bluuebunny/crossref_metadata_2025 huggingface dataset:
Search and characterization of T-type planetary mass candidates in the σ Orionis cluster
Authors: Ramírez Karla Peña , Zapatero Osorio Maria R. , Béjar Victor J.S.
Published: November 2011

We present new photometric and astrometric data available for S Ori 70 and 73, the two T-type planetary-mass member candidates in the σ Orionis cluster (~3 ± 2 Myr, d~360 pc). S Ori 70 (J ~ 19.9 mag) has a spectral type of T5.5 ± 1.0 measured from published near-infrared spectra, while no spectroscopic data are available for S Ori 73 (J ~ 21 mag). We estimate the spectral type of S Ori 73 by using J, H, and CH4off (λc=1.575 μm, Δλ=0.112 μm) photometry and comparing the H-CH4off index of S Ori 73 with the colors of field stars and brown dwarfs of spectral types in the range F to late T. The locations of S Ori 70 and 73 in the J-H vs H-CH4off color-color diagram are consistent with spectral types T8 ± 1 and T4 ± 1, respectively. Proper motion measurements of the two sources are larger than the motion of the central σ Ori star, making their cluster membership somehow uncertain.
Two bodies with high eccentricity around the cataclysmic variable QS Vir
Authors: Almeida Leonardo A. , Jablonski Francisco
Published: November 2011

QS Vir is an eclipsing cataclysmic variable with 3.618 hrs orbital period. This system has the interesting characteristics that it does not show mass transfer between the components through the L1 Lagrangian point and shows a complex orbital period variation history. Qian et al. (2010) associated the orbital period variations to the presence of a giant planet in the system plus angular momentum loss via magnetic braking. Parsons et al. (2010) obtained new eclipse timings and observed that the orbital period variations associated to a hypothetical giant planet disagree with their measurements and concluded that the decrease in orbital period is part of a cyclic variation with period ~16 yrs. In this work, we present 28 new eclipse timings of QS Vir and suggest that the orbital period variations can be explained by a model with two circumbinary bodies. The best fitting gives the lower limit to the masses M1 sin(i) ~ 0.0086 M⊙ and M2 sin(i) ~ 0.054 M⊙; orbital periods P1 ~ 14.4 yrs and P2 ~ 16.99 yrs, and eccentricities e1 ~ 0.62 and e2~0.92 for the two external bodies. Under the assumption of coplanarity among the two external bodies and the inner binary, we obtain a giant planet with ~0.009 M⊙ and a brown dwarf with ~ 0.056 M⊙ around the eclipsing binary QS Vir.
Evolution of planetary systems in dissipating gas disks
Authors: Matsumura Soko , Thommes Edward W. , Chatterjee Sourav , Rasio Frederic A.
Published: November 2011

In a recently published paper Matsumura et al. (2010) (hereafter M10), we have studied the evolution of three-planet systems in dissipating gas disks by using a hybrid N-body and one-dimensional gas disk evolution code. In this article, we highlight some results which are only briefly mentioned in M10.
Tidal evolution of a close-in planet with a more massive outer companion
Authors: Rodríguez Adrian , Ferraz-Mello Sylvio , Michtchenko Tatiana A. , Beaugé Cristian , Miloni Octavio
Published: November 2011

We investigate the motion of a two-planet coplanar system under the combined effects of mutual interaction and tidal dissipation. The secular behavior of the system is analyzed using two different approaches, restricting to the case of a more massive outer planet. First, we solve the exact equations of motion through the numerical simulation of the system evolution. We also compute the stationary solutions of the mean equations of motion based on a Hamiltonian formalism. An application to the real system CoRoT-7 is investigated.
3D MHD simulations of planet migration in turbulent stratified disks
Authors: Uribe Ana , Klahr Hubert , Flock Mario , Henning Thomas
Published: November 2011

We performed 3D MHD numerical simulations of planet migration in stratified disks using the Godunov code PLUTO (Mignone et al. 2007). The disk is invaded by turbulence generated by the magnetorotational instability (MRI). We study the migration for planets with different mass to primary mass ratio. The migration of the low-mass planet (q=Mp/Ms=10−5) is dominated by random fluctuations in the torque and there is no defined direction of migration on timescales of 100 orbits. The intermediate-mass planet (q=Mp/Ms=10−4) can experience systematic outwards migration that was sustained for the times we were able to simulate.
Planetesimal and protoplanet dynamics in a turbulent protoplanetary disk
Authors: Yang Chao-Chin , Mac Low Mordecai-Mark , Menou Kristen
Published: November 2011

Due to the gravitational influence of density fluctuations driven by magneto-rotational instability in the gas disk, planetesimals and protoplanets undergo diffusive radial migration as well as changes of other orbital properties. The magnitude of the effect on particle orbits has important consequences for planet formation scenarios. We use the local-shearing-box approximation to simulate an ideal, isothermal, magnetized gas disk with vertical density stratification and simultaneously evolve numerous massless particles moving under the gravity of the gas and the host star. Although the results converge with resolution for fixed box dimensions, we find there exists no convergence of the response of the particles to the gravity of the gas against the horizontal box size, up to 16 disk scale heights. This lack of convergence indicate that caution should be exercised when interpreting local-shearing-box models involving gravitational physics of magneto-rotational turbulence.
CARMENES: Calar Alto high-Resolution search for M dwarfs with Exo-earths with Near-infrared and optical Echelle Spectrographs
Authors: Quirrenbach Andreas , Amado Pedro J. , Caballero José A. , Mandel Holger , Mundt Reinhard , Reiners Ansgar , Ribas Ignasi , Sánchez Carrasco Miguel A. , Seifert Walter ,   the CARMENES Consortium
Published: November 2011

CARMENES (Calar Alto high-Resolution search for M dwarfs with Exo-earths with Near-infrared and optical Echelle Spectrographs) is a next-generation instrument for the 3.5 m telescope at the Calar Alto Observatory. CARMENES will conduct a five-year exoplanet survey targeting ~300 M stars. The CARMENES instrument consists of two separate fiber-fed spectrographs covering the wavelength range from 0.52 to 1.7 μm at a spectral resolution of R = 85,000. The spectrographs are housed in a temperature-stabilized environment in vacuum tanks, to enable a 1 m/s radial velocity precision employing a simultaneous emission-line calibration.
The LCOGT Network
Authors: Shporer Avi , Brown Tim , Lister Tim , Street Rachel , Tsapras Yiannis , Bianco Federica , Fulton Benjamin , Howell Andy
Published: November 2011

Motivated by the increasing need for observational resources for the study of time varying astronomy, the Las Cumbres Observatory Global Telescope (LCOGT) is a private foundation, whose goal is to build a global network of robotic telescopes for scientific research and education. Once completed, the network will become a unique tool, capable of continuous monitoring from both the Northern and Southern Hemispheres. The network currently includes 2 × 2.0 m telescopes, already making an impact in the field of exoplanet research. In the next few years they will be joined by at least 12 × 1.0 m and 20 × 0.4 m telescopes. The increasing amount of LCOGT observational resources in the coming years will be of great service to the astronomical community in general, and the exoplanet community in particular.
Millimeter-wave rotational spectroscopy of FeCN (X 4Δi) and FeNC (X 6Δi): Determining the lowest energy isomer
Authors: Flory M. A. , Ziurys L. M.
Published: November 2011

The pure rotational spectrum of FeCN has been recorded in the frequency range 140-500 GHz using millimeter/sub-millimeter direct absorption techniques. The species was created in an ac discharge of Fe(CO)5 and cyanogen. Spectra of the 13C, 54Fe, and 57Fe isotopologues were also measured, confirming the linear cyanide structure of this free radical. Lines originating from several Renner-Teller components in the v2 bending mode were also observed. Based on the observed spin-orbit pattern, the ground state of FeCN is 4Δi, with small lambda-doubling splittings apparent in the Ω = 5/2, 3/2, and 1/2 components. In addition, a much weaker spectrum of the lowest spin-orbit component of FeNC, Ω = 9/2, was recorded; these data are consistent with the rotational parameters of previous optical studies. The data for FeCN were fit with a Hund's case (a) Hamiltonian and rotational, spin-orbit, spin-spin, and lambda-doubling parameters were determined. Rotational constants were also established from a case (c) analysis for the other isotopologues, excited vibronic states, and for FeNC. The r0 bond lengths of FeCN were determined to be rFe−C = 1.924 Å and rC−N = 1.157 Å, in agreement with theoretical predictions for the 4Δi state. These measurements indicate that FeCN is the lower energy isomer and is more stable than FeNC by ∼1.9 kcal/mol.
Enhanced photorefractive effect in liquid crystal structures co-doped with semiconductor quantum dots and metallic nanoparticles
Authors: Anczykowska A. , Bartkiewicz S. , Nyk M. , Myśliwiec J.
Published: November 2011

In this paper, we present strong enhancement of optical properties of hybrid liquid crystal structures functionalized with metallic and semiconductor nanoparticles. Several experiments done in two wave mixing experimental set-up have reported that diffraction efficiency can be improved by up to 14 times by introducing nanoparticles of cadmium selenide or gold into the photoconducting polymer adjacent to the liquid crystal layer. Our research may open up a possible route for the development of faster and more efficient holographic materials which can be used in dynamic data processing systems.
A broadband acoustic omnidirectional absorber comprising positive-index materials
Authors: Li Rui-Qi , Zhu Xue-Feng , Liang Bin , Li Yong , Zou Xin-Ye , Cheng Jian-Chun
Published: November 2011

We propose a broadband acoustic omnidirectional absorber (AOA) made of acoustic metamaterials having a positive index, which guides an incident acoustic wave into a central cavity spirally without backscattering. Numerical simulations show that the AOA has an absorption cross section remarkably larger than its cavity within a broad band, which is of potential practical significance to various applications such as sound absorption and noise control. A possible scheme for the practical realization of the AOA is also briefly discussed.
Single-molecule measurement of strand breaks on large DNA induced by atmospheric pressure plasma jet
Authors: Kurita Hirofumi , Nakajima Tomoko , Yasuda Hachiro , Takashima Kazunori , Mizuno Akira , Wilson John I. B. , Cunningham Samia
Published: November 2011

We report a single-molecule-based analysis of strand breakages on large DNA molecules induced by an atmospheric pressure plasma jet. We exposed DNA solution to an argon plasma jet; single-molecule observation that involved molecular combing was then used to measure the length of individual DNA molecules. The measured DNA length showed that plasma exposure caused a marked change in length of DNA molecules. The rate of plasma-induced strand breakage on large random-coiled DNA molecules was determined using a simple mathematical model. For strand breaks on large DNA molecules the rate was estimated.
Note: Detection of micro-cracks in the interlayer dielectric film by the stress based light scattering method
Authors: Sakai Kazufumi , Nonaka Kazuhiro
Published: November 2011

A phenomenon was discovered wherein light scattering strength from cracks increases when tensile stress is applied to micro-cracks produced in the interlayer dielectric film by chemical mechanical polishing treatment. It is likely that the change in light scattering intensity occurs because a region of high stress concentration (region with high variation in index of refraction) is produced near the crack tip due to stress, thus forming a type of scatterer. With this method, it is possible to detect only scatterers which respond to stress, and thus, it is possible to classify and separately detect cracks and particles.
Cognitive tools to support learning about farming system management: a case study in grazing systems
Authors: Duru Michel , Martin-Clouaire Roger
Published: November 2011

The complex challenge of farm management has prompted a search for ways in which scientific knowledge can be acquired and combined with practical know-how and experience to enhance the adaptability, profitability and environmental soundness of agricultural systems. Cognitive tools offer a kind of model-based learning support that facilitates and stimulates critical thinking about the functioning of agricultural production processes and the ways to control them in various and changing situations. The purpose of this paper is to delineate, illustrate and analyse the concept of cognitive tool together with the learning process and conditions in which such a tool would be used. We review three such tools built to help understand, improve, adapt or design grazing management practices in pasture-based livestock farms. For each of them we examine the knowledge content of the tool, the way it is represented, the kind of use and the nature of the support it provides to its users.
Epidermal growth factor upregulates endometrial CYR61 expression via activation of the JAK2/STAT3 pathway
Authors: Klein Rebecca , Stiller Simone , Gashaw Isabella
Published: November 2011

Endometrial cysteine-rich protein 61 (CYR61, CCN1) is a growth factor-inducible gene whose expression is elevated during the proliferative phase of the menstrual cycle and which has been implicated in the pathogenesis of endometriosis. This study aimed to define the mediators of epidermal growth factor (EGF) signalling on CYR61 expression in spontaneously immortalised human endometrial epithelial cells (HES) as a model system. After 30 min of EGF treatment, the receptor was phosphorylated and internalised as well as mRNA CYR61 increased in HES cells. However, neither inhibition of C-terminal EGF receptor (EGFR)-phosphorylation nor blockage of the mitogen-activated proteinkinase/extracellular signal-regulated kinase (MAPK/ERK) pathway was able to reduce CYR61 levels. Surprisingly, the HES cells showed upregulation of CYR61 mRNA expression after inhibition of the MAPK/ERK pathway when treated with EGF. Specific inhibitor studies identified the contribution of Janus kinase 2 (JAK2) and the signal transducer and activator of transcription protein STAT3 to the regulation of CYR61 expression. The JAK2/STAT3 interaction contributed to the basal expression of CYR61 and mediated EGF-driven regulation of CYR61 after 30 and 120 min of treatment. In summary, EGF-mediated CYR61 upregulation in HES cells involves STAT3 and is counter-regulated by the EGFR/MAPK/ERK pathway.
Safer sex and condom use: a convenience sample of Aboriginal young people in New South Wales
Authors: Bryant Joanne , Ward James , Worth Heather , Hull Peter , Solar Sarina , Bailey Sandra
Published: November 2011

Background This paper examines condom use in a sample of Aboriginal young people in New South Wales (NSW) aged 16–30 years. Methods: Cross-sectional data were collected using hand-held computer devices from 293 Aboriginal people attending two Aboriginal events in NSW. Results: Almost two-thirds of respondents reported having had a casual sex partner in the previous 6 months. Of these, 39.2% reported always using a condom with casual partners. Having always used a condom with casual partners varied among respondents, and was more likely among younger respondents (adjusted odds ratio (AOR): 2.7, 95% confidence interval (CI): 1.2–6.1) and less likely among those who used illicit drugs (AOR: 0.2, 95% CI: 0.1–0.7). Conclusions: In comparison to published studies of other Australians, casual sex appears to be more common among this sample of Aboriginal young people; however, the proportion who report having always used condoms with casual partners is very similar. This suggests that although casual sex is more common, Aboriginal young people do not engage in risky behaviour any more often than other young Australians. Further work should be conducted with those who do not always use condoms, such as those who are older and who use illicit drugs, particularly with regards to how abstinence from drug use supports protective behaviours such as condom use among this population of Aboriginal young people.
Compression-induced percolation in low filler composites based on polyvinylidene fluoride and nickel particles
Authors: Li Weiping , Wang Xinming , Tong Chaohui , Zhu Yuejin
Published: November 2011

Low filler composites based on polyvinylidene fluoride and nickel particles are compressed with different strain rates. It is found that the percolative process can be induced by a compression, which is denoted as the compression-induced percolation (CIP). Because of the CIP effect, the maximum of dielectric permittivity is up to 178 at 100 Hz (10 times enhancement over the uncompressed sample) and the loss is controlled in the range 0–0.15 at a low frequency. The CIP effect is beneficial to the preparation and optimization of high dielectric permittivity and low loss percolative composites.
Dependence of Chs2 ER export on dephosphorylation by cytoplasmic Cdc14 ensures that septum formation follows mitosis
Authors: Chin Cheen Fei , Bennett Alexis M. , Ma Wai Kit , Hall Mark C. , Yeong Foong May
Published: November 2011

Cytokinesis, which leads to the physical separation of two dividing cells, is normally restrained until after nuclear division. In Saccharomyces cerevisiae, chitin synthase 2 (Chs2), which lays down the primary septum at the mother–daughter neck, also ensures proper actomyosin ring constriction during cytokinesis. During the metaphase-to-anaphase transition, phosphorylation of Chs2 by the mitotic cyclin-dependent kinase (Cdk1) retains Chs2 at the endoplasmic reticulum (ER), thereby preventing its translocation to the neck. Upon Cdk1 inactivation at the end of mitosis, Chs2 is exported from the ER and targeted to the neck. The mechanism for triggering Chs2 ER export thus far is unknown. We show here that Chs2 ER export requires the direct reversal of the inhibitory Cdk1 phosphorylation sites by Cdc14 phosphatase, the ultimate effector of the mitotic exit network (MEN). We further show that only Cdc14 liberated by the MEN after completion of chromosome segregation, and not Cdc14 released in early anaphase by the Cdc fourteen early anaphase release pathway, triggers Chs2 ER exit. Presumably, the reduced Cdk1 activity in late mitosis further favors dephosphorylation of Chs2 by Cdc14. Thus, by requiring declining Cdk1 activity and Cdc14 nuclear release for Chs2 ER export, cells ensure that septum formation is contingent upon chromosome separation and exit from mitosis.
Wavelet-based image fusion in multi-view three-dimensional microscopy
Authors: Rubio-Guivernau Jose L. , Gurchenkov Vasily , Luengo-Oroz Miguel A. , Duloquin Louise , Bourgine Paul , Santos Andres , Peyrieras Nadine , Ledesma-Carbayo Maria J.
Published: November 2011

Motivation: Multi-view microscopy techniques such as Light-Sheet Fluorescence Microscopy (LSFM) are powerful tools for 3D + time studies of live embryos in developmental biology. The sample is imaged from several points of view, acquiring a set of 3D views that are then combined or fused in order to overcome their individual limitations. Views fusion is still an open problem despite recent contributions in the field.

Results: We developed a wavelet-based multi-view fusion method that, due to wavelet decomposition properties, is able to combine the complementary directional information from all available views into a single volume. Our method is demonstrated on LSFM acquisitions from live sea urchin and zebrafish embryos. The fusion results show improved overall contrast and details when compared with any of the acquired volumes. The proposed method does not need knowledge of the system's point spread function (PSF) and performs better than other existing PSF independent fusion methods.

Availability and Implementation: The described method was implemented in Matlab (The Mathworks, Inc., USA) and a graphic user interface was developed in Java.

The software, together with two sample datasets, is available at http://www.die.upm.es/im/software/SPIMFusionGUI.zip

A public release, free of charge for non-commercial use, is planned after the publication of this article.

Contact:  jlrubio@die.upm.es; nadine.peyrieras@inaf.cnrs-gif.fr; mledesma@die.upm.es

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Decompositions of large-scale biological systems based on dynamical properties
Authors: Soranzo Nicola , Ramezani Fahimeh , Iacono Giovanni , Altafini Claudio
Published: November 2011

Motivation: Given a large-scale biological network represented as an influence graph, in this article we investigate possible decompositions of the network aimed at highlighting specific dynamical properties.

Results: The first decomposition we study consists in finding a maximal directed acyclic subgraph of the network, which dynamically corresponds to searching for a maximal open-loop subsystem of the given system. Another dynamical property investigated is strong monotonicity. We propose two methods to deal with this property, both aimed at decomposing the system into strongly monotone subsystems, but with different structural characteristics: one method tends to produce a single large strongly monotone component, while the other typically generates a set of smaller disjoint strongly monotone subsystems.

Availability: Original heuristics for the methods investigated are described in the article.

Contact:  altafini@sissa.it
Comparison of the shell structure of two tropical Thecosomata (Creseis acicula and Diacavolinia longirostris) from 1963 to 2009: potential implications of declining aragonite saturation
Authors: Roger Liza M. , Richardson Anthony J. , McKinnon A. David , Knott Brenton , Matear Richard , Scadding Cameron
Published: November 2011

Roger, L. M., Richardson, A. J., McKinnon, A. D., Knott, B., Matear, R., and Scadding, C. 2012. Comparison of the shell structure of two tropical Thecosomata (Creseis acicula and Diacavolinia longirostris) from 1963 to 2009: potential implications of declining aragonite saturation. – ICES Journal of Marine Science, 69: 465–474. Thecosomata (shelled pteropod molluscs) are calcifiers that play an important role in the ocean carbonate cycle. Ocean acidification as a result of the uptake of CO2 affects pteropods by increasing dissolution rates of their aragonite skeletons. Two species of pteropod found in Australian tropical waters were studied, Creseis acicula and Diacavolinia longirostris. To assess the changes in their aragonite shells, shell morphology, growth patterns, structure, size, and porosity are described for both species, from material collected at seven sites between the 1960s and the 2000s. Shell characteristics were used to explore variations over time potentially related to ocean acidification. The aragonite saturation level (Ωarag) of surface waters was hindcast and a decline equivalent to −10% (average of the seven sites) was found. Simultaneously, variations in shell thickness were recorded (C. acicula by −4.43 µm, D. longirostris by −5.37 µm) over the study period along with a significant increase in shell porosity (C. acicula: +1.43%, D. longirostris: +8.69%). The work, although not conclusive, does suggest that pteropods off Northern Australia may have been influenced by the decline in Ωarag over the past few decades. Such adverse effects could ultimately affect thecosome survival and that of their predators.
MGOS: Development of a Community Annotation Database for Magnaporthe oryzae
Authors: Kour Anupreet , Greer Kevin , Valent Barbara , Orbach Marc J. , Soderlund Carol
Published: November 2011

Magnaporthe oryzae causes rice blast disease, which is the most serious disease of cultivated rice worldwide. We previously developed the Magnaporthe grisea–Orzya sativa (MGOS) database as a repository for the M. oryzae and rice genome sequences together with a comprehensive set of functional interaction data generated by a major consortium of U.S. researchers. The MGOS database has now undergone a major redesign to include data from the international blast research community, accessible with a new intuitive, easy-to-use interface. Registered database users can manually annotate gene sequences and features as well as add mutant data and literature on individual gene pages. Over 900 genes have been manually curated based on various biological databases and the scientific literature. Gene names and descriptions, gene ontology annotations, published and unpublished information on mutants and their phenotypes, responses in diverse microarray analyses, and related literature have been incorporated. Thus far, 362 M. oryzae genes have associated information on mutants. MGOS is now poised to become a one-stop repository for all structural and functional data available on all genes of this critically important rice pathogen.
First Report of Root Rot Caused by Sclerotium rolfsii on Daucus carota var. sativa in Southern Korea
Authors: Kwon J.-H. , Lee Y. H. , Shim H.-S. , Kim J.
Published: November 2011

Carrot (Daucus carota var. sativa DC.), an important root vegetable, is cultivated widely because of its dietary fiber and beta carotene. In June 2009 and June 2010, a disease suspected as root rot of carrot caused by Sclerotium rolfsii occurred in a 5-ha field in Jinju, Korea. Early symptoms consisted of water-soaked lesions on root and lower stem tissue near the soil line. Infected plants gradually withered and white mycelial mats appeared on the surface of roots. Numerous sclerotia were often produced on stem and root surfaces in contact with the soil. The heavily infected carrots became rotted and blighted and the whole plant eventually died. The freshly isolated pathogenic fungus was grown on potato dextrose agar (PDA) and examined microscopically. Optimum temperature for mycelia growth or sclerotia formation was 25 to 30°C. Numerous globoid sclerotia formed on the PDA after 18 days of mycelial growth. The sclerotia (1 to 3 mm in diameter) were white at first and then gradually turned dark brown. Aerial mycelia usually formed, consisting of many narrow hyphal strands 3 to 9 μm wide. The white mycelium formed a typical clamp connection after 5 days of growth at optimum temperature. To fulfill Koch's postulates, 10 carrot seedlings were inoculated with colonized agar discs (6 mm in diameter) of the causal fungus directly on the root and incubated in a humid chamber at 25°C for 24 h. Ten carrot seedlings were inoculated similarly with agar discs as the control treatment. After this period, the inoculated and noninoculated plants were maintained in a greenhouse. Eight days after inoculation, the disease symptoms seen in the field were reproduced and the fungus was reisolated from the artificially inoculated plants. To confirm identity of the causal fungus, the complete internal transcribed spacer (ITS) rDNA region of the causal fungus was amplified using the primers ITS1 and ITS4 (2) and sequenced. The resulting sequence of 684 bp was deposited in GenBank (Accession No. JF342557). The sequence was 99% similar to sequences of Athelia rolfsii (Sclerotium rolfsii) in GenBank. Cultures of S. rolfsii have been deposited with the Korean Agricultural Culture Collection (KACC 45154), National Academy of Agricultural Science, Korea. On the basis of symptoms, fungal colonies, the ITS sequence, and the pathogenicity test on the host plant, this fungus was identified as S. rolfsii Saccardo (1). To our knowledge, this is the first report of root rot of carrot caused by S. rolfsii in Korea. This disease is highly dependent upon environmental conditions, including warm weather and high humidity. Recent occurrence of the disease suggests that S. rolfsii could spread widely.

References: (1) J. E. M. Mordue. CMI Descriptions of Pathogenic Fungi and Bacteria. No. 410, 1974. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, Inc., New York, 1990.
Calosphaeria Canker of Sweet Cherry Caused byCalosphaeria pulchellain California and South Australia
Authors: Trouillas F. P. , Peduto F. , Lorber J. D. , Sosnowski M. R. , Grant J. , Coates W. W. , Anderson K. K. , Caprile J. , Gubler W. D.
Published: November 2011

California is the second largest sweet cherry producer in the United States with annual revenues up to $200 million. The South Australian cherry industry generates about 10% of Australia's overall production with approximately 1,500 metric tons of cherries produced yearly. In California, perennial canker diseases and subsequent branch dieback are responsible for extensive damage throughout sweet cherry orchards, reducing annual yields and tree longevity. Surveys of cherry orchards and isolation work were conducted in California to identify the main canker-causing agents. Calosphaeria pulchella was the main fungus isolated from cankers, followed by Eutypa lata and Leucostoma persoonii, respectively. Preliminary surveys in cherry orchards in South Australia documented C. pulchella and L. persoonii in cankers. The pathogenicity of C. pulchella in sweet cherry was confirmed following field inoculations of 2- to 3-year-old branches. C. pulchella was able to infect healthy wood and produce cankers with as much virulence as E. lata or L. persoonii. Spore trapping studies were conducted in two sweet cherry orchards in California to investigate the seasonal abundance of C. pulchella spores. Experiments showed that rain and sprinkler irrigation were important factors for aerial dissemination. Finally, this study illustrates the symptoms and signs of the new disease Calosphaeria canker.
Phylogenetic and Pathogenic Analyses Show That the Causal Agent of Apple Ring Rot in China Is Botryosphaeria dothidea
Authors: Tang W. , Ding Z. , Zhou Z. Q. , Wang Y. Z. , Guo L. Y.
Published: November 2011

Apple ring rot and Botryosphaeria canker are severe diseases affecting apple production in China, but there is confusion regarding which pathogens cause these diseases and their similarity to other diseases, such as white rot of apple, and ring rot and Botryosphaeria canker of pear. In this study, the pathogen of apple ring rot in China was compared with the pathogen of apple ring rot in Japan and Korea, the pathogen of Botryosphaeria canker of apple and pear in China, the pathogen of pear ring rot in China, and the pathogen of white rot of apple in the United States. Comparisons were based on morphology, pathogenicity on branches and fruit, and sequences of rDNA in the internal transcribed spacer region and of the β-tubulin and actin genes. Results showed that the causal agent of apple ring rot and Botryosphaeria canker of apple in China was Botryosphaeria dothidea, which has also been reported to be the pathogen of apple ring rot in Korea and Japan. Pathogenicity tests showed that B. dothidea infection on apple and pear branches may induce wart or canker symptoms depending on the conditions. These results are consistent with the hypothesis that the same pathogen causes the wart symptom of apple ring rot and the Botryosphaeria canker symptom on apple branches in China. The results also suggest that apple ring rot and white rot are the same disease and are caused by B. dothidea. Finally, B. dothidea isolates from pear and other fruit or forest trees may serve as inoculum for apple ring rot.
The reverse, but coordinated, roles of Tor2 (TORC1) and Tor1 (TORC2) kinases for growth, cell cycle and separase-mediated mitosis inSchizosaccharomyces pombe
Authors: Ikai Nobuyasu , Nakazawa Norihiko , Hayashi Takeshi , Yanagida Mitsuhiro
Published: November 2011

Target of rapamycin complexes (TORCs), which are vital for nutrient utilization, contain a catalytic subunit with the phosphatidyl inositol kinase-related kinase (PIKK) motif. TORC1 is required for cell growth, while the functions of TORC2 are less well understood. We show here that the fission yeastSchizosaccharomyces pombeTORC2 has a cell cycle role through determining the proper timing of Cdc2 Tyr15 dephosphorylation and the cell size under limited glucose, whereas TORC1 restrains mitosis and opposes securin–separase, which are essential for chromosome segregation. These results were obtained using the previously isolated TORC1 mutanttor2-L2048Sin the phosphatidyl inositol kinase (PIK) domain and a new TORC2 mutanttor1-L2045D, which harbours a mutation in the same site. While mutated TORC1 and TORC2 displayed diminished kinase activity and FKBP12/Fkh1-dependent rapamycin sensitivity, their phenotypes were nearly opposite in mitosis. Premature mitosis and the G2–M delay occurred in TORC1 and TORC2 mutants, respectively. Surprisingly, separase/cut1—securin/cut2 mutants were rescued by TORC1/tor2-L2048Smutation or rapamycin addition or even Fkh1 deletion, whereas these mutants showed synthetic defect with TORC2/tor1-L2045D. TORC1 and TORC2 coordinate growth, mitosis and cell size control, such as Wee1 and Cdc25 do for the entry into mitosis.
Evidence for benefit vs novelty in new intubation equipment
Authors: Behringer E. C. , Kristensen M. S.
Published: November 2011

A myriad of new intubation equipment has been introduced commercially since the appearance of Macintosh/Miller blades in the 1940s. We review the role of devices that are relevant to current clinical practice based on their presence in the scientific literature. The comparative performance of new vs traditional direct laryngoscopes, their complications, their use in awake intubation techniques and the prediction of unsuccessful intubation with new devices are reviewed. Manikin studies are of limited value in this area. We conclude that in both predicted and unpredicted difficult or failed intubation, carefully selected new intubation equipment has a high success rate for tracheal intubation. Ideally, such devices should be available in all settings where tracheal intubation is performed. Most importantly, experience and competence with any of the new devices are critical for their successful use in any clinical setting.
Expression and regulation ofCCL15 by human airway smooth muscle cells
Authors: Joubert P. , Lajoie‐Kadoch S. , Wellemans V. , Létuvé S. , Tulic M. K. , Halayko A. J. , Hamid Q.
Published: November 2011

Background

Structural cells are an important reservoir of chemokines that coordinate the influx of various immune cells to the lungs of asthmatics. Airway smooth muscle cells (ASMC) are an important source of these chemokines.CCL15 is a recently described chemo‐attractant for neutrophils, eosinophils, monocytes and lymphocytes.

Objective

To determine the production and the regulation ofCCL15 byASMCand to investigate its production in asthmatic airways.

Methods

HumanASMCwere obtained from main bronchial airway segments of patients with mild, moderate and severe asthma. To induce chemokine production, cells were incubated withIL‐4,IL‐13,TNF‐α orIFN‐γ in presence or absence of dexamethasone, mithramycin A (SP‐1 inhibitor) or theIKK‐2 inhibitor,AS602868.CCL15 mRNAexpression was evaluated by real‐timePCR. ImmunoreactiveCCL15 was detected by immuno‐fluorescence andCCL15 protein concentration in the supernatant was measured usingELISA.

Results

CCL15 is constitutively expressed in humanASMCand is strongly up‐regulated byTNF‐α. This up‐regulation is inhibited by dexamethasone, mithramycin A andAS602868.TNF‐α‐inducedCCL15 levels can be synergistically enhanced by the presence ofIFN‐γ, at both the transcriptional and translation level. This synergism isNF‐κB‐dependent. Asthmatic biopsies demonstrated higher expression ofCCL15 compared with non‐asthmatic controls.

Conclusion and Clinical Relevance

Our results show thatASMCare a potent source ofCCL15 in the airways and may directly participate in the recruitment of inflammatory cells to asthmatic airways. Targeting the production ofCCL15 byASMCmight reduce the inflammatory response within the airways of asthmatic patients.
Cardiopulmonary assessment in primary ciliary dyskinesia
Authors: Valerio Giuliana , Giallauria Francesco , Montella Silvia , Vaino Nicola , Vigorito Carlo , Mirra Virginia , Santamaria Francesca
Published: November 2011

Eur J Clin Invest 2012; 42 (6): 617–622

Background  Primary ciliary dyskinesia (PCD) is a rare, usually autosomal recessive disorder of ciliary dysfunction associated with lung involvement, which has a great impact on health. There is limited information concerning the aerobic fitness of children and adolescents with PCD. The aim of this study was to assess cardiopulmonary functional capacity and its relationship with pulmonary function and physical activity (PA) levels in patients with PCD.

Design  Ten patients with PCD (age 13·2 ± 2·8 years) underwent spirometry and cardiopulmonary exercise testing. PA was investigated through a questionnaire. Eight age‐ and body mass index‐matched healthy children were enrolled as controls. Main variables were forced expiratory volume at 1 s, peak oxygen uptake (VO2peak) and time spent in PA.

Results  Forty per cent of patients with PCD had impaired lung function as expressed by FEV1 < 85% predicted. Only patients with impaired lung function exhibited reduced VO2peak (18·1 ± 7·9 mL/kg/min). Time spent in total daily PA was slightly lower in patients than controls, with no difference between patients with normal or reduced lung function. In multiple regression models, male gender (β = 0·518, P = 0·018), age (β = 0·752, P = 0·035) and time spent in vigorous PA (β = 0·353, P = 0·049) were independent predictors of aerobic fitness.

Conclusions  Assessment of resting pulmonary function and cardiopulmonary functional capacity could contribute to the evaluation of pulmonary impairment in PCD. Given the benefit of physical exercise on airway clearance and on general health and quality of life, patients with PCD should be encouraged to adopt an active lifestyle.
Use of atorvastatin to inhibit hypoxia‐induced myocardin expression
Authors: Chiu Chiung‐Zuan , Wang Bao‐Wei , Shyu Kou‐Gi
Published: November 2011

Eur J Clin Invest 2012; 42 (5): 564–571

Background  Hypoxia induces the formation of reactive oxygen species (ROS), myocardin expression and cardiomyocyte hypertrophy. The 3‐hydroxy‐3‐methylglutaryl coenzyme A reductase inhibitors (statins) have been demonstrated to have both antioxidant and antihypertrophic effects. We evaluated the pathways of atorvastatin in repressing ROS and myocardin after hypoxia to prevent cardiomyocyte hypertrophy.

Materials and methods  Cultured rat neonatal cardiomyocytes were subjected to hypoxia, and the expression of myocardin and ROS were evaluated. Different signal transduction inhibitors, atorvastatin and N‐acetylcysteine (NAC) were used to identify the pathways that inhibited myocardin expression and ROS. Electrophoretic motility shift assay (EMSA) and luciferase assay were used to identify the binding of myocardin/serum response factor (SRF) and transcription to cardiomyocytes. Cardiomyocyte hypertrophy was assessed by 3H‐proline incorporation assay.

Results  Myocardin expression after hypoxia was inhibited by atorvastatin, RhoA/Rho kinase inhibitor (Y27632), extracellular signal‐regulated kinase (ERK) small interfering RNA (siRNA)/ERK pathway inhibitor (PD98059), myocardin siRNA and NAC. Bindings of myocardin/SRF, transcription of myocardin/SRF to cardiomyocytes, presence of myocardin in the nuclei of cardiomyocytes and protein synthesis after hypoxia were identified by EMSA, luciferase assay, confocal microscopy and 3H‐proline assay and were suppressed by atorvastatin, Y27632, PD98059 and NAC.

Conclusions  Hypoxia in neonatal cardiomyocytes increases myocardin expression and ROS to cause cardiomyocyte hypertrophy, which can be prevented by atorvastatin by suppressing ROS and myocardin expression.
Macrophytes respond to reach‐scale river restorations
Authors: Lorenz Armin W. , Korte Thomas , Sundermann Andrea , Januschke Kathrin , Haase Peter
Published: November 2011

1. In recent years, river restoration science has been searching for biological indicators of improvement in the physical habitats of streams. To date, research has mainly focused on the use of fish and macroinvertebrates as indicators. Despite their importance in aquatic ecosystems, the response of macrophytes to habitat restoration has been rarely studied.

2. We investigated the macrophyte communities of 40 restored river reaches in the lowland and lower mountainous areas of Germany. Each restored reach was compared to an upstream, unrestored reach using a space‐for‐time‐substitution approach. At each reach, a 100 m stretch was surveyed for submerged and emergent macrophytes, recording the quantity, abundance and growth form of each species. Additionally, microhabitat patterns (substrate, depth, current velocity) and channel parameters (mean and bankfull width, number of channel elements) were recorded.

3. Restored reaches had a significantly higher macrophyte cover, richness, diversity and number of growth forms. Macrophyte diversity and richness were both positively correlated with depth, current and substrate.

4. The analysis of growth forms showed that Lemnids, Helodids, Parvopotamids, Elodids, Peplids and Juncids are all significant indicators of restoration. These species all responded directly to the restoration measures either by highly increasing in abundance or by being present in the restored reaches and absent in the unrestored reaches. While the restored reaches of the lowland rivers were characterized by a high abundance of Peplids and Parvopotamids, the restored reaches of the mountain rivers showed a significantly higher presence and abundance of Lemnids and Helodids.

5. Three macrophyte species (Lemna minor, Persicaria hydropiper, Potamogeton crispus) were regarded as significant indicators of restoration. No species were found to be indicators of unrestored reaches.

6.
Synthesis and applications. Macrophyte communities benefit from river restoration by showing increased cover, abundance and diversity. The main drivers of this enhancement are more natural and diverse substrates and an increased floodplain area in the restored reaches, as well as a greater variability of current and depth patterns. Monitoring of macrophytes could thus be an easy and cost‐effective means to gauge the success of river restoration measures.
Evolution of the large genome in Capsicum annuum occurred through accumulation of single‐type long terminal repeat retrotransposons and their derivatives
Authors: Park Minkyu , Park Jongsun , Kim Seungill , Kwon Jin‐Kyung , Park Hye Mi , Bae Ik Hyun , Yang Tae‐Jin , Lee Yong‐Hwan , Kang Byoung‐Cheorl , Choi Doil
Published: November 2011

Although plant genome sizes are extremely diverse, the mechanism underlying the expansion of huge genomes that did not experience whole‐genome duplication has not been elucidated. The pepper, Capsicum annuum, is an excellent model for studies of genome expansion due to its large genome size (2700 Mb) and the absence of whole genome duplication. As most of the pepper genome structure has been identified as constitutive heterochromatin, we investigated the evolution of this region in detail. Our findings show that the constitutive heterochromatin in pepper was actively expanded 20.0–7.5 million years ago through a massive accumulation of single‐type Ty3/Gypsy‐like elements that belong to the Del subgroup. Interestingly, derivatives of the Del elements, such as non‐autonomous long terminal repeat retrotransposons and long‐unit tandem repeats, played important roles in the expansion of constitutive heterochromatic regions. This expansion occurred not only in the existing heterochromatic regions but also into the euchromatic regions. Furthermore, our results revealed a repeat of unit length 18–24 kb. This repeat was found not only in the pepper genome but also in the other solanaceous species, such as potato and tomato. These results represent a characteristic mechanism for large genome evolution in plants.
Herbicidal activity of phenolic compounds from hairy root cultures of Fagopyrum tataricum
Authors: UDDIN M R , LI X , WON O J , PARK S U , PYON J Y
Published: November 2011

Uddin MR, Li X, Won OJ, Park SU & Pyon JY (2011). Herbicidal activity of phenolic compounds from hairy root cultures of Fagopyrum tataricum. Weed Research 52, 25–33.

The hairy root of Fagopyrum tataricum (Tartary buckwheat) has been shown to produce allelochemicals that have herbicidal activity. The hairy root culture technique has been previously employed with F. tataricum to isolate several phenolic compounds. The purpose of this study was firstly to optimise the hairy root culture of F. tataricum using different growth media, supplemented with varying concentrations (0.1–1.0 mg L−1) of auxin, for phenolic compound production and secondly to evaluate the phenolic compounds for herbicidal activity to different weed species both in growth chamber and in glasshouse studies. The results suggest that hairy roots grown in half‐strength Schenk and Hildebrandt medium showed the highest levels of growth (10.8 g L−1) and the maximal production of gallic acid, chlorogenic acid and rutin. Among the different auxin treatments, indole‐3‐butyric acid at 0.5 mg L−1 produced 24% more hairy root mass than the control. Hairy root extracts of F. tataricum suppressed germination and shoot and root growth in tested weeds, with the grass weed species showing greater susceptibility than the broad‐leaved weed species in a growth chamber bioassay. In the glasshouse experiments, post‐emergence application of the extract on 21‐day‐old seedlings had a greater inhibitory effect than the pre‐emergence application of hairy root extract. Setaria viridis and Aeschynomene indica were the most susceptible species among grass and broad‐leaved weed species, respectively. This study demonstrated that hairy root extract of F. tataricum contained allelopathic compounds and that their phytotoxicity varied with weed species.
Application of synthetic herbivore‐induced plant volatiles causes increased parasitism of herbivores in the field
Authors: Uefune M. , Choh Y. , Abe J. , Shiojiri K. , Sano K. , Takabayashi J.
Published: November 2011

We previously reported that Cotesia vestalis (Hymenoptera, Braconidae), a parasitoid of diamondback moth (DBM) (Plutella xylostella; Lepidoptera, Plutellidae) larvae, was attracted to volatiles from crucifer plants infested by moth larvae kept in a desktop acrylic box, and that a blend of four DBM‐induced plant volatiles was responsible for this attraction. In this study, using a specially designed dispenser to release the four compounds, we demonstrated that the wasp was attracted to intact komatsuna plants (Brassica rapa var. perviridis). The experiments were performed in a climate‐controlled room, which was approximately 1000 times larger than the acrylic box used previously. Similarly, using the dispenser in the field, C. vestalis females were attracted to intact komatsuna plants with the dispenser from a distance of three metres. We also examined the effect of the volatile blend on the incidence of parasitism of DBM larvae in the field. Three small containers containing DBM‐infested komatsuna plants with dispensers, and three control containers containing only infested plants (control) were arranged in two lines running perpendicular to a komatsuna field in which both DBM larvae and C. vestalis populations were maintained, at distances of 12, 30 and 70 m. The results showed that the incidence of DBM parasitism was significantly higher in containers containing dispensers than in the control containers, suggesting that the blend could potentially be applied to DBM control in agroecosystems.