bluuebunny/crossref_metadata_2025 huggingface dataset:
Rupture prone aneurysm of the inferior mesenteric artery complicated by mid aortic syndrome with occluded celiac and superior mesenteric arteries
Authors: Werth  , Rodionov  , Hinterseher  , Beyer-Westendorf  , Stroszczynski  , Weiss  , Bergert
Published: January 2011

We present the case of a 45-year-old male patient with a large aneurysm of the inferior mesenteric artery complicated by mid aortic syndrome with occlusion of the celiac trunk and superior mesenteric artery. The vascular pathology was detected by CT imaging after presentation and hospitalization with symptoms of acute cholecystitis. After resolve of the acute symptoms, the aneurysm was resected and the proximal inferior mesenteric artery interponated with a reversed saphenous vein bypass graft. Besides presenting this case we review the literature concerning the rare descriptions of inferior mesenteric artery aneurysms.
The impact of buoyancy on front spreading in heterogeneous porous media in two‐phase immiscible flow
Authors: Bolster Diogo , Neuweiler Insa , Dentz Marco , Carrera Jesus
Published: February 2011

We study the influence of buoyancy and spatial heterogeneity on the spreading of the saturation front of a displacing fluid during injection into a porous medium saturated with another, immiscible fluid. To do so we use a stochastic modeling framework. We derive an effective large‐scale flow equation for the saturation of the displacing fluid that is characterized by six nonlocal flux terms, four that resemble dispersive type terms and two that have the appearance of advection terms. From the effective large‐scale flow equation we derive measures for the spreading of the saturation front. A series of full two‐phase numerical solutions are conducted to complement the analytical developments. We find that the interplay between density and heterogeneity leads to an enhancement of the front spreading on one hand and to a renormalization of the evolution of the mean front position compared with an equivalent homogeneous medium. The quantification of these phenomena plays an important role in several applications, including, for example, carbon sequestration and enhanced oil recovery.
Temperature dependence of a high-performance narrow-stripe (1 μm) single quantum-well transistor laser
Authors: Feng M. , Holonyak N. , James A.
Published: February 2011

Data are presented on the thermal behavior of a high performance 1 μm wide stripe quantum-well (QW) transistor laser in continuous-wave single-mode operation up to 40 °C, multimode to 55 °C. The electrical and optical outputs of the TL are found to be complementary across temperature, directly correlated with the spontaneous and stimulated radiative recombination process. The QW transistor laser operates on two states, lower and upper, at two characteristic temperatures, T0 (ITH=I0 exp(T/T0)). On the lower state transition, T00=40 K, and on the upper state, T01=70 K, the difference in performance and speed (bandwidth) connected directly to the different recombination lifetimes on each state and the confining barrier heights of the lower |0⟩ and upper state |1⟩.
Enhanced annealing of implantation-induced defects in 4H-SiC by thermal oxidation
Authors: Løvlie L. S. , Svensson B. G.
Published: February 2011

Annealing of the prominent Z1/2 defect in 4H-SiC has been studied after thermal treatment in N2 and O2 atmospheres at 1150 °C subsequent to implantation with MeV Si-ions to doses in the range of (1–4)×108 cm−2. The annealing rate is found to be significantly enhanced under oxidizing conditions, while in N2 atmosphere Z1/2 remains stable. Hence, a substantial lowering of the annealing temperature required for defect removal in 4H-SiC doped by ion-implantation may be expected using oxidizing annealing atmosphere. Concentration versus depth profiles of Z1/2 clearly show that it is annihilated by defect species injected from the SiO2/4H-SiC interface during oxidation. The injection rate of the in-diffusing species is found to be about (1.2±0.2)×106 cm−2 s−1, and the concentration ratio of the injected species relative to the native atoms originally present in the oxidized volume is ∼1×10−7. A model where the annihilating species are injected from the surface with a diffusion coefficient of about 10−8 cm2/s yields excellent agreement with the experimental data.
The high-transmission photonic crystal heterostructure Y-branch waveguide operating at photonic band region
Authors: Pei Ting-Hang , Huang Yang-Tung
Published: February 2011

We design a high-efficiency two-dimensional photonic crystal (PhC) Y-branch waveguide formed as a heterostructure with two different triangular PhCs composed of air holes. At photonic-band frequency regions corresponding to circular equifrequency surfaces, the two PhCs could be taken as effective homogeneous media with effective refractive indices. A triangular coupler composed of the PhC is designed at the input port in order to divide the incident beam into two parts. The two parts finally propagate into different channels. A case demonstrated here shows that the total transmission of light passing through the Y-branch waveguide is about 91.2%. The propagation phenomena can be explained by the mechanism of total internal reflection very well.
A method for temperature profile measurement of silicon wafers in high-temperature environments
Authors: Appapillai Anjuli T. , Sachs Emanuel M.
Published: February 2011

This paper describes the development of a method to characterize the temperature profile of silicon wafers in high-temperature environments. Monocrystalline wafers are implanted on one surface with B and P ions, which diffuse into the wafer at different rates based on the temperature-dependent diffusivity of the ions during a 30 min soak in the high-temperature environment between 1000 and 1400 °C. The use of two different dopant species, instead of one, yields higher sensitivity of the measured resistance to changes in temperature in this high-temperature range. The ρ-T relation is simulated using TSUPREM-4 and calibrated using a furnace of known temperature. The final sheet resistance varies spatially between 50 and 250 Ω/sq, and can be related to the temperature of each part of the wafer during the soak step, with a sensitivity of ∼0.5 Ω/°C, and a two-dimensional temperature map can be extracted. The method is demonstrated on wafers by characterizing the hot zone of a high-temperature furnace.
A single-electron transistor and an even-odd effect in chemically synthesized Ge nanowires
Authors: Huang Shaoyun , Shin Sung-Kwon , Fukata Naoki , Ishibashi Koji
Published: February 2011

Single-electron transistors have been fabricated with individual n-type monocrystalline germanium nanowires to realize an electron single-spin in a quantum dot. At low temperatures, well-pronounced Coulomb oscillations, with almost equidistant peak spacings and strongly varied peak amplitudes, were observed in a wide range of the back-gate voltage (Vg). The charge-stability diagram showed almost identical diamond-shaped dimensions and the charging energy turned out to be 110 μeV. In some Vg range, the two-electron periodicity in the addition energy was found, indicating the even-odd effect due to an alternate change of electron spin between 0 and 1/2. This work suggests the possible application to an electron-spin quantum-bit even with many electrons residing in the dot.
A multiscale model to evaluate the efficacy of anticancer therapies based on chimeric polypeptide nanoparticles
Authors: Paiva L. R. , Martins M. L.
Published: February 2011

A multiscale model for tumor growth and its chemotherapy using conjugate nanoparticles is presented, and the corresponding therapeutic outcomes are evaluated. It is found that doxorubicin assembled into chimeric polypeptide nanoparticles cannot eradicate either vascularized primary tumors or avascular micrometastasis even administrated at loads close to their maximum tolerated doses. Furthermore, an effective and safety treatment demands for conjugate nanoparticles targeted to the malignant cells with much higher specificity and affinity than those currently observed in order to leave most of the normal tissues unaffected and to ensure a fast intracellular drug accumulation.
Evolution of the surface morphology of rubrene under ambient conditions
Authors: Thompson R. J. , Yadin B. , Grout Z. J. , Hudziak S. , Kloc C. L. , Mitrofanov O. , Curson N. J.
Published: February 2011

Evolution of the surface morphology and local conductivity on cleaved surfaces of rubrene single crystals is characterized with atomic force microscopy. The cleaved surface was found to exhibit molecular reorganization that results in the formation of nanoscale beads aligned along molecular step edges and fingers, narrow molecular structures, one molecule high, and in excess of 1 μm long. The beads show insulating behavior and a band bending effect on the surface nearby. Their formation has a strong environmental dependence, which has implications for the operation of rubrene field-effect transistors in the ambient environment.
Modelling phloem transport within a pruned dwarf bean: a 2-source-3-sink system
Authors: Thorpe Michael R. , Lacointe André , Minchin Peter E. H.
Published: January 2011

A mechanistic model of carbon partitioning, based on the Münch hypothesis of phloem transport and implemented with PIAF-Münch modelling platform (Lacointe and Minchin 2008), was tested for an architecture more complex than any tested previously. Using 11C to label photosynthate, responses in transport of photosynthate within a heavily pruned dwarf bean plant (Phaseolus vulgaris L.) to changes in source and sink activities were compared with model predictions. The observed treatment responses were successfully predicted. However, the observations could not be completely explained if the modelled stem contained only one phloem pathway: tracer from a labelled leaf was always detected in both shoot apex and root, whichever of the two leaves was labelled. This shows that bidirectional flow occurred within the stem, with solute moving simultaneously in both directions. Nevertheless, a model architecture with very little more complexity could incorporate such bidirectional flow. We concluded that the model could explain the observations, and that the PIAF-Münch model platform can be expected to describe partitioning in even more complex architectures.
RNAi screen of the protein kinome identifies checkpoint kinase 1 (CHK1) as a therapeutic target in neuroblastoma
Authors: Cole Kristina A. , Huggins Jonathan , Laquaglia Michael , Hulderman Chase E. , Russell Mike R. , Bosse Kristopher , Diskin Sharon J. , Attiyeh Edward F. , Sennett Rachel , Norris Geoffrey , Laudenslager Marci , Wood Andrew C. , Mayes Patrick A. , Jagannathan Jayanti , Winter Cynthia , Mosse Yael P. , Maris John M.
Published: February 2011

Neuroblastoma is a childhood cancer that is often fatal despite intense multimodality therapy. In an effort to identify therapeutic targets for this disease, we performed a comprehensive loss-of-function screen of the protein kinome. Thirty kinases showed significant cellular cytotoxicity when depleted, with loss of the cell cycle checkpoint kinase 1 (CHK1/CHEK1) being the most potent. CHK1 mRNA expression was higher in
MYC–Neuroblastoma-related (MYCN)–
amplified (
P
< 0.0001) and high-risk (
P
= 0.03) tumors. Western blotting revealed that CHK1 was constitutively phosphorylated at the ataxia telangiectasia response kinase target site Ser345 and the autophosphorylation site Ser296 in neuroblastoma cell lines. This pattern was also seen in six of eight high-risk primary tumors but not in control nonneuroblastoma cell lines or in seven of eight low-risk primary tumors. Neuroblastoma cells were sensitive to the two CHK1 inhibitors SB21807 and TCS2312, with median IC
50
values of 564 nM and 548 nM, respectively. In contrast, the control lines had high micromolar IC
50
values, indicating a strong correlation between CHK1 phosphorylation and CHK1 inhibitor sensitivity (
P
= 0.0004). Furthermore, cell cycle analysis revealed that CHK1 inhibition in neuroblastoma cells caused apoptosis during S-phase, consistent with its role in replication fork progression. CHK1 inhibitor sensitivity correlated with total MYC(N) protein levels, and inducing MYCN in retinal pigmented epithelial cells resulted in CHK1 phosphorylation, which caused growth inhibition when inhibited. These data show the power of a functional RNAi screen to identify tractable therapeutical targets in neuroblastoma and support CHK1 inhibition strategies in this disease.
Slob, a Slowpoke channel–binding protein, modulates synaptic transmission
Authors: Ma Huifang , Zhang Jiaming , Levitan Irwin B.
Published: January 2011

Modulation of ion channels by regulatory proteins within the same macromolecular complex is a well-accepted concept, but the physiological consequences of such modulation are not fully understood. Slowpoke (Slo), a potassium channel critical for action potential repolarization and transmitter release, is regulated by Slo channel–binding protein (Slob), a Drosophila melanogaster Slo (dSlo) binding partner. Slob modulates the voltage dependence of dSlo channel activation in vitro and exerts similar effects on the dSlo channel in Drosophila central nervous system neurons in vivo. In addition, Slob modulates action potential duration in these neurons. Here, we investigate further the functional consequences of the modulation of the dSlo channel by Slob in vivo, by examining larval neuromuscular synaptic transmission in flies in which Slob levels have been altered. In Slob-null flies generated through P-element mutagenesis, as well as in Slob knockdown flies generated by RNA interference (RNAi), we find an enhancement of synaptic transmission but no change in the properties of the postsynaptic muscle cell. Using targeted transgenic rescue and targeted expression of Slob-RNAi, we find that Slob expression in neurons (but not in the postsynaptic muscle cell) is critical for its effects on synaptic transmission. Furthermore, inhibition of dSlo channel activity abolishes these effects of Slob. These results suggest that presynaptic Slob, by regulating dSlo channel function, participates in the modulation of synaptic transmission.
Voltage- and cold-dependent gating of single TRPM8 ion channels
Authors: Fernández José A. , Skryma Roman , Bidaux Gabriel , Magleby Karl L. , Scholfield C. Norman , McGeown J. Graham , Prevarskaya Natalia , Zholos Alexander V.
Published: January 2011

Transient receptor potential (TRP) channels play critical roles in cell signaling by coupling various environmental factors to changes in membrane potential that modulate calcium influx. TRP channels are typically activated in a polymodal manner, thus integrating multiple stimuli. Although much progress has been made, the underlying mechanisms of TRP channel activation are largely unknown. The TRPM8 cation channel has been extensively investigated as a major neuronal cold sensor but is also activated by voltage, calcium store depletion, and some lipids as well as by compounds that produce cooling sensations, such as menthol or icilin. Several models of TRPM8 activation have been proposed to explain the interaction between these diverse stimuli. However, a kinetic scheme is not yet available that can describe the detailed single-channel kinetics to gain further insight into the underlying gating mechanism. To work toward this goal, we investigated voltage-dependent single-channel gating in cell-attached patches at two different temperatures (20 and 30°C) using HEK293 cells stably expressing TRPM8. Both membrane depolarization and cooling increased channel open probability (Po) mainly by decreasing the duration of closed intervals, with a smaller increase in the duration of open intervals. Maximum likelihood analysis of dwell times at both temperatures indicated gating in a minimum of five closed and two open states, and global fitting over a wide range of voltages identified a seven-state model that described the voltage dependence of Po, the single-channel kinetics, and the response of whole-cell currents to voltage ramps and steps. The major action of depolarization and cooling was to accelerate forward transitions between the same two sets of adjacent closed states. The seven-state model provides a general mechanism to account for TRPM8 activation by membrane depolarization at two temperatures and can serve as a starting point for further investigations of multimodal TRP activation.
The long activations of α2 glycine channels can be described by a mechanism with reaction intermediates (“flip”)
Authors: Krashia Paraskevi , Lape Remigijus , Lodesani Francesco , Colquhoun David , Sivilotti Lucia G.
Published: January 2011

The α2 glycine receptor (GlyR) subunit, abundant in embryonic neurons, is replaced by α1 in the adult nervous system. The single-channel activity of homomeric α2 channels differs from that of α1-containing GlyRs, as even at the lowest glycine concentration (20 µM), openings occurred in long (>300-ms) groups with high open probability (Popen; 0.96; cell-attached recordings, HEK-expressed channels). Shut-time intervals within groups of openings were dominated by short shuttings of 5–10 µs. The lack of concentration dependence in the groups of openings suggests that they represent single activations, separated by very long shut times at low concentrations. Several putative mechanisms were fitted by maximizing the likelihood of the entire sequence of open and shut times, with exact missed-events allowance (program hjcfit). Records obtained at several glycine concentrations were fitted simultaneously. The adequacy of the different schemes was judged by the accuracy with which they predicted not only single-channel data but also the time course and concentration dependence of macroscopic responses elicited by rapid glycine applications to outside-out patches. The data were adequately described only with schemes incorporating a reaction intermediate in the activation, and the best was a flip mechanism with two binding sites and one open state. Fits with this mechanism showed that for α2 channels, the opening rate constant is very fast, ∼130,000 s−1, much as for α1β GlyRs (the receptor in mature synapses), but the estimated true mean open time is 20 times longer (around 3 ms). The efficacy for the flipping step and the binding affinity were lower for α2 than for α1β channels, but the overall efficacies were similar. As we previously showed for α1 homomeric receptors, in α2 glycine channels, maximum Popen is achieved when fewer than all five of the putative binding sites in the pentamer are occupied by glycine.
Fabrication of ultrathin epitaxial γ-Fe2O3 films by reactive sputtering
Authors: Li Peng , Jiang E Y , Bai H L
Published: February 2011

Ultrathin epitaxial γ-Fe2O3 (0 0 1) and (0 1 1) films are synthesized by reactive sputtering on corresponding MgO substrates. The average roughness of the epitaxial films increases with decreasing film thickness, and that of ∼5 nm thick films is ∼4.2 Å. The easy axis of the epitaxial γ-Fe2O3 films is verified to be ⟨1 1 1⟩ by angular dependence of hysteresis loops measured by a vibrating sample magnetometer with a sample rotator. The saturation magnetization of the ultrathin epitaxial γ-Fe2O3 films is close to the bulk value of ∼390 emu cm−3 and independent of film thickness when the thickness is above 5 nm, which is crucial for their practical applications in spin filter devices.
Controlling branching in streamer discharge by laser background ionization
Authors: Takahashi E , Kato S , Sasaki A , Kishimoto Y , Furutani H
Published: February 2011

Irradiation with a KrF laser controlled the positive streamer branching in atmospheric argon gas. This laser irradiation changed the amount of background ionization before the streamer discharge. Measuring the ionization current allowed us to evaluate the initial electron density formed by the KrF laser. We observed characteristic feather-like branching structure and found that it was only suppressed in the irradiated region. The threshold of ionization density which can influence the branching was evaluated to be 5 × 105 cm−3. The relationship between the size of avalanche head and mean distance between initial electrons explained this suppression behaviour. These experimental results support that the feather-like structure originates from the branching model of Loeb–Meek, a probabilistic merging of individual avalanches.
Design and fabrication of ultrathin and highly thermal-stable α-Ta/graded Ta(N)/TaN multilayer as diffusion barrier for Cu interconnects
Authors: Liu C H , Wang Y , Liu B , An Z , Song Z X , Xu K W
Published: February 2011

A one-step strategy of magnetron sputtering deposition with dynamic regulation of sputtering atmosphere was developed to prepare α-Ta/graded Ta(N)/TaN multilayer films on the Si substrate. The evolution of Ta clusters shows a significant effect on the crystal structure of the Ta film. The experimental results validate that the formation of α-Ta was attributed to the nucleation of larger Ta clusters. After being annealed at 600 °C, the α-Ta/graded Ta(N)/TaN multilayer film can still effectively block the diffusion of Cu. The mechanisms of the forming of the α-Ta and the thermal stability of the film stacks are characterized in detail.
Multiple zeros of nonlinear systems
Authors: Dayton Barry , Li Tien-Yien , Zeng Zhonggang
Published: February 2011

As an attempt to bridge between numerical analysis and algebraic geometry, this paper formulates the multiplicity for the general nonlinear system at an isolated zero, presents an algorithm for computing the multiplicity structure, proposes a depth-deflation method for accurate computation of multiple zeros, and introduces the basic algebraic theory of the multiplicity.

Furthermore, this paper elaborates and proves some fundamental properties of the multiplicity, including local finiteness, consistency, perturbation invariance, and depth-deflatability.

As a justification of this formulation, the multiplicity is proved to be consistent with the multiplicity defined in algebraic geometry for the special case of polynomial systems.

The proposed algorithms can accurately compute the multiplicity and the multiple zeros using floating point arithmetic even if the nonlinear system is perturbed.
FAK phosphorylation at Tyr-925 regulates cross-talk between focal adhesion turnover and cell protrusion
Authors: Deramaudt Therese B. , Dujardin Denis , Hamadi Abdelkader , Noulet Fanny , Kolli Kaouther , De Mey Jan , Takeda Kenneth , Rondé Philippe
Published: February 2011

Cell migration is a highly complex process that requires the coordinated formation of membrane protrusion and focal adhesions (FAs). Focal adhesion kinase (FAK), a major signaling component of FAs, is involved in the disassembly process of FAs through phosphorylation and dephosphorylation of its tyrosine residues, but the role of such phosphorylations in nascent FA formation and turnover near the cell front and in cell protrusion is less well understood. In the present study, we demonstrate that, depending on the phosphorylation status of Tyr-925 residue, FAK modulates cell migration via two specific mechanisms. FAK−/−mouse embryonic fibroblasts (MEFs) expressing nonphosphorylatable Y925F-FAK show increased interactions between FAK and unphosphorylated paxillin, which lead to FA stabilization and thus decreased FA turnover and reduced cell migration. Conversely, MEFs expressing phosphomimetic Y925E-FAK display unchanged FA disassembly rates, show increase in phosphorylated paxillin in FAs, and exhibit increased formation of nascent FAs at the cell leading edges. Moreover, Y925E-FAK cells present enhanced cell protrusion together with activation of the p130CAS/Dock180/Rac1 signaling pathway. Together, our results demonstrate that phosphorylation of FAK at Tyr-925 is required for FAK-mediated cell migration and cell protrusion.
Easyfig: a genome comparison visualizer
Authors: Sullivan Mitchell J. , Petty Nicola K. , Beatson Scott A.
Published: January 2011

Summary: Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures.

Availability: Easyfig is freely available (under a GPL license) for download (for Mac OS X, Unix and Microsoft Windows) from the SourceForge web site: http://easyfig.sourceforge.net/.

Contact:  s.beatson@uq.edu.au
Learning effect of a conditional cash transfer programme on poor rural women’s selection of delivery care in Mexico
Authors: Sosa-Rubí Sandra G , Walker Dilys , Serván Edson , Bautista-Arredondo Sergio
Published: January 2011

Background The Mexican programme Oportunidades/Progresa conditionally transfers money to beneficiary families. Over the past 10 years, poor rural women have been obliged to attend antenatal care (ANC) visits and reproductive health talks. We propose that the length of time in the programme influences women’s preferences, thus increasing their use not only of services directly linked to the cash transfers, but also of other services, such as clinic-based delivery, whose utilization is not obligatory.

Objective To analyse the long-term effect of Oportunidades on women’s use of antenatal and delivery care.

Methodology 5051 women aged between 15 and 49 years old with at least one child aged less than 24 months living in rural localities were analysed. Multilevel probit and logit models were used to analyse ANC visits and physician/nurse attended delivery, respectively. Models were adjusted with individual and socio-economic variables and the locality’s exposure time to Oportunidades.

Findings On average women living in localities with longer exposure to Oportunidades report 2.1% more ANC visits than women living in localities with less exposure. Young women aged 15–19 and 20–24 years and living in localities with longer exposure to Oportunidades (since 1998) have 88% and 41% greater likelihood of choosing a physician/nurse vs. traditional midwife for childbirth, respectively. Women of indigenous origin are 68.9% less likely to choose a physician/nurse for delivery care than non-indigenous women.

Conclusions An increase in the average number of ANC visits has been achieved among Oportunidades beneficiaries. An indirect effect is the increased selection of a physician/nurse for delivery care among young women living in localities with greater exposure time to Oportunidades. Disadvantaged women in Mexico (indigenous women) continue to have less access to skilled delivery care. Developing countries must develop strategies to increase access and use of skilled obstetric care for marginalized women.
Physicochemical, Textural, and Nutritional Characterization of Mexican Rice Cultivars
Authors: Chávez‐Murillo Carolina E. , Wang Ya‐Jane , Quintero‐Gutierrez Adrian G. , Bello‐Pérez Luis A.
Published: January 2011

The physicochemical properties, textural properties, and starch digestibility of rice cultivars grown in Mexico were evaluated. Variations existed in grain dimensions, and the rice grains were classified as medium, long, and extra long. Huimanguillo had the highest amylose content (30.4%), and A06, A92, A98, and Champoton presented the lowest amylose content (24.3–25.2%). The protein content was 7.1–11.0% and the lipid level was 0.47–1.22% among these Mexican cultivars. Champoton showed the highest temperature and enthalpy of gelatinization, and this with A98, Culiacan, and Huimanguillo had the highest enthalpy of retrogradation. Cotaxtla had the highest pasting peak, setback, and final viscosity. The texture assessment in cooked rice showed that A06 had the highest hardness, and A96 and A98 had the highest stickiness. There was little difference in the rapidly digestible starch, slowly digestible starch, and resistant starch content of tested Mexican rice cultivars. The differences in the physicochemical properties could be used to determine the end use of these Mexican rice cultivars.
Evaluation of a Dynamic Model for Primary Infections Caused by Plasmopara viticola on Grapevine in Quebec
Authors: Caffi Tito , Rossi Vittorio , Carisse Odile
Published: January 2011

Downy mildew is major grape disease in several areas of the world. Recently, a dynamic model for primary infections of grapes by Plasmopara viticola, forecasting time of primary lesions emergence, was developed in Italy. The model simulates the development of predicted oospore cohorts during the primary infection period. The efficacy of this disease-cycle-based model was evaluated in eastern Canada by comparing the time of lesion emergence predicted by the model with field observations in 20 and 23 vineyards in 2008 and 2009, respectively. For each vineyard, one to 20 simulation runs were performed depending on the number of oospore cohorts expected to form, for a total of 545 simulations. The model evaluation was based on the true positive proportion (lesion emergence was predicted and observed) and the true negative proportion (lesion emergence was not predicted and not observed) which were 0.996, and 0.907, respectively. A total of 313 simulations resulted in no infection among which 284 corresponded to no lesion emergence. In only one situation, lesions were observed and not predicted by the model. On the contrary, in 29 simulations run, lesion emergence was predicted but not observed in the field. Further validation of this model is required, but the results of this study are encouraging and this model may be used to improve timing of fungicide sprays against P. viticola.

Accepted for publication 17 November 2010. Published 26 January 2011.
A Strain of Japanese holly fern mottle virus Infecting Leatherleaf Fern in the United States
Authors: Valverde Rodrigo A. , Sabanadzovic Sead
Published: January 2011

Leatherleaf fern, a popular cut foliage plant for use in flower arrangements, was found showing virus-like symptoms at a local nursery in Baton Rouge, LA. The causal agent of the disease was determined to be a strain of Japanese holly fern mottle virus. The virus was identified by dsRNA, RT-PCR, and sequence analyses. The potential negative impact of this pathogen on leatherleaf fern production and its spread within the crop should be a concern for leatherleaf fern growers.

Accepted for publication 17 December 2010. Published 28 January 2011.
Exploring Soil Bacterial Communities in Different Peanut-Cropping Sequences Using Multiple Molecular Approaches
Authors: Sudini Hari , Liles Mark R. , Arias Covadonga R. , Bowen Kira L. , Huettel Robin N.
Published: January 2011

Soil bacterial communities have significant influence on soilborne plant pathogens and, thus, crop health. The present study focuses on ribotyping soil bacterial communities in different peanut-cropping sequences in Alabama. The objective was to identify changes in microbial assemblages in response to cropping sequences that can play a role in managing soilborne plant pathogens in peanut. Four peanut-cropping sequences were sampled at the Wiregrass Research Station, Headland, AL in 2006 and 2007, including continuous peanut, 4 years of bahiagrass followed by peanut, peanut-cotton, and peanut-corn-cotton. Soil sampling was done at early and mid-season and at harvest. Bacterial community structure was assessed using ribosomal intergenic spacer analysis (RISA) combined with 16S rRNA cloning and sequencing. RISA results indicated >70% dissimilarities among different cropping sequences. However, 90% similarities were noticed among replicated plots of the same cropping sequences. Cropping sequences and time of soil sampling had considerable effect on soil microbial community structure. Bahiagrass rotation with peanut was found to have the highest bacterial diversity, as indicated by a high Shannon Weaver Diversity index. Overall, higher bacterial diversity was observed with bahiagrass and corn rotations compared with continuous peanut. The bacterial divisions Proteobacteria, Acidobacteria, Firmicutes, Bacteroidetes, and Actinomycetes were the predominant bacterial phyla found in all peanut-cropping sequences. The Proteobacteria taxa in these soils were negatively correlated with the abundance of members of division Firmicutes but, conversely, had a significant positive correlation with Gemmatimonadetes taxa. The prevalence of the division Actinomycetes was negatively correlated with the relative abundance of members of division Verrucomicrobia. These results indicate complex interactions among soil bacteria that are important contributors to crop health.
Structure and formation of ant transportation networks
Authors: Latty Tanya , Ramsch Kai , Ito Kentaro , Nakagaki Toshiyuki , Sumpter David J. T. , Middendorf Martin , Beekman Madeleine
Published: February 2011

Many biological systems use extensive networks for the transport of resources and information. Ants are no exception. How do biological systems achieve efficient transportation networks in the absence of centralized control and without global knowledge of the environment? Here, we address this question by studying the formation and properties of inter-nest transportation networks in the Argentine ant (
Linepithema humile
). We find that the formation of inter-nest networks depends on the number of ants involved in the construction process. When the number of ants is sufficient and networks do form, they tend to have short total length but a low level of robustness. These networks are topologically similar to either minimum spanning trees or Steiner networks. The process of network formation involves an initial construction of multiple links followed by a pruning process that reduces the number of trails. Our study thus illuminates the conditions under and the process by which minimal biological transport networks can be constructed.
The Anthropocene and the international law of the sea
Authors: Vidas Davor
Published: January 2011

The current law of the sea provides a framework for various specific issues, but is incapable of responding adequately to the overall challenges facing humankind, now conceivably already living in the Anthropocene. The linkages between the development of the law of the sea and the current process towards formal recognition of an Anthropocene epoch are twofold. First, there is a linkage of origin. The ideological foundations of the law of the sea facilitated the emergence of forces that were to lead to the Industrial Revolution and, eventually, to levels of development entailing ever-greater human impacts on the Earth System. Second, there are linkages in interaction. Geological information has prompted key developments in the law of the sea since the introduction of the continental shelf concept in the mid-twentieth century. With the formalization of the Anthropocene epoch, geology might again act as a trigger for new developments needed in the law of the sea. This article explores those two aspects of linkages and examines prospects for further development of the law of the sea framework, through concepts such as the responsibility for the seas as well as those related to new approaches to global sustainability such as the ‘planetary boundaries’.
Sediment flux and the Anthropocene
Authors: Syvitski James P. M. , Kettner Albert
Published: January 2011

Data and computer simulations are reviewed to help better define the timing and magnitude of human influence on sediment flux—the Anthropocene epoch. Impacts on the Earth surface processes are not spatially or temporally homogeneous. Human influences on this sediment flux have a secondary effect on floodplain and delta-plain functions and sediment dispersal into the coastal ocean. Human impact on sediment production began 3000 years ago but accelerated more widely 1000 years ago. By the sixteenth century, societies were already engineering their environment. Early twentieth century mechanization has led to global signals of increased sediment flux in most large rivers. By the 1950s, this sediment disturbance signal reversed for many rivers owing to the proliferation of dams, and sediment load reduction below pristine conditions is the dominant signal today. A delta subsidence signal began in the 1930s and is now a dominant signal in terms of sea level for many coastal environments, overwhelming even the global warming imprint on sea level. Humans have engineered how most water and sediment are discharged into the coastal ocean. Hyperpycnal flow events have become more common for some rivers, and less common for other rivers. Bottom trawling is now widespread, suggesting that even continental shelves have received a significant but as yet quantified Anthropocene impact. The Anthropocene attains the level of a geological climate event, such as that seen in the transition between the Pleistocene and the Holocene.
Anthropogenic transformation of the terrestrial biosphere
Authors: Ellis Erle C.
Published: January 2011

Human populations and their use of land have transformed most of the terrestrial biosphere into anthropogenic biomes (anthromes), causing a variety of novel ecological patterns and processes to emerge. To assess whether human populations and their use of land have directly altered the terrestrial biosphere sufficiently to indicate that the Earth system has entered a new geological epoch, spatially explicit global estimates of human populations and their use of land were analysed across the Holocene for their potential to induce irreversible novel transformation of the terrestrial biosphere. Human alteration of the terrestrial biosphere has been significant for more than 8000 years. However, only in the past century has the majority of the terrestrial biosphere been transformed into intensively used anthromes with predominantly novel anthropogenic ecological processes. At present, even were human populations to decline substantially or use of land become far more efficient, the current global extent, duration, type and intensity of human transformation of ecosystems have already irreversibly altered the terrestrial biosphere at levels sufficient to leave an unambiguous geological record differing substantially from that of the Holocene or any prior epoch. It remains to be seen whether the anthropogenic biosphere will be sustained and continue to evolve.
Anthropocene streams and base-level controls from historic dams in the unglaciated mid-Atlantic region, USA
Authors: Merritts Dorothy , Walter Robert , Rahnis Michael , Hartranft Jeff , Cox Scott , Gellis Allen , Potter Noel , Hilgartner William , Langland Michael , Manion Lauren , Lippincott Caitlin , Siddiqui Sauleh , Rehman Zain , Scheid Chris , Kratz Laura , Shilling Andrea , Jenschke Matthew , Datin Katherine , Cranmer Elizabeth , Reed Austin , Matuszewski Derek , Voli Mark , Ohlson Erik , Neugebauer Ali , Ahamed Aakash , Neal Conor , Winter Allison , Becker Steven
Published: January 2011

Recently, widespread valley-bottom damming for water power was identified as a primary control on valley sedimentation in the mid-Atlantic US during the late seventeenth to early twentieth century. The timing of damming coincided with that of accelerated upland erosion during post-European settlement land-use change. In this paper, we examine the impact of local drops in base level on incision into historic reservoir sediment as thousands of ageing dams breach. Analysis of lidar and field data indicates that historic milldam building led to local base-level rises of 2–5 m (typical milldam height) and reduced valley slopes by half. Subsequent base-level fall with dam breaching led to an approximate doubling in slope, a significant base-level forcing. Case studies in forested, rural as well as agricultural and urban areas demonstrate that a breached dam can lead to stream incision, bank erosion and increased loads of suspended sediment, even with no change in land use. After dam breaching, key predictors of stream bank erosion include number of years since dam breach, proximity to a dam and dam height. One implication of this work is that conceptual models linking channel condition and sediment yield exclusively with modern upland land use are incomplete for valleys impacted by milldams. With no equivalent in the Holocene or late Pleistocene sedimentary record, modern incised stream-channel forms in the mid-Atlantic region represent a transient response to both base-level forcing and major changes in land use beginning centuries ago. Similar channel forms might also exist in other locales where historic milling was prevalent.
The Anthropocene: a new epoch of geological time?
Authors: Zalasiewicz Jan , Williams Mark , Haywood Alan , Ellis Michael
Published: January 2011

Anthropogenic changes to the Earth’s climate, land, oceans and biosphere are now so great and so rapid that the concept of a new geological epoch defined by the action of humans, the Anthropocene, is widely and seriously debated. Questions of the scale, magnitude and significance of this environmental change, particularly in the context of the Earth’s geological history, provide the basis for this Theme Issue. The Anthropocene, on current evidence, seems to show global change consistent with the suggestion that an epoch-scale boundary has been crossed within the last two centuries.
Underwater linear polarization: physical limitations to biological functions
Authors: Shashar Nadav , Johnsen Sönke , Lerner Amit , Sabbah Shai , Chiao Chuan-Chin , Mäthger Lydia M. , Hanlon Roger T.
Published: January 2011

Polarization sensitivity is documented in a range of marine animals. The variety of tasks for which animals can use this sensitivity, and the range over which they do so, are confined by the visual systems of these animals and by the propagation of the polarization information in the aquatic environment. We examine the environmental physical constraints in an attempt to reveal the depth, range and other limitations to the use of polarization sensitivity by marine animals. In clear oceanic waters, navigation that is based on the polarization pattern of the sky appears to be limited to shallow waters, while solar-based navigation is possible down to 200–400 m. When combined with intensity difference, polarization sensitivity allows an increase in target detection range by 70–80% with an upper limit of 15 m for large-eyed animals. This distance will be significantly smaller for small animals, such as plankton, and in turbid waters. Polarization-contrast detection, which is relevant to object detection and communication, is strongly affected by water conditions and in clear waters its range limit may reach 15 m as well. We show that polarization sensitivity may also serve for target distance estimation, when examining point source bioluminescent objects in the photic mesopelagic depth range.
Behavioural and physiological mechanisms of polarized light sensitivity in birds
Authors: Muheim Rachel
Published: January 2011

Polarized light (PL) sensitivity is relatively well studied in a large number of invertebrates and some fish species, but in most other vertebrate classes, including birds, the behavioural and physiological mechanism of PL sensitivity remains one of the big mysteries in sensory biology. Many organisms use the skylight polarization pattern as part of a sun compass for orientation, navigation and in spatial orientation tasks. In birds, the available evidence for an involvement of the skylight polarization pattern in sun-compass orientation is very weak. Instead, cue-conflict and cue-calibration experiments have shown that the skylight polarization pattern near the horizon at sunrise and sunset provides birds with a seasonally and latitudinally independent compass calibration reference. Despite convincing evidence that birds use PL cues for orientation, direct experimental evidence for PL sensitivity is still lacking. Avian double cones have been proposed as putative PL receptors, but detailed anatomical and physiological evidence will be needed to conclusively describe the avian PL receptor. Intriguing parallels between the functional and physiological properties of PL reception and light-dependent magnetoreception could point to a common receptor system.
Central neural coding of sky polarization in insects
Authors: Homberg Uwe , Heinze Stanley , Pfeiffer Keram , Kinoshita Michiyo , el Jundi Basil
Published: January 2011

Many animals rely on a sun compass for spatial orientation and long-range navigation. In addition to the Sun, insects also exploit the polarization pattern and chromatic gradient of the sky for estimating navigational directions. Analysis of polarization–vision pathways in locusts and crickets has shed first light on brain areas involved in sky compass orientation. Detection of sky polarization relies on specialized photoreceptor cells in a small dorsal rim area of the compound eye. Brain areas involved in polarization processing include parts of the lamina, medulla and lobula of the optic lobe and, in the central brain, the anterior optic tubercle, the lateral accessory lobe and the central complex. In the optic lobe, polarization sensitivity and contrast are enhanced through convergence and opponency. In the anterior optic tubercle, polarized-light signals are integrated with information on the chromatic contrast of the sky. Tubercle neurons combine responses to the UV/green contrast and e-vector orientation of the sky and compensate for diurnal changes of the celestial polarization pattern associated with changes in solar elevation. In the central complex, a topographic representation of e-vector tunings underlies the columnar organization and suggests that this brain area serves as an internal compass coding for spatial directions.
Behavioural relevance of polarization sensitivity as a target detection mechanism in cephalopods and fishes
Authors: Pignatelli Vincenzo , Temple Shelby E. , Chiou Tsyr-Huei , Roberts Nicholas W. , Collin Shaun P. , Marshall N. Justin
Published: January 2011

Aquatic habitats are rich in polarized patterns that could provide valuable information about the environment to an animal with a visual system sensitive to polarization of light. Both cephalopods and fishes have been shown to behaviourally respond to polarized light cues, suggesting that polarization sensitivity (PS) may play a role in improving target detection and/or navigation/orientation. However, while there is general agreement concerning the presence of PS in cephalopods and some fish species, its functional significance remains uncertain. Testing the role of PS in predator or prey detection seems an excellent paradigm with which to study the contribution of PS to the sensory assets of both groups, because such behaviours are critical to survival. We developed a novel experimental set-up to deliver computer-generated, controllable, polarized stimuli to free-swimming cephalopods and fishes with which we tested the behavioural relevance of PS using stimuli that evoke innate responses (such as an escape response from a looming stimulus and a pursuing behaviour of a small prey-like stimulus). We report consistent responses of cephalopods to looming stimuli presented in polarization and luminance contrast; however, none of the fishes tested responded to either the looming or the prey-like stimuli when presented in polarization contrast.