micelles. The function and the phylogenetic distribution of
aupA
and
aupB
suggest that they might be one attribute of the remarkable adaptation of marine hydrocarbonoclastic bacteria that allow them to take advantage of hydrocarbons.
Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research
Authors: Schloss Patrick D.
Published: June 2018

The “reproducibility crisis” in science affects microbiology as much as any other area of inquiry, and microbiologists have long struggled to make their research reproducible. We need to respect that ensuring that our methods and results are sufficiently transparent is difficult. This difficulty is compounded in interdisciplinary fields such as microbiome research. There are many reasons why a researcher is unable to reproduce a previous result, and even if a result is reproducible, it may not be correct. Furthermore, failures to reproduce previous results have much to teach us about the scientific process and microbial life itself. This Perspective delineates a framework for identifying and overcoming threats to reproducibility, replicability, robustness, and generalizability of microbiome research. Instead of seeing signs of a crisis in others’ work, we need to appreciate the technical and social difficulties that limit reproducibility in the work of others as well as our own.
Emergence and Evolution of Novel Reassortant Influenza A Viruses in Canines in Southern China
Authors: Chen Ying , Trovão Nídia S. , Wang Guojun , Zhao Weifeng , He Ping , Zhou Huabo , Mo Yanning , Wei Zuzhang , Ouyang Kang , Huang Weijian , García-Sastre Adolfo , Nelson Martha I.
Published: June 2018

The capacity of influenza A viruses (IAVs) to host jump from animal reservoir species to humans presents an ongoing pandemic threat. Birds and swine are considered major reservoirs of viral genetic diversity, whereas equines and canines have historically been restricted to one or two stable IAV lineages with no transmission to humans. Here, by sequencing the complete genomes of 16 IAVs obtained from canines in southern China (Guangxi Zhuang Autonomous Region [Guangxi]) in 2013 to 2015, we demonstrate that the evolution of canine influenza viruses (CIVs) in Asian dogs is increasingly complex, presenting a potential threat to humans. First, two reassortant H1N1 virus genotypes were introduced independently from swine into canines in Guangxi, including one genotype associated with a zoonotic infection. The genomes contain segments from three lineages that circulate in swine in China: North American triple reassortant H3N2, Eurasian avian-like H1N1, and pandemic H1N1. Furthermore, the swine-origin H1N1 viruses have transmitted onward in canines and reassorted with the CIV-H3N2 viruses that circulate endemically in Asian dogs, producing three novel reassortant CIV genotypes (H1N1r, H1N2r, and H3N2r [r stands for reassortant]). CIVs from this study were collected primarily from pet dogs presenting with respiratory symptoms at veterinary clinics, but dogs in Guangxi are also raised for meat, and street dogs roam freely, creating a more complex ecosystem for CIV transmission. Further surveillance is greatly needed to understand the full genetic diversity of CIV in southern China, the nature of viral emergence and persistence in the region’s diverse canine populations, and the zoonotic risk as the viruses continue to evolve.

IMPORTANCE
Mammals have emerged as critically underrecognized sources of influenza virus diversity, including pigs that were the source of the 2009 pandemic and bats and bovines that harbor highly divergent viral lineages. Here, we identify two reassortant IAVs that recently host switched from swine to canines in southern China, including one virus with known zoonotic potential. Three additional genotypes were generated via reassortment events in canine hosts, demonstrating the capacity of dogs to serve as “mixing vessels.” The continued expansion of IAV diversity in canines with high human contact rates requires enhanced surveillance and ongoing evaluation of emerging pandemic threats.
Engineering Nitrogen Fixation Activity in an Oxygenic Phototroph
Authors: Liu Deng , Liberton Michelle , Yu Jingjie , Pakrasi Himadri B. , Bhattacharyya-Pakrasi Maitrayee
Published: June 2018

Biological nitrogen fixation is catalyzed by nitrogenase, a complex metalloenzyme found only in prokaryotes. N
2
fixation is energetically highly expensive, and an energy-generating process such as photosynthesis can meet the energy demand of N
2
fixation. However, synthesis and expression of nitrogenase are exquisitely sensitive to the presence of oxygen. Thus, engineering nitrogen fixation activity in photosynthetic organisms that produce oxygen is challenging. Cyanobacteria are oxygenic photosynthetic prokaryotes, and some of them also fix N
2
. Here, we demonstrate a feasible way to engineer nitrogenase activity in the nondiazotrophic cyanobacterium
Synechocystis
sp. PCC 6803 through the transfer of 35 nitrogen fixation (
nif
) genes from the diazotrophic cyanobacterium
Cyanothece
sp. ATCC 51142. In addition, we have identified the minimal
nif
cluster required for such activity in
Synechocystis
6803. Moreover, nitrogenase activity was significantly improved by increasing the expression levels of
nif
genes. Importantly, the O
2
tolerance of nitrogenase was enhanced by introduction of uptake hydrogenase genes, showing this to be a functional way to improve nitrogenase enzyme activity under micro-oxic conditions. To date, our efforts have resulted in engineered
Synechocystis
6803 strains that, remarkably, have more than 30% of the N
2
fixation activity of
Cyanothece
51142, the highest such activity established in any nondiazotrophic oxygenic photosynthetic organism. This report establishes a baseline for the ultimate goal of engineering nitrogen fixation ability in crop plants.

IMPORTANCE
Application of chemically synthesized nitrogen fertilizers has revolutionized agriculture. However, the energetic costs of such production processes and the widespread application of fertilizers have raised serious environmental issues. A sustainable alternative is to endow to crop plants the ability to fix atmospheric N
2
in situ
. One long-term approach is to transfer all
nif
genes from a prokaryote to plant cells and to express nitrogenase in an energy-producing organelle, chloroplast, or mitochondrion. In this context,
Synechocystis
6803, the nondiazotrophic cyanobacterium utilized in this study, provides a model chassis for rapid investigation of the necessary requirements to establish diazotrophy in an oxygenic phototroph.