bluuebunny/crossref_metadata_2025 huggingface dataset:
TBAI/TBHP-catalyzed [3 + 2]cycloaddition/oxidation/aromatization cascade and online ESI-MS mechanistic studies: synthesis of pyrrolo[2,1-a]isoquinolines and indolizino[8,7-b]indoles
Authors: Nekkanti Shalini , Kumar Niggula Praveen , Sharma Pankaj , Kamal Ahmed , Nachtigall Fabiane M. , Forero-Doria Oscar , Santos Leonardo S. , Shankaraiah Nagula
Published: December 2015

A facile [3 + 2]cycloaddition/oxidation/aromatization cascade reaction for the synthesis of pyrrolo[2,1-a]isoquinolines and indolizino[8,7-b]indoles has been developed by employing tert-butyl hydroperoxide (TBHP) and tetrabutylammonium iodide (TBAI).
Synthesis and properties of the derivatives of triphenylamine and 1,8-naphthalimide with the olefinic linkages between chromophores
Authors: Gudeika Dalius , Sini Gjergji , Jankauskas Vygintas , Sych Galyna , Grazulevicius Juozas V.
Published: December 2015

Two donor–acceptor type molecules consisting of triphenylamine and 1,8-naphthalimide moieties with the olefinic linkages between chromophores were synthesized by Heck reaction.
Synthesis of γ-Fe2O3@SiO2@polypyrrole core/shell/shell nanospheres with flexible controllability of electromagnetic properties
Authors: Zhang Yajie , Zhang Zhiming , Xu Shicong , Yu Liangmin , Long Yunze , Tang Qunwei
Published: December 2015

A possible formation mechanism for γ-Fe2O3@SiO2@PPy core/shell/shell nanospheres with flexible controllability of electromagnetic properties is proposed.
Bacteria-triggered degradation of nanofilm shells for release of antimicrobial agents
Authors: Craig Marina , Altskär Annika , Nordstierna Lars , Holmberg Krister
Published: December 2015

Stimuli-responsive nanofilm shells on hollow microcapsules exposing drugs in the presence of Pseudomonas aeruginosa.
Molecular engineering of starburst triarylamine donor with selenophene containing π-linker for dye-sensitized solar cells
Authors: Ho Po-Yu , Siu Chi-Ho , Yu Wai-Hong , Zhou Panwang , Chen Tao , Ho Cheuk-Lam , Lee Lawrence Tien Lin , Feng Ying-Hsuan , Liu Jianyong , Han Keli , Lo Yih Hsing , Wong Wai-Yeung
Published: December 2015

New starburst triarylamine donor with selenophene containing π-linker were synthesized. Such donor can minimize dye aggregation on TiO2 and slow down charge recombination kinetics in dye-sensitized solar cells.
Electronic band structure, optical, dynamical and thermodynamic properties of cesium chloride (CsCl) from first-principles
Authors: Bingol Suat , Erdinc Bahattin , Akkus Harun
Published: December 2015

The geometric structural optimization, electronic band structure, total density of states for valence electrons, density of states for phonons, optical, dynamical, and thermodynamical features of cesium chloride have been investigated by linearized augmented plane wave method using the density functional theory under the generalized gradient approximation. Ground state properties of cesium chloride are studied. The calculated ground state properties are consistent with experimental results. Calculated band structure indicates that the cesium chloride structure has an indirect band gap value of 5.46 eV and is an insulator. From the obtained phonon spectra, the cesium chloride structure is dynamically stable along the various directions in the Brillouin zone. Temperature dependent thermodynamic properties are studied using the harmonic approximation model.
Spectroscopic study on deuterated benzenes. I. Microwave spectra and molecular structure in the ground state
Authors: Kunishige Sachi , Katori Toshiharu , Baba Masaaki , Nakajima Masakazu , Endo Yasuki
Published: December 2015

We observed microwave absorption spectra of some deuterated benzenes and accurately determined the rotational constants of all H/D isotopomers in the ground vibrational state. Using synthetic analysis assuming that all bond angles are 120°, the mean bond lengths were obtained to be r0(C–C) = 1.3971 Å and r0(C–H) = r0(C–D) = 1.0805 Å. It has been concluded that the effect of deuterium substitution on the molecular structure is negligibly small and that the mean bond lengths of C–H and C–D are identical unlike small aliphatic hydrocarbons, in which r0(C–D) is about 5 mÅ shorter than r0(C–H). It is considered that anharmonicity is very small in the C–H stretching vibration of aromatic hydrocarbons.
Double layers and other phenomena in low-pressure plasma columns generated by ultra-violet light
Authors: Valentini H.-B. , Kaiser D.
Published: December 2015

Low-pressure steady-state plasmas are analysed by means of a two-fluid model in both plane and cylindrical geometries. The charged particles are generated by UV illumination. Both a Gaussian and a one-step profile of the ionization are taken into account. Numerical results reveal various types of solutions depending on the ionization profile and the collisionality. The first state arises if the ionization spreads from the centre over a great part of the plasma. It has an almost quasineutral plasma core and a positively charged boundary sheath. The curvature of the number density of the charge particles is negative, except the boundary sheath. The second state occurs if the ionization is mainly localized in the vicinity of the centre and the collisionality is below a threshold. A slightly positive plasma core is surrounded by a double layer there where the ionization falls off steeply. Between the double layer and the boundary sheath a broad zone can exist where the plasma is nearly quasi-neutral and the electric field is small. Within the double layer the ion drift speed attains the Bohm velocity in collisionless plasmas, it is smaller in collisional cases. In a broad domain, the curvature of the number density of the charged particles can be positive. This is a feature of the so-called contracted columns. The transition between both the states occurs abruptly under collisonless conditions and becomes smooth as the collisionality increases. The minimum of the space charge density can become positive in this case. Several layers are possible, as well. Using the Gaussian profile analytical criteria can be given for a few of the mentioned phenomena. Probably, ionization profiles prescribed by photons allow to understand the origin of the contracted column more completely than up to now.
The dynamics of carbon nanostructures at detonation of condensed high explosives
Authors: Satonkina Nataliya P.
Published: December 2015

Based on the obtained earlier experimental conductivity graphs at detonation of five different high explosives, an analysis was performed which shows a correlation between the carbon content and the conductivity magnitude. An assumption was put forward that the conductivity in the whole detonation wave is provided by the contact mechanism along conductive carbon nanostructures.
Approaching the limits of two-phase boiling heat transfer: High heat flux and low superheat
Authors: Palko J. W. , Zhang C. , Wilbur J. D. , Dusseault T. J. , Asheghi M. , Goodson K. E. , Santiago J. G.
Published: December 2015

We demonstrate capillary fed porous copper structures capable of dissipating over 1200 W cm−2 in boiling with water as the working fluid. Demonstrated superheats for this structure are dramatically lower than those previously reported at these high heat fluxes and are extremely insensitive to heat input. We show superheats of less than 10 K at maximum dissipation and varying less than 5 K over input heat flux ranges of 1000 W cm−2. Fabrication of the porous copper layers using electrodeposition around a sacrificial template allows fine control of both microstructure and bulk geometry, producing structures less than 40 μm thick with active region lateral dimensions of 2 mm × 0.3 mm. The active region is volumetrically Joule heated by passing an electric current through the porous copper bulk material. We analyze the heat transfer performance of the structures and suggest a strong influence of pore size on superheat. We compare performance of the current structure to existing wick structures.
Dislocation related droop in InGaN/GaN light emitting diodes investigated via cathodoluminescence
Authors: Pozina Galia , Ciechonski Rafal , Bi Zhaoxia , Samuelson Lars , Monemar Bo
Published: December 2015

Today's energy saving solutions for general illumination rely on efficient white light emitting diodes (LEDs). However, the output efficiency droop experienced in InGaN based LEDs with increasing current injection is a serious limitation factor for future development of bright white LEDs. We show using cathodoluminescence (CL) spatial mapping at different electron beam currents that threading dislocations are active as nonradiative recombination centers only at high injection conditions. At low current, the dislocations are inactive in carrier recombination due to local potentials, but these potentials are screened by carriers at higher injection levels. In CL images, this corresponds to the increase of the dark contrast around dislocations with the injection (excitation) density and can be linked with droop related to the threading dislocations. Our data indicate that reduction of droop in the future efficient white LED can be achieved via a drastic reduction of the dislocation density by using, for example, bulk native substrates.
Phase stability and magnetic behavior of FeCrCoNiGe high-entropy alloy
Authors: Huang Shuo , Vida Ádám , Molnár Dávid , Kádas Krisztina , Varga Lajos Károly , Holmström Erik , Vitos Levente
Published: December 2015

We report an alternative FeCrCoNiGe magnetic material based on FeCrCoNi high-entropy alloy with Curie point far below the room temperature. Investigations are done using first-principles calculations and key experimental measurements. Results show that the equimolar FeCrCoNiGe system is decomposed into a mixture of face-centered cubic and body-centered cubic solid solution phases. The increased stability of the ferromagnetic order in the as-cast FeCrCoNiGe composite, with measured Curie temperature of 640 K, is explained using the exchange interactions.
Revealing localized plastic flow in apparent elastic region before yielding in metallic glasses
Authors: Zhao L. Z. , Xue R. J. , Li Y. Z. , Wang W. H. , Bai H. Y.
Published: December 2015

The microscopically localized flow before yielding in metallic glass (MG) is hard to be detected using conventional mechanical tests due to its extremely slow process with a long time scale and lack of structural information. We present a stress relaxation approach to circumvent the experimental problem and to reveal the evolution of the flow before yielding in MG by detecting the evolution of structural heterogeneity and activation energy barrier spectra of flow units. We report on explicit correlations among dynamical heterogeneities, nanoscale flow units, and yielding, revealing a transition from the microscopically flow to macroscopic yielding in MG.
Analysis of fluid motion and heat transport on magnetohydrodynamic boundary layer past a vertical power law stretching sheet with hydrodynamic and thermal slip effects
Authors: Alkahtani Badr , Abel M. Subhas , Aly Emad H.
Published: December 2015

The present model is committed to the study of MHD boundary layer flow and heat transfer past a nonlinear vertically stretching porous stretching sheet with the effects of hydrodynamic and thermal slip. The boundary value problem, consisting of boundary layer equations of motion and heat transfer, which are nonlinear partial differential equations are transformed into nonlinear ordinary differential equations, with the aid of similarity transformation. This problem has been solved, using Runge Kutta fourth order method with shooting technique. The effects of various physical parameters, such as, stretching parameter m, magnetic parameter M, porosity parameter fw, buoyancy parameter λ, Prandtl number Pr, Eckert number Ec, hydrodynamic slip parameter γ, and thermal slip parameter δ, on flow and heat transfer characteristics, are computed and represented graphically.
A molecular dynamics study of melting and dissociation of tungsten nanoparticles
Authors: Li Min , Wang Jun , Fu Baoqin , Hou Qing
Published: December 2015

Molecular dynamics simulations were conducted to study the melting and dissociation of free tungsten nanoparticles. For the various interatomic potentials applied, the melting points of the tungsten nanoparticles increased with increasing nanoparticle diameter. Combining these results with the melting point of bulk tungsten in the experiment, the melting point of nanoparticles with diameters ranging from 4 to 12 nm could be determined. As the temperature increases, free nanoparticles are subject to dissociation phenomena. The dissociation rate was observed to follow Arrhenius behavior, and the Meyer–Neldel rule was obeyed. These results are useful in understanding the behavior of tungsten dust generated in nuclear fusion devices as well as for the preparation, formation, and application of tungsten powders.
Self-assembled Ag nanoparticle network passivated by a nano-sized ZnO layer for transparent and flexible film heaters
Authors: Seo Ki-Won , Kim Min-Yi , Chang Hyo-Sik , Kim Han-Ki
Published: December 2015

We investigated a self-assembled Ag nanoparticle network electrode passivated by a nano-sized ZnO layer for use in high-performance transparent and flexible film heaters (TFFHs). The low temperature atomic layer deposition of a nano-sized ZnO layer effectively filled the uncovered area of Ag network and improved the current spreading in the self-assembled Ag network without a change in the sheet resistance and optical transmittance as well as mechanical flexibility. The time-temperature profiles and heat distribution analysis demonstrate that the performance of the TFTH with the ZnO/Ag network is superior to that of a TFFH with Ag nanowire electrodes. In addition, the TFTHs with ZnO/Ag network exhibited better stability than the TFFH with a bare Ag network due to the effective current spreading through the nano-sized ZnO layer.
On the extent of fire-induced forest degradation in Mato Grosso, Brazilian Amazon, in 2000, 2005 and 2010
Authors: Miettinen Jukka , Shimabukuro Yosio E. , Beuchle René , Grecchi Rosana C. , Gomez Marcela Velasco , Simonetti Dario , Achard Frédéric
Published: December 2015

In this paper we analyse the extent of fire-induced forest degradation in Mato Grosso State, Brazil. We utilise a sample based approach used in a previous pan-tropical deforestation survey to derive information on land cover and burned areas in the two major biomes of Mato Grosso: Amazon and Cerrado. Land cover and burned area are mapped for three years (2000–2005–2010) over 77 sample sites (10 000 ha each) distributed systematically throughout the state which covers 90.337 Mha. Our results indicate continuing forest degradation by fires in the state and potentially increasing fire susceptibility of the Amazon forests, regardless of the decrease in deforestation. 2010 witnessed the most extensive fire-induced forest degradation (~300 000 ha) in the forests of the Amazon biome among the study years, regardless of the fact that the fire season was less severe than in 2005. Deforestation in the Amazon biome in Mato Grosso dropped from 590 000 ha year–1 in the 2000–2005 period to 190 000 ha year–1 in the second half of the decade. The findings of this study advocate the inclusion of forest fire effects into carbon accounting initiatives.
Climate change and agricultural development: a challenge for water management.
Authors: Hoanh C. T. , Johnston R. , Smakhtin V.
Published: December 2015

Freshwater-related risks of climate change increase significantly with increasing global temperatures. Globally, the negative impacts of future climate change on freshwater systems are expected to outweigh the benefits, and agriculture and irrigation, as the largest consumers of water globally, are most at risk. This book analyses the potential impacts of climate change on water for agriculture, and the adaptation strategies in water management to deal with these impacts, drawing on global assessments and regional studies. This chapter introduces the book, sets the scene for research on climate change in agricultural water management, and synthesizes the issues, methodologies and findings in the chapters to follow. Chapters 2 and 3 provide an overview of global assessment of climate change impacts and water requirement for future agriculture. Chapters 4-7 provide analyses of crop water requirements in four case studies in developing countries. Chapters 8 and 9 are studies of irrigation management under sea-level rise in Vietnam's Mekong Delta. Chapters 10-12 discuss examples of adaptation alternatives such as water-saving techniques and groundwater exploitation, and related policy settings. The last chapter links the dominant approach of uncertainty presented in the climate change discourse with policy discussions on climate adaptation strategies.
Lubrication of aluminium versus diamond-like carbon contacts with hydrophobin proteins
Authors: Shi Zhen , Hakala Timo J. , Metsäjoki Jarkko , Szilvay Géza R. , Li Feng
Published: December 2015

Hydrogenated diamond-like carbon coatings (a-C:H) and silicon-doped diamond-like carbon coatings (a-C:H(Si)) of 1 μm thickness were deposited on stainless steel substrates by the inductively coupled plasma chemical vapour deposition technique, including a 300 nm-thick SiN x interlayer. Tribological experiments for both types of coating under pure and hydrophobin-containing water lubrication were performed using a pin-on-disc tribometer. To better understand wear behaviour, studies of hardness, surface morphology, water contact angle and chemical bonding were carried out using a nano-indenter, atomic force microscopy, contact angle measurement and X-ray photoelectron spectroscopy, respectively. Silicon doping in the a-C:H coating was found to slightly increase the surface roughness and wettability. The lowest friction coefficient (0.09) was obtained for the a-C:H(Si) coating sliding against an aluminium counterpart in water. The addition of HFBII hydrophobins to water increased both friction and wear of the aluminium counter body, and oxide tribofilm formation was prevented on the aluminium surface.
Participatory Photography for Peace: Using Images to Open up Dialogue after Violence
Authors: Baú Valentina
Published: December 2015

This article begins with a literature review of Participatory Photography (PP) that highlights how this tool has been mostly implemented for action research, advocacy, and public health purposes. It shows how scholars have only quite recently begun to recognise its ability to generate change among PP participants. This is followed by a description of the project that was carried out in Kenya, including its background, objectives and daily activities related to peacebuilding. Offering insight into crucial aspects of this work, examples of the photographs taken by participants and related stories are presented. The conclusion is preceded by reflections on the effectiveness, limitations and potential risks involved in carrying out PP projects in post-conflict settings.
XCR1+ dendritic cells promote memory CD8+ T cell recall upon secondary infections with Listeria monocytogenes or certain viruses
Authors: Alexandre Yannick O. , Ghilas Sonia , Sanchez Cindy , Le Bon Agnès , Crozat Karine , Dalod Marc
Published: December 2015

Naive CD8+ T cell priming during tumor development or many primary infections requires cross-presentation by XCR1+ dendritic cells (DCs). Memory CD8+ T lymphocytes (mCTLs) harbor a lower activation threshold as compared with naive cells. However, whether their recall responses depend on XCR1+ DCs is unknown. By using a new mouse model allowing fluorescent tracking and conditional depletion of XCR1+ DCs, we demonstrate a differential requirement of these cells for mCTL recall during secondary infections by different pathogens. XCR1+ DCs were instrumental to promote this function upon secondary challenges with Listeria monocytogenes, vesicular stomatitis virus, or Vaccinia virus, but dispensable in the case of mouse cytomegalovirus. We deciphered how XCR1+ DCs promote mCTL recall upon secondary infections with Listeria. By visualizing for the first time the in vivo choreography of XCR1+ DCs, NK cells and mCTLs during secondary immune responses, and by neutralizing in vivo candidate molecules, we demonstrate that, very early after infection, mCTLs are activated, and attracted in a CXCR3-dependent manner, by NK cell–boosted, IL-12–, and CXCL9-producing XCR1+ DCs. Hence, depending on the infectious agent, strong recall of mCTLs during secondary challenges can require cytokine- and chemokine-dependent cross-talk with XCR1+ DCs and NK cells.
Black Holes: A Very Short Introduction
Authors: Blundell Katherine
Published: December 2015

Black holes are a constant source of fascination to many due to their mysterious nature. Black Holes: A Very Short Introduction addresses a variety of questions, including what a black hole actually is, how they are characterized and discovered, and what would happen if you came too close to one. It explains how black holes form and grow—by stealing material that belongs to stars—as well as how many there may be in the Universe. It also explores the large black holes found in the centres of galaxies, and how black holes power quasars and lie behind other spectacular phenomena in the cosmos.
Improving Food Bank Gleaning Operations: An Application in New York State
Authors: Sönmez Erkut , Lee Deishin , Gómez Miguel I. , Fan Xiaoli
Published: December 2015

Gleaning is increasingly attracting the attention of food safety networks, including food banks, as a valuable tool that simultaneously reduces food loss and alleviates food insecurity. However, managing gleaning operations can be challenging because the arrival of gleaning opportunities and the attendance of gleaner volunteers are both stochastic. We develop a stochastic optimization model to characterize and optimize a gleaning operation. The food bank chooses the gleaning schedule, which affects the gleaner capacity and the number of gleaning opportunities scheduled. In a specific field study of the Food Bank of the Southern Tier in New York, we analyze the tradeoff between call and volume service levels to find the optimum schedule that maximizes the expected total volume gleaned. Moreover, we find that increasing the gleaning window and increasing slot availability can be used as substitute mechanisms for increasing the total volume gleaned. Additionally, we use our model to assess the impact of recruiting more volunteer gleaners.
The Welfare Impacts of Commodity Price Volatility: Reply
Authors: Bellemare Marc F. , Barrett Christopher B. , Just David R.
Published: December 2015

It was with delight that we read McBride's comment on our work (Bellemare, Barrett, and Just 2013), first because we welcome more light on a topic on which we spent almost seven years before the AJAE accepted it for publication, and second because a dialogue such as this one is, in our view, part and parcel of what makes the research endeavor worthwhile.

In this response to McBride's comment, we bring further light to this topic by discussing the difference between willingness to pay (WTP) as a proportion of income calculated at mean income versus mean WTP as a proportion of income. We then discuss the necessary limitations imposed on researchers doing work of the nature of that done in Bellemare, Barrett, and Just (2013) by the use of observational data. We conclude by briefly discussing potential solutions to those limitations.
Association of Urinary Sodium Excretion With Blood Pressure and Cardiovascular Clinical Events in 17,033 Latin Americans
Authors: Lamelas Pablo M. , Mente Andrew , Diaz Rafael , Orlandini Andres , Avezum Alvaro , Oliveira Gustavo , Lanas Fernando , Seron Pamela , Lopez-Jaramillo Patricio , Camacho-Lopez Paul , O′Donnell Martin J. , Rangarajan Sumathy , Teo Koon , Yusuf Salim
Published: December 2015

BACKGROUND

Information on actual sodium intake and its relationships with blood pressure (BP) and clinical events in South America is limited. The aim of this cohort study was to assess the relationship of sodium intake with BP, cardiovascular (CV) events, and mortality in South America.

METHODS

We studied 17,033 individuals, aged 35–70 years, from 4 South American countries (Argentina, Brazil, Chile, and Colombia). Measures of sodium excretion, estimated from morning fasting urine, were used as a surrogate for daily sodium intake. We measured BP and monitored the composite outcome of death and major CV events.

RESULTS

Overall mean sodium excretion was 4.70±1.43g/day. A positive, nonuniform association between sodium and BP was detected, with a significant steeper slope for the relationship at higher sodium excretion levels ( P < 0.001 for interaction). With a median follow-up of 4.7 years, the primary composite outcome (all-cause death, myocardial infarction, stroke, or heart failure) occurred in 568 participants (3.4%). Compared with sodium excretion of 5–6g/day (reference group), participants who excreted >7g/day had increased risks of the primary outcome (odds ratio (OR) 1.73; 95% confidence interval (CI) 1.24 to 2.40; P < 0.001), as well as death from any cause (OR 1.87; 95% CI 1.23 to 2.83; P = 0.003) and major CV disease (OR 1.77; 95% CI 1.12 to 2.81; P = 0.014). Sodium excretion of <3g/day was associated with a statistically nonsignificant increased risk of the primary outcome (OR 1.20; 95% CI 0.86 to 1.65; P = 0.26) and death from any cause (OR 1.25; 95% CI 0.81 to 1.93; P = 0.29), and a significant increased risk of major CV disease (OR 1.50; 95% CI 1.01 to 2.24; P = 0.048), as compared to the reference group.

CONCLUSIONS

Our results support a positive, nonuniform association between estimated urinary sodium excretion and BP, and a possible J-shaped pattern of association between sodium excretion over the entire range and clinical outcomes.
Epigenetics of drought-induced trans-generational plasticity: consequences for range limit development
Authors: Alsdurf Jacob , Anderson Cynthia , Siemens David H.
Published: December 2015

Genetic variation gives plants the potential to adapt to stressful environments that often exist beyond their geographic range limits. However, various genetic, physiological or developmental constraints might prevent the process of adaptation. Alternatively, environmentally induced epigenetic changes might sustain populations for several generations in stressful areas across range boundaries, but previous work on Boechera stricta , an upland mustard closely related to Arabidopsis , documented a drought-induced trans-generational plastic trade-off that could contribute to range limit development. Offspring of parents who were drought treated had higher drought tolerance, but lower levels of glucosinolate toxins. Both drought tolerance and defence are thought to be needed to expand the range to lower elevations. Here, we used methylation-sensitive amplified fragment length polymorphisms to determine whether environmentally induced DNA methylation and thus epigenetics could be a mechanism involved in the observed trans-generational plastic trade-off. We compared 110 offspring from the same self-fertilizing lineages whose parents were exposed to experimental drought stress treatments in the laboratory. Using three primer combinations, 643 polymorphic epi-loci were detected. Discriminant function analysis (DFA) on the amount of methylation detected resulted in significant combinations of epi-loci that distinguished the parent drought treatments in the offspring. Principal component (PC) and univariate association analyses also detected the significant differences, even after controlling for lineage, planting flat, developmental differences and multiple testing. Univariate tests also indicated significant associations between the amount of methylation and drought tolerance or glucosinolate toxin concentration. One epi-locus that was implicated in DFA, PC and univariate association analysis may be directly involved in the trade-off because increased methylation at this site on the genome decreased drought tolerance, but increased glucosinolate concentration.
traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals
Authors: Chen Li , Qin Zhaohui S.
Published: December 2015

Summary: Genome-wide association studies (GWASs) have successfully identified many sequence variants that are significantly associated with common diseases and traits. Tens of thousands of such trait-associated SNPs have already been cataloged, which we believe form a great resource for genomic research. Recent studies have demonstrated that the collection of trait-associated SNPs can be exploited to indicate whether a given genomic interval or intervals are likely to be functionally connected with certain phenotypes or diseases. Despite this importance, currently, there is no ready-to-use computational tool able to connect genomic intervals to phenotypes. Here, we present traseR, an easy-to-use R Bioconductor package that performs enrichment analyses of trait-associated SNPs in arbitrary genomic intervals with flexible options, including testing method, type of background and inclusion of SNPs in LD.

Availability and implementation: The traseR R package preloaded with up-to-date collection of trait-associated SNPs are freely available in Bioconductor

Contact:  zhaohui.qin@emory.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Limited effects of increased CO2 and temperature on metal and radionuclide bioaccumulation in a sessile invertebrate, the oyster Crassostrea gigas
Authors: Belivermiş Murat , Warnau Michel , Metian Marc , Oberhänsli François , Teyssié Jean-Louis , Lacoue-Labarthe Thomas
Published: December 2015

This study investigated the combined effects of reduced pH and increased temperature on the capacities of the Pacific cupped oyster Crassostrea gigas to bioconcentrate radionuclide and metals. Oysters were exposed to dissolved radiotracers (110mAg, 241Am, 109Cd, 57Co, 54Mn, and 65Zn) at three pH (7.5, 7.8, 8.1) and two temperatures (21 and 24°C) under controlled laboratory conditions. Although calcifying organisms are recognized as particularly vulnerable to ocean acidification, the oyster did not accumulate differently the studied metals when exposed under the different pH conditions. However, temperature alone or in combination with pH somewhat altered the bioaccumulation of the studied elements. At pH 7.5, Cd was accumulated with an uptake rate constant twofold higher at 24°C than 21°C. Bioaccumulation of Mn was significantly affected by an interactive effect between seawater pH and temperature, with a decreased uptake rate at pH 7.5 when temperature increased (27 ± 1 vs. 17 ± 1 d−1 at 21 and 24°C, respectively). Retention of Co and Mn tended also to decrease at the same pH with decreasing temperature. Neither pH nor temperature affected strongly the elements distribution between shell and soft tissues. Significant effects of pH were found on the bioaccessibility of Mn, Zn, and 241Am during experimental in vitro simulation of human digestion.
Association Between Bagrada hilaris Density and Feeding Damage in Broccoli: Implications for Pest Management
Authors: Palumbo John C. , Carrière Yves
Published: December 2015

Bagrada hilaris (Burmeister) (Hemiptera:Pentatomidae) has become a serious economic pest of brassica crops in Arizona and southern California. Feeding damage on broccoli can result in excessive seedling mortality and, on established plants, in malformed plants which are not commercially marketable. Although management tactics have been developed for this new pest, a reliable sampling technique for estimating adult density is lacking. Here, we analyzed data from 18 insecticide trials conducted from 2011 to 2014 in plots planted to broccoli to determine if estimates of fresh feeding damage on broccoli plants can be used to forecast B. hilaris densities. The proportion of plants with fresh feeding damage in a plot was significantly affected by year, trial nested within year, number of insecticides applied, and time after insecticide application. Average density of B. hilaris adults per plant in a plot was significantly affected by year, trial nested within year, and number of insecticides applied, while time after insecticide application had a marginal effect on population density. Across plots and years, the proportion of plants with fresh feeding damage was strongly and positively associated with the average number of B. hilaris adults per plant. Our results suggest that sampling young plants for signs of fresh feeding damage will provide a reliable and accurate sampling technique for monitoring B. hilaris in broccoli fields. We recommend that growers and pest control advisers focus their monitoring efforts on sampling broccoli plants for the presence of fresh feeding damage, rather than adults alone, when making pest management decisions.

Accepted for publication 10 November 2015. Published 12 November 2015.
Translocation of bacteria from the gut to the eggs triggers maternal transgenerational immune priming in
Tribolium castaneum
Authors: Knorr Eileen , Schmidtberg Henrike , Arslan Derya , Bingsohn Linda , Vilcinskas Andreas
Published: December 2015

Invertebrates can be primed to enhance their protection against pathogens they have encountered before. This enhanced immunity can be passed maternally or paternally to the offspring and is known as transgenerational immune priming. We challenged larvae of the red flour beetle
Tribolium castaneum
by feeding them on diets supplemented with
Escherichia coli
,
Micrococcus luteus
or
Pseudomonas entomophila
, thus mimicking natural exposure to pathogens. The oral uptake of bacteria induced immunity-related genes in the offspring, but did not affect the methylation status of the egg DNA. However, we observed the translocation of bacteria or bacterial fragments from the gut to the developing eggs via the female reproductive system. Such translocating microbial elicitors are postulated to trigger bacterial strain-specific immune responses in the offspring and provide an alternative mechanistic explanation for maternal transgenerational immune priming in coleopteran insects.
A Yankee at Oxford: John William Draper at the British Association for the Advancement of Science at Oxford, 30 June 1860
Authors: Ungureanu James C.
Published: December 2015

This paper contributes to the revisionist historiography on the legendary encounter between Samuel Wilberforce and Thomas Henry Huxley at the 1860 meeting in Oxford of the British Association for the Advancement of Science. It discusses the contents of a series of letters written by John William Draper and his family reflecting on his experience at that meeting. The letters have recently been rediscovered and have been neither published nor examined at full length. After a preliminary discussion on the historiography of the Oxford debate, the paper discloses the contents of the letters and then assesses them in the light of other contemporary accounts. The letters offer a nuanced reinterpretation of the event that supports the growing move towards a revisionist account.
Hodgkin–Huxley revisited: reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods
Authors: Daly Aidan C. , Gavaghan David J. , Holmes Chris , Cooper Jonathan
Published: December 2015

As cardiac cell models become increasingly complex, a correspondingly complex ‘genealogy’ of inherited parameter values has also emerged. The result has been the loss of a direct link between model parameters and experimental data, limiting both reproducibility and the ability to re-fit to new data. We examine the ability of approximate Bayesian computation (ABC) to infer parameter distributions in the seminal action potential model of Hodgkin and Huxley, for which an immediate and documented connection to experimental results exists. The ability of ABC to produce tight posteriors around the reported values for the gating rates of sodium and potassium ion channels validates the precision of this early work, while the highly variable posteriors around certain voltage dependency parameters suggests that voltage clamp experiments alone are insufficient to constrain the full model. Despite this, Hodgkin and Huxley's estimates are shown to be competitive with those produced by ABC, and the variable behaviour of posterior parametrized models under complex voltage protocols suggests that with additional data the model could be fully constrained. This work will provide the starting point for a full identifiability analysis of commonly used cardiac models, as well as a template for informative, data-driven parametrization of newly proposed models.
The influence of social preferences and reputational concerns on intergroup prosocial behaviour in gains and losses contexts
Authors: Everett Jim A. C. , Faber Nadira S. , Crockett Molly J.
Published: December 2015

To what extent do people help ingroup members based on a social preference to improve ingroup members’ outcomes, versus strategic concerns about preserving their reputation within their group? And do these motives manifest differently when a prosocial behaviour occurs in the context of helping another gain a positive outcome (study 1), versus helping another to avoid losing a positive outcome (study 2)? In both contexts, we find that participants are more prosocial towards ingroup (versus outgroup members) and more prosocial when decisions are public (versus private) but find no interaction between group membership and either anonymity of the decision or expected economic value of helping. Therefore, consistent with a preference-based account of ingroup favouritism, people appear to prefer to help ingroup members more than outgroup members, regardless of whether helping can improve their reputation within their group. Moreover, this preference to help ingroup members appears to take the form of an intuitive social heuristic to help ingroup members, regardless of the economic incentives or possibility of reputation management. Theoretical and practical implications for the study of intergroup prosocial behaviour are discussed.
Peculiar macrophagous adaptations in a new Cretaceous pliosaurid
Authors: Fischer Valentin , Arkhangelsky Maxim S. , Stenshin Ilya M. , Uspensky Gleb N. , Zverkov Nikolay G. , Benson Roger B. J.
Published: December 2015

During the Middle and Late Jurassic, pliosaurid plesiosaurs evolved gigantic body size and a series of craniodental adaptations that have been linked to the occupation of an apex predator niche. Cretaceous pliosaurids (i.e. Brachaucheninae) depart from this morphology, being slightly smaller and lacking the macrophagous adaptations seen in earlier forms. However, the fossil record of Early Cretaceous pliosaurids is poor, concealing the evolution and ecological diversity of the group. Here, we report a new pliosaurid from the Late Hauterivian (Early Cretaceous) of Russia. Phylogenetic analyses using reduced consensus methods recover it as the basalmost brachauchenine. This pliosaurid is smaller than other derived pliosaurids, has tooth alveoli clustered in pairs and possesses trihedral teeth with complex serrated carinae. Maximum-likelihood ancestral state reconstruction suggests early brachauchenines retained trihedral teeth from their ancestors, but modified this feature in a unique way, convergent with macrophagous archosaurs or sphenacodontoids. Our findings indicate that Early Cretaceous marine reptile teeth with serrated carinae cannot be unequivocally assigned to metriorhynchoid crocodylomorphs. Furthermore, they extend the known diversity of dental adaptations seen in Sauropterygia, the longest lived clade of marine tetrapods.
Evolution of the immune system in humans from infancy to old age
Authors: Simon A. Katharina , Hollander Georg A. , McMichael Andrew
Published: December 2015

This article reviews the development of the immune response through neonatal, infant and adult life, including pregnancy, ending with the decline in old age. A picture emerges of a child born with an immature, innate and adaptive immune system, which matures and acquires memory as he or she grows. It then goes into decline in old age. These changes are considered alongside the risks of different types of infection, autoimmune disease and malignancy.
Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge
Sycon ciliatum
Authors: Bråte Jon , Adamski Marcin , Neumann Ralf S. , Shalchian-Tabrizi Kamran , Adamska Maja
Published: December 2015

Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation was important for the evolution of developmental complexity in animals. However, most studies of lncRNA gene regulation have been performed using model animal species, and very little is known about this type of gene regulation in non-bilaterians. We have therefore analysed RNA-Seq data derived from a comprehensive set of embryogenesis stages in the calcareous sponge
Sycon ciliatum
and identified hundreds of developmentally expressed intergenic lncRNAs (lincRNAs) in this species.
In situ
hybridization of selected lincRNAs revealed dynamic spatial and temporal expression during embryonic development. More than 600 lincRNAs constitute integral parts of differentially expressed gene modules, which also contain known developmental regulatory genes, e.g. transcription factors and signalling molecules. This study provides insights into the non-coding gene repertoire of one of the earliest evolved animal lineages, and suggests that RNA-based gene regulation was probably present in the last common ancestor of animals.
Evolutionary rescue and the coexistence of generalist and specialist competitors: an experimental test
Authors: Bono Lisa M. , Gensel Catharine L. , Pfennig David W. , Burch Christina L.
Published: December 2015

Competition for resources is thought to play a critical role in both the origins and maintenance of biodiversity. Although numerous laboratory evolution experiments have confirmed that competition can be a key driver of adaptive diversification, few have demonstrated its role in the maintenance of the resulting diversity. We investigate the conditions that favour the origin and maintenance of alternative generalist and specialist resource-use phenotypes within the same population. Previously, we confirmed that competition for hosts amongφ6 bacteriophage in a mixed novel (non-permissive) and ancestral (permissive) host microcosm triggered the evolution of a generalist phenotype capable of infecting both hosts. However, because the newly evolved generalists tended to competitively exclude the ancestral specialists, coexistence between the two phenotypes was rare. Here, we show that reducing the relative abundance of the novel host slowed the increase in frequency of the generalist phenotype, allowing sufficient time for the specialist to further adapt to the ancestral host. This adaptation resulted in ‘evolutionary rescue’ of the specialists, preventing their competitive exclusion by the generalists. Thus, our results suggest that competition promotes both the origin and maintenance of biodiversity when it is strong enough to favour a novel resource-use phenotype, but weak enough to allow adaptation of both the novel and ancestral phenotypes to their respective niches.
Cardiac regeneration: epicardial mediated repair
Authors: Kennedy-Lydon Teresa , Rosenthal Nadia
Published: December 2015

The hearts of lower vertebrates such as fish and salamanders display scarless regeneration following injury, although this feature is lost in adult mammals. The remarkable capacity of the neonatal mammalian heart to regenerate suggests that the underlying machinery required for the regenerative process is evolutionarily retained. Recent studies highlight the epicardial covering of the heart as an important source of the signalling factors required for the repair process. The developing epicardium is also a major source of cardiac fibroblasts, smooth muscle, endothelial cells and stem cells. Here, we examine animal models that are capable of scarless regeneration, the role of the epicardium as a source of cells, signalling mechanisms implicated in the regenerative process and how these mechanisms influence cardiomyocyte proliferation. We also discuss recent advances in cardiac stem cell research and potential therapeutic targets arising from these studies.
Ancestral genome estimation reveals the history of ecological diversification inAgrobacterium
Authors: Lassalle Florent , Planel Rémi , Penel Simon , Chapulliot David , Barbe Valérie , Dubost Audrey , Calteau Alexandra , Vallenet David , Mornico Damien , Bigot Thomas , Guéguen Laurent , Vial Ludovic , Muller Daniel , Daubin Vincent , Nesme Xavier
Published: December 2015

Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes inAgrobacteriumbiovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of co-transferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of keyAgrobacteriumclades. This pattern of gene co-evolution rejects a neutral model of transfer, in which neighbouring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of co-functioning genes probably drove the ecological diversification ofAgrobacteriumand defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.
Structure of TSA2 reveals novel features of the active-site loop of peroxiredoxins
Authors: Nielsen Maja Holch , Kidmose Rune Thomas , Jenner Lasse Bohl
Published: December 2015

Saccharomyces cerevisiaeTSA2 belongs to the family of typical 2-Cys peroxiredoxins, a ubiquitously expressed family of redox-active enzymes that utilize a conserved peroxidatic cysteine to reduce peroxides. Typical 2-Cys peroxiredoxins have been shown to be involved in protection against oxidative stress and in hydrogen peroxide signalling. Furthermore, several 2-Cys peroxiredoxins, includingS. cerevisiaeTSA1 and TSA2, are able to switch to chaperone activity upon hyperoxidation of their peroxidatic cysteine. This makes the sensitivity to hyperoxidation of the peroxidatic cysteine a very important determinant for the cellular function of a peroxiredoxin under different cellular conditions. Typical 2-Cys peroxiredoxins exist as dimers, and in the course of the reaction the peroxidatic cysteine forms a disulfide with a resolving cysteine located in the C-terminus of its dimeric partner. This requires a local unfolding of the active site and the C-terminus. The balance between the fully folded and locally unfolded conformations is of key importance for the reactivity and sensitivity to hyperoxidation of the different peroxiredoxins. Here, the structure of a C48S mutant of TSA2 fromS. cerevisiaethat mimics the reduced state of the peroxidatic cysteine has been determined. The structure reveals a novel conformation for the strictly conserved Pro41, which is likely to affect the delicate balance between the fully folded and locally unfolded conformations of the active site, and therefore the reactivity and the sensitivity to hyperoxidation. Furthermore, the structure also explains the observed difference in the pKavalues of the peroxidatic cysteines ofS. cerevisiaeTSA1 and TSA2 despite their very high sequence identity.