bluuebunny/crossref_metadata_2025 huggingface dataset:
Band gap tuning of armchair silicene nanoribbons using periodic hexagonal holes
Authors: Mehdi Aghaei Sadegh , Calizo Irene
Published: September 2015

The popularity of graphene owing to its unique and exotic properties has triggered a great deal of interest in other two-dimensional nanomaterials. Among them silicene shows considerable promise for electronic devices with a carrier mobility comparable to graphene, flexible buckled structure, and expected compatibility with silicon electronics. Using first-principle calculations based on density functional theory, the electronic properties of armchair silicene nanoribbons perforated with periodic nanoholes (ASiNRPNHs) are investigated. Two different configurations of mono-hydrogenated (:H) and di-hydrogenated (:2H) silicene edges are considered. Pristine armchair silicene nanoribbons (ASiNRs) can be categorized into three branches with width W = 3P − 1, 3P, and 3P + 1, P is an integer. The order of their energy gaps change from “EG (3P − 1) < EG (3P) < EG (3P + 1)” for W-ASiNRs:H to “EG (3P + 1) < EG (3P − 1) < EG (3P)” for W-ASiNRs:2H. We found the band gaps of W-ASiNRs:H and (W + 2)-ASiNRs:2H are slightly different, giving larger band gaps for wider ASiNRs:2H. ASiNRPNHs' band gaps changed based on the nanoribbon's width, nanohole's repeat periodicity and position relative to the nanoribbon's edge compared to pristine ASiNRs because of changes in quantum confinement strength. ASiNRPNHs:2H are more stable than ASiNRPNHs:H and their band gaps are noticeably greater than ASiNRPNHs:H. We found that the value of energy band gap for 12-ASiNRPNHs:2H with repeat periodicity of 2 is 0.923 eV. This value is about 2.2 times greater than pristine ASiNR:2H and double that of the 12-ASiNRPNHs:H with repeat periodicity of 2.
Enhancement of magnetoresistance and ferromagnetic coupling in the complex perovskites CaCu3(Mn4−xAlx)O12 (x = 0, 0.2, 0.4, and 0.6): A neutron diffraction study
Authors: Ben Hassine R. , Cherif W. , Sánchez-Benítez J. , Mompean F. J. , Fernández-Díaz M. T. , Elhalouani F. , Alonso J. A.
Published: September 2015

New compounds of the series CaCu3(Mn4−xAlx)O12 have been prepared under high pressure conditions (2 GPa), in the presence of KClO4 as oxidizing agent to stabilize Mn3+,4+ mixed valence. The polycrystalline samples have been characterized by x-ray diffraction, neutron powder diffraction (NPD), magnetic, and magnetotransport measurements. All the samples are cubic, space group Im-3. These oxides adopt a superstructure of ABO3 perovskite given by the long-range 1:3 ordering of Ca2+ and Cu2+ ions at the A sublattice. The NPD study for x = 0.4 shows that Al3+ ions are statistically distributed at the octahedral positions, being the (Mn,Al)O6 octahedra strongly tilted, with superexchange (Mn,Al)-O-(Mn,Al) angles of 142.1°. Also, neutron data clearly show that some Mn3+ ions (0.65(2) per formula) are located together with Cu2+ at the square-planar 6b positions. Regarding the magnetic properties, all the compounds present a spontaneous increase of the magnetization below TC, typical of ferro-or ferrimagnetic materials, with TC decreasing upon Al introduction. The magnetic structure determined from low-temperature NPD data unveils a ferromagnetic coupling between (Cu2+, Mn3+)6b spins and Mn8c spins at octahedral positions; this is in contrast with the ferrimagnetic structure observed for RCu3Mn4O12 and CaCu3Mn4O12, where an AFM coupling is observed between both magnetic sublattices. Interestingly, an enhancement of the magnetoresistance effect is observed for x = 0.2, well beyond that found for the parent compound. This effect, in materials subtly doped with non-magnetic elements at the Mn positions, may be of interest for applications.
Oxygen and germanium migration at low temperature influenced by the thermodynamic nature of the materials used in germanium metal-insulator-semiconductor structures
Authors: Kato Kimihiko , Taoka Noriyuki , Sakashita Mitsuo , Nakatsuka Osamu , Zaima Shigeaki
Published: September 2015

The influence of the reductive character of the metals used for the gate electrode on O migration in gate stacks and following reductive or oxidative reactions at an interface between a high permittivity (high-k) insulating layer and Ge or Si was investigated. The magnitude of the increase or decrease of Ge or Si oxides in the gate stacks caused by the metal layer deposition can be systematically correlated with the oxygen chemical potential (μO) of gate metals for both Ge and Si systems. However, the influence of the gate metals on oxidative/reductive reactions of a semiconductor element is more significant for the Ge gate stacks than the Si system. Detailed investigations of Ge oxide as a function of depth were used to determine that the strong μO dependence of the increase or decrease in the Ge oxide is because of the high diffusivity of Ge into the high-k oxide. In particular, migration of Ge into the high-k oxide occurs concurrently with O migration towards the reductive metal layer, and the strong reductive character of the metal significantly influences the decrease in the amount of Ge oxide. These results indicate the importance of the selection of gate metals based on μO for controlling high-k/Ge interfacial structures.
X-ray standing wave analysis of nanostructures using partially coherent radiation
Authors: Tiwari M. K. , Das Gangadhar , Bedzyk M. J.
Published: September 2015

The effect of longitudinal (or temporal) coherence on total reflection assisted x-ray standing wave (TR-XSW) analysis of nanoscale materials is quantitatively demonstrated by showing how the XSW fringe visibility can be strongly damped by decreasing the spectral resolution of the incident x-ray beam. The correction for nonzero wavelength dispersion (δλ ≠ 0) of the incident x-ray wave field is accounted for in the model computations of TR-XSW assisted angle dependent fluorescence yields of the nanostructure coatings on x-ray mirror surfaces. Given examples include 90 nm diameter Au nanospheres deposited on a Si(100) surface and a 3 nm thick Zn layer trapped on top a 100 nm Langmuir-Blodgett film coating on a Au mirror surface. Present method opens up important applications, such as enabling XSW studies of large dimensioned nanostructures using conventional laboratory based partially coherent x-ray sources.
Magnetocaloric cycle with six stages: Possible application of graphene at low temperature
Authors: Reis M. S.
Published: September 2015

The present work proposes a thermodynamic hexacycle based on the magnetocaloric oscillations of graphene, which has either a positive or negative adiabatic temperature change depending on the final value of the magnetic field change. For instance, for graphenes at 25 K, an applied field of 2.06 T/1.87 T promotes a temperature change of ca. −25 K/+3 K. The hexacycle is based on the Brayton cycle and instead of the usual four steps, it has six stages, taking advantage of the extra cooling provided by the inverse adiabatic temperature change. This proposal opens doors for magnetic cooling applications at low temperatures.
Tunnel junction enhanced nanowire ultraviolet light emitting diodes
Authors: Sarwar A. T. M. Golam , May Brelon J. , Deitz Julia I. , Grassman Tyler J. , McComb David W. , Myers Roberto C.
Published: September 2015

Polarization engineered interband tunnel junctions (TJs) are integrated in nanowire ultraviolet (UV) light emitting diodes (LEDs). A ∼6 V reduction in turn-on voltage is achieved by the integration of tunnel junction at the base of polarization doped nanowire UV LEDs. Moreover, efficient hole injection into the nanowire LEDs leads to suppressed efficiency droop in TJ integrated nanowire LEDs. The combination of both reduced bias voltage and increased hole injection increases the wall plug efficiency in these devices. More than 100 μW of UV emission at ∼310 nm is measured with external quantum efficiency in the range of 4–6 m%. The realization of tunnel junction within the nanowire LEDs opens a pathway towards the monolithic integration of cascaded multi-junction nanowire LEDs on silicon.
High pressure synthesis of amorphous TiO2 nanotubes
Authors: Li Quanjun , Liu Ran , Wang Tianyi , Xu Ke , Dong Qing , Liu Bo , Liu Jing , Liu Bingbing
Published: September 2015

Amorphous TiO2 nanotubes with diameters of 8-10 nm and length of several nanometers were synthesized by high pressure treatment of anatase TiO2 nanotubes. The structural phase transitions of anatase TiO2 nanotubes were investigated by using in-situ high-pressure synchrotron X-ray diffraction (XRD) method. The starting anatase structure is stable up to ∼20GPa, and transforms into a high-density amorphous (HDA) form at higher pressure. Pressure-modified high- to low-density transition was observed in the amorphous form upon decompression. The pressure-induced amorphization and polyamorphism are in good agreement with the previous results in ultrafine TiO2 nanoparticles and nanoribbons. The relationship between the LDA form and α-PbO2 phase was revealed by high-resolution transmission electron microscopy (HRTEM) study. In addition, the bulk modulus (B0 = 158 GPa) of the anatase TiO2 nanotubes is smaller than those of the corresponding bulks and nanoparticles (180-240 GPa). We suggest that the unique open-ended nanotube morphology and nanosize play important roles in the high pressure phase transition of TiO2 nanotubes.
Building links between town and gown: an innovative organisation in south-eastern Melbourne
Authors: Advocat Jenny , Russell Grant , Mathews Mary
Published: September 2015

Primary care is the foundation of a nation’s health care system. Real world research is a requirement of a health system built to deliver the benefits of a strong primary care community. In the last decade, new approaches to optimising the impact of research on practice and policy have been formulated across disciplines. However, in Australia, the primary care research community remains small and primary care researchers are not well represented in either receiving support for or governing research. While practice-based research networks (PBRNs) have brought GPs and, sometimes, other clinicians together with academics, few have managed to bring local decision makers and other primary health care stakeholders into partnerships where they can work together on common problems. This paper outlines a novel three-way partnership between a health authority, a primary care organisation and a university in the south-eastern suburbs of Melbourne. A case study was undertaken based on author experience of the Southern Academic Primary Care Research Unit (SAPCRU) and semi-structured interviews with representatives from partner organisations. Interviews elicited perceived barriers and facilitators, including complex financial, human resources and governance challenges, associated with bridging the gap between research and practice. It was found that SAPCRU has been successful in engaging with research partners and has begun to develop links with policy makers and orient research themes to the needs of its varied communities. Especially with the introduction of Primary Health Networks (PHNs), the model has the potential to translate to different settings but barriers should be noted.
From maternity paper hand-held records to electronic health records: what do women tell us about their use?
Authors: Hawley Glenda , Hepworth Julie , Wilkinson Shelley A. , Jackson Claire
Published: September 2015

The paper hand-held record (PHR) has been used extensively in general practice (GP) shared care management of pregnant women, and recently, the first Mater Shared Electronic Health Record (MSEHR) was introduced. The aim of this qualitative study was to examine women’s experiences using the records and the contribution of the records to integrate care. At the 36-week antenatal visit in a maternity tertiary centre clinic, women were identified as a user of either the PHR or the MSEHR and organised into Phase 1 and Phase 2 studies respectively. Fifteen women were interviewed in Phase 1 and 12 women in Phase 2. Semi-structured interviews were used for data collection, and analysed using qualitative content analysis. Four main themes were identified: (1) purpose of the record, (2) perceptions of the record; (3) content of the record, and (4) sharing the record. Findings indicate that the PHR is a well-liked maternity tool. The findings also indicate there is under-usage of the MSEHR due to health-care providers failing to follow up and discuss the option of using the electronic health record option or if a woman has completed the log-in process. This paper adds to an already favourable body of knowledge about the use of the PHR. It is recommended that continued implementation of the MSEHR be undertaken to facilitate its use.
Client perceptions of group education in the management of type 2 diabetes mellitus in South Australia
Authors: Smith Cynthia , McNaughton Darlene A. , Meyer Samantha
Published: September 2015

Type 2 diabetes mellitus (T2DM) is a progressive chronic disease that requires significant self-surveillance and adherence to the treatment protocols for successful management and future health. There is a growing body of evidence suggesting that diabetes education is beneficial for patient outcomes. However, there is some debate about how best to deliver diabetes education, whether individually or in groups. Although several studies have investigated the role of group education in improving the management of T2DM, few studies have examined this issue from the client’s perspective. It is here that this study makes a contribution to understanding diabetes management. Drawing on systematic observation of group education sessions provided by diabetic resource nurses and in-depth interviews with clients, this paper describes the experiences, perspectives and significance of these sessions to clients. Our results suggest that group education sessions were seen as valuable to the clients for: the opportunity they provided to meet others living with diabetes; to improve motivation for managing the disease; and to enhance knowledge of diabetes, its management and long-term implications. In short, this study demonstrates that the clients value group education sessions for the social contact, increasing knowledge about the disease for self-management and support they provide; factors recognised as important to maintaining health. In addition, group education sessions appear to be a cost-effective method for diabetes self-management that funders need to consider.
Critical design features for establishing a childhood obesity monitoring program in Australia
Authors: Lacy Kathleen E. , Nichols Melanie S. , de Silva Andrea M. , Allender Steven E. , Swinburn Boyd A. , Leslie Eva R. , Jones Laura V. , Kremer Peter J.
Published: September 2015

Efforts to combat childhood obesity in Australia are hampered by the lack of quality epidemiological data to routinely monitor the prevalence and distribution of the condition. This paper summarises the literature on issues relevant to childhood obesity monitoring and makes recommendations for implementing a school-based childhood obesity monitoring program in Australia. The primary purpose of such a program would be to collect population-level health data to inform both policy and the development and evaluation of community-based obesity prevention interventions. Recommendations are made for the types of data to be collected, data collection procedures and program management and evaluation. Data from an obesity monitoring program are crucial for directing and informing policies, practices and services, identifying subgroups at greatest risk of obesity and evaluating progress towards meeting obesity-related targets. Such data would also increase the community awareness necessary to foster change.
The effectiveness and cost of camera traps for surveying small reptiles and critical weight range mammals: a comparison with labour-intensive complementary methods
Authors: Welbourne Dustin J. , MacGregor Christopher , Paull David , Lindenmayer David B.
Published: September 2015

Context Biodiversity studies often require wildlife researchers to survey multiple species across taxonomic classes. To detect terrestrial squamate and mammal species, often multiple labour-intensive survey techniques are required. Camera traps appear to be more effective and cost-efficient than labour-intensive methods for detecting some mammal species. Recent developments have seen camera traps used for detecting terrestrial squamates. However, the performance of camera traps to survey terrestrial squamate and mammal species simultaneously has not been evaluated. Aim We compared the effectiveness and financial cost of a camera trapping method capable of detecting small squamates and mammals with a set of labour-intensive complementary methods, which have been used in a long-term monitoring program. Methods We compared two survey protocols: one employed labour-intensive complementary methods consisting of cage traps, Elliott traps and artificial refuges; the second utilised camera traps. Comparisons were made of the total number of species detected, species detectability, and cost of executing each type of survey. Key results Camera traps detected significantly more target species per transect than the complementary methods used. Although camera traps detected more species of reptile per transect, the difference was not significant. For the initial survey, camera traps were more expensive than the complementary methods employed, but for realistic cost scenarios camera traps were less expensive in the long term. Conclusions Camera traps are more effective and less expensive than the complementary methods used for acquiring incidence data on terrestrial squamate and mammal species. Implications The camera trapping method presented does not require customised equipment; thus, wildlife managers can use existing camera trapping equipment to detect cryptic mammal and squamate species simultaneously.
Neighborhood effects on use of African-American Vernacular English
Authors: Rickford John R. , Duncan Greg J. , Gennetian Lisa A. , Gou Ray Yun , Greene Rebecca , Katz Lawrence F. , Kessler Ronald C. , Kling Jeffrey R. , Sanbonmatsu Lisa , Sanchez-Ordoñez Andres E. , Sciandra Matthew , Thomas Ewart , Ludwig Jens
Published: September 2015

Significance

We provide, to our knowledge, the first experimental evidence of neighborhood effects on the use by low-income minority youth of African-American Vernacular English (AAVE). Rising U.S. residential economic segregation may be contributing to growing differences within the population in AAVE use, which has benefits to in-group solidarity and identity but is associated with discrimination in schools and workplaces and so may exacerbate the disadvantages of youth growing up in high-poverty areas. To the extent that the association between AAVE use and income represents a causal effect of AAVE use, our illustrative calculations suggest that neighborhood effects on speech could increase lifetime earnings by approximately $18,000 (∼3–4% of lifetime income).
Isoflurane inhibits synaptic vesicle exocytosis through reduced Ca
2+
influx, not Ca
2+
-exocytosis coupling
Authors: Baumgart Joel P. , Zhou Zhen-Yu , Hara Masato , Cook Daniel C. , Hoppa Michael B. , Ryan Timothy A. , Hemmings Hugh C.
Published: September 2015

Significance

Clarification of the presynaptic actions of general anesthetics is critical to understanding the molecular and cellular mechanisms of their prominent effects on synaptic transmission. We show that the ether anesthetic isoflurane inhibits synaptic vesicle exocytosis through inhibition of presynaptic Ca
2+
influx in the absence of significant alteration of the Ca
2+
sensitivity of exocytosis. The greater inhibition of glutamate release compared with GABA release is explained by the relative anesthetic resistance of Ca
2+
influx in GABAergic boutons, consistent with overall reduction in excitatory synaptic tone.
Suburbanization, estrogen contamination, and sex ratio in wild amphibian populations
Authors: Lambert Max R. , Giller Geoffrey S. J. , Barber Larry B. , Fitzgerald Kevin C. , Skelly David K.
Published: September 2015

Significance

We focus on a critical issue, the influence of human-derived contaminants on wildlife populations. Endocrine disrupting chemicals that act through hormonal pathways are capable of having large influences even when concentrations are relatively low. While there is evidence that such endocrine disruption can result from the application of agricultural pesticides and through exposure to wastewater effluent, we have identified a diversity of endocrine disrupting chemicals within suburban neighborhoods. Sampling populations of a local frog species, we found a strong association between the degree of landscape development and frog offspring sex ratio. Our study points to rarely studied contamination sources, like vegetation landscaping and impervious surface runoff, that may be associated with endocrine disruption environments around suburban homes.
Dissecting repulsion linkage in the dwarfing gene
Dw3
region for sorghum plant height provides insights into heterosis
Authors: Li Xin , Li Xianran , Fridman Eyal , Tesso Tesfaye T. , Yu Jianming
Published: September 2015

Significance

Heterosis, the better performance of hybrids over their parents, holds great economic and biological significance. Different theories have been proposed, but specific examples with detailed dissection are limited. If close linkage of alleles with opposite effects exists, the superiority of hybrids over inbreds is observed and may appear as overdominance at a single locus. We present a case of pseudo-overdominance generated by repulsion linkage between two quantitative trait loci in sorghum plant height. A combination of approaches were used: linkage mapping under a defined genetic background, genome-wide association study with a diversity panel, computer simulation, and designed crosses with selected genetic stocks. Our findings provide insights into heterosis and a tool box for plant breeders to develop ideal cultivars.
Origami tubes assembled into stiff, yet reconfigurable structures and metamaterials
Authors: Filipov Evgueni T. , Tachi Tomohiro , Paulino Glaucio H.
Published: September 2015

Significance

Origami, the ancient art of folding paper, has recently emerged as a method for creating deployable and reconfigurable engineering systems. These systems tend to be flexible because the thin sheets bend and twist easily. We introduce a new method of assembling origami into coupled tubes that can increase the origami stiffness by two orders of magnitude. The new assemblages can deploy through a single flexible motion, but they are substantially stiffer for any other type of bending or twisting movement. This versatility can be used for deployable structures in robotics, aerospace, and architecture. On a smaller scale, assembling thin sheets into these tubular assemblages can create metamaterials that can be deployed, stiffened, and tuned.
Rapid and transient palmitoylation of the tyrosine kinase Lck mediates Fas signaling
Authors: Akimzhanov Askar M. , Boehning Darren
Published: September 2015

Significance

Protein palmitoylation has been proposed to mediate the recruitment of signaling proteins into lipid rafts. However, a significant shortcoming of this hypothesis is that the proposed kinetics of protein palmitoylation/depalmitoylation heretofore have been too slow to mediate very rapid signaling events. Using a combination of a highly sensitive palmitoylation assay with pulsed metabolic labeling, we were able to detect a population of the Src kinase Lck undergoing extremely rapid palmitoylation and depalmitoylation subsequent to Fas receptor stimulation. The rapid rise and fall in Lck palmitoylation was highly synchronized with other signaling events occurring during the first minutes after activation of the Fas pathway, suggesting the existence of a previously undescribed signal transduction mechanism.
Glass-to-cryogenic-liquid transitions in aqueous solutions suggested by crack healing
Authors: Kim Chae Un , Tate Mark W. , Gruner Sol M.
Published: September 2015

Significance

For decades, physicists, physical chemists, and biologists have been tremendously intrigued by the unusual thermodynamic and kinetic properties of supercooled water. Theories have been proposed to account for the properties but these theories remain contentious for lack of experimental evidence. We investigated phase behavior of water at cryogenic temperatures and showed clear experimental evidence that the two cryogenic glassy states of water (high-density amorphous and low-density amorphous) undergo glass-to-cryogenic-liquid transitions and they are thermodynamically separated by a first-order phase transition. The results provide insight into the physical origin of the anomalous properties of supercooled water.
Evidence for superconductivity in Li-decorated monolayer graphene
Authors: Ludbrook B. M. , Levy G. , Nigge P. , Zonno M. , Schneider M. , Dvorak D. J. , Veenstra C. N. , Zhdanovich S. , Wong D. , Dosanjh P. , Straßer C. , Stöhr A. , Forti S. , Ast C. R. , Starke U. , Damascelli A.
Published: September 2015

Significance

Although superconductivity is well-known in intercalated bulk graphite, the ultimate goal of inducing superconductivity in single-layer graphene has not yet been achieved. We have here developed an experiment that combines ultralow-temperature (5 K) and ultrahigh-vacuum (10
−11
torr) sample preparation with high-resolution angle-resolved photoemission spectroscopy (ARPES). We show that decorating monolayer graphene with a layer of lithium atoms enhances the electron–phonon coupling to the point where a superconducting state can be stabilized at low temperature. Measurements of the size of the superconducting gap by ARPES suggest a

T
c

of about 5.9 K. This result constitutes the first observation, to our knowledge, of superconductivity in monolayer graphene. Given the massive scientific and technological interest in graphene, our findings will have significant cross-disciplinary impact.
Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse
Authors: Perera Lalith , Freudenthal Bret D. , Beard William A. , Shock David D. , Pedersen Lee G. , Wilson Samuel H.
Published: September 2015

Significance

DNA polymerases use a general two-metal ion mechanism for DNA synthesis. Recent time-lapse crystallographic studies identified additional adjunct metal ions in the polymerase active site. One of these ions correlates with appearance of pyrophosphate and was proposed to be involved in pyrophosphorolysis (reverse reaction of DNA synthesis). Because DNA polymerases can use pyrophosphorolysis to remove chain-terminating nucleotides during chemotherapies, a better understanding of this reaction is warranted. Through site-directed mutagenesis, pyrophosphorolysis measurements, and computational analysis, we examine the role of metal ions in the reverse reaction. The results indicate that the product-associated metal ion facilitates pyrophosphorolysis during the early stages of the reaction but deters the reaction at later stages, suggesting dynamic metal behavior that can modulate the chemical equilibrium.
Widespread convergence in toxin resistance by predictable molecular evolution
Authors: Ujvari Beata , Casewell Nicholas R. , Sunagar Kartik , Arbuckle Kevin , Wüster Wolfgang , Lo Nathan , O’Meally Denis , Beckmann Christa , King Glenn F. , Deplazes Evelyne , Madsen Thomas
Published: September 2015

Significance

Convergence has strong bearing on the fundamental debate about whether evolution is stochastic and unpredictable or subject to constraints. Here we show that, in certain circumstances, evolution can be highly predictable. We demonstrate that several lineages of insects, amphibians, reptiles, and mammals have utilized the same molecular solution, via the process of convergence, to evolve resistance to toxic cardiac glycosides produced defensively by plants and bufonid toads. The repeatability of this process across the animal kingdom demonstrates that evolution can be constrained to proceed along highly predictable pathways at molecular and functional levels. Our study has important implications for conservation biology by providing a predictive framework for assessing the vulnerability of native fauna to the introduction of invasive toxic toads.
Candida albicans
adapts to host copper during infection by swapping metal cofactors for superoxide dismutase
Authors: Li Cissy X. , Gleason Julie E. , Zhang Sean X. , Bruno Vincent M. , Cormack Brendan P. , Culotta Valeria Cizewski
Published: September 2015

Significance

During infection, the host is known to elevate Cu to attack invading microbes with Cu toxicity. Because Cu is also a micronutrient, pathogens must capture Cu while defending against its toxicity. Here we describe an innovative method by which the fungal pathogen
Candida albicans
adapts to extremes in Cu. Specifically,
C. albicans
maintains its antioxidant defense over a spectrum of Cu conditions by expressing either Cu-dependent or Cu-independent forms of superoxide dismutase (SOD). This switching of fungal SODs becomes prevalent during a mouse model for disseminated candidiasis, where serum Cu rises and kidney Cu declines. The host both elevates and restricts Cu for invading pathogens and
C. albicans
adapts by modulating Cu uptake and metal cofactor selection for SODs.
Accelerating molecular simulations of proteins using Bayesian inference on weak information
Authors: Perez Alberto , MacCallum Justin L. , Dill Ken A.
Published: September 2015

Significance

An important challenge has been to develop computer methods that can predict protein native structures from their sequences and satisfy the thermodynamic principle of Boltzmann's Law, which requires that the sampling method obey detailed balance. The latter is needed to study mechanisms and dynamics, which require an understanding of relative populations of states. These dual goals are met by atomistic model simulations, but they have been too expensive computationally. Here, we join together molecular dynamics (MD) with Bayesian inferences derived from loose insights (proteins have “hydrophobic cores” and “secondary structures”). We show that this method can speed up MD simulations by up to five orders of magnitude, allowing for the accurate predictions of small native protein structures with only atomistic potentials.
Hopanoids as functional analogues of cholesterol in bacterial membranes
Authors: Sáenz James P. , Grosser Daniel , Bradley Alexander S. , Lagny Thibaut J. , Lavrynenko Oksana , Broda Martyna , Simons Kai
Published: September 2015

Significance

The function of the cell membrane as a barrier and a matrix for biochemical activity relies on the properties imparted by lipids. In eukaryotes, sterols are crucial for modulating the molecular order of membranes. Sterol ordering provides the basis for membrane lateral segregation and promotes a fluid, mechanically robust plasma membrane. How do organisms that lack sterols determine membrane order? Hopanoids are bacterial membrane lipids that have been demonstrated to have sterol-like properties in vitro. We now explore the distribution of hopanoids and their effect on membranes in
Methylobacterium extorquens
. We find that hopanoids determine bacterial outer membrane order in a manner analogous to sterol ordering in the eukaryotic plasma membrane, and that their deletion impairs energy-dependent multidrug efflux.
Extremes of 𝛼(𝑡)-locally stationary Gaussian random fields
Authors: Hashorva Enkelejd , Ji Lanpeng
Published: September 2015

The main result of this contribution is the derivation of the exact asymptotic behavior of the supremum of a class of

α
(

t

)

\alpha (\mathbf {t})

-locally stationary Gaussian random fields. We present two applications of our result: the first one deals with the extremes of aggregate multifractional Brownian motions, whereas the second one establishes the exact asymptotics of the supremum of the

χ
\chi

-process generated by multifractional Brownian motions.
Balanced harvesting in fisheries: a preliminary analysis of management implications‡
Authors: Garcia S. M. , Rice J. , Charles A.
Published: September 2015

Balanced harvest (BH) proposes to distribute a moderate mortality from fishing across the widest possible range of species, stocks, and sizes in an ecosystem, in proportion to their natural productivity so that the relative size and species composition are maintained, in line with the CBD requirement for sustainable use. This proposal has many and not always intuitive implications for fisheries management, e.g. in relation to selectivity, protection of juveniles and spawning sites, models of harvesting strategies, a focus on size and species, the impacts of discarding, aspects of emblematic species and ecosystem services, operational complexity, partial implementation, ecosystem rebuilding, and relations with broader management frameworks. The paper closes with a discussion of BH implementation, concluding that a logical step would be to integrate several separate initiatives to move fisheries into a more ecosystem-conscious context. Implementation challenges will be encountered, but there are lessons to be drawn from fishery ecosystems already close to BH, as in some tropical multispecies fisheries, and further, the implementation challenges are already being taken on in many well-managed fisheries and areas as management begins to address the realities of what ecosystem-based fishery management actually entails.
Aeromicrobium camelliae sp. nov., isolated from Pu′er tea
Authors: Niu Lili , Xiong Mengjie , Tang Tianyi , Song Lei , Hu Xing , Zhao Meng , Zhang Kegui
Published: September 2015

A novel Gram-reaction-positive, aerobic and non-spore-forming rod-shaped bacterial strain, YS17T, was isolated from ripened Pu′er tea. Growth of the strain was observed at 15–50 °C (optimum 30–37 °C) and at pH 5.5–10.5 (optimum 6.0–9.5). Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain represented a member of the genus Aeromicrobium. The strains most closely related to YS17T were Aeromicrobium erythreum DSM 8599T, Aeromicrobium alkaliterrae JCM 13518T and Aeromicrobium ginsengisoli JCM 14732T, with 16S rRNA gene sequence similarities of 96.8, 96.8 and 96.7 %, respectively. DNA–DNA hybridization of YS17T with the type strains of the most closely related species, A. erythreum DSM 8599T, A. alkaliterrae JCM 13518T and A. ginsengisoli JCM 14732T, yielded reassociation values of 10.9, 16.8 and 10.9 %, respectively. The diagnostic diamino acid of the cell wall peptidoglycan was ll-diaminopimelic acid. The predominant menaquinones were menaquinone MK-9(H4) (76 %) and MK-8(H4) (17 %). The major fatty acids were C16 : 0, 10-methyl C18 : 0 and C18 : 1ω9c. The DNA G+C content of YS17T was 66 mol%. YS17T could be differentiated from recognized species of the genus Aeromicrobium on the basis of phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA–DNA hybridization data. On the basis of evidence from the polyphasic analyses performed as part of this study a novel species, Aeromicrobium camelliae sp. nov., is proposed, with strain YS17T ( = CGMCC 1.12942T = JCM 30952T) as the type strain.
Formosa haliotis sp. nov., a brown-alga-degrading bacterium isolated from the gut of the abalone Haliotis gigantea
Authors: Tanaka Reiji , Cleenwerck Ilse , Mizutani Yukino , Iehata Shunpei , Shibata Toshiyuki , Miyake Hideo , Mori Tetsushi , Tamaru Yutaka , Ueda Mitsuyoshi , Bossier Peter , Vandamme Peter
Published: September 2015

Four brown-alga-degrading, Gram-stain-negative, aerobic, non-flagellated, gliding and rod-shaped bacteria, designated LMG 28520T, LMG 28521, LMG 28522 and LMG 28523, were isolated from the gut of the abalone Haliotis gigantea obtained in Japan. The four isolates had identical random amplified polymorphic DNA patterns and grew optimally at 25 °C, at pH 6.0–9.0 and in the presence of 1.0–4.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences placed the isolates in the genus Formosa with Formosa algae and Formosa arctica as closest neighbours. LMG 28520T and LMG 28522 showed 100 % DNA–DNA relatedness to each other, 16–17 % towards F. algae LMG 28216T and 17–20 % towards F. arctica LMG 28318T; they could be differentiated phenotypically from these established species. The predominant fatty acids of isolates LMG 28520T and LMG 28522 were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 1 G and iso-C15 : 0. Isolate LMG 28520T contained menaquinone-6 (MK-6) as the major respiratory quinone and phosphatidylethanolamine, two unknown aminolipids and an unknown lipid as the major polar lipids. The DNA G+C content was 34.4 mol% for LMG 28520T and 35.5 mol% for LMG 28522. On the basis of their phylogenetic and genetic distinctiveness, and differential phenotypic properties, the four isolates are considered to represent a novel species of the genus Formosa, for which the name Formosa haliotis sp. nov. is proposed. The type strain is LMG 28520T ( = NBRC 111189T).
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach
Authors: Chauve Cedric , Ponty Yann , Peirera Zanetti João Paulo
Published: September 2015

Context

The reconstruction of evolutionary scenarios for whole genomes in terms of genome rearrangements is a fundamental problem in evolutionary and comparative genomics. The DeCo algorithm, recently introduced by Bérardet al., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. However, as for many combinatorial optimization algorithms, there can exist many co-optimal, or slightly sub-optimal, evolutionary scenarios that deserve to be considered.

Contribution

We extend the DeCo algorithm to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution, and also to compute Boltzmann probabilities for specific ancestral adjacencies.

Results

We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies.
Combining niche modelling, land use-change, and genetic information to assess the conservation status ofPouteria splendenspopulations in Central Chile
Authors: Morales Narkis S , Fernandez Ignacio C , Carrasco Basilio A , Orchard Cristina
Published: September 2015

Background:Pouteria splendens(lúcumo chileno) is an endemic shrub to the coastal areas of Central Chile classified as Endangered and Rare by the Chilean threatened species list, but as Lower Risk (LR) by IUCN. Based in historical records some authors have hypothesized thatP. splendensoriginally formed a large metapopulation, but due to habitat loss and fragmentation these populations have been reduced to two main areas separated by 100 km, neither of both currently protected by the Chilean system of protected areas. Knowledge about this species is scarce and no studies have provided evidence to support the large metapopulation hypothesis. This gap of knowledge limits our availability to gauge the real urgency to conserve remainingP. splendenspopulations, which can generate tragic consequences in light of the increasing land-use change and climatic change that are facing these populations. In this study we combined niche modelling, land-use information, future climatic scenarios, and conservation genetics techniques, to test the hypothesis of a potential original large metapopulation, evaluate the role of land-use change in population decline, assess the threats this species may face in the future, and combine the generated information to re-assess its conservation status using the IUCN criteria. Results: Our results show that locations withP. splendensare fewer than described in the literature. Results from the niche modelling and genetic analyses support the hypothesis of an originally large metapopulation that was recently reduced and fragmented by anthropogenic land-use change. Future climate change could increase the range of suitable habitats forP. splendenstowards inland areas; however the high level of fragmentation of these new areas is expected to preclude colonization processes. Conclusions: Based on our results we recommend urgent actions towards the conservation of this species, including (1) re-evaluating its current IUCN conservation status and reclassifying it as Endangered (EN), and (2) take immediate actions to develop strategies that effectively protect the remaining populations.
Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three relatedPopulusspecies
Authors: Wang Jing , Street Nathaniel R , Scofield Douglas G , Ingvarsson Pär K
Published: September 2015

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome re-sequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum and population-scaled recombination rates in three species ofPopulus:P. tremula, P. tremuloidesandP. trichocarpa. We find thatP. tremuloideshas the highest level of genome-wide variation, skewed allele frequencies and population-scaled recombination rates, whereasP. trichocarpaharbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, both due to purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination are largely explaining the disparate magnitudes and signatures of linked selection we observe among species. The present work provides the first phylogenetic comparative study at genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.
HacDivSel: Two new methods (haplotype-based and outlier-based) for the detection of divergent selection in pairs of populations
Authors: Carvajal-Rodríguez A.
Published: September 2015

The detection of genomic regions involved in local adaptation is an important topic in current population genetics. There are several detection strategies available depending on the kind of genetic and demographic information at hand. A common drawback is the high risk of false positives. In this study we introduce two complementary methods for the detection of divergent selection from populations connected by migration. Both methods have been developed with the aim of being robust to false positives. The first method combines haplotype information with inter-population differentiation (FST). Evidence of divergent selection is concluded only when both the haplotype pattern and theFSTvalue support it. The second method is developed for independently segregating markers i.e. there is no haplotype information. In this case, the power to detect selection is attained by developing a new outlier test based on detecting a bimodal distribution. The test computes theFSToutliers and then assumes that those of interest would have a different mode. We demonstrate the utility of the two methods through simulations and the analysis of real data. The simulation results showed power ranging from 60-95% in several of the scenarios whilst the false positive rate was controlled below the nominal level. The analysis of real samples consisted of phased data from the HapMap project and unphased data from intertidal marine snail ecotypes. The results illustrate that the proposed methods could be useful for detecting locally adapted polymorphisms. The software HacDivSel implements the methods explained in this manuscript.
General methods for evolutionary quantitative genetic inference from generalised mixed models.
Authors: de Villemereuil Pierre , Schielzeth Holger , Nakagawa Shinichi , Morrissey Michael
Published: September 2015

Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioural traits, have inherently non-normal distributions. The generalised linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for non-normal traits. However, whereas GLMMs provide inference on a statistically-convenient latent scale, it is sometimes desirable to express quantitative genetic parameters on the scale upon which traits are expressed. The parameters of a fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal for this effect by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulae for quantities such as heritability of traits with Binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation, and apply our approach to data from a wild pedigreed vertebrate population.
Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice
Authors: Zhang Xiangqian , Sun Jing , Cao Xiaofeng , Song Xianwei
Published: September 2015

Heritable epigenetic variants of genes, termed epialleles, can broaden genetic and phenotypic diversity in eukaryotes. Epialleles may also provide a new source of beneficial traits for crop breeding, but very few epialleles related to agricultural traits have been identified in crops. Here, we identified Epi-rav6, a gain-of-function epiallele of rice (Oryza sativa) RELATED TO ABSCISIC ACID INSENSITIVE3 (ABI3)/VIVIPAROUS1 (VP1) 6 (RAV6), which encodes a B3 DNA-binding domain-containing protein. The Epi-rav6 plants show larger lamina inclination and smaller grain size; these agronomically important phenotypes are inherited in a semidominant manner. We did not find nucleotide sequence variation of RAV6. Instead, we found hypomethylation in the promoter region of RAV6, which caused ectopic expression of RAV6 in Epi-rav6 plants. Bisulfite analysis revealed that cytosine methylation of four CG and two CNG loci within a continuous 96-bp region plays essential roles in regulating RAV6 expression; this region contains a conserved miniature inverted repeat transposable element transposon insertion in cultivated rice genomes. Overexpression of RAV6 in the wild type phenocopied the Epi-rav6 phenotype. The brassinosteroid (BR) receptor BR INSENSITIVE1 and BR biosynthetic genes EBISU DWARF, DWARF11, and BR-DEFICIENT DWARF1 were ectopically expressed in Epi-rav6 plants. Also, treatment with a BR biosynthesis inhibitor restored the leaf angle defects of Epi-rav6 plants. This indicates that RAV6 affects rice leaf angle by modulating BR homeostasis and demonstrates an essential regulatory role of epigenetic modification on a key gene controlling important agricultural traits. Thus, our work identifies a unique rice epiallele, which may represent a common phenomenon in complex crop genomes.