bluuebunny/crossref_metadata_2025 huggingface dataset:
A High-Fat High-Sucrose Diet Rapidly Alters Muscle Integrity, Inflammation and Gut Microbiota in Male Rats
Authors: Collins Kelsey H. , Paul Heather A. , Hart David A. , Reimer Raylene A. , Smith Ian C. , Rios Jaqueline L. , Seerattan Ruth A. , Herzog Walter
Published: November 2016

The chronic low-level inflammation associated with obesity is known to deleteriously affect muscle composition. However, the manner in which obesity leads to muscle loss has not been explored in detail or in an integrated manner following a short-term metabolic challenge. In this paper, we evaluated the relationships between compromised muscle integrity, diet, systemic inflammatory mediators, adipose tissue, and gut microbiota in male Sprague-Dawley rats. We show that intramuscular fat, fibrosis, and the number of pro-inflammatory cells increased by 3-days and was sustained across 28-days of high-fat high-sugar feeding compared to control-diet animals. To understand systemic contributors to muscle damage, dynamic changes in gut microbiota and serum inflammatory markers were evaluated. Data from this study links metabolic challenge to persistent compromise in muscle integrity after just 3-days, a finding associated with altered gut microbiota and systemic inflammatory changes. These data contribute to our understanding of early consequences of metabolic challenge on multiple host systems, which are important to understand as obesity treatment options are developed. Therefore, intervention within this early period of metabolic challenge may be critical to mitigate these sustained alterations in muscle integrity.
Lent-On-Plus Lentiviral vectors for conditional expression in human stem cells
Authors: Benabdellah Karim , Muñoz Pilar , Cobo Marién , Gutierrez-Guerrero Alejandra , Sánchez-Hernández Sabina , Garcia-Perez Angélica , Anderson Per , Carrillo-Gálvez Ana Belén , Toscano Miguel G. , Martin Francisco
Published: November 2016

Conditional transgene expression in human stem cells has been difficult to achieve due to the low efficiency of existing delivery methods, the strong silencing of the transgenes and the toxicity of the regulators. Most of the existing technologies are based on stem cells clones expressing appropriate levels of tTA or rtTA transactivators (based on the TetR-VP16 chimeras). In the present study, we aim the generation of Tet-On all-in-one lentiviral vectors (LVs) that tightly regulate transgene expression in human stem cells using the original TetR repressor. By using appropriate promoter combinations and shielding the LVs with the Is2 insulator, we have constructed the Lent-On-Plus Tet-On system that achieved efficient transgene regulation in human multipotent and pluripotent stem cells. The generation of inducible stem cell lines with the Lent-ON-Plus LVs did not require selection or cloning, and transgene regulation was maintained after long-term cultured and upon differentiation toward different lineages. To our knowledge, Lent-On-Plus is the first all-in-one vector system that tightly regulates transgene expression in bulk populations of human pluripotent stem cells and its progeny.
Genetic determination of the enhanced drought resistance of rice maintainer HuHan2B by pedigree breeding
Authors: Wei Haibin , Feng Fangjun , Lou Qiaojun , Xia Hui , Ma Xiaosong , Liu Yunhua , Xu Kai , Yu Xinqiao , Mei Hanwei , Luo Lijun
Published: November 2016

The ongoing deficit of fresh water resource in rice growing regions has made the selection of water-saving and drought-resistance rice (WDR) a crucial factor in developing sustainable cultivation. HuHan2B, a new japonica maintainer for WDR breeding, had the same yield potential as recurrent parent HanFengB but showed improved drought resistance in fields. We investigated the genomic content accumulation and candidate genes passed from parent to offspring using the genomic and transcriptomic approaches. The genomic constitution indicated that the genetic similarity was 84% between HuHan2B and HanFengB; additionally, 7,256 genes with specific alleles were inherited by HuHan2B from parents other than HanFengB. The differentially expressed genes (DEGs) under drought stress showed that biological function was significantly enriched for transcript regulation in HuHan2B, while the oxidation-reduction process was primarily enriched in HanFengB. Furthermore, 36 DEGs with specific inherited alleles in HuHan2B were almost involved in the regulatory network of TFs and target genes. These findings suggested that major-effect genes were congregated and transformed into offspring in manner of interacting network by breeding. Thus, exploiting the potential biological function of allelic-influencing DEGs would be of great importance for improving selection efficiency and the overall genetic gain of multiple complex traits.
Novel Podophyllotoxin Derivatives as Partial PPARγ Agonists and their Effects on Insulin Resistance and Type 2 Diabetes
Authors: Zhang Xiangming , Liu Huijuan , Sun Bo , Sun Yan , Zhong Weilong , Liu Yanrong , Chen Shuang , Ling Honglei , Zhou Lei , Jing Xiangyan , Qin Yuan , Xiao Ting , Sun Tao , Zhou Honggang , Yang Cheng
Published: November 2016

Peroxisome proliferator-activated receptor γ (PPARγ) is recognized as a key regulator of insulin resistance. In this study, we searched for novel PPARγ agonists in a library of structurally diverse organic compounds and determined that podophyllotoxin exhibits partial agonist activity toward PPARγ. Eight novel podophyllotoxin-like derivatives were synthesized and assayed for toxicity and functional activity toward PPARγ to reduce the possible systemic toxic effects of podophyllotoxin and to maintain partial agonist activity toward PPARγ. Cell-based transactivation assays showed that compounds (E)-3-(hydroxy(3,4,5-trimethoxyphenyl)methyl)-4-(4(trifluoromethyl)styryl)dihydrofuran-2(3H)-one (3a) and (E)-4-(3-acetylstyryl)-3-(hydroxyl (3,4,5-trimethoxyphenyl)methyl)dihydrofuran-2(3H)-one (3f) exhibited partial agonist activity. An experiment using human hepatocarcinoma cells (HepG2) that were induced to become an insulin-resistant model showed that compounds 3a and 3f improved insulin sensitivity and glucose consumption. In addition, compounds 3a and 3f significantly improved hyperglycemia and insulin resistance in high-fat diet-fed streptozotocin (HFD-STZ)-induced type 2 diabetic rats at a dose of 15 mg/kg/day administered orally for 45 days, without significant weight gain. Cell toxicity testing also showed that compounds 3a and 3f exhibited weaker toxicity than pioglitazone. These findings suggested that compounds 3a and 3f improved insulin resistance in vivo and in vitro and that the compounds exhibited potential for the treatment of type 2 diabetes mellitus.
Atomic Layering, Intermixing and Switching Mechanism in Ge-Sb-Te based Chalcogenide Superlattices
Authors: Yu Xiaoming , Robertson John
Published: November 2016

GeSbTe-based chalcogenide superlattice (CSLs) phase-change memories consist of GeSbTe layer blocks separated by van der Waals bonding gaps. Recent high resolution electron microscopy found two types of disorder in CSLs, a chemical disorder within individual layers, and SbTe bilayer stacking faults connecting one block to an adjacent block which allows individual block heights to vary. The disorder requires a generalization of the previous switching models developed for CSL systems. Density functional calculations are used to describe the stability of various types of intra-layer disorder, how the block heights can vary by means of SbTe-based stacking faults and using a vacancy-mediated kink motion, and also to understand the nature of the switching process in more chemically disordered CSLs.
Genome wide transcriptome profiling of Fusarium oxysporum f sp. ciceris conidial germination reveals new insights into infection-related genes
Authors: Sharma Mamta , Sengupta Anindita , Ghosh Raju , Agarwal Gaurav , Tarafdar Avijit , Nagavardhini A , Pande Suresh , Varshney Rajeev K
Published: November 2016

Vascular wilt caused by Fusarium oxysporum f. sp. ciceris (Foc) is a serious disease of chickpea (Cicer arietinum L.) accounting for approximately 10–15% annual crop loss. The fungus invades the plant via roots, colonizes the xylem vessels and prevents the upward translocation of water and nutrients. Infection is initiated by conidia that invade the host tissue often by penetration of intact epidermal cells. Here, we report the characterization of the transcriptome of Foc sequenced using Illumina Hiseq technology during its conidial germination at different time points. Genome-wide expression profiling revealed that genes linked to fungal development are transcribed in successive ways. Analysis showed that Foc have large sets of germination-related genes and families of genes encoding secreted effectors, cell wall/pectin-degrading enzymes, metabolism related enzymes, transporters and peptidases. We found that metabolism related enzymes are up-regulated at early time point whereas most transporters and secondary metabolites important for tissue colonization and pathogenicity are up-regulated later as evident from the qRT-PCR. The study demonstrated that early conidial germination in Foc is accompanied by rapid shifts in gene expression that prepare the fungus for germ tube outgrowth, host cell invasion and pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction.
Acidic pH promotes intervertebral disc degeneration: Acid-sensing ion channel -3 as a potential therapeutic target
Authors: Gilbert Hamish T. J. , Hodson Nathan , Baird Pauline , Richardson Stephen M. , Hoyland Judith A.
Published: November 2016

The aetiology of intervertebral disc (IVD) degeneration remains poorly understood. Painful IVD degeneration is associated with an acidic intradiscal pH but the response of NP cells to this aberrant microenvironmental factor remains to be fully characterised. The aim here was to address the hypothesis that acidic pH, similar to that found in degenerate IVDs, leads to the altered cell/functional phenotype observed during IVD degeneration, and to investigate the involvement of acid-sensing ion channel (ASIC) -3 in the response. Human NP cells were treated with a range of pH, from that of a non-degenerate (pH 7.4 and 7.1) through to mildly degenerate (pH 6.8) and severely degenerate IVD (pH 6.5 and 6.2). Increasing acidity of pH caused a decrease in cell proliferation and viability, a shift towards matrix catabolism and increased expression of proinflammatory cytokines and pain-related factors. Acidic pH resulted in an increase in ASIC-3 expression. Importantly, inhibition of ASIC-3 prevented the acidic pH induced proinflammatory and pain-related phenotype in NP cells. Acidic pH causes a catabolic and degenerate phenotype in NP cells which is inhibited by blocking ASIC-3 activity, suggesting that this may be a useful therapeutic target for treatment of IVD degeneration.
The structure and dynamics of Nano Particles encapsulated by the SDS monolayer collapse at the water/TCE interface
Authors: Shi Wenxiong
Published: November 2016

The super-saturated surfactant monolayer collapses with the nanoparticles (NPs) at the water/trichloroethylene (TCE) interface are investigated using molecular dynamics (MD) simulations. The results show that sodium alkyl sulfate (SDS) monolayer collapse is initiated by buckling and followed primarily by budding and the bud encapsulating the NPs and oil molecules. The developed bud detaches from the monolayer into a water phase and forms the swollen micelle emulsion with NPs and oil molecules. We investigate the wavelength of the initial budding and the theoretical description of the budding process. The wavelength of the monolayer increases with bending modulus. The energy barrier of the budding can be easily overcome by thermal fluctuation energy, which indicates that budding process proceeds rapidly.
Tunable high-performance microwave absorption for manganese dioxides by one-step Co doping modification
Authors: Lv Guocheng , Xing Xuebing , Wu Limei , Jiang Wei-Teh , Li Zhaohui , Liao Libing
Published: November 2016

The frequencies of microwave absorption can be affected by the permanent electric dipole moment which could be adjusted by modifying the crystal symmetry of the microwave absorbing materials. Herein, we corroborate this strategy experimentally and computationally to the microwave absorption of manganese dioxides. Nanosized Co-doped cryptomelane (Co-Cryp) was successfully synthesized by a one-step reaction. The introduction of Co(III) induced a change of crystal symmetry from tetragonal to monlclinic, which could lead to an increase of its permanent electric dipole moment. As a result, the frequencies of maximum microwave absorption were regulated in the range of 7.4 to 13.9 GHz with a broadened bandwidths. The results suggested that microwave absorption of manganese dioxides can be tailored with Co doping to expand their potential uses for abatement of various microwave pollutions.
Emerging investigators series: a critical review of decision support systems for water treatment: making the case for incorporating climate change and climate extremes
Authors: Raseman William J. , Kasprzyk Joseph R. , Rosario-Ortiz Fernando L. , Stewart Jenna R. , Livneh Ben
Published: November 2016

We present potential impacts of climate on drinking water treatment and review decision support systems for these utilities.
Discovery of selective cystathionine β-synthase inhibitors by high-throughput screening with a fluorescent thiol probe
Authors: Niu Weining , Wu Ping , Chen Fei , Wang Jun , Shang Xiaoya , Xu Chunlan
Published: November 2016

Screening of a natural product library identified several selective cystathionine β-synthase inhibitors, which suppressed the proliferation of HT29 cancer cells.
Donor–acceptor conjugated polymers based on two-dimensional thiophene derivatives for bulk heterojunction solar cells
Authors: Dong Xin , Tian Hongkun , Xie Zhiyuan , Geng Yanhou , Wang Fosong
Published: November 2016

D–A conjugated polymers based on accessible 2D conjugated (E)-1,2-bis(5-alkyl-[2,3′-bithiophen]-2′-yl)ethene units possess low bandgaps, shorter π–π stacking distances, higher mobility and higher photovoltaic performance.
Janus nanoparticles inside polymeric materials: interfacial arrangement toward functional hybrid materials
Authors: Yang Qiuyan , Loos Katja
Published: November 2016

Recent advances and successes in interfacial behavior of Janus NPs at interfaces are summarized, with the hope to motivate additional efforts in the studies of Janus NPs in polymer matrix for the design of functional hybrid nanostructures and devices with engineered, desired and tailored properties for real-life applications.
One-pot synthesis of electro-active polymer gels via Cu(0)-mediated radical polymerization and click chemistry
Authors: Boujioui Fadoi , Bertrand Olivier , Ernould Bruno , Brassinne Jérémy , Janoschka Tobias , Schubert Ulrich S. , Vlad Alexandru , Gohy Jean-François
Published: November 2016

Electro-active polymer gels are prepared via one-pot Cu(0)-mediated radical polymerization and click chemistry.
Discovery of novel quinazolinones and their acyclic analogues as multi-kinase inhibitors: design, synthesis, SAR analysis and biological evaluation
Authors: El Sayed Nehad A. , Eissa Amal A. , El Masry Ghada F. , Abdullah Mohamed M. , Arafa Reem K.
Published: November 2016

MCF-7 IC50 = 0.000012 μM; MDA-MB-231 IC50 = 0.00010 μM; HS-578T IC50 = 0.00045 μM, ABL IC50 = 0.011 nM.
Application of response surface methodology for investigation of membrane fouling behaviours in microalgal membrane bioreactor: the effect of aeration rate and biomass concentration
Authors: Alipourzadeh Atefeh , Mehrnia Mohammad Reza , Hallaj Sani Ahmad , Babaei Azadeh
Published: November 2016

This study was performed to investigate membrane fouling phenomena and to optimize fouling parameters in a submerged membrane bioreactor.
Enhanced ethanol gas sensing performance of zinc–tin–vanadium oxide nanocomposites at room temperature
Authors: Chitra M. , Uthayarani K. , Rajasekaran N. , Neelakandeswari N. , Girija E. K. , Padiyan D. Pathinettam , Mangamma G.
Published: November 2016

Zinc–tin–vanadium oxide (ZTV) nanocomposite room temperature ethanol sensor (98.96% for 300 ppm) with fast adsorption (32 s) and desorption (6 s) rate is reported for first time and the mechanism is elucidated based on its structure and morphology.
Halogenation of organic compounds using continuous flow and microreactor technology
Authors: Cantillo David , Kappe C. Oliver
Published: November 2016

Halogenation reactions involving highly reactive halogenating agents can be performed safely and with improved efficiency and selectivity under continuous flow conditions.
Covalent tethering of photo-responsive superficial layers on hydrogel surfaces for photo-controlled release
Authors: Chen Lie , Yao Xi , Gu Zhandong , Zheng Kaikai , Zhao Chuangqi , Lei Wenwei , Rong Qinfeng , Lin Ling , Wang Jiaobing , Jiang Lei , Liu Mingjie
Published: November 2016

A facile strategy that can functionalize the surfaces of hydrogels, while keeping the interior network unchanged, was reported.
Vertically aligned two-dimensional SnS2 nanosheets with a strong photon capturing capability for efficient photoelectrochemical water splitting
Authors: Liu Guangbo , Li Zhonghua , Hasan Tawfique , Chen Xiaoshuang , Zheng Wei , Feng Wei , Jia Dechang , Zhou Yu , Hu PingAn
Published: November 2016

Two-dimensional (2D) metal dichalcogenides have emerged as attractive materials for application in photoelectrochemical (PEC) water splitting due to their unique structure and strong interaction with light.
Drastic solid-state luminescence color tuning of an archetypal Ir(iii) complex using polyoxometalates and its application as a vapoluminescence chemosensor
Authors: Bolle P. , Serier-Brault H. , Génois R. , Faulques E. , Boulmier A. , Oms O. , Lepeltier M. , Marrot J. , Dolbecq A. , Mialane P. , Dessapt R.
Published: November 2016

New assemblies based on the archetypal [IrIII(ppy)2(bpy)]+ complex and a series of polyoxometalates exhibit highly tunable phosphorescence and vapoluminescence properties for detection of volatile organic compounds.
Muscular activity and physical interaction forces during lower limb exoskeleton use
Authors: Wilcox Matthew , Rathore Ashish , Morgado Ramirez Dafne Zuleima , Loureiro Rui C.V. , Carlson Tom
Published: November 2016

Spinal cord injury (SCI) typically manifests with a loss of sensorimotor control of the lower limbs. In order to overcome some of the disadvantages of chronic wheelchair use by such patients, robotic exoskeletons are an emerging technology that has the potential to transform the lives of patients. However, there are a number of points of contact between the robot and the user, which lead to interaction forces. In a recent study, the authors have shown that peak interaction forces are particularly prominent at the anterior aspect of the right leg. This study uses a similar experimental protocol with additional electromyography (EMG) analysis to examine whether such interaction forces are due to the muscular activity of the participant or the movement of the exoskeleton itself. Interestingly, the authors found that peak forces preceded peak EMG activity. This study did not find a significant correlation between EMG activity and force data, which would indicate that the interaction forces can largely be attributed to the movement of the exoskeleton itself. However, we also report significantly higher correlation coefficients in muscle/force pairs located at the anterior aspect of the right leg. In their previous research, the authors have shown peak interaction forces at the same locations, which suggests that muscular activity of the participant makes a more significant contribution to the interaction forces at these locations. The findings of this study are of significance for incomplete SCI patients, for whom EMG activity may provide an important input to an intuitive control schema.
Fabrication of high aspect ratio broadband antireflection porous nano-network on glass using candle soot as a sacrificial layer for solar energy utilization
Authors: Kumar Arvind , Putta Veerender , Barshilia Harish C.
Published: November 2016

In this paper, we report the fabrication of broadband antireflection porous nano-network on the glass substrate using the combination of candle soot and HF-based vapor phase etching method. Candle soot layer plays a key role to control the pore size during the etching process. Field emission electron microscopy results showed that the pores have the tapering profile, and the pores size was restricted to the sub-wavelength dimension. Therefore, an excellent broadband antireflection with an enhancement of ∼7% in the maximum total transmittance as compared to plain glass has been achieved. Moreover, reflectance from the etched surface remains quite low (<4%) over a broad range of incident angles up to 58°. The broadband antireflection property was further examined by finite difference time domain simulation. Further, we demonstrate a relative improvement of ∼6% in the Jsc (ΔJsc/Jsc) of solar cell covered with the etched glass.
State of the art about dissimilar metal friction stir welding
Authors: Simar Aude , Avettand-Fènoël Marie-Noëlle
Published: November 2016

Friction stir welding is a rather recent welding process (patented in 1991 by Thomas et al., ‘Improvements to friction welding’ UK patent application no. 9125978.8, US Patent 5460317, 1995) that has shown great potential for welding dissimilar materials even of different metallic nature, e.g. Al to steel, Mg to steel, Al to Ti, Mg to Ti, Al to Cu, Al to Mg. This review presents the specific microstructural features and mechanical properties, in particular tensile strength, of such welds. A focus will be on the material flow and welding defects, on the intermetallic compounds, on constitutional liquation, on particularities related to dissimilar lap welding and finally on process modifications to improve dissimilar friction stir weldability.
Multivalent Rab interactions determine tether-mediated membrane fusion
Authors: Lürick Anna , Gao Jieqiong , Kuhlee Anne , Yavavli Erdal , Langemeyer Lars , Perz Angela , Raunser Stefan , Ungermann Christian
Published: November 2016

Membrane fusion at endomembranes requires cross-talk between Rab GTPases and tethers to drive SNARE-mediated lipid bilayer mixing. Several tethers have multiple Rab-binding sites with largely untested function. Here we dissected the lysosomal HOPS complex as a tethering complex with just two binding sites for the Rab7-like Ypt7 protein to determine their relevance for fusion. Using tethering and fusion assays combined with HOPS mutants, we show that HOPS-dependent fusion requires both Rab-binding sites, with Vps39 being the stronger Ypt7 interactor than Vps41. The intrinsic amphipathic lipid packaging sensor (ALPS) motif within HOPS Vps41, a target of the vacuolar kinase Yck3, is dispensable for tethering and fusion but can affect tethering if phosphorylated. In combination, our data demonstrate that a multivalent tethering complex uses its two Rab bindings to determine the place of SNARE assembly and thus fusion at endomembranes.
Killing in Self-Defense
Authors: Miller Seumas
Published: November 2016

In this chapter the main contemporary theories of justifiable killing in self-defense are criticized and an alternative account elaborated: the fault-based internalist suspendable-rights theory (FIST). FIST is a partialist account. The rights not to be killed are such that when one member of the set of rights is suspended, the other rights remain in force. Thus, if A’s right not to be killed by B is suspended, then B no longer has an obligation not to kill A. However, A still has a right not to be killed by C, and thus C’s obligation not to kill A remains in force. In addition, on FIST, a culpable attacker suspends his or her right not to be killed by a defender even in cases in which it is not necessary (necessity condition) for the defender to kill the attacker to save his or her own life.
Becoming Conquered (The 1560s)
Authors: Townsend Camilla
Published: November 2016

The 1560s were a pivotal decade for the Nahuas. For the first time, the urban Indians had to pay a head tax like all other Mexican indigenous peoples. They made extraordinary efforts to prevent this change, which they foresaw would impoverish them, and they recorded for their posterity traditional histories or annals recounting their efforts. Because of high unrest, a plot against the Crown by don Martín Cortés, son of Hernando Cortés, reverberated in terrible ways. Several indigenous texts illuminate not only the political moment but also the traditional indigenous notions of historiography, among them the Codex Aubin, the Codex Osuna, and the Annals of Juan Bautista.
Forging Friendship with Franciscans (1560s–1580s)
Authors: Townsend Camilla
Published: November 2016

Franciscan friars at missions established by the Spanish conquerors taught the Nahuas the roman alphabet. As some of their earliest students attained adulthood and became intellectuals in their own right, they occasionally found themselves arguing with their former mentors. Two indigenous men in this position were don Mateo Sánchez of Tecamachalco, a friend of fray Francisco Toral, and don Pedro de San Buenaventura of Cuauhtitlan, a friend of fray Bernardino de Sahagún. The sets of annals they wrote reveal both their knowledge of their people’s past and present and also their participation in dialog with Europeans. As intermediaries, they suffered and were empowered in unique ways.
Collective dynamics in plasmas—I. Hydrodynamics and transport
Authors: Bers Abraham
Published: November 2016

This chapter presents simple, illustrative descriptions of collective dynamics in plasmas—in particular, in fully-ionized plasmas. These descriptions entail choices of collective plasma models, and the simplest models of plasma dynamics which describe collective modes spanning regimes from LF and long-wavelengths to HF and short-wavelengths. The chapter also addresses reduced hydrodynamic model equations appropriate for the first regime with emphasis on the Braginskii transport equations and the magnetohydrodynamics (MHD) model equations. The topics covered here are critical to students in two dimensions: The first is important in evaluating the validity of a result that follows from a reduced hydrodynamic description. The second is important to appreciate and understand the quasi-steady state, classical properties of a magnetically-confined plasma, and to compare these to experiments in current magnetic confinement fusion (MCF) plasmas exhibiting “anomalous” transport. Additionally, it is also important to be able to appreciate and evaluate the time and space scales of such collisional transport.
Drift-free cold plasma, magnetized—II. Linear modes; principal waves
Authors: Bers Abraham
Published: November 2016

This chapter offers a detailed study and exposition of linear natural modes in a homogeneous, magnetized, drift-free cold plasma. These linear modes are stable waves; at a given frequency, and in the absence of collisions, they propagate or evanesce relative to magnetization and are of a large variety in the structure of their field polarization. In addition, the linear natural modes description presented in the chapter emphasizes the electric fields of the modes, all other field variables having been expressed in terms of the electric field. The chapter concludes with an examination of the dispersion tensor to other coordinates and the dispersion relation under various constraints as well as some of the more detailed aspects of the principal wave.
Streaming instabilities in cold plasmas
Authors: Bers Abraham
Published: November 2016

This chapter provides detailed analyses of streaming instabilities in cold, collisionless plasmas. It highlights one-d electrostatic (ES) instabilities, which are most prominent due to having the largest growth rates. Their large growth rates justify (in most cases) the neglect of collisions (and sometimes even thermal effects) in their initial evolution, but they also imply that nonlinear effects set in rapidly. Hence, the linear description of each of these instabilities is supplemented by giving results from computer simulations that show the nonlinear evolution and saturation of these instabilities. The analyses here, although limited in dynamics, given an initial, qualitative understanding of some nonlinear phenomena that play an important role in these instabilities. In addition, the chapter includes a relativistic analysis of small amplitude modes in a beam drifting along an externally-applied magnetic field, allowing for wave propagation in arbitrary directions.
A Dictionary of Atheism
Authors: Bullivant Stephen , Lee Lois
Published: November 2016

Over 150 entries

This new dictionary provides definitions of terms related to the subject of atheism, ranging from those of historic importance, including the history of the term ‘atheist’ itself, to crucial concepts in the contemporary study of atheism and related topics, such as nonreligion and postsecular. Coverage includes secular and humanist organizations, significant events in the history of atheism such as the Scopes Monkey Trial, neologisms by or about atheists including ‘Bright’ and ‘New Atheism’, and parodic religions and deities such as Pastafarianism and the Flying Spaghetti Monster. Atheism is a growing subject of study with a significant scholarly presence emerging online, and many of the new terms covered represent the first authoritative definitions for this subject.
RENT+: an improved method for inferring local genealogical trees from haplotypes with recombination
Authors: Mirzaei Sajad , Wu Yufeng
Published: November 2016

Motivation

Haplotypes from one or multiple related populations share a common genealogical history. If this shared genealogy can be inferred from haplotypes, it can be very useful for many population genetics problems. However, with the presence of recombination, the genealogical history of haplotypes is complex and cannot be represented by a single genealogical tree. Therefore, inference of genealogical history with recombination is much more challenging than the case of no recombination.

Results

In this paper, we present a new approach called RENT+ for the inference of local genealogical trees from haplotypes with the presence of recombination. RENT+ builds on a previous genealogy inference approach called RENT, which infers a set of related genealogical trees at different genomic positions. RENT+ represents a significant improvement over RENT in the sense that it is more effective in extracting information contained in the haplotype data about the underlying genealogy than RENT. The key components of RENT+ are several greatly enhanced genealogy inference rules. Through simulation, we show that RENT+ is more efficient and accurate than several existing genealogy inference methods. As an application, we apply RENT+ in the inference of population demographic history from haplotypes, which outperforms several existing methods.

Availability and Implementation

RENT+ is implemented in Java, and is freely available for download from: https://github.com/SajadMirzaei/RentPlus.

Supplementary information

Supplementary data are available at Bioinformatics online.
Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography
Authors: Chen Julian C.-H. , Unkefer Clifford J.
Published: November 2016

The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002–2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallography in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.
Honest signals to maintain a long‐lasting relationship: floral colour change prevents plant‐level avoidance by experienced pollinators
Authors: Makino Takashi T. , Ohashi Kazuharu
Published: November 2016

Honest signals prevail when those signals manipulate receivers to benefit the senders more than deceptive signals do. Floral colour change (FCC), reported in hundreds of species, is a well‐known example of honest signalling in plant–pollinator interactions. It occurs in fully turgid flowers, and usually correlates with a cessation of reward production in individual flowers. This trait has been considered a plant strategy that enhances distant pollinator attraction by extended displays, while minimizing visits to non‐reproductive flowers by honest colour signals.

Here, we propose an additional, overlooked benefit of FCC, which emerges when we consider the spatial learning ability of pollinators to avoid unprofitable plants. If a plant retains rewardless flowers without FCC, it is difficult for pollinators to visually locate the rewarding flowers. Although the enhanced display initially attracts more pollinators, its low profitability for foraging may cause plant‐level avoidance by them. The avoidance resulting from rewardless flower retention may be prevented by FCC because it helps pollinators to find rewarding flowers. To test this hypothesis, we observed the behavioural changes of bumblebees foraging in an array of artificial plants.

We found that rewardless flowers without FCC could initially attract bees by increasing the plant's display size, but their lack of reward resulted in plant‐level avoidance by those bees with spatial memories. The FCC in rewardless flowers, in contrast, encouraged bees to return by helping them to find rewards on plants. Consequently, honest plants with FCC received more visits than those dishonest plants that did not display colour change.

Floral colour change thus can prevent plant‐level avoidance by pollinators that use spatial memory when choosing plants. The spatial learning ability of pollinators may, therefore, be one of the keys to understanding why both colour‐changing and non‐colour‐changing plant species occur among angiosperms.

A lay summary is available for this article.
Connexin32 deficiency is associated with liver injury, inflammation and oxidative stress in experimental non‐alcoholic steatohepatitis
Authors: Tiburcio Taynã Cristina , Willebrords Joost , da Silva Tereza Cristina , Pereira Isabel Veloso Alves , Nogueira Marina Sayuri , Crespo Yanguas Sara , Maes Michaël , Silva Elisangela dos Anjos , Dagli Maria Lucia Zaidan , de Castro Inar Alves , Oliveira Cláudia Pinto , Vinken Mathieu , Cogliati Bruno
Published: November 2016

Non‐alcoholic steatohepatitis is a highly prevalent liver pathology featured by hepatocellular fat deposition and inflammation. Connexin32, which is the major building block of hepatocellular gap junctions, has a protective role in hepatocarcinogenesis and is downregulated in chronic liver diseases. However, the role of connexin32 in non‐alcoholic steatohepatitis remains unclear. Connexin32−/− mice and their wild‐type littermates were fed a choline‐deficient high‐fat diet. The manifestation of non‐alcoholic steatohepatitis was evaluated based on a battery of clinically relevant read‐outs, including histopathological examination, diverse indicators of inflammation and liver damage, in‐depth lipid analysis, assessment of oxidative stress, insulin and glucose tolerance, liver regeneration and lipid‐related biomarkers. Overall, more pronounced liver damage, inflammation and oxidative stress were observed in connexin32−/− mice compared to wild‐type animals. No differences were found in insulin and glucose tolerance measurements and liver regeneration. However, two lipid‐related genes, srebf1 and fabp3, were upregulated in Cx32−/− mice in comparison with wild‐type animals. These findings suggest that connexin32‐based signalling is not directly involved in steatosis as such, but rather in the sequelae of this process, which underlie progression of non‐alcoholic steatohepatitis.
Synergistic attraction of pine sawyer Monochamus saltuarius (Coleoptera: Cerambycidae) to monochamol and α‐pinene
Authors: Lee Sung‐Min , Hong Do Kyung , Jang Sei‐Heon , Lee Kyeong‐Yeoll , Lee ChangWoo
Published: November 2016

Monochamus (Coleoptera: Cerambycidae) species are longhorn pine sawyers that serve as insect vectors of the pinewood nematode Bursaphelenchus xylophilus (Nematoda: Parasitaphelenchidae), which are responsible for debilitating pine wilt disease. An aggregation pheromone, 2‐(1‐undecyloxy)‐1‐ethanol (hereafter referred to as monochamol), was shown to be effective at attracting Monochamus species. However, attraction of the pine sawyers to aggregation pheromones varied depending on semiochemicals, including host plant volatiles and kairomones. In this study, we investigated the abilities of monochamol and the host‐plant volatiles α‐pinene and ethanol to attract M. saltuarius in a pine forest in Cheongsong, Gyeongsangbuk‐do, Korea. A total of 91 M. saltuarius (28 males and 63 females) were captured. The combination of monochamol (700 mg) with α‐pinene and ethanol exhibited a synergistic effect on attracting M. saltuarius (11.0 beetles per trap), whereas monochamol alone and a mixture of α‐pinene and ethanol resulted in the capture of 3.2 beetles and 3.6 beetles per trap, respectively. Our results suggest that multi‐funnel traps baited with a blend of monochamol, α‐pinene and ethanol are highly effective for monitoring M. saltuarius and M. alternatus in pine forests.
Ezetimibe: Use, costs, and adverse events in Australia
Authors: Hollingworth Samantha A. , Ostini Remo , David Michael C. , Martin Jennifer H. , Tett Susan E.
Published: November 2016

Aim

To analyze the subsidized use and reported adverse events of ezetimibe, used to lower cholesterol, in Australia over the 11 years following its inclusion on the Pharmaceutical Benefits Scheme (PBS) in 2004.

Methods

Pharmacoepidemiological analysis of dispensed prescriptions from Medicare Australia. Adverse event data were obtained from the Therapeutic Goods Administration. Use was measured by the defined daily dose (DDD) per 1000 population per day for each calendar year. Adverse events were counted by organ class system.

Results

Total ezetimibe use rose to 8.46 DDD/1000 population/d in the 11 years to 2015. Ezetimibe as a sole active ingredient was the most commonly dispensed formulation followed by the two combination products containing ezetimibe and 40 mg or 80 mg simvastatin. The average yearly increase in utilization was 19% with a 24% annual increase in costs to government (2006‐2015) to $169.0 million in 2015. There were substantial differences in ezetimibe use between states, with no relationship to deaths from ischaemic heart disease (IHD) in each jurisdiction. The major reported adverse events were musculoskeletal and connective tissue disorders and gastrointestinal disorders.

Conclusions

Ezetimibe use has increased rapidly in Australia since receiving public subsidy. Although the indications for subsidy are very restricted, there appears to have been widespread use, not explained by differential geographical IHD death rates. Latest guidelines still question the value of ezetimibe, so further discussion about whether the public spending on this medication for any potential improvement in population health outcomes is justified.
He‐Ar‐S‐Pb Isotopic Compositions of Pyrite: Constraints on the Source of Ore‐forming Materials of the Chengchao Skarn Iron Deposit, SE Hubei Province, Eastern China
Authors: LI Wei , XIE Guiqing , ZHU Qiaoqiao
Published: November 2016

The Chengchao iron deposit, the largest high‐grade skarn iron deposit in southeastern Hubei Province, contains considerable amounts of magnetite and by‐product anhydrite. To obtain better understanding of the ore‐formation process, this study carried out He‐Ar‐S‐Pb multi‐isotopic analyses on the pyrites formed during two stages of mineralization. The results indicate that the δ34S values (ranging from 14.0‰ to 17.6‰) of pyrites formed from the two stages have no obvious differences, suggesting that they were not derived from a single magmatic sulfur source. The δ34S values of anhydrite mostly range from 21.9‰ to 28.4‰, similar to that of the Middle Triassic sedimentary anhydrite in the Middle‐Lower Yangtze River metallogenic belt (MLYRB). The Pb isotopic compositions of the pyrites of both stages are homogeneous, with values of 208Pb/204Pb, 207Pb/204Pb, and206Pb/204Pb being 38.006–38.257, 15.523–15.556, and 17.806–18.052, respectively, indicating a mixed crust‐mantle source. The He‐Ar results exhibit different compositions of the two stages: the 3He/4He (R/Ra) and 40Ar/36Ar values for the early‐stage pyrite are 0.46–0.63 and 311–322, respectively, whereas the values for late‐stage pyrite are 0.23–0.34 and 305–361, respectively. Both stages of pyrites indicate the multiple sources of the ore‐forming fluids, with decreasing amount of magmatic water and increasing amount of modified meteoric water(MASW) during fluid evolution. The Triassic evaporites played an important role in the mineralization process.
Executive Gender Pay Gaps: The Roles of Female Risk Aversion and Board Representation
Authors: Carter Mary Ellen , Franco Francesca , Gine Mireia
Published: November 2016

Using a large sample of executives in S&P 1500 firms over 1996–2010, we document significant salary and total compensation gaps between female and male executives and explore two possible explanations for the gaps. We find support for greater female risk aversion as one contributing factor. Female executives hold significantly lower equity incentives and demand larger salary premiums for bearing a given level of compensation risk. These results suggest that females’ risk aversion contributes to the observed lower pay levels through its effect on ex ante compensation structures. We also find evidence that the lack of gender diversity on corporate boards affects the size of the gaps. In firms with a higher proportion of female directors on the board, the gaps in salary and total pay levels are lower. Together, these findings suggest that female higher risk aversion may act as a barrier to full pay convergence, despite the mitigating effect from greater gender diversity on the board.
Preparing to lead: Mayoral transition planning in Canadian cities
Authors: Spicer Zachary , Graham Kate
Published: November 2016

Transition teams are often used to help Prime Ministers and Premiers move into their new roles. At the municipal level, the use of transition teams is relatively new. As such, we know little about what these groups do in comparison to federal and provincial transition teams. In this article, we examine mayoral transition teams and find that the increased use of these groups is a reflection of the enhanced organizational complexity of Canadian local government. Additionally, local conditions and candidate experience often dictate the shape and function of transition teams. Overall, we argue that more resources should be devoted to the municipal transition process.
Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska
Authors: West Catherine , Hofman Courtney A. , Ebbert Steve , Martin John , Shirazi Sabrina , Dunning Samantha , Maldonado Jesus E.
Published: November 2016

The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating mammals classified as invasive species. The Arctic ground squirrel(Urocitellus parryii)is of concern because it affects vegetation and seabirds on Gulf of Alaska islands. This animal is assumed to have been introduced by historic settlers; however, ground squirrel remains in the prehistoric archaeological record of Chirikof Island, Alaska, challenge this timeline and suggest they colonized the islands long ago. We used 3 lines of evidence to address this problem: direct radiocarbon dating of archaeological squirrel remains; evidence of prehistoric human use of squirrels; and ancient DNA analysis of dated squirrel remains. Chirikof squirrels dated to at least 2000 years ago, and cut marks on squirrel bones suggested prehistoric use by people. Ancient squirrels also shared a mitochondrial haplotype with modern Chirikof squirrels. These results suggest that squirrels have been on Chirikof longer than previously assumed and that the current population of squirrels is closely related to the ancient population. Thus, it appears ground squirrels are not a recent, human‐mediated introduction and may have colonized the island via a natural dispersal event or an ancient human translocation.
Incidental Learning of Melodic Structure of North Indian Music
Authors: Rohrmeier Martin , Widdess Richard
Published: November 2016

Musical knowledge is largely implicit. It is acquired without awareness of its complex rules, through interaction with a large number of samples during musical enculturation. Whereas several studies explored implicit learning of mostly abstract and less ecologically valid features of Western music, very little work has been done with respect to ecologically valid stimuli as well as non‐Western music. The present study investigated implicit learning of modal melodic features in North Indian classical music in a realistic and ecologically valid way. It employed a cross‐grammar design, using melodic materials from two modes (rāgas) that use the same scale. Findings indicated that Western participants unfamiliar with Indian music incidentally learned to identify distinctive features of each mode. Confidence ratings suggest that participants' performance was consistently correlated with confidence, indicating that they became aware of whether they were right in their responses; that is, they possessed explicit judgment knowledge. Altogether our findings show incidental learning in a realistic ecologically valid context during only a very short exposure, they provide evidence that incidental learning constitutes a powerful mechanism that plays a fundamental role in musical acquisition.