bluuebunny/crossref_metadata_2025 huggingface dataset:
Screening of resonant magnetic perturbations taking into account a self-consistent electric field
Authors: Kaveeva E. , Rozhansky V.
Published: May 2012

Steady-state screening of resonant magnetic perturbations (RMPs) in a tokamak is analysed taking into account a self-consistent electric field. On the one hand, the self-consistent radial electric field is determined by the balance of the electron radial conductivity in a stochastic magnetic field screened by the plasma and by the neoclassical ion conductivity. On the other hand, the parallel current of electrons, the radial projection of which is balanced by the ion current, determines the screening of RMPs. In this work, the self-consistent electric field and RMP screening are calculated. Two different regimes of screening are found: the ‘ion’ branch which corresponds to the negative radial electric field and the ‘electron’ branch for which the electric field is positive. Predictions of the model are compared with the experimental data and results of the simulation with various codes. The corresponding toroidal rotation and pump-out effect are discussed.
Edge topology and flows in the reversed-field pinch
Authors: Spizzo G. , Agostini M. , Scarin P. , Vianello N. , White R. B. , Cappello S. , Puiatti M. E. , Valisa M.
Published: May 2012

Edge topology and plasma flow deeply influence transport in the reversed-field pinch as well as in all fusion devices, playing an important role in many practical aspects of plasma performance, such as access to enhanced confinement regimes, the impact on global power balance and operative limits, such as the density limit (Spizzo G. et al 2010 Plasma Phys. Control. Fusion
52 095011).

A central role is played by the edge electric field, which is determined by the ambipolar constraint guaranteeing quasi-neutrality in a sheath next to the plasma wall. Its radial component is experimentally determined in RFX over the whole toroidal angle by means of a diagnostic set measuring edge plasma potential and flow with different techniques (Scarin P. et al 2011 Nucl. Fusion
51 073002). The measured radial electric field is used to construct the potential in the form Φ(ψp, θ, ζ) (ψp radial coordinate, θ, ζ angles), by means of the Hamiltonian guiding-centre code ORBIT. Simulations show that a proper functional form of the potential can balance the differential radial diffusion of electrons and ions subject to m = 0 magnetic island O- and X-points. Electrons spend more time in the X-points of such islands than in O-points; ions have comparatively larger drifts and their radial motion is more uniform over the toroidal angle. The final spatial distribution of Φ(ψp, θ, ζ) results in a complex 3D pattern, with convective cells next to the wall. Generally speaking, an edge topology dominating parallel transport with a given symmetry brings about an edge potential with the same symmetry. This fact helps us to build a first step of a unified picture of the effect of magnetic topology on the Greenwald limit, and, more generally, on flows in the edge of RFPs and tokamaks.
Magnetic barriers and their q95 dependence at DIII-D
Authors: Volpe F.A. , Kessler J. , Ali H. , Evans T.E. , Punjabi A.
Published: May 2012

It is well known that externally generated resonant magnetic perturbations (RMPs) can form islands in the plasma edge. In turn, large overlapping islands generate stochastic fields, which are believed to play a role in the avoidance and suppression of edge localized modes (ELMs) at DIII-D. However, large coalescing islands can also generate, in the middle of these stochastic regions, KAM surfaces effectively acting as ‘barriers’ against field-line dispersion and, indirectly, particle diffusion. It was predicted in Ali and Punjabi (2007 Plasma Phys. Control. Fusion
49 1565–82) that such magnetic barriers can form in piecewise analytic DIII-D plasma equilibria. In this work, the formation of magnetic barriers at DIII-D is corroborated by field-line tracing calculations using experimentally constrained EFIT (Lao et al 1985 Nucl. Fusion
25 1611) DIII-D equilibria perturbed to include the vacuum field from the internal coils utilized in the experiments. According to these calculations, the occurrence and location of magnetic barriers depend on the edge safety factor q
95. It was thus suggested that magnetic barriers might contribute to narrowing the edge stochastic layer and play an indirect role in the RMPs failing to control ELMs for certain values of q
95. The analysis of DIII-D discharges where q
95 was varied, however, does not show anti-correlation between barrier formation and ELM suppression.
OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing
Authors: Das Shreepriya , Vikalo Haris
Published: May 2012

Motivation: Next-generation DNA sequencing platforms are becoming increasingly cost-effective and capable of providing enormous number of reads in a relatively short time. However, their accuracy and read lengths are still lagging behind those of conventional Sanger sequencing method. Performance of next-generation sequencing platforms is fundamentally limited by various imperfections in the sequencing-by-synthesis and signal acquisition processes. This drives the search for accurate, scalable and computationally tractable base calling algorithms capable of accounting for such imperfections.

Results: Relying on a statistical model of the sequencing-by-synthesis process and signal acquisition procedure, we develop a computationally efficient base calling method for Illumina's sequencing technology (specifically, Genome Analyzer II platform). Parameters of the model are estimated via a fast unsupervised online learning scheme, which uses the generalized expectation–maximization algorithm and requires only 3 s of running time per tile (on an Intel i7 machine @3.07GHz, single core)—a three orders of magnitude speed-up over existing parametric model-based methods. To minimize the latency between the end of the sequencing run and the generation of the base calling reports, we develop a fast online scalable decoding algorithm, which requires only 9 s/tile and achieves significantly lower error rates than the Illumina's base calling software. Moreover, it is demonstrated that the proposed online parameter estimation scheme efficiently computes tile-dependent parameters, which can thereafter be provided to the base calling algorithm, resulting in significant improvements over previously developed base calling methods for the considered platform in terms of performance, time/complexity and latency.

Availability: A C code implementation of our algorithm can be downloaded from http://www.cerc.utexas.edu/OnlineCall/

Contact:  hvikalo@ece.utexas.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Exploring single-sample SNP and INDEL calling with whole-genomede novoassembly
Authors: Li Heng
Published: May 2012

Motivation: Eugene Myers in his string graph paper suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a graph, provided that it can be constructed correctly, is in fact a lossless representation of reads. In principle, every analysis based on whole-genome shotgun sequencing (WGS) data, such as SNP and insertion/deletion (INDEL) calling, can also be achieved with unitigs.

Results: To explore the feasibility of using de novo assembly in the context of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads into unitigs while preserving most of information of the input reads. SNPs and INDELs can be called by mapping the unitigs against a reference genome. By applying the method on 35-fold human resequencing data, we showed that in comparison to the standard pipeline, our approach yields similar accuracy for SNP calling and better results for INDEL calling. It has higher sensitivity than other de novo assembly based methods for variant calling. Our work suggests that variant calling with de novo assembly can be a beneficial complement to the standard variant calling pipeline for whole-genome resequencing. In the methodological aspects, we propose FMD-index for forward–backward extension of DNA sequences, a fast algorithm for finding all super-maximal exact matches and one-pass construction of unitigs from an FMD-index.

Availability:  http://github.com/lh3/fermi

Contact:  hengli@broadinstitute.org
Role of Nitrogen-Metabolism Genes Expressed During Pathogenicity of the Alkalinizing Colletotrichum gloeosporioides and Their Differential Expression in Acidifying Pathogens
Authors: Miyara I. , Shnaiderman C. , Meng X. , Vargas W. A. , Diaz-Minguez J. M. , Sherman A. , Thon M. , Prusky D.
Published: May 2012

Pathogens can actively alter fruit pH around the infection site, signaling modulation of pathogenicity-factor expression, as found for alkalinizing (Colletotrichum and Alternaria spp.) and acidifying (Penicillium, Botrytis, and Sclerotinia spp.) fungi. The nitrogen-metabolism genes GDH2, GS1, GLT, and MEP genes are differentially expressed during colonization by Colletotrichum gloeosporioides, and a Δgdh2 strain reduces ammonia accumulation and pathogenicity. We analyzed the contribution of transporters GLT and MEPB to C. gloeosporiodes pathogenicity. Germinating spores of Δglt strains showed reduced appressorium formation; those of ΔmepB mutants showed rapid ammonia uptake and accumulation inside the hyphae, indicating deregulated uptake. Both mutants reduced pathogenicity, indicating that these transporters function during alkalinizing species pathogenicity. We compared the expressions of these genes in C. gloeosporioides and Sclerotinia sclerotiorum, and found five to 10-fold higher expression at the transcript level in the former. Interestingly, GLT and MEPB in the alkalinizing species showed no and very low sequence identity, respectively, with their counterparts in the acidifying species. Knockout analysis of GLT and MEPB and their differential transcript regulation in the alkalinizing and acidifying species suggest that the ammonia accumulation contributing to pathogenicity in the former is modulated by factors at the gene-regulation levels that are lacking in the acidifying species.
First Report of Iris yellow spot virus Infecting Onion in Pennsylvania
Authors: Hoepting C. A. , Fuchs M. F.
Published: May 2012

Iris yellow spot virus (IYSV; genus Tospovirus; family Bunyaviridae) is an economically important pathogen of onion. It is vectored by onion thrips (Thrips tabaci Lindeman) and causes widespread disease of onion in all major onion growing states in the western United States (1). In the eastern United States, IYSV was first reported in Georgia in 2004 (4) and then in New York in 2006 (2). In mid-July of 2010, symptomatic onion (Allium cepa) plants (cv. Candy) were found in New Holland, Pennsylvania, in Lancaster County on a small, diversified commercial farm (40.06°N, 76.06°W). Bleached, elongated lesions with tapered ends occurred on middle-aged leaves on approximately 30% of the 13,760 plants in an area approximately one tenth of an acre. Leaf tissue from five symptomatic plants tested positive for IYSV in a double-antibody sandwich (DAS)-ELISA with IYSV-specific serological reagents from Agdia Inc. (Elkhart, IN). A reverse transcription (RT)-PCR assay was used to verify the presence of IYSV in a subset of symptomatic leaf samples that reacted to IYSV antibodies in DAS-ELISA. Primers specific to the nucleocapsid (N) gene of IYSV (5′-ACTCACCAATGTCTTCAAC-3′ and 5′-GGCTTCCTCTGGTAAGTGC-3′) were used to characterize a 402-bp fragment (3). The resulting amplicons were ligated in TOPO TA cloning vector (Invitrogen, Carlsbad, CA) and two clones of each isolate were sequenced in both directions. Sequence analysis showed a consensus sequence for the partial N gene of the five IYSV isolates from Pennsylvania (GenBank Accession No. JQ952568) and an 87 to 100% nucleotide sequence identity with other IYSV N gene sequences that are available in GenBank. The highest nucleotide sequence identity (100%) was with an IYSV isolate from Texas (GenBank Accession No. DQ658242) and the lowest was with an isolate from India (GenBank Accession No. EU310291). To our knowledge, this is the first report of IYSV infection of onion in Pennsylvania. This finding confirms further spread of the virus within North America. Further study is warranted to determine the impact of IYSV on the Pennsylvania onion industry and to determine viable management strategies, if necessary.

References: (1) D. H. Gent et al. Plant Dis. 88:446, 2004 (2) C. A. Hoepting et al. Plant Dis. 91:327, 2007 (3) C. L. Hsu et al. Plant Dis. 95:735-743. (4) S. W. Mullis et al. Plant Dis. 88: 1285, 2004.
First Report of Elm Yellows Subgroup 16SrV-B Phytoplasma Infecting Chinese Tulip Tree in China
Authors: Li Z. Y. , Dong Z. P. , Hao Z. M. , Dong J. G.
Published: May 2012

Chinese tulip tree (Liriodendron chinensis) is native to China and is planted all around the country as an ornamental tree. In July of 2011, some Chinese tulip trees with typical phytoplasma symptoms were found in Baoding City, Hebei Province, China. Symptoms included yellowing of leaves, slow decline, little leaves, and death of entire plants. To confirm phytoplasma infection of these plants, total DNA was extracted from 100 mg of fresh leaf midribs collected from leaves of nine symptomatic and eight asymptomatic plants with a plant DNA extract kit (Tiangen, Beijing, China) according to the manufacturer's protocols. Using 16S rRNA phytoplasma universal primer pairs P1/P7 followed by R16F2n/R16R2, a nest PCR was carried out (1,2). The results showed that the phytoplasma was only detected in symptomatic samples by nested PCR, while the asymptomatic were negative. An approximate 1.2-kb specific fragment was obtained from the DNA of nine symptomatic plants, but no product was amplified from the leaves of eight healthy ones. The amplified products were cloned and sequenced. The sequence was deposited in GenBank Data Libraries under Accession No. JQ585925 and shared the highest homology of 99% with Puna chicory flat stem phytoplasma (GenBank Accession No. JN582266), Apricot leaf roll phytoplasma (GenBank Accession No. FJ572660), Jujube witches'-broom phytoplasma (GenBank Accession No. AY197661), and other elm yellows group phytoplasmas by BLAST analysis with that of other phytoplasmas from GenBank. Meanwhile, the sequence data was analyzed by iPhyClassifier software and the result showed that the 16S rDNA F2nR2 fragment was identical (similarity coefficient 1.00) to the reference patterns of 16Sr group V, subgroup B (GenBank Accession No.AB052876) (3). Combining the BLAST analysis in GenBank and the analysis of iPhyClassifier, we classified the phytoplasma causing Chinese tulip tree yellow leaves disease into subgroup 16SrV-B. To our knowledge, this is the first report of the 16SrVB group phytoplasmas infecting Chinese tulip tree in China.

References: (1) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (2) I. M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004. (3) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
Molecular Variation of Sporisorium scitamineum in Mainland China Revealed by RAPD and SRAP Markers
Authors: Que Y. , Xu L. , Lin J. , Chen R. , Grisham M. P.
Published: May 2012

Sugarcane smut caused by Sporisorium scitamineum occurs worldwide, causing serious losses in sugar yield and quality. To study the molecular variation of S. scitamineum, 23 S. scitamineum isolates collected from the six primary sugarcane production areas in mainland China (Guangxi, Yunnan, Guangdong, Hainan, Fujian, and Jiangxi provinces) were assessed by random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) markers. The results of RAPD, SRAP, and RAPD-SRAP combined analysis showed that, whereas the molecular variation of S. scitamineum was associated with geographic origin, there was no evidence of co-evolution between sugarcane and the pathogen. The results of RAPD, SRAP, or RAPD-SRAP combined analysis also did not provide any information about race differentiation of S. scitamineum. This suggests that the mixture of spores from sori collected from different areas should be used in artificial inoculations for resistance breeding and selection.
A Systems Approach for Management of Pests and Pathogens of Nursery Crops
Authors: Parke Jennifer L. , Grünwald Niklaus J.
Published: May 2012

Horticultural nurseries are heterogeneous and spatially complex agricultural systems, which present formidable challenges to management of diseases and pests. Moreover, nursery plants shipped interstate and internationally can serve as important vectors for pathogens and pests that threaten both agriculture and forestry. Current regulatory strategies to prevent this movement of pathogens and pests with nursery plants are based on visual inspections of plants just before shipping, a process that is costly and inadequate. Here we propose the application of a systems approach for horticultural nurseries modeled after the Hazard Analysis of Critical Control Points (HACCP) approach widely used in the food processing industry. We evaluated aspects of the systems approach to analyze contamination hazards by Phytophthora species and then implemented management practices targeting specific critical control points. The systems approach for analyzing and correcting unsafe practices offers a potential alternative strategy for preventing plant contamination that could be broadly applied to many pests and pathogens. One of the hallmarks of this approach is its flexibility, including the ability to improve and adapt the approaches as new technologies are developed or improved and to provide the grower with management options.
Characterization of Alternaria alternata Causing Black Spot Disease of Pomegranate in Israel Using a Molecular Marker
Authors: Gat Tami , Liarzi Orna , Skovorodnikova Yulia , Ezra David
Published: May 2012

Black spot disease of pomegranate is a relatively new disease in Israel that is caused by Alternaria alternata. The symptoms include black spots on leaves and fruit. Only the outer part of the fruit is damaged; the edible tissue remains unaffected. In this study, we obtained 50 isolates of A. alternata from infected pomegranate plants that were classified based on pathogenicity tests using detached leaves. Using an arbitrarily primed polymerase chain reaction, we identified one primer (primer CAG) that reacted only with DNA of isolates that induced the most severe disease symptoms. Based on the sequence of the amplified fragment, we generated a specific primer (primer C) that recognizes these highly virulent isolates. Therefore, we suggest that primer C can be utilized as a molecular marker for the detection of A. alternata isolates that cause black spot disease of pomegranate.
Compartment-Specific Antioxidative Defense in Arabidopsis Against Virulent and Avirulent Pseudomonas syringae
Authors: Großkinsky Dominik K. , Koffler Barbara E. , Roitsch Thomas , Maier Romana , Zechmann Bernd
Published: May 2012

The accumulation of reactive oxygen species (ROS) during biotic stress is either part of a hypersensitive response of the plant or induced directly by the pathogen. Antioxidants such as ascorbate and glutathione counteract the accumulation of ROS and are part of the defense reaction. The aim of the present study was to investigate the compartment-specific importance of ascorbate and glutathione during a virulent and avirulent Pseudomonas syringae infection in Arabidopsis thaliana. Peroxisomes were found to be the hotspot for glutathione accumulation reaching 452% and 258% of control levels 24 h postinoculation during the virulent and avirulent infection, respectively. An accumulation of ascorbate could also be observed in vacuoles during Pseudomonas syringae infection, whereas glutathione remained absent in this cell compartment. Neither glutathione nor ascorbate accumulated in the apoplast during pathogen infection demonstrating an only negligible role of these antioxidants in the apoplast during pathogen infection. Compartment-specific changes followed a recently proposed stress model with an increase of ascorbate and glutathione in most cell compartments at the early stages of infection and a strong drop at the later stage of infection when a strong accumulation of ROS and symptoms occurred in the leaves. This study highlights the importance of certain cell compartments and antioxidants in general for the protection of pathogen-induced ROS accumulation.
Increased oceanic microplastic debris enhances oviposition in an endemic pelagic insect
Authors: Goldstein Miriam C. , Rosenberg Marci , Cheng Lanna
Published: May 2012

Plastic pollution in the form of small particles (diameter less than 5 mm)—termed ‘microplastic’—has been observed in many parts of the world ocean. They are known to interact with biota on the individual level, e.g. through ingestion, but their population-level impacts are largely unknown. One potential mechanism for microplastic-induced alteration of pelagic ecosystems is through the introduction of hard-substrate habitat to ecosystems where it is naturally rare. Here, we show that microplastic concentrations in the North Pacific Subtropical Gyre (NPSG) have increased by two orders of magnitude in the past four decades, and that this increase has released the pelagic insect
Halobates sericeus
from substrate limitation for oviposition. High concentrations of microplastic in the NPSG resulted in a positive correlation between
H. sericeus
and microplastic, and an overall increase in
H. sericeus
egg densities. Predation on
H. sericeus
eggs and recent hatchlings may facilitate the transfer of energy between pelagic- and substrate-associated assemblages. The dynamics of hard-substrate-associated organisms may be important to understanding the ecological impacts of oceanic microplastic pollution.
The benefits of maternal effects in novel and in stable environments
Authors: Hoyle Rebecca B. , Ezard Thomas H. G.
Published: May 2012

Natural selection favours phenotypes that match prevailing ecological conditions. A rapid process of adaptation is therefore required in changing environments. Maternal effects can facilitate such responses, but it is currently poorly understood under which circumstances maternal effects may accelerate or slow down the rate of phenotypic evolution. Here, we use a quantitative genetic model, including phenotypic plasticity and maternal effects, to suggest that the relationship between fitness and phenotypic variance plays an important role. Intuitive expectations that positive maternal effects are beneficial are supported following an extreme environmental shift, but, if too strong, that shift can also generate oscillatory dynamics that overshoot the optimal phenotype. In a stable environment, negative maternal effects that slow phenotypic evolution actually minimize variance around the optimum phenotype and thus maximize population mean fitness.
Airflow elicits a spider's jump towards airborne prey. I. Airflow around a flying blowfly
Authors: Klopsch Christian , Kuhlmann Hendrik C. , Barth Friedrich G.
Published: May 2012

The hunting spiderCupiennius saleiuses airflow generated by flying insects for the guidance of its prey-capture jump. We investigated the velocity field of the airflow generated by a freely flying blowfly close to the flow sensors on the spider's legs. It shows three characteristic phases (I–III). (I) When approaching, the blowfly induces an airflow signal near the spider with only little fluctuation (0.013 ± 0.006 m s−1) and a strength that increases nearly exponentially with time (maximum: 0.164 ± 0.051 m s−1s.d.). The spider detects this flow while the fly is still 38.4 ± 5.6 mm away. The fluctuation of the airflow above the sensors increases linearly up to 0.037 m s−1with the fly's altitude. Differences in the time of arrival and intensity of the fly signal at different legs probably inform the spider about the direction to the prey. (II) Phase II abruptly follows phase I with a much higher degree of fluctuation (fluctuation amplitudes: 0.114 ± 0.050 m s−1). It starts when the fly is directly above the sensor and corresponds to the time-dependent flow in the wake below and behind the fly. Its onset indicates to the spider that its prey is now within reach and triggers its jump. The spider derives information on the fly's position from the airflow characteristics, enabling it to properly time its jump. The horizontal velocity of the approaching fly is reflected by the time of arrival differences (ranging from 0.038 to 0.108 s) of the flow at different legs and the exponential velocity growth rate (16–79 s−1) during phase I. (III) The air flow velocity decays again after the fly has passed the spider.
Design of gecko-inspired fibrillar surfaces with strong attachment and easy-removal properties: a numerical analysis of peel-zone
Authors: Zhou Ming , Pesika Noshir , Zeng Hongbo , Wan Jin , Zhang Xiangjun , Meng Yonggang , Wen Shizhu , Tian Yu
Published: May 2012

Despite successful fabrication of gecko-inspired fibrillar surfaces with strong adhesion forces, how to achieve an easy-removal property becomes a major concern that may restrict the wide applications of these bio-inspired surfaces. Research on how geckos detach rapidly has inspired the design of novel adhesive surfaces with strong and reversible adhesion capabilities, which relies on further fundamental understanding of the peeling mechanisms. Recent studies showed that the peel-zone plays an important role in the peeling off of adhesive tapes or fibrillar surfaces. In this study, a numerical method was developed to evaluate peel-zone deformation and the resulting mechanical behaviour due to the deformations of fibrillar surfaces detaching from a smooth rigid substrate. The effect of the geometrical parameters of pillars and the stiffness of backing layer on the peel-zone and peel strength, and the strong attachment and easy-removal properties have been analysed to establish a design map for bio-inspired fibrillar surfaces, which shows that the optimized strong attachment and easy-removal properties can vary by over three orders of magnitude. The adhesion and peeling design map established provides new insights into the design and development of novel gecko-inspired fibrillar surfaces.
Karhunen–Loeve representation of stochastic ocean waves
Authors: Sclavounos Paul D.
Published: May 2012

A new stochastic representation of a seastate is developed based on the Karhunen–Loeve spectral decomposition of stochastic signals and the use of Slepian prolate spheroidal wave functions with a tunable bandwidth parameter. The new representation allows the description of stochastic ocean waves in terms of a few independent sources of uncertainty when the traditional representation of a seastate in terms of Fourier series requires an order of magnitude more independent components. The new representation leads to parsimonious stochastic models of the ambient wave kinematics and of the nonlinear loads and responses of ships and offshore platforms. The use of the new representation is discussed for the derivation of critical wave episodes, the derivation of up-crossing rates of nonlinear loads and responses and the joint stochastic representation of correlated wave and wind profiles for use in the design of fixed or floating offshore wind turbines. The forecasting is also discussed of wave elevation records and vessel responses for use in energy yield enhancement of compliant floating wind turbines.
The finite-dipole dynamical system
Authors: Tchieu Andrew A. , Kanso Eva , Newton Paul K.
Published: May 2012

The notion of a
finite dipole
is introduced as a pair of equal and opposite strength point vortices (i.e. a vortex dipole) separated by a finite distance. Equations of motion for
N
finite dipoles interacting in an unbounded inviscid fluid are derived from the modified interaction of 2
N
independent vortices subject to the constraint that the inter-vortex spacing of each constrained dipole, ℓ, remains constant. In the absence of all other dipoles and background flow, a single dipole moves in a straight line along the perpendicular bisector of the line segment joining the two point vortices comprising the dipole, with a self-induced velocity inversely proportional to ℓ. When more than one dipole is present, the velocity of the dipole centre is the sum of the self-induced velocity and the average of the induced velocities on each vortex comprising the pair due to all the other dipoles. Each dipole orients in the direction of shear gradient based on the difference in velocities on each of the two vortices in the pair. Several numerical experiments are shown to illustrate the interactions between two and three dipoles in abreast and tandem configurations. We also show that equilibria (multi-poles) can form as a result of the interactions, and we study the stability of polygonal equilibria, showing that the
N
=3 case is linearly stable, whereas the
N
>3 case is linearly unstable.
Structures of inactive retinoblastoma protein reveal multiple mechanisms for cell cycle control
Authors: Burke Jason R. , Hura Greg L. , Rubin Seth M.
Published: May 2012

Cyclin-dependent kinase (Cdk) phosphorylation of the Retinoblastoma protein (Rb) drives cell proliferation through inhibition of Rb complexes with E2F transcription factors and other regulatory proteins. We present the first structures of phosphorylated Rb that reveal the mechanism of its inactivation. S608 phosphorylation orders a flexible “pocket” domain loop such that it mimics and directly blocks E2F transactivation domain (E2FTD) binding. T373 phosphorylation induces a global conformational change that associates the pocket and N-terminal domains (RbN). This first multidomain Rb structure demonstrates a novel role for RbN in allosterically inhibiting the E2FTD–pocket association and protein binding to the pocket “LxCxE” site. Together, these structures detail the regulatory mechanism for a canonical growth-repressive complex and provide a novel example of how multisite Cdk phosphorylation induces diverse structural changes to influence cell cycle signaling.
CML42-Mediated Calcium Signaling Coordinates Responses to Spodoptera Herbivory and Abiotic Stresses in Arabidopsis
Authors: Vadassery Jyothilakshmi , Reichelt Michael , Hause Bettina , Gershenzon Jonathan , Boland Wilhelm , Mithöfer Axel
Published: May 2012

In the interaction between Arabidopsis (Arabidopsis thaliana) and the generalist herbivorous insect Spodoptera littoralis, little is known about early events in defense signaling and their link to downstream phytohormone pathways. S. littoralis oral secretions induced both Ca2+ and phytohormone elevation in Arabidopsis. Plant gene expression induced by oral secretions revealed up-regulation of a gene encoding a calmodulin-like protein, CML42. Functional analysis of cml42 plants revealed more resistance to herbivory than in the wild type, because caterpillars gain less weight on the mutant, indicating that CML42 negatively regulates plant defense; cml42 also showed increased aliphatic glucosinolate content and hyperactivated transcript accumulation of the jasmonic acid (JA)-responsive genes VSP2 and Thi2.1 upon herbivory, which might contribute to increased resistance. CML42 up-regulation is negatively regulated by the jasmonate receptor Coronatine Insensitive1 (COI1), as loss of functional COI1 resulted in prolonged CML42 activation. CML42 thus acts as a negative regulator of plant defense by decreasing COI1-mediated JA sensitivity and the expression of JA-responsive genes and is independent of herbivory-induced JA biosynthesis. JA-induced Ca2+ elevation and root growth inhibition were more sensitive in cml42, also indicating higher JA perception. Our results indicate that CML42 acts as a crucial signaling component connecting Ca2+ and JA signaling. CML42 is localized to cytosol and nucleus. CML42 is also involved in abiotic stress responses, as kaempferol glycosides were down-regulated in cml42, and impaired in ultraviolet B resistance. Under drought stress, the level of abscisic acid accumulation was higher in cml42 plants. Thus, CML42 might serve as a Ca2+ sensor having multiple functions in insect herbivory defense and abiotic stress responses.
One-dimensional coordination polymers generated from a new triazole bridging ligand and HgX2(X= Cl, Br and I): characterization and luminescent properties
Authors: Qin Na , Zhao Chao-Wei , Ma Jian-Ping , Liu Qi-Kui , Dong Yu-Bin
Published: May 2012

The new 4-amino-1,2,4-triazole asymmetric bridging ligand 4-amino-5-(pyridin-3-yl)-3-[4-(pyridin-4-yl)phenyl]-4H-1,2,4-triazole (L) has been used to generate three novel isomorphic one-dimensional coordination polymers,viz. catena-poly[[tris[dichloridomercury(II)]-bis{μ3-4-amino-5-(pyridin-3-yl)-3-[4-(pyridin-4-yl)phenyl]-4H-1,2,4-triazole}] acetonitrile monosolvate], {[Hg3Cl6(C18H14N6)2]·CH3CN}n, (I), and the bromido, {[Hg3Br6(C18H14N6)2]·CH3CN}n, (II), and iodido, {[Hg3I6(C18H14N6)2]·CH3CN}n, (III), analogs. The asymmetric ligand acts as a tridentate ligand to coordinate the three different HgIIcenters (two of which are symmetry-related). Two ligands and two symmetry-related HgIIcenters form centrosymmetric rectangular units which are linked into one-dimensional chainsviathe other unique Hg atoms, which sit on mirror planes. The chains are elaborated into a three-dimensional structureviainterchain hydrogen bonds. The acetonitrile solvent molecules are located in ellipsoidal cavities. The luminescent character of these three coordination complexes was investigated in the solid state.
Suppressive effect of recombinant human thioredoxin on ultraviolet light‐induced inflammation and apoptosis in murine skin
Authors: ONO Ryusuke , MASAKI Taro , DIEN Siphora , YU Xijun , FUKUNAGA Atsushi , YODOI Junji , NISHIGORI Chikako
Published: May 2012

Thioredoxin (TRX) is a small ubiquitous protein, which regulates cellular redox status and scavenges reactive oxygen species. The present study was conducted to investigate the effect of TRX on ultraviolet (UV)‐B‐mediated inflammatory and apoptotic responses. Ear swelling after UV‐B irradiation was significantly reduced in TRX‐transgenic mice compared to wild‐type mice. Administration i.p. of recombinant human TRX also reduced acute skin inflammatory reaction, such as skin erythema and swelling. Histologically, numbers of inflammatory cells including neutrophils and lymphocytes were significantly reduced and the average size of the caliber of blood vessels were also reduced in recombinant human TRX‐injected mice. The number of apoptotic keratinocytes, in terms of sunburn cells, activated‐caspase‐3‐positive cells and terminal deoxynucleotidyl transferase dUTP nick end labeling‐positive cells were all significantly reduced in recombinant human TRX‐injected mice. Immunohistochemical intensity of 8‐hydroxy‐2′‐deoxyguanosine was strikingly reduced in recombinant human TRX‐injected mouse. Western blotting showed that administration of recombinant human TRX attenuated duration of phosphorylation of p38 mitogen‐activated protein kinases and intensity of phosphorylation of c‐Jun N‐terminal kinase in the early phase, which play important roles in inflammatory and apoptotic signaling. Collectively, these findings indicated that recombinant human TRX attenuated inflammatory and apoptotic responses caused by UV‐B. Possible mechanisms for this might be via redox regulation of stress signaling and reduction of reactive oxygen species.
Alcohol consumption and psoriatic risk: A meta‐analysis of case–control studies
Authors: ZHU Kun‐Ju , ZHU Cheng‐Yao , FAN Yi‐Ming
Published: May 2012

Psoriasis is one of the most common dermatological disorders. The association between alcohol consumption and psoriasis has been inconsistent among studies. To examine the magnitude of the risk of developing psoriasis for drinking populations compared to those with non‐drinking, and to determine causes of the variation in odds ratios (OR) between various case–control studies, we performed a comprehensive published work search and a meta‐analysis of case–control studies considering prevalence. We did electronic searches on Medline, and searched reports to identify case–control studies of prevalent of psoriasis. We did meta‐analyses of study‐specific incremental estimates to determine the risk of psoriasis associated with drinking. The magnitude of the OR was analyzed by combining 15 case–control studies that matched defined criteria. The variance in OR between studies was explored. The overall OR of psoriasis for drinking persons compared to those with non‐drinking was 1.531 (95% confidence interval [CI] = 1.164–2.014, P = 0.002) and the association remains statistically significant across a number of stratified analyses in European descent subgroup (OR = 1.432, 95% CI = 1.085–1.889, P = 0.011) and also persists in sensitivity analyses performed to assess the potential effect of varying psoriasis outcome definitions. Alcohol consumption is associated with increased risk of psoriasis. These epidemiological observations should inform the exploration of biological mechanisms that link alcohol consumption with psoriasis.
Genetic alterations in systemic nodal and extranodal non‐cutaneous lymphomas derived from mature T cells and natural killer cells
Authors: Boi Michela , Stathis Anastasios , Zucca Emanuele , Inghirami Giorgio , Bertoni Francesco
Published: May 2012

Mature (peripheral) T‐cell and natural killer (NK)‐cell lymphomas comprise a series of rather different neoplasms. Based on morphologic, immunophenotypic, genetic, and clinical data, the World Health Organization classification recognizes more than 20 entities or provisional entities. The variable clinical presentations, the objective recognition and pathological stratification, the difficulties regarding treatment, and the hardly predictable response to therapy indicate that the management of these entities requires novel tools. In contrast to B‐cell lymphomas or precursor T‐cell neoplasms, few recurrent translocations have been identified so far in T‐cell non‐Hodgkin's and NK‐cell lymphomas. Additionally, some of the entities recognized by the World Health Organization classification are very rare and very scarce molecular data are available for T‐cell lymphomas. Here, we have reviewed published reports focusing on the genetic lesions and gene expression profiling underlying systemic nodal and extranodal non‐cutaneous mature T‐cell and NK‐cell lymphomas. We also provide a summary of new agents in clinical development and outline some future directions. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02321.x, 2012)
Clinical significance of granulocytic sarcoma in adult patients with acute myeloid leukemia
Authors: Shimizu Hiroaki , Saitoh Takayuki , Hatsumi Nahoko , Takada Satoru , Yokohama Akihiko , Handa Hiroshi , Jimbo Tkahiro , Sakura Toru , Tsukamoto Norifumi , Murakami Hirokazu , Miyawaki Shuichi , Nojima Yoshihisa
Published: May 2012

To investigate the clinical significance of granulocytic sarcoma (GS) in adults with acute myeloid leukemia (AML), 434 consecutive patients with AML were analyzed retrospectively. Forty‐five patients (10.4%) with GS at diagnosis were younger (P < 0.001), presented with higher white blood cell counts (P = 0.03) and were more likely to conform to French–American–British M4 (P = 0.001) and M5 (P = 0.045) classifications than those without GS. In contrast, no significant difference in frequency of cytogenetic abnormalities was found between the GS and non‐GS groups. Treatment outcomes in 260 patients (40 with GS) who underwent intensive chemotherapy, excluding patients with acute promyelocytic leukemia, were investigated. Complete remission rates did not differ significantly between the GS and non‐GS groups (75.0% vs 79.1%; P = 0.192, respectively) or the 5‐year overall survival (OS) rates (39.9% vs 38.7%; P = 0.749, respectively). However, the GS group had a significantly higher relapse rate than the non‐GS group (74.2% vs 55.3%; P = 0.048) and a significantly lower 5‐year disease‐free survival rate (8.2% vs 25.7%, respectively; P = 0.005). When considered together with the results of multivariate analysis, which identified the presence of GS as an independent predictor for disease‐free survival time, these findings indicate that GS might identify a high‐risk subset of patients with AML. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02324.x, 2012)
Nonclonal growth of preneoplastic cells positive for glutathione S‐transferase P‐form in the rat liver
Authors: Satoh Kimihiko , Yamakawa Daishi , Kasai Kosuke , Hayakari Makoto , Uchida Koji , Miura Tomisato
Published: May 2012

We investigated the process of induction of preneoplastic cells positive for glutathione S‐transferase P‐form (GST‐P) in the rat liver. AAF (2‐Acetylaminofluorene) mixed with normal rat chow at high concentration (0.04%) induced 517 000 ± 86 000 GST‐P+ single hepatocytes/g liver after 2 weeks followed by induction of a few foci and nodules after 4–6 weeks. Overproduction of GST‐P+ single hepatocytes was dose‐ and time‐dependent, and the induction kinetics were typical of first‐order consecutive reaction, by which induction of the positive cells was nongenetic. Quantitative analysis indicated that the estimated numbers of cells in foci and nodules at 4–6 weeks after exposure to AAF ranged from 2.7 × 104 (214.7) to 3.6 × 106 (221.7) cells, and 2.0 × 104 (214.3) to 2.7 × 106 (221.4) cells, respectively, when analyzed by using two equations. According to the initiated cell theory of Farber, foci and nodules are formed through sequential cell division of 14 to 21‐times or more within a short time period. The rapid growth exceeded the rate of cell division, indicating that the growth of preneoplastic cells is based on a nonclonal penetration mechanism. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02325.x, 2012)
Differences and similarities between carbon nanotubes and asbestos fibers during mesothelial carcinogenesis: Shedding light on fiber entry mechanism
Authors: Nagai Hirotaka , Toyokuni Shinya
Published: May 2012

The emergence of nanotechnology represents an important milestone, as it opens the way to a broad spectrum of applications for nanomaterials in the fields of engineering, industry and medicine. One example of nanomaterials that have the potential for widespread use is carbon nanotubes, which have a tubular structure made of graphene sheets. However, there have been concerns that they may pose a potential health risk due to their similarities to asbestos, namely their high biopersistence and needle‐like structure. We recently found that despite these similarities, carbon nanotubes and asbestos differ in certain aspects, such as their mechanism of entry into mesothelial cells. In the study, we showed that non‐functionalized, multi‐walled carbon nanotubes enter mesothelial cells by directly piercing through the cell membrane in a diameter‐ and rigidity‐dependent manner, whereas asbestos mainly enters these cells through the process of endocytosis, which is independent of fiber diameter. In this review, we discuss the key differences, as well as similarities, between asbestos fibers and carbon nanotubes. We also summarize previous reports regarding the mechanism of carbon nanotube entry into non‐phagocytic cells. As the entry of fibers into mesothelial cells is a crucial step in mesothelial carcinogenesis, we believe that a comprehensive study on the differences by which carbon nanotubes and asbestos fibers enter into non‐phagocytic cells will provide important clues for the safer manufacture of carbon nanotubes through strict regulation on fiber characteristics, such as diameter, surface properties, length and rigidity. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02326.x, 2012)
Associations between substance use disorders and major depression in parents and late adolescent–emerging adult offspring: an adoption study
Authors: Marmorstein Naomi R. , Iacono William G. , McGue Matt
Published: May 2012

Aims

To examine whether major depressive disorder (MDD) and substance use disorders [SUDs: specifically, nicotine dependence (ND), alcohol use disorders (AUDs), and cannabis use disorders (CUDs)] in parents predicted increased risk for these disorders in late adolescent–emerging adult offspring and, specifically, the extent to which the pattern of risk differed for adopted and non‐adopted youth.

Participants

Late adolescent and emerging adult participants from the Sibling Interaction and Behavior Study (mean age = 18.8), a community‐based investigation of adopted and non‐adopted adolescents, and their parents (adoptive parents of adopted youth, biological parents of non‐adopted adolescents) were included.

Measurements

Structured interviews were used to assess these disorders.

Findings

(i) When the same disorder in parents and adolescents was examined, parental MDD was associated with increased risk for MDD among both adopted (P < 0.001) and non‐adopted (P < 0.01) adolescents; in contrast, SUDs were associated with increased risk for the same SUD in non‐adopted offspring (all P < 0.01). (ii) When cross‐SUD effects were examined, for the most part, each SUD was associated with increased risk for other SUDs among non‐adopted but not adopted offspring (most P < 0.05). (iii) When MDD‐SUD associations were examined, parental ND and CUDs predicted increased risk for MDD in non‐adopted (P < 0.001), but not adopted, adolescents. These effects tended to remain significant when adjusting for within‐person comorbidity (P < 0.05).

Conclusions

Major depressive disorder in parents appears to be a risk factor for late adolescent–emerging adult major depressive disorder but not substance use disorder in offspring, with this risk being environmentally mediated. Substance use disorder in parents appears, via genetic mediation, to increase risk of substance use disorder in adolescent offspring, and cannabis and nicotine use disorders in parents contribute similarly to major depressive disorder in those offspring.
Does it matter who you see to help you stop smoking? Short‐term quit rates across specialist stop smoking practitioners in England
Authors: Brose Leonie S. , McEwen Andy , West Robert
Published: May 2012

Aims

A network of Stop Smoking Services has been set up within the National Health Service (NHS) in England. The services deliver a combination of behavioural support and medication. It is important to establish the degree of variability in quit rates attributable to differences between individual practitioners, to gauge the scope for improvement by training and professional support. The aim of the present analysis was to examine how far short‐term quit rates depend on the practitioner delivering the intervention after adjusting for potential confounding variables.

Design

Observational study using routinely collected data.

Setting

Thirty‐one NHS Stop Smoking Services in England.

Participants

Data from 46 237 one‐to‐one treatment episodes (supported quit attempts) delivered by specialist practitioners.

Measurements

Three‐level logistic regression models were fitted for carbon monoxide (CO)‐validated short‐term (4‐week) quit rates. Models adjusted for age, gender, exemption from prescription charges, medication and intervention setting for each treatment episode, number of clients for each practitioner and economic deprivation at the level of the Stop Smoking Service. Secondary analyses included (i) the Heaviness‐of‐Smoking Index (HSI) as predictor and (ii) 4‐week quit rates whether or not confirmed by CO.

Findings

Differences between individual specialist practitioners explained 7.6% of the variance in CO‐verified quit rates after adjusting for client demographics, intervention characteristics and practitioner and service variables (P < 0.001). HSI had little impact on this figure; in quits not necessarily validated by CO, practitioners explained less variance.

Conclusions

Individual stop smoking practitioners appear to differ to a significant degree in effectiveness. It is important to examine what underlies these differences in order to improve selection, training and professional development.