bluuebunny/crossref_metadata_2025 huggingface dataset:
The size and diffusion effect of gold on silicon nanowire sidewall faceting
Authors: Seo Deok-Won , Kim Gil-Sung , Lee Chan-Yang , Lee Seung-Yong , Hyung Jung-Hwan , Choi Chel-Jong , Lee Sang-Kwon
Published: February 2012

Single crystalline silicon nanowires (SiNWs) were grown using a gold (Au)-catalyzed vapor-liquid-solid (VLS) approach. In this study, we examine the influence of the size of Au catalyst droplets on the size of SiNWs and discuss the effect of Au diffusion and surface passivation on SiNW sidewall faceting and roughening in the VLS process. To simultaneously cover a variety of sizes of SiNWs on the same substrate, 2-nm-thick Au film was used on Si (111) substrate as a catalyst, since it is known that Au thin film–based seed offers relatively less control of the NW size, due to the randomness of the film breakup at reaction temperature. We then found that the grown SiNWs have two main types of surface morphologies on the sidewall of the nanowires (NWs). One type had a small and coarse surface morphology with no Au-Si droplets at the top of the NWs. The other type had a long and smooth surface and still had Au-Si droplets at the end. The fact that resulting SiNWs have two main different surface morphologies can be explained by three reasons: the size difference of Au-Si droplets, Au diffusion to the surface of the SiNWs, and surface passivation on the SiNW surface. Furthermore, we proposed a combined VLS and vapor-solid (VS) growth model to describe the creation of the facets and roughening of the sidewall of the NWs. Our results point toward the exciting possibility that the proposed well-controlled and coarse-surfaced SiNWs could be promising thermoelectric materials with low thermal conductivity, since the thermal conductivity is greatly reduced at the rough surface due to the enhancement of phonon scattering.
Dynamics of fibers in a wide microchannel
Authors: Słowicka Agnieszka M. , Ekiel-Jeżewska Maria L. , Sadlej Krzysztof , Wajnryb Eligiusz
Published: February 2012

Dynamics of single flexible non-Brownian fibers, tumbling in a Poiseuille flow between two parallel solid plane walls, is studied with the use of the HYDROMULTIPOLE numerical code, based on the multipole expansion of the Stokes equations, corrected for lubrication. Fibers, which are closer to a wall, more flexible (less stiff) or longer, deform more significantly and, for a wide range of the system parameters, they faster migrate towards the middle plane of the channel. For the considered systems, fiber velocity along the flow is only slightly smaller than (and can be well approximated by) the Poseuille flow velocity at the same position. In this way, the history of a fiber migration across the channel is sufficient to determine with a high accuracy its displacement along the flow.
Micromagnetic analysis of the Rashba field on current-induced domain wall propagation
Authors: Martinez Eduardo
Published: February 2012

The current-driven domain wall propagation along a thin ferromagnetic strip with high perpendicular magnetocrystalline anisotropy is studied by means of micromagnetic simulations with emphasis on the role of the Rashba field, which has been predicted to play a dominant role in multilayer stacks with structure inversion asymmetry. Taking into account the surface roughness and thermal fluctuations, the results show a current dependence of the domain wall velocity in good qualitative agreement with recent experimental observations. It depicts (i) a low-current creep regime, where the domain wall velocity increases exponentially and (ii) a high-current linear regime where the wall propagates rigidly with a higher mobility than the one expected in the turbulent Walker regime. The analysis seems to be essential in order to get a better understanding of the magnitude of the non-adiabatic torque by direct comparison with experimental measurements.
Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA
Authors: Sivak David A. , Geissler Phillip L.
Published: February 2012

The wormlike chain model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for elasticity at the 1–10 basepair (bp) scale, which holds particular interest in biological contexts. Here, we examine a class of microscopic models which allow for disruption of base pairing (i.e., a “melt” or “kink”, generically an “excitation”) and consequently enhanced local flexibility. We first analyze the effect on the excitation free energy of integrating out the spatial degrees of freedom in a wormlike chain. Based on this analysis, we present a formulation of these models that ensures consistency with the well-established thermodynamics of melting in long chains. Using a new method to calculate cyclization statistics of short chains from enhanced-sampling Monte Carlo simulations, we compute J-factors of a meltable wormlike chain over a broad range of chain lengths, including very short molecules (30 bp) that have not yet been explored experimentally. For chains longer than about 120 bp, including most molecules studied to date in the laboratory, we find that melting excitations have little impact on cyclization kinetics. Strong signatures of melting, which might be resolved within typical experimental scatter, emerge only for shorter chains.
Tapping-mode force spectroscopy using cantilevers with interferometric high-bandwidth force sensors
Authors: Fatih Sarioglu A. , Magonov Sergei , Solgaard Olav
Published: February 2012

We quantitatively map the surface forces and elastic modulus in tapping-mode atomic force microscopy (AFM). To achieve this, we use custom-built cantilevers with interferometric high-bandwidth force sensors that can resolve nonlinear tip-sample interaction forces, combined with a set of algorithms to process the force sensor signals in real-time. Our technique achieves quantitative mechanical measurements, while retaining nanoscale spatial resolution and minimal loading forces in tapping-mode AFM. Moreover, conventional tapping-mode AFM images are not affected and can simultaneously be acquired. As a practical demonstration, we use our technique to quantify the mechanical properties of a polystyrene and linear low-density polyethylene blend.
Melting and superheating of sI methane hydrate: Molecular dynamics study
Authors: Smirnov Grigory S. , Stegailov Vladimir V.
Published: February 2012

Melting and decay of the superheated sI methane structure are studied using molecular dynamics simulation. The melting curve is calculated by the direct coexistence simulations in a wide range of pressures up to 5000 bar for the SPC/E, TIP4P/2005 and TIP4P/Ice water models and the united-atom model for methane. We locate the kinetic stability boundary of the superheated metastable sI structure that is found to be surprisingly high comparing with the predictions based on the classical nucleation theory.
Structural phase transition of graphene caused by GaN epitaxy
Authors: Gohda Y. , Tsuneyuki S.
Published: February 2012

We report first-principles predictions, where the structure of graphene changes drastically with the epitaxial growth of GaN (which has been performed experimentally). We identify GaN-3×3/graphene-2 × 2 superstructure as the most probable interface atomic structure, where three C-C bonds are replaced with C-N-C bonds preserving the Dirac cones. As the GaN epitaxy proceeds expanding graphene gradually, the tensile strain for graphene is released suddenly by partial breaking of the C-bond network, attributable to the two-dimensionality of graphene. In contrast, graphene retains its honeycomb structure at the AlN-graphene interface. Both of GaN- and AlN-graphene interfaces exhibit spin polarization.
A versatile cantilever beam magnetometer for ex situ characterization of magnetic materials
Authors: Adhikari R. , Sarkar A. , Das A. K.
Published: February 2012

We have designed, fabricated, and made operational an ex situ cantilever beam magnetometer (CBM), which is versatile in the sense that it can measure most of the magnetic properties of a material in all probable shapes. The working principle of a CBM is discussed considering the magnetic torque into the beam theory. The individual components of the instrument are described in details and experiments were performed on the bulk materials, pellets of nanoparticles, ribbon samples, and thin films, and the magnetization, magnetostriction, and magnetocrystalline anisotropy were studied. This magnetometer is inexpensive, but versatile and would be suitable for the research as well as teaching laboratories.
Pseudobinary Al2Te3-Sb2Te3 material for high speed phase change memory application
Authors: Ren Kun , Rao Feng , Song Zhitang , Lv Shilong , Cheng Yan , Wu Liangcai , Peng Cheng , Zhou Xilin , Xia Mengjiao , Liu Bo , Feng Songlin
Published: February 2012

Al2Sb2Te6 is a pseudobinary material constructed by Sb2Te3 (fast crystallization speed but thermally unstable) and Al2Te3 (thermally stable but without memory switching ability). Al2Sb2Te6 material possesses advantages of these two binary compounds showing good memory switching ability with fast switching speed and good thermal stability. These improvements are believed to be closely related to the coordination situations of Al atoms in Al2Sb2Te6 material. Phase change memory device using Al2Sb2Te6 showed high speed (∼5 ns), low power consumption, and high endurance (∼106 cycles). Thus, we consider that Al2Sb2Te6 can be one of the most promising materials for phase change memory use.
Transmission enhancement in a non-adiabatic tapered nano-aperture waveguide
Authors: Chen Yongzhu , Xie Xiangsheng , Li Yongyao , Zhou Jianying
Published: February 2012

Transmission enhancement via transverse mode control through an aluminum hollow tapered waveguide with a sub-100 nm aperture is simulated with optical wavefront modulations via a binary optical element. Efficient delivery of an input field by exciting the fundamental propagating mode near the apex is realized, giving rise to a significant transmission enhancement through the nano-tip.
2-bit operation based on modulated Fowler-Nordheim tunneling in charge-trapping flash memory cell
Authors: Hung Min-Feng , Wu Yung-Chun , Chen Jiang-Hung
Published: February 2012

This work proposes a spatially charge tunneling method for program/erase (P/E) based on the drain-modulated Fowler-Nordheim (MFN) tunneling in a polycrystalline silicon channel charge-trap type flash memory device. The program mechanism and the simulation of the MFN are discussed. 2-bit operations based on MFN and channel hot electron injection were demonstrated. MFN 2-bit operation and conventional 2-bit operation present different transfer curves, indicating that charge is injected into the different regions. The MFN P/E operation provides flexibility in flash memory applications.
Top-gate hybrid complementary inverters using pentacene and amorphous InGaZnO thin-film transistors with high operational stability
Authors: Kim J. B. , Fuentes-Hernandez C. , Hwang D. K. , Potscavage W. J. , Kippelen B.
Published: February 2012

We report on the operational stability of low-voltage hybrid organic-inorganic complementary inverters with a top-gate bottom source-drain geometry. The inverters are comprised of p-channel pentacene and n-channel amorphous InGaZnO thin-film transistors (TFTs) with bi-layer gate dielectrics formed from an amorphous layer of a fluoropolymer (CYTOP) and a high-k layer of Al2O3. The p- and n- channel TFTs show saturation mobility values of 0.1 ± 0.01 and 5.0 ± 0.5 cm2/Vs, respectively. The individual transistors show high electrical stability with less than 6% drain-to-source current variations after 1 h direct current (DC) bias stress. Complementary inverters yield hysteresis-free voltage transfer characteristics for forward and reverse input biases with static DC gain values larger than 45 V/V at 8 V before and after being subjected to different conditions of electrical stress. Small and reversible variations of the switching threshold voltage of the inverters during these stress tests are compatible with the observed stability of the individual TFTs.
Climate scientists not cowed by relentless climate change deniers
Authors: Feder Toni
Published: February 2012

Groups that provide moral support, legal counsel, and swift rebuttals of misinformation are sprouting up.
Small business technology program gains new lease on life
Authors: Kramer David
Published: February 2012

Six-year extension of grants act will give small companies a leg up in the scramble for increasingly scarce federal research dollars.
Radiation meets food
Authors: Dickson James S.
Published: February 2012

It’s no secret that some people are wary of irradiated food. But radiation levels that effectively control pathogens have no demonstrated harmful effects on humans.
Hierarchical processing of complex motion along the primate dorsal visual pathway
Authors: Mineault Patrick J. , Khawaja Farhan A. , Butts Daniel A. , Pack Christopher C.
Published: February 2012

Neurons in the medial superior temporal (MST) area of the primate visual cortex respond selectively to complex motion patterns defined by expansion, rotation, and deformation. Consequently they are often hypothesized to be involved in important behavioral functions, such as encoding the velocities of moving objects and surfaces relative to the observer. However, the computations underlying such selectivity are unknown. In this work we have developed a unique, naturalistic motion stimulus and used it to probe the complex selectivity of MST neurons. The resulting data were then used to estimate the properties of the feed-forward inputs to each neuron. This analysis yielded models that successfully accounted for much of the observed stimulus selectivity, provided that the inputs were combined via a nonlinear integration mechanism that approximates a multiplicative interaction among MST inputs. In simulations we found that this type of integration has the functional role of improving estimates of the 3D velocity of moving objects. As this computation is of general utility for detecting complex stimulus features, we suggest that it may represent a fundamental aspect of hierarchical sensory processing.
Effects of Smallmouth Bass on Atlantic Salmon Habitat Use and Diel Movements in an Artificial Stream
Authors: Wathen Gus , Zydlewski Joseph , Coghlan Stephen M. , Trial Joan G.
Published: February 2012

Invasive smallmouth bass Micropterus dolomieu have been introduced to some of the last remaining watersheds that contain wild anadromous Atlantic salmon Salmo salar, yet little is known about the interactions between these species. We used an artificial stream equipped with passive integrated transponder tag antenna arrays to monitor habitat use and movements of age‐0 Atlantic salmon and age‐0 smallmouth bass in sympatry and allopatry. We used additive and substitutive designs to test for changes in habitat use, diel movements, and diel activity patterns of prior‐resident Atlantic salmon or smallmouth bass resulting from the addition of conspecifics or heterospecifics. Atlantic salmon prior residents did not change their habitat use in the presence of conspecific or heterospecific invaders. However, Atlantic salmon invaders did lessen riffle habitat use by smallmouth bass prior residents during daytime. Atlantic salmon and smallmouth bass displayed different diel activity patterns of movement (Atlantic salmon were more nocturnal; smallmouth bass were more diurnal), which were affected by heterospecific introductions. Because the two species tended to favor different habitat types and displayed different diel activity patterns, we suggest that under the conditions tested, the level of interspecific competition for habitat was low. Age‐0 Atlantic salmon and smallmouth bass may be able to avoid intense interspecific competition through spatial and temporal habitat partitioning. These data do not, however, predict the potential for competition under different seasonal or ontogenetic circumstances.
A Method for an Image‐Analysis‐Based Two‐Dimensional Computational Fluid Dynamics Simulation of Moving Fish
Authors: Garvin Justin W. , Kureksiz Ozge , Breczinski Philip J. , Garvin Mona K.
Published: February 2012

Studies involving how fish respond given different flow field conditions are important in understanding phenomena such as fish schooling as well as larger‐scale migrations. Simulating a fish moving under various flow field conditions is a difficult task, however, due to the fact that fish responses are dependent upon the environment. This makes the traditional use of analytical expressions to model the movement of fish bodies intractable. Thus, the main focus of the present study was to establish a method for coupling the use of image‐analysis‐based techniques for determining fish body motion with the use of a computational fluid dynamics (CFD) simulation. In particular, we focused on the simulation of a fish (rainbow trout Oncorhynchus mykiss) swimming behind a D‐section cylinder. This simulation was based on previous experiments that studied how vortices being shed from a blunt body affected fish movement. The individual frames of a video depicting a fish swimming behind a D‐section cylinder were segmented, and the resulting x, y coordinates of the fish's body were supplied to a CFD simulation to capture the fish motion. The CFD simulations were performed by using a k– turbulence model to calculate the flow field. Previous experimental results showed that the fish traversed between the shedding vortices. Our computational results show that the propulsive force is greatest when the shedding vortices pass along the sides of the fish body in order to aid in its movement. Future work entails extending the analysis to three dimensions and including more details in the fish geometry.
Growing confidence in educational research: Threats and opportunities
Authors: James Mary
Published: February 2012

We live in difficult times—socially, economically and politically—and it is right that learned societies, such as the British Educational Research Association, reflect on their purpose and direction. We cannot take for granted the social contract that supports the funding of social science and educational research. This paper reflects on enduring themes and new pressures and argues for special attention to: collaboration within and beyond the community of university‐based educational researchers; support for, and recognition of, the importance of reviews of research; the development of accessible forms of communication of findings and their implications, to guide sound decision making; more direct engagement with practitioners, policy makers and the public. It argues that it is time for communities of educational researchers to have confidence to become outward looking and strengthen alliances with other groups of researchers at home and abroad, across disciplines, with different types of research institutions and also with practitioners and policy makers. What drives this should be our principal aim to pursue educational research and its application for the improvement of education and the public benefit.
Laboratory and Production Scale Disinfection of Salmonid Eggs with Hydrogen Peroxide
Authors: Wagner Eric J , Oplinger Randall W , Bartley Matthew
Published: February 2012

Disinfection tests were conducted on eggs from rainbow trout Oncorhynchus mykiss, cutthroat trout O. clarkii, and brown trout Salmo trutta to evaluate hydrogen peroxide (H2O2) as an egg disinfectant. A daily drip of 500 mg/L hydrogen peroxide for 35 min on eyed brown trout eggs safely led to significantly reduced bacterial abundance relative to untreated controls, but abundance did not differ significantly from that in a formalin treatment (2,000 mg/L for 15 min). Using water-hardened cutthroat trout eggs, hydrogen peroxide concentrations of (1) 10 g/L for 2 min, (2) 10 g/L for 3 min, (3) 15 g/L for 2 min, and (4) 1,000 mg/L for 15 min were compared with two controls (untreated; 100 mg/L iodine). Bacteria were significantly more abundant in the untreated eggs, but abundance did not significantly differ among chemical treatments. In another test, rainbow trout eggs treated the day before hatch with 15 g/L H2O2 for 2 min had significantly higher mortality than the controls. In production-scale tests, 10–15 g/L H2O2 for 2 min was safe for rainbow and cutthroat trout eggs and significantly reduced bacterial abundance relative to that in untreated eggs. Complete disinfection was not achievable with either iodine or hydrogen peroxide. Daily drip treatment with either formalin or hydrogen peroxide significantly reduced bacterial growth and is recommended.
Effects of ferromagnet–molecule chemical bonding on spin injection in an Fe3O4–molecule granular system
Authors: Yue F J , Wang S , Lin L , Ding H F , Wu D
Published: February 2012

Spin injection at the interface of Fe3O4/stearic acid molecule is investigated in a comparative study of Fe3O4 nanoparticles chemically bonded with molecules (ChemNPs) and Fe3O4 nanoparticles with physically absorbed molecules (PhyNPs). The resistance of PhyNPs is two orders of magnitude larger than that of ChemNPs, indicating that the resistance of PhyNPs is dominated by the energy barrier at the Fe3O4–molecule interface. A magnetoresistance of −12% under a field of 5.8 kOe at room temperature is observed in ChemNPs, in sharp contrast to the zero magnetoresistance in PhyNPs, reflecting that the chemical bonding is crucial for spin injection. We attribute this result to the induced magnetic moment in molecules by proximity effect, which is likely the origin of the spin-dependent tunnelling through molecules. In addition, the estimated relatively large spin polarization of ChemNPs suggests electronic hybridization at the interface and improved oxygen stoichiometry of the Fe3O4 surface.
Benchmarking ICRF full-wave solvers for ITER
Authors: Budny R.V. , Berry L. , Bilato R. , Bonoli P. , Brambilla M. , Dumont R.J. , Fukuyama A. , Harvey R. , Jaeger E.F. , Indireshkumar K. , Lerche E. , McCune D. , Phillips C.K. , Vdovin V. , Wright J.
Published: February 2012

Benchmarking full-wave solvers for ion-cyclotron range of frequency (ICRF) simulations is performed using plasma profiles and equilibria obtained from integrated self-consistent modelling predictions of four ITER plasmas. One is for a high-performance baseline (5.3 T, 15 MA) DT H-mode. The others are for half-field, half-current plasmas of interest for the pre-activation phase with bulk plasma ion species being either hydrogen or He4. The predicted profiles are used by six full-wave solver groups to simulate the ICRF electromagnetic fields and heating, and by three of these groups to simulate the current drive. Approximate agreement is achieved by four of the solvers for the heating power partitions for the DT and He4 cases. Factor of two or more disagreements are found for the heating power partitions for the cases with second harmonic He3 heating in bulk H cases. Approximate agreement is achieved simulating the ICRF current-drive 1D profiles.
Core and edge toroidal rotation study in JT-60U
Authors: Yoshida M. , Sakamoto Y. , Honda M. , Kamada Y. , Takenaga H. , Oyama N. , Urano H.
Published: February 2012

The relation between toroidal rotation velocities (V
t) in the core and edge regions is investigated in H-mode plasmas with a small external torque input from the viewpoint of momentum transport. The toroidal rotation velocity in the core region (core-V
t) gradually varies on a timescale of ∼20 ms after a rapid change in the toroidal rotation velocity in the edge region (edge-V
t) at the L–H transition. This timescale of ∼20 ms is consistent with a transport timescale using the momentum diffusivity (χϕ) and convection velocity (V
conv). In steady state, a linear correlation between the core- and edge-V
t is observed in H-mode plasmas when the ion pressure gradient (∇P
i) is small. This relation between core- and edge-V
t is also explained by momentum transport. The V
t profiles with a large ∇P
i are reproduced in the core region of r/a ∼ 0.2–0.7 by adopting a residual stress term ‘Πres = α
k
χϕ∇P
i’ proposed in this paper. Here r/a is the normalized plasma radius and α
k1 is a radial constant. Using this formula, V
t profiles are reproduced over a wide range of plasma conditions. Parameter dependences of the edge-V
t are investigated at a constant ripple loss power, ripple amplitude and plasma current. A reduction in the CTR-rotation is observed with decreasing ion temperature gradient (∇T
i). Here CTR refers to the counter-I
P direction.
First Report of a New TTKSF Race of Wheat Stem Rust (Puccinia graminis f. sp. tritici) in South Africa and Zimbabwe
Authors: Pretorius Z. A. , Szabo L. J. , Boshoff W. H. P. , Herselman L. , Visser B.
Published: February 2012

Seven races have been described in the Ug99 race group of Puccinia graminis f. sp. tritici (2). Ug99-related races previously recorded in South Africa are TTKSF, TTKSP, and PTKST (4). In December 2010, severe stem rust infection of the winter wheat cv. Matlabas was observed for the first time in South Africa. Race analysis using the 20 North American (NA) stem rust differential lines and letter code system classified the race as TTKSF. In comparative infection studies in a greenhouse, cv. Matlabas seedlings were susceptible (infection type [IT] 4) to isolate UVPgt61/1 (TTKSF+) collected from Afrikaskop in the eastern Free State, whereas the cultivar was resistant (IT 1 to 2) to stem rust isolates 2013 (TTKSF), UVPgt55 (TTKSF), UVPgt59 (TTKSP), and UVPgt60 (PTKST). Isolate 2013 represents the original collection of race TTKSF in South Africa (1). In addition to the NA differentials, no variation in the IT range of seedlings of lines with Sr7a, 8b, 12, 13, 14, 16, 18, 19, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 39, 41, 42, 43, 44, Em, R, Tt2, and Satu was observed between UVPgt61/1 and UVPgt55. With the exception of cv. Matlabas, ITs of 106 South African cultivars likewise did not differentiate UVPgt61/1 and UVPgt55. Seedling IT studies were conducted at least twice. Microsatellite analysis (4) showed that all single pustule isolates established from the original Matlabas isolate formed part of the Ug99 group. When characterized with selected single nucleotide polymorphisms (SNPs), all single pustule isolates shared an identical genotype that differed from UVPgt55 (TTKSF), a foreign introduction into South Africa (1,3). SNP genotype analysis suggests that UVPgt61/1 is genetically dissimilar to UVPgt55, as is Zim1009, another TTKSF+ isolate that was collected from Birchenough in Zimbabwe. Studies are underway to determine the identity of the defeated Sr gene in Matlabas and the cultivar has been added to the South African stem rust differential set. TTKSF+ is the eighth race detected in the Ug99 group. Since no other cultivars or advanced lines were found to carry the Matlabas gene, it is unlikely that race TTKSF+ will threaten wheat production in South Africa. However, the occurrence of a new Ug99-related race emphasizes the variability within this internationally important group.

References: (1) W. H. P. Boshoff et al. Plant Dis. 86:922, 2002. (2) R. F. Park et al. Euphytica 179:109, 2011. (3) B. Visser et al. Mol. Plant Pathol. 10:213, 2009. (4) B. Visser et al. Euphytica 179:119, 2011.
Can clade age alone explain the relationship between body size and diversity?
Authors: Etienne Rampal S. , de Visser Sara N. , Janzen Thijs , Olsen Jeanine L. , Olff Han , Rosindell James
Published: February 2012

One of the most striking patterns observed among animals is that smaller-bodied taxa are generally much more diverse than larger-bodied taxa. This observation seems to be explained by the mere fact that smaller-bodied taxa tend to have an older evolutionary origin and have therefore had more time to diversify. A few studies, based on the prevailing null model of diversification (i.e. the stochastic constant-rate birth–death model), have suggested that this is indeed the correct explanation, and body-size dependence of speciation and extinction rates does not play a role. However, there are several potential shortcomings to these studies: a suboptimal statistical procedure and a relatively narrow range of body sizes in the analysed data. Here, we present a more coherent statistical approach, maximizing the likelihood of the constant-rate birth–death model with allometric scaling of speciation and extinction rates, given data on extant diversity, clade age and average body size in each clade. We applied our method to a dataset compiled from the literature that includes a wide range of Metazoan taxa (range from midges to elephants). We find that the higher diversity among small animals is indeed, partly, caused by higher clade age. However, it is also partly caused by the body-size dependence of speciation and extinction rates. We find that both the speciation rate and extinction rate decrease with body size such that the net diversification rate is close to 0. Even more interestingly, the allometric scaling exponent of speciation and extinction rates is approximately −0.25, which implies that theper generationspeciation and extinction rates areindependentof body size. This suggests that the observed relationship between diversity and body size pattern can be explained by clade age alone, but only if clade age is measured in generations rather than years. Thus, we argue that the most parsimonious explanation for the observation that smaller-bodied taxa are more diverse is that their evolutionary clock ticks faster.
New construction of algebro-geometric solutions to the Camassa–Holm equation and their numerical evaluation
Authors: Kalla C. , Klein C.
Published: February 2012

An independent derivation of solutions to the Camassa–Holm equation in terms of multi-dimensional theta functions is presented using an approach based on Fay’s identities. Reality and smoothness conditions are studied for these solutions from the point of view of the topology of the underlying real hyperelliptic surface. The solutions are studied numerically for concrete examples, also in the limit where the surface degenerates to the Riemann sphere, and where solitons and cuspons appear.
Drosophila melanogaster
females change mating behaviour and offspring production based on social context
Authors: Billeter Jean-Christophe , Jagadeesh Samyukta , Stepek Nancy , Azanchi Reza , Levine Joel D.
Published: February 2012

In
Drosophila melanogaster
, biological rhythms, aggression and mating are modulated by group size and composition. However, the fitness significance of this group effect is unknown. By varying the composition of groups of males and females, we show that social context affects reproductive behaviour and offspring genetic diversity. Firstly, females mating with males from the same strain in the presence of males from a different strain are infecund, analogous to the Bruce effect in rodents, suggesting a social context-dependent inbreeding avoidance mechanism. Secondly, females mate more frequently in groups composed of males from more than one strain; this mitigates last male sperm precedence and increases offspring genetic diversity. However, smell-impaired
Orco
mutant females do not increase mating frequency according to group composition; this indicates that social context-dependent changes in reproductive behaviour depend on female olfaction, rather than direct male–male interactions. Further, variation in mating frequency in wild-type strains depends on females and not males. The data show that group composition can affect variance in the reproductive success of its members, and that females play a central role in this process. Social environment can thus influence the evolutionary process.
Host genetics and population structure effects on parasitic disease
Authors: Williams-Blangero Sarah , Criscione Charles D. , VandeBerg John L. , Correa-Oliveira Rodrigo , Williams Kimberly D. , Subedi Janardan , Kent Jack W. , Williams Jeff , Kumar Satish , Blangero John
Published: February 2012

Host genetic factors exert significant influences on differential susceptibility to many infectious diseases. In addition, population structure of both host and parasite may influence disease distribution patterns. In this study, we assess the effects of population structure on infectious disease in two populations in which host genetic factors influencing susceptibility to parasitic disease have been extensively studied. The first population is the Jirel population of eastern Nepal that has been the subject of research on the determinants of differential susceptibility to soil-transmitted helminth infections. The second group is a Brazilian population residing in an area endemic for
Trypanosoma cruzi
infection that has been assessed for genetic influences on differential disease progression in Chagas disease. For measures of
Ascaris
worm burden, within-population host genetic effects are generally more important than host population structure factors in determining patterns of infectious disease. No significant influences of population structure on measures associated with progression of cardiac disease in individuals who were seropositive for
T. cruzi
infection were found.
FGF21 regulates PGC-1α and browning of white adipose tissues in adaptive thermogenesis
Authors: Fisher ffolliott M. , Kleiner Sandra , Douris Nicholas , Fox Elliott C. , Mepani Rina J. , Verdeguer Francisco , Wu Jun , Kharitonenkov Alexei , Flier Jeffrey S. , Maratos-Flier Eleftheria , Spiegelman Bruce M.
Published: February 2012

Certain white adipose tissue (WAT) depots are readily able to convert to a “brown-like” state with prolonged cold exposure or exposure to β-adrenergic compounds. This process is characterized by the appearance of pockets of uncoupling protein 1 (UCP1)-positive, multilocular adipocytes and serves to increase the thermogenic capacity of the organism. We show here that fibroblast growth factor 21 (FGF21) plays a physiologic role in this thermogenic recruitment of WATs. In fact, mice deficient in FGF21 display an impaired ability to adapt to chronic cold exposure, with diminished browning of WAT. Adipose-derived FGF21 acts in an autocrine/paracrine manner to increase expression of UCP1 and other thermogenic genes in fat tissues. FGF21 regulates this process, at least in part, by enhancing adipose tissue PGC-1α protein levels independently of mRNA expression. We conclude that FGF21 acts to activate and expand the thermogenic machinery in vivo to provide a robust defense against hypothermia.
Structural basis of agrin–LRP4–MuSK signaling
Authors: Zong Yinong , Zhang Bin , Gu Shenyan , Lee Kwangkook , Zhou Jie , Yao Guorui , Figueiredo Dwight , Perry Kay , Mei Lin , Jin Rongsheng
Published: February 2012

Synapses are the fundamental units of neural circuits that enable complex behaviors. The neuromuscular junction (NMJ), a synapse formed between a motoneuron and a muscle fiber, has contributed greatly to understanding of the general principles of synaptogenesis as well as of neuromuscular disorders. NMJ formation requires neural agrin, a motoneuron-derived protein, which interacts with LRP4 (low-density lipoprotein receptor-related protein 4) to activate the receptor tyrosine kinase MuSK (muscle-specific kinase). However, little is known of how signals are transduced from agrin to MuSK. Here, we present the first crystal structure of an agrin–LRP4 complex, consisting of two agrin–LRP4 heterodimers. Formation of the initial binary complex requires the z8 loop that is specifically present in neuronal, but not muscle, agrin and that promotes the synergistic formation of the tetramer through two additional interfaces. We show that the tetrameric complex is essential for neuronal agrin-induced acetylcholine receptor (AChR) clustering. Collectively, these results provide new insight into the agrin–LRP4–MuSK signaling cascade and NMJ formation and represent a novel mechanism for activation of receptor tyrosine kinases.
Translating cancer ‘omics’ to improved outcomes: Figure 1.
Authors: Vucic Emily A. , Thu Kelsie L. , Robison Keith , Rybaczyk Leszek A. , Chari Raj , Alvarez Carlos E. , Lam Wan L.
Published: February 2012

The genomics era has yielded great advances in the understanding of cancer biology. At the same time, the immense complexity of the cancer genome has been revealed, as well as a striking heterogeneity at the whole-genome (or omics) level that exists between even histologically similar tumors. The vast accrual and public availability of multi-omics databases with associated clinical annotation including tumor histology, patient response, and outcome are a rich resource that has the potential to lead to rapid translation of high-throughput omics to improved overall survival. We focus on the unique advantages of a multidimensional approach to genomic analysis in this new high-throughput omics age and discuss the implications of the changing cancer demographic to translational omics research.
Using Cultured Mammalian Cells to Study Mitosis
Authors: Wadsworth Patricia
Published: February 2012

Diverse cell types have been used to study various aspects of mitosis. Early investigators focused primarily on cells that were suited to morphological studies. More recently, experimental systems have been developed to study both morphology and the molecular basis of chromosome motion and cell-cycle regulation. This article briefly reviews cell types that have been used to study mitosis in live cells. It then discusses cell lines that have been used to examine mitosis in cultured mammalian cells and summarizes the methods that are used to culture and study these cells.
Design and Construction of 2A Peptide-Linked Multicistronic Vectors
Authors: Szymczak-Workman Andrea L. , Vignali Kate M. , Vignali Dario A.A.
Published: February 2012

The need for reliable, multicistronic vectors for multigene delivery is at the forefront of biomedical technology. This article describes the design and construction of 2A peptide-linked multicistronic vectors, which can be used to express multiple proteins from a single open reading frame (ORF). The small 2A peptide sequences, when cloned between genes, allow for efficient, stoichiometric production of discrete protein products within a single vector through a novel “cleavage” event within the 2A peptide sequence. Expression of more than two genes using conventional approaches has several limitations, most notably imbalanced protein expression and large size. The use of 2A peptide sequences alleviates these concerns. They are small (18–22 amino acids) and have divergent amino-terminal sequences, which minimizes the chance for homologous recombination and allows for multiple, different 2A peptide sequences to be used within a single vector. Importantly, separation of genes placed between 2A peptide sequences is nearly 100%, which allows for stoichiometric and concordant expression of the genes, regardless of the order of placement within the vector.
Fiber-Optic Calcium Monitoring of Dendritic Activity In Vivo
Authors: Murayama Masanori , Larkum Matthew
Published: February 2012

Observing dendritic activity in active animals presents great challenges and there are currently not many options available. This protocol describes the fiber-optic-based “periscope” method for recording from populations of layer 5 (L5) neocortical pyramidal dendrites. This is an inexpensive, convenient, and robust method for recording dendritic activity during behavior. The limitations of this approach are discussed and tips are provided for how it might be adapted for different purposes and brain areas.
Genetic Crosses between Ectocarpus Strains: Figure 1.
Authors: Coelho Susana M. , Scornet Delphine , Rousvoal Sylvie , Peters Nick , Dartevelle Laurence , Peters Akira F. , Cock J. Mark
Published: February 2012

This article describes a procedure for conducting crosses between different strains of Ectocarpus. Crossing gametophytes to obtain the sporophyte generation is the most technically challenging stage of this process because diploid sporophytes have to be distinguished from the haploid partheno-sporophytes that result from the parthenogenetic germination of unfused gametes. This requires careful monitoring of the progeny of the genetic cross until they have developed sufficiently to be transferred to a separate Petri dish. Genetic crosses allow several classical genetic methodologies to be applied in Ectocarpus, including allelic complementation tests, backcrosses, combination of different genetic mutations, and outcrosses to create mapping populations.
Germ cells and fertilization differences among Japanese flounder Paralichthys olivaceus, summer flounder Paralichthys dentatus and their first and second generations
Authors: Sui J. , Ma D. Y. , Liu Q. H. , Xu S. H. , Xiao Z. Z. , Lin F. , Xiao Y. S. , Li J.
Published: February 2012

The morphology of gametes and the fertilization biology of Japanese flounder Paralichthys olivaceus (Po), summer flounder Paralichthys dentatus (Pd) and their hybrids were examined. Multiple generations (two hybrids: Po♀× Pd♂ (F1) and Pd♀× Po♂; two backcrosses: F1♀× Po♂ and F1♀× Pd♂) were obtained by artificial insemination. Comparison of egg ultrastructure among Po, Pd and F1 showed the morphology of micropyle region and the distribution density of pores were species specific. There were c. 100–200 accessory openings around the micropyle in Po, but not in Pd and F1. The zona radiata thickness and number of parallel bands were similar between F1 and Po, which were different from Pd. Comparison of spermatozoa ultrastructure revealed a close relationship between Po and Pd. Cytologically, the six crosses obeyed normal fertilization and cleavage processes, and only one male pronucleus was observed in a fertilized egg, indicating a monospermic fertilization pattern. Analysis of the time distribution from fertilization to first cleavage revealed an obvious delay at pronucleus fusion in the Pd × Po cross. The delay might indicate some cytoplasmic‐nuclear incompatibility during the process of fertilization.
Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing
Authors: STASSEN JOOST H. M. , SEIDL MICHAEL F. , VERGEER PIM W. J. , NIJMAN ISAÄC J. , SNEL BEREND , CUPPEN EDWIN , VAN DEN ACKERVEKEN GUIDO
Published: February 2012

Lettuce downy mildew (Bremia lactucae) is a rapidly adapting oomycete pathogen affecting commercial lettuce cultivation. Oomycetes are known to use a diverse arsenal of secreted proteins (effectors) to manipulate their hosts. Two classes of effector are known to be translocated by the host: the RXLRs and Crinklers. To gain insight into the repertoire of effectors used by B. lactucae to manipulate its host, we performed massively parallel sequencing of cDNA derived from B. lactucae spores and infected lettuce (Lactuca sativa) seedlings. From over 2.3 million 454 GS FLX reads, 59 618 contigs were assembled representing both plant and pathogen transcripts. Of these, 19 663 contigs were determined to be of B. lactucae origin as they matched pathogen genome sequences (SOLiD) that were obtained from >270 million reads of spore‐derived genomic DNA. After correction of cDNA sequencing errors with SOLiD data, translation into protein models and filtering, 16 372 protein models remained, 1023 of which were predicted to be secreted. This secretome included elicitins, necrosis and ethylene‐inducing peptide 1‐like proteins, glucanase inhibitors and lectins, and was enriched in cysteine‐rich proteins. Candidate host‐translocated effectors included 78 protein models with RXLR effector features. In addition, we found indications for an unknown number of Crinkler‐like sequences. Similarity clustering of secreted proteins revealed additional effector candidates. We provide a first look at the transcriptome of B. lactucae and its encoded effector arsenal.
Differential expression of forkhead box M1 and its downstream cyclin‐dependent kinase inhibitors p27kip1 and p21waf1/cip1 in the diagnosis of pulmonary neuroendocrine tumours
Authors: Ha Seung Yeon , Lee Chang Hun , Chang Hee Kyung , Chang Sunhee , Kwon Kun Young , Lee Eun Hee , Roh Mee Sook , Seo Boram
Published: February 2012

Ha S Y, Lee C H, Chang H K, Chang S, Kwon K Y, Lee E H, Roh M S & Seo B  (2012) Histopathology 60, 731–739 Differential expression of forkhead box M1 and its downstream cyclin‐dependent kinase inhibitors p27kip1 and p21waf1/cip1 in the diagnosis of pulmonary neuroendocrine tumours

Aims:  Pulmonary neuroendocrine (NE) tumours represent a spectrum of phenotypically distinct entities with different biological behaviours. Difficulties in classifying these tumours are frequently encountered in clinical practice. Forkhead box M1 (FoxM1) is essential for the development of various cancers and is a proliferation‐specific transcription factor that regulates transcription of cell cycle genes, including cyclin‐dependent kinase inhibitors p27kip1 and p21waf1/cip1. This study was performed to determine the utility of FoxM1, p27kip1 and p21waf1/cip1 as immunomarkers for subtyping pulmonary NE tumours.

Methods and results:  FoxM1, p27kip1 and p21waf1/cip1 expression was evaluated by immunohistochemistry in 60 pulmonary NE tumours [19 typical carcinoids (TCs), six atypical carcinoids (ACs), 17 large cell neuroendocrine carcinomas (LCNECs) and 18 small cell lung cancers (SCLCs)]. The frequencies of FoxM1 and p21waf1/cip1 expression were significantly different between TCs and ACs (each P = 0.009), and those of FoxM1 and p27kip1 expression were significantly different between LCNECs and SCLCs (P = 0.012 and P = 0.002, respectively). The combined FoxM1(−)/p21waf1/cip1(−) and FoxM1(+)/p27kip1(high) phenotypes had the best diagnostic accuracy for distinguishing TCs from ACs, and SCLCs from LCNECs, respectively.

Conclusions:  FoxM1, p27kip1 and p21waf1/cip1 showed distinct immunoreactivity according to histological subtype, which may be of value as an ancillary test in the differential diagnosis of pulmonary NE tumours.
Increased levels of deleted in malignant brain tumours 1 (DMBT1) in active bacteria‐related appendicitis
Authors: Kaemmerer Elke , Schneider Ursula , Klaus Christina , Plum Patrick , Reinartz Andrea , Adolf Maximilian , Renner Marcus , Wolfs Tim G A M , Kramer Boris W , Wagner Norbert , Mollenhauer Jan , Gassler Nikolaus
Published: February 2012

Kaemmerer E, Schneider U, Klaus C, Plum P, Reinartz A, Adolf M, Renner M, Wolfs T G A M, Kramer B W, Wagner N, Mollenhauer J & Gassler N  (2012) Histopathology 60, 561–569 Increased levels of deleted in malignant brain tumours 1 (DMBT1) in active bacteria‐related appendicitis

Aims:  Deleted in malignant brain tumours 1 (DMBT1; gp340) is a secreted glycoprotein which is found in the surface lining epithelia of human small and large intestine. DMBT1 is suggested to play a role in enterocyte differentiation and surface protection from intestinal bacteria. The aim of this study was to elucidate DMBT1 expression in bacteria‐related active intestinal inflammation such as appendicitis.

Methods and results:  mRNA and protein levels of DMBT1 were analysed in surgical resections of 50 appendices (active inflammation: n = 25). In non‐actively inflamed appendices, inter‐individual differences in basal DMBT1 levels of enterocytes and some non‐epithelial cells were found. In active appendicitis, enterocytic DMBT1 mRNA expression was increased approximately fivefold, which was paralleled by a corresponding increase of cytoplasmic and secreted DMBT1 protein levels. Increased DMBT1 expression was predominant in enterocytes adjacent to erosive lesions or ulcers.

Conclusions:  Our data demonstrate that bacteria‐related active inflammation results in a sharp increase of DMBT1 levels in enterocytes. These findings substantiate the view that DMBT1 is of functional relevance for host defence and modulation of the course of intestinal bacteria‐related inflammatory responses.