bluuebunny/crossref_metadata_2025 huggingface dataset:
Problems of Oxfordian and Kimmeridgian stratigraphy in northern Central Siberia (Nordvik Peninsula section)
Authors: Nikitenko B.L. , Knyazev V.G. , Lebedeva N.K. , Peshchevitskaya E.B. , Kutygin R.V.
Published: August 2011

The Oxfordian–Lower Hauterivian section of the Nordvik Peninsula (northern Central Siberia) is a reference for developing zonal scales for various fossil groups and improving the Boreal zonal standard. In the middle 1950s–late 1980s, it was studied extensively by geologists, stratigraphers, lithologists, and experts on various fossil groups. These studies yielded rich fossil and microfossil collections and a set of parallel zonal scales for various faunal groups. Recently, a new detailed ammonite zonation of the Oxfordian and Kimmeridgian units of this section has been proposed. These results contradict the previous biostratigraphic data on ammonites, foraminifers, and palynomorphs. In the present paper, all the biostratigraphic data on the Oxfordian and Kimmeridgian units of the Nordvik Peninsula (Cape Urdyuk-Khaya) and northern Central Siberia undergo a comprehensive analysis and comparison with those on the Boreal Realm. The ammonite-constrained stratigraphic position of the lower Upper Jurassic in the Cape Urdyuk-Khaya section is interpreted as Upper Oxfordian or Middle Oxfordian. In our view, this difference in the understanding is due to the misidentification of some Oxfordian ammonite forms. The zones based on other fossil groups (foraminifers, dinocysts) which were distinguished in the Upper Oxfordian and Kimmeridgian sections of the Nordvik Peninsula are well traceable circumarctically. Their stratigraphic position in various regions of the Northern Hemisphere is constrained by ammonites and bivalves. However, if we use the last alternative ammonite zonation of this section part, hardly explicable contradictions will appear in interregional foraminiferal and dinocyst correlations.
Tectonic interpretation of the thermochronological data and PT-conditions of rock metamorphism in the Bodonchin zonal complex (Mongolian Altay)
Authors: Polyansky O.P. , Sukhorukov V.P. , Travin A.V. , Alekhin I.G. , Yudin D.S.
Published: August 2011

Based on the new petrological and thermochronological data, analysis of the metamorphism conditions and tectonic evolution of the Bodonchin zonal complex in the Mongolian Altay was performed. Using mineral geothermometers and geobarometers, the parameters of the thermal state of the Mongolian Altay crust site during the collision of terranes were estimated, and the paleogeotherm at the peak of syncollisional metamorphism was reconstructed. The thermal state of the crust was determined by either a high concentration of radioactive heat sources or a high mantle heat flow. The estimated metamorphism temperatures and pressures of rocks in two zones (staurolite-kyanite schists and migmatites) of the Bodonchin complex correspond to the paleogeotherms with average temperature gradients ∂T/∂z = 25.5 and 27.2 ºC/km. The results of isotope dating of zircons and metamorphic minerals were used to construct a thermochronological model for the regressive stage of evolution of the polymetamorphic complex. The rates of the ascent of metamorphic rocks to the surface as a result of thrusts in the Bulgan Fault zone were estimated at 0.3–1 mm/year.
Genauigkeit von Lehrerurteilen über die Lesekompetenz ihrer Schülerinnen und Schüler in der Sekundarstufe I – Eine Frage der Spezifität?
Authors: Karing Constance , Matthäi Jacqueline , Artelt Cordula
Published: August 2011

Zusammenfassung. In der vorliegenden Studie wurde die Akkuratheit von globalen (Konstruktebene) und aufgabenspezifischen (Aufgabenebene) Lehrereinschätzungen von Schülerleistungen im Bereich des Lesens untersucht und verglichen. Darüber hinaus wurde der Einfluss des Geschlechts und des sozioökonomischen Status auf die Lehrerurteile überprüft. Die Ergebnisse beziehen sich auf 64 Deutschlehrkräfte und deren Klassen der fünften Jahrgangsstufe, die an der BiKS-Studie teilnahmen. Die Lehrerurteile wiesen sowohl auf der Konstrukt- als auch auf der Aufgabenebene nur geringe Zusammenhänge mit den Schülerleistungen auf. Dabei fielen die globalen Lehrerurteile akkurater aus als die aufgabenspezifischen Einschätzungen. In ihren Urteilen auf Aufgabenebene überschätzten die Deutschlehrkräfte im Mittel das Niveau der Lesekompetenz, schätzten aber die Streuung akkurat ein und wiesen eine mittelhohe Trefferquote auf. Zudem zeigte sich, dass diese Komponenten nur gering miteinander korrelierten. Weiterhin konnten wir in dieser Studie feststellen, dass weder der sozioökonomische Status noch das Geschlecht der Schülerinnen und Schüler über die Schülerleistung hinaus einen signifikanten Einfluss auf die globalen und aufgabenspezifischen Lehrereinschätzungen hatten.
Momentan verfügbare ­Selbstkontrollkraft – Vorstellung eines Messinstruments und erste Befunde aus pädagogisch-­psychologischen Kontexten
Authors: Bertrams Alex , Unger und Alexander , Dickhäuser Oliver
Published: August 2011

Zusammenfassung.Selbstkontrolle spielt in pädagogischen Kontexten oft eine entscheidende Rolle, beispielsweise wenn Lernende attraktiven Handlungsalternativen widerstehen müssen. Etliche Studien zeigen, dass die erfolgreiche Ausübung von Selbstkontrolle von der momentanen Verfügbarkeit an Selbstkontrollkraft abhängt. Zur Erfassung der momentanen Selbstkontrollkraft in deutschsprachigen Stichproben, wurde die State Self-Control Capacity Scale ins Deutsche adaptiert. In der vorliegenden Arbeit wird über fünf Teilstudien berichtet, in denen die psychometrische Güte dieser Skala überprüft wurde. Über alle Studien hinweg erwies sich die eindimensionale Skala als sehr reliabel (Cronbachs Alphas ≥ .93). Bezüglich ihrer Validität zeigten sich erwartete Zusammenhänge mit Validitätskriterien (z. B. Angst, Stress, am gegenwärtigen Tag bereits in Lehrveranstaltungen verbrachte Zeit); zusätzlich gelang die empirische Trennung von verschiedenen Stimmungsaspekten. Des Weiteren bildete die neue Skala (quasi-) experimentell im Labor und im Feld (Hochschule) induzierte Unterschiede in der Selbstkontrollkraft ab. Auch eine aus zehn Items bestehende Kurzskala erwies sich als hinreichend reliabel und valide.
Generalisten oder Spezialisten? ­Bereichsspezifität und leistungs­bezogene Zusammenhänge des schulischen Selbstkonzepts von Schulanfängern
Authors: Poloczek Sebastian , Karst Karina , Praetorius Anna-Katharina , Lipowsky Frank
Published: August 2011

Zusammenfassung. In der vorliegenden Studie wird erstens untersucht, ob sich wenige Wochen nach der Einschulung bereits domänenspezifische Facetten des schulischen Selbstkonzepts (Lesen, Schreiben und Rechnen) unterscheiden lassen, und zweitens, in welchem Ausmaß sich die Selbstkonzeptfacetten Lesen und Rechnen durch Lese- und Rechenleistungen sowie durch Leistungs­einschät­zungen der Eltern vorhersagen lassen. Die Ergebnisse der konfirmatorischen Faktorenanalysen mit Selbsteinschätzungen von 693 Kindern des 1. Schuljahres zeigen, dass ein Dreifaktorenmodell mit den Facetten Lesen, Schreiben und Rechnen am besten zu den Daten passt. Des Weiteren zeigen sich schon in diesem Alter signifikante, allerdings gering ausgeprägte Zusammenhänge zwischen Leistungen bzw. elterlichen Leistungs­einschätzungen und den korrespondierenden schulischen Selbstkonzeptfacetten der Kinder. Die vom I/E-Modell postulierten negativen Pfade zwischen Leistungen und nicht-korrespondierenden Selbsteinschätzungen lassen sich nicht nachweisen. Zusammengenommen sprechen die Ergebnisse dafür, dass sich schon ca. zwei Monate nach der Einschulung verschiedene Facetten des schulischen Selbstkonzepts unterscheiden lassen, auch wenn die Facetten vergleichsweise hoch korreliert sind. Aufgrund der Zusammenhänge mit Leistungen sowie Elterneinschätzungen lässt sich vermuten, dass Erstklässlerinnen und Erstklässler beginnen, durch Perspektivübernahme sowie soziale Vergleiche gewonnene Informationen in ihr Selbstkonzept zu integrieren.
Application of acoustic full waveform inversion to retrieve high‐resolution temperature and salinity profiles from synthetic seismic data
Authors: Kormann J. , Biescas B. , Korta N. , de la Puente J. , Sallarès V.
Published: August 2011

Recent works show that multichannel seismic (MCS) systems are able to provide detailed information on the oceans' fine structure. The aim of this paper is to analyze whether 1‐D full waveform inversion algorithms are suitable to recover the extremely weak acoustic impedance contrasts associated to the oceans' fine structure, as well as their potential to image meso‐scale objects such as meddies. We limited our analysis to synthetic, noise‐free data, in order to identify some methodological issues related to this approach under idealistic conditions (e.g., 1‐D wave propagation, noise‐free data, known source wavelet). We first discuss the influence of the starting model in the context of the multi‐scale strategy that we have implemented. Then we show that it is possible to retrieve not only sound speed but also salinity and temperature contrasts within reasonable bounds from the seismic data using Neural Network relationships trained with regional oceanographic data sets. Potentially, the vertical resolution of the obtained models, which depends on the maximum frequency inverted, is of the order of 5–10 m, whereas the root mean square error of the inverted properties is shown to be ∼0.5 m/s for sound speed, 0.1°C for temperature, and 0.06 for salinity. To conclude this study, we have inverted synthetic data simulated along an oceanographic transect acquired during the EU‐funded Geophysical Oceanography (GO) project. The results demonstrate the applicability of the method for synthetic data, as well as its potential to define oceanographic features along 2‐D transects at full ocean depth with excellent lateral resolution.
Diastolic Dysfunction and Intraventricular Dyssynchrony Are Restored by Low Intensity Exercise Training in Obese Men
Authors: Schuster Iris , Vinet Agnès , Karpoff Lucie , Startun Aliona , Jourdan Nathalie , Dauzat Michel , Nottin Stephane , Perez‐Martin Antonia
Published: August 2011

The aim of this study was to evaluate the impact of a low‐intensity training program on subclinical cardiac dysfunction and on dyssynchrony in moderately obese middle aged men. Ten obese and 14 age‐matched normal‐weight men (BMI: 33.6 ± 1.0 and 24.2 ± 0.5 kg/m2) were included. Obese men participated in an 8‐week low‐intensity training program without concomitant diet. Cardiac function and myocardial synchrony were assessed by echocardiography with tissue Doppler imaging (TDI) and speckle tracking echocardiography (STE). At baseline, obese men showed diastolic dysfunction on standard echocardiography, lower strain values (systolic strain: 15.9 ± 0.9 vs. 18.8 ± 0.3%, diastolic strain rate: 0.81 ± 0.09 vs. 1.05 ± 0.06 s−1), and significant intraventricular dyssynchrony (systolic: 13.3 ± 2.1 vs. 5.4 ± 2.1 ms, diastolic: 17.4 ± 3.2 vs. 9.1 ± 2.1 ms) (P < 0.05 vs. controls for all variables). Training improved aerobic fitness, decreased systolic blood pressure and heart rate, and reduced fat mass without weight loss. Diastolic function, strain values (systolic strain: 17.4 ± 0.9%, diastolic strain rate: 0.96 ± 0.12 s−1) and intraventricular dyssynchrony (systolic: 3.3 ± 1.7 ms, diastolic: 5.5 ± 3.4 ms) improved significantly after training (P < 0.05 vs. baseline values for all variables), reaching levels similar to those of normal‐weight men. In conclusion, in obese men, a short and easy‐to‐perform low intensity training program restored diastolic function and cardiac synchrony and improved body composition without weight loss.
A New and Easy Technique of Maxillomandibular Fixation in Treatment of Mandibular Fractures
Authors: Singh Virendra , Bhagol Amrish
Published: August 2011

The present work evaluated the success of maxillomandibular fixation (MMF) by a new and simplified technique in management of minimally displaced mandibular fractures. A total of 20 patients who sustained various types of mandibular fractures were treated at the Government Dental College, Rohtak, India by a new MMF technique. The patients were evaluated by preoperative and postoperative radiography, and clinical testing was performed to assess the degree of tooth mobility adjacent to the site of MMF. The time required for MMF was also noted. Patient recovery was uneventful in all 20 cases, and the period of MMF ranged from 2 to 4 weeks (mean 21 days). The outcome was good. The mean time for performing MMF was 12 minutes (range, 10 to 15 minutes). It is a simple, quick, economical, and minimally invasive technique. Its mechanical principle provides an advantage in preventing postoperative periodontal problems.
Dendritic Myxofibrolipoma: Often Misdiagnosed as Sarcoma
Authors: Al-Maskery Awatif Y. , Al-Sidairy Salem M. , Al-Hamadani Aisha S.
Published: August 2011

The author describes a benign soft tissue tumor that could be easily mistaken for sarcoma. It represents a combined feature of solitary fibrous tumor and spindle cell lipoma. The clinical presentation, diagnosis, and management of this lesion are discussed. It highlights the importance of proper diagnosis to prevent unnecessary and ineffective treatment by clinicians as the complete excision of this lesion is the treatment of choice and recurrence is very unlikely. It is believed that this case is the first reported case of dendritic myxofibrolipoma occurring in the lower lip mucosa in an Omani patient.
On duality and negative dimensions in the theory of Lie groups and symmetric spaces
Authors: Mkrtchyan Ruben L. , Veselov Alexander P.
Published: August 2011

We give one more interpretation of the symbolic formulas U( − N) = U(N) and Sp( − 2N) = SO(2N) and show that they can be extended to the classical symmetric spaces using Macdonald duality for Jack and Jacobi symmetric functions.
How much do we spend on prescription medicines? Out-of-pocket costs for patients in Australia and other OECD countries
Authors: Kemp Anna , Preen David B. , Glover John , Semmens James , Roughead Elizabeth E.
Published: August 2011

Objectives. To determine changes in out-of-pocket expenditure on prescription medicines for Australian patients, and how patient expenditure compares with other Organisation for Economic Co-operation and Development (OECD) countries. Methods. We examined out-of-pocket expenditure on prescription medicines by patients in Australia between 1970 and 2007, and between Australia and 15 other OECD countries (Canada, Czech Republic, Denmark, Finland, France, Germany, Japan, Republic of Korea (South Korea), Luxembourg, Poland, Slovak Republic, Spain, Sweden, Switzerland and the United States) in 2005. Findings. Spending on publicly subsidised medicines by Australian patients increased from $16 per person in 1971 to $62 in 2007. Patient expenditure on all prescription medicines had risen to $134 per person in 2007. Out-of-pocket expenditure for Australian patients ranked 4th of 14 OCED countries with universal pharmaceutical subsidies. Australian patients pay 28% of national pharmaceutical expenditure; more than patients in South Korea (27%), Slovak Republic (26%), Sweden (22%), France, Luxembourg, Japan and Switzerland (17%), Germany (15%), Czech Republic (11%) and Spain (6%), but less than patients in Finland (36%), Denmark (33%) and Poland (34%). Conclusions. Compared to other OECD countries, Australian out-of-pocket costs are now in the mid to upper range. Further increases have the potential to significantly affect access to care. What is known about the topic? In Australia and internationally, increases in the portion of prescription medicines paid by patients have been associated with falls in utilisation. Despite the pharmaceutical subsidies patients receive under the Australian Pharmaceutical Benefits Scheme, prescription medicine costs are a barrier to access for many low income, elderly and other vulnerable patients. What does this paper add? The findings demonstrate that the prescription medicine expenditure of Australian patients has increased substantially over recent years, and is double that indicated by benefit-paid data alone. Out-of-pocket expenditure in Australia is moderate-to-high by international standards. What are the implications for practitioners? Patient out-of-pocket expenditure for prescription medicines in Australia has increased in recent decades, accounting for higher proportions of household and national medicine expenditure. Lack of patient involvement in treatment decisions is associated with patients forgoing medicines due to costs. Practitioners are encouraged to discuss treatment decisions, cost-barriers and possible strategies to overcome cost-barriers with their patients.
Dynamics of the plague–wildlife–human system in Central Asia are controlled by two epidemiological thresholds
Authors: Samia Noelle I. , Kausrud Kyrre Linné , Heesterbeek Hans , Ageyev Vladimir , Begon Mike , Chan Kung-Sik , Stenseth Nils C.
Published: August 2011

Plague (caused by the bacteriumYersinia pestis) is a zoonotic reemerging infectious disease with reservoirs in rodent populations worldwide. Using one-half of a century of unique data (1949–1995) from Kazakhstan on plague dynamics, including data on the main rodent host reservoir (great gerbil), main vector (flea), human cases, and external (climate) conditions, we analyze the full ecoepidemiological (bubonic) plague system. We show that two epidemiological threshold quantities play key roles: one threshold relating to the dynamics in the host reservoir, and the second threshold relating to the spillover of the plague bacteria into the human population.
Functional melanocytes derived from human pluripotent stem cells engraft into pluristratified epidermis
Authors: Nissan Xavier , Larribere Lionel , Saidani Manoubia , Hurbain Ilse , Delevoye Cédric , Feteira Jessica , Lemaitre Gilles , Peschanski Marc , Baldeschi Christine
Published: August 2011

Melanocytes are essential for skin homeostasis and protection, and their defects in humans lead to a wide array of diseases that are potentially extremely severe. To date, the analysis of molecular mechanisms and the function of human melanocytes have been limited because of the difficulties in accessing large numbers of cells with the specific phenotypes. This issue can now be addressed via a differentiation protocol that allows melanocytes to be obtained from pluripotent stem cell lines, either induced or of embryonic origin, based on the use of moderate concentrations of a single cytokine, bone morphogenic protein 4. Human melanocytes derived from pluripotent stem cells exhibit all the characteristic features of their adult counterparts. This includes the enzymatic machinery required for the production and functional delivery of melanin to keratinocytes. Melanocytes also integrate appropriately into organotypic epidermis reconstructed in vitro. The availability of human cells committed to the melanocytic lineage in vitro will enable the investigation of those mechanisms that guide the developmental processes and will facilitate analysis of the molecular mechanisms responsible for genetic diseases. Access to an unlimited resource may also prove a vital tool for the treatment of hypopigmentation disorders when donors with matching haplotypes become available in clinically relevant banks of pluripotent stem cell lines.
NLRP3 inflammasome plays a critical role in the pathogenesis of hydroxyapatite-associated arthropathy
Authors: Jin Chengcheng , Frayssinet Patrick , Pelker Richard , Cwirka Diane , Hu Bo , Vignery Agnès , Eisenbarth Stephanie C. , Flavell Richard A.
Published: August 2011

The proinflammatory and catabolic cytokine IL-1β has been implicated in the pathogenesis of osteoarthritis (OA) by mediating synovial inflammation and cartilage degeneration. Although synovial macrophages are suggested to be the source of IL-1β, the mechanism remains unclear. Ectopic deposition of hydroxyapatite (HA) crystals in joints is closely associated with OA and other arthropathies, but the precise role of HA in arthritis pathogenesis has not been clearly demonstrated. Here we show that HA crystals of a particular size and shape can stimulate robust secretion of proinflammatory cytokines IL-1β and IL-18 from murine macrophages in a NLRP3 inflammasome-dependent manner. HA-induced inflammasome activation is dependent on potassium efflux, generation of reactive oxygen species (ROS), and lysosomal damage, but independent of cell death. Mice lacking the inflammasome components are protected against HA-induced neutrophilic inflammation in the air-pouch model of synovitis, and they show decreased joint pathology accompanying spontaneous HA deposition in the
ank
-deficient mouse model of arthritis. Moreover, calcium crystal positive synovial fluids from some OA patients exhibited inflammasome-stimulatory activity in vitro. These results demonstrate that the NLRP3 inflammasome mediates the pathological effect of HA crystals in vitro and in vivo and suggest a critical role for the inflammasome in the pathogenesis of OA.
The Establishment of the Position of Marja'iyyt-i Taqlid in the Twelver-Shi'i Community
Authors: Moussavi Ahmad Kazemi
Published: August 2011

Nineteenth-century Iran witnessed the advent of a new socioreligious institution. While the theory of a divinely appointed Imam (Imām al-Manṣūb) increasingly became eschatological in nature, a highly centralized religious position came into being whose source of power was not to be found in the classical Shi'i doctrine. The position of marjaᶜ-i taqlīd is a product of several religious developments that characterized the nineteenth-century Shi'i community. The prevalence of the Uṣūlī school and the formulation of two important doctrines, i.e., aᶜlamiyyat (more knowledgeability) and vilāyat-i faqīh (the governance of the jurist) are held as three major juridical impetuses underlying the birth of the institution of marjaᶜiyyat-i taqlīd. Therefore, we will first deal with the Uṣūlī process, then the doctrines of aᶜlamiyyat and vilāyat-i faqīh, then with the qualifications of a marjᶜ, and the question of who the first marjaᶜ of the Twelver-Shi'i community was, and finally the place of marjaᶜ-i taqlīd in the political life of Shi'i Iran.
Exfoliation of the tungsten fibreform nanostructure by unipolar arcing in the LHD divertor plasma
Authors: Tokitani M. , Kajita S. , Masuzaki S. , Hirahata Y. , Ohno N. , Tanabe T.
Published: August 2011

The tungsten nanostructure (W-fuzz) created in the linear divertor simulator (NAGDIS) was exposed to the Large Helical Device (LHD) divertor plasma for only 2 s (1 shot) to study exfoliation/erosion and microscopic modifications due to the high heat/particle loading under high magnetic field conditions. Very fine and randomly moved unipolar arc trails were clearly observed on about half of the W-fuzz area (6 × 10 mm2). The fuzzy surface was exfoliated by continuously moving arc spots even for the very short exposure time. This is the first observation of unipolar arcing and exfoliation of some areas of the W-fuzz structure itself in a large plasma confinement device with a high magnetic field. The typical width and depth of each arc trail were about 8 µm and 1 µm, respectively, and the arc spots moved randomly on the micrometre scale. The fractality of the arc trails was analysed using a box-counting method, and the fractal dimension (D) of the arc trails was estimated to be D ≈ 1.922. This value indicated that the arc spots moved in Brownian motion, and were scarcely influenced by the magnetic field. One should note that such a large scale exfoliation due to unipolar arcing may enhance the surface erosion of the tungsten armour and act as a serious impurity source for fusion plasmas.
Linear microstability analysis of a low-Z impurity doped tokamak plasma
Authors: Romanelli M. , Szepesi G. , Peeters A.G. , Apicella M.L. , Marinucci M. , Mazzotta C. , Mazzitelli G. , Frigione D.
Published: August 2011

Improved electron and deuterium energy and particle confinement in the presence of low-Z impurities have been observed in many tokamaks under various experimental conditions. Peaked electron density profiles have been obtained in the Frascati Tokamak Upgrade (FTU) ohmic plasmas where a high concentration of lithium has been detected following the installation of a Liquid Lithium Limiter (LLL). This paper presents the results of a gyrokinetic study on the effects of lithium and other low-Z impurities on the linear stability of deuterium and electron temperature driven modes and their associated fluxes for plasma parameters such as those found in the core of LLL-FTU plasmas.

Simulations show that a lithium concentration in excess of n
Li/n
e = 15%, as estimated in the initial phase of a reference FTU discharge, is found to have a strong stabilizing effect on the TEM and high-frequency ETG modes. A significant stabilization of the electron driven modes can still be observed when the lithium concentration is reduced to 3%.

In the presence of a significant impurity concentration (n
Li/n
e = 3–15%) the long wavelength ITG modes drive an inward electron and deuterium flux and outward lithium flux. This process may lead eventually to an increased electron and deuterium density peaking and a reduced Z
eff (lithium density below n
Li/n
e = 1%).
Equilibrium and transport for quasi-helical reversed field pinches
Authors: Cappello S. , Bonfiglio D. , Escande D.F. , Guo S.C. , Predebon I. , Sattin F. , Veranda M. , Zanca P. , Angioni C. , Chacón L. , Dong J.Q. , Garbet X. , Liu S.F.
Published: August 2011

This paper presents the most recent results in theoretical/numerical studies on the physics of the quasi-helical regime in reversed field pinch (RFP) configurations. Such regime systematically characterizes RFX-mod experiments at high currents (I
p > 1.2 MA), producing clear internal electron transport barriers. Several approaches, ranging from a macroscopic (MHD) to a microscopic (transport) description, have been used to tackle the related complex physics. From the macroscopic point of view, we derive analytically the electrostatic velocity field consistent with a generic helical ohmic equilibrium. We also provide the first MHD initial-value simulation results in toroidal geometry obtained with the PIXIE3D code. Concerning transport, the effect of magnetic chaos healing by mode separatrix expulsion, believed to favour the formation of transport barriers, is discussed. Results indicate that helical equilibria originated by non-resonant modes are more resilient to chaos formation. Finally, gyrofluid and gyrokinetic tools have been used towards a first assessment of the role of microturbulence in the RFP. Concerning the electrostatic branches, ion temperature gradient mode stability is robustly improved in RFP with respect to tokamaks, due to stronger Landau damping effects, and the marginality condition is estimated to be only spottily reached in present experimental regimes, unless the effects of impurities are considered. Impurities, which in RFX-mod accumulate in the edge, may also significantly impact the stability of the impurity-driven modes. On the electromagnetic side, microtearing turbulence is found to probably play a role at the transport barriers.
Prospects for pilot plants based on the tokamak, spherical tokamak and stellarator
Authors: Menard J.E. , Bromberg L. , Brown T. , Burgess T. , Dix D. , El-Guebaly L. , Gerrity T. , Goldston R.J. , Hawryluk R.J. , Kastner R. , Kessel C. , Malang S. , Minervini J. , Neilson G.H. , Neumeyer C.L. , Prager S. , Sawan M. , Sheffield J. , Sternlieb A. , Waganer L. , Whyte D. , Zarnstorff M.
Published: August 2011

A potentially attractive next-step towards fusion commercialization is a pilot plant, i.e. a device ultimately capable of small net electricity production in as compact a facility as possible and in a configuration scalable to a full-size power plant. A key capability for a pilot-plant programme is the production of high neutron fluence enabling fusion nuclear science and technology (FNST) research. It is found that for physics and technology assumptions between those assumed for ITER and nth-of-a-kind fusion power plant, it is possible to provide FNST-relevant neutron wall loading in pilot devices. Thus, it may be possible to utilize a single facility to perform FNST research utilizing reactor-relevant plasma, blanket, coil and auxiliary systems and maintenance schemes while also targeting net electricity production. In this paper three configurations for a pilot plant are considered: the advanced tokamak, spherical tokamak and compact stellarator. A range of configuration issues is considered including: radial build and blanket design, magnet systems, maintenance schemes, tritium consumption and self-sufficiency, physics scenarios and a brief assessment of research needs for the configurations.
Role of Survivin in cytokinesis revealed by a separation-of-function allele
Authors: Szafer-Glusman Edith , Fuller Margaret T. , Giansanti Maria Grazia
Published: August 2011

The chromosomal passenger complex (CPC), containing Aurora B kinase, Inner Centromere Protein, Survivin, and Borealin, regulates chromosome condensation and interaction between kinetochores and microtubules at metaphase, then relocalizes to midzone microtubules at anaphase and regulates central spindle organization and cytokinesis. However, the precise role(s) played by the CPC in anaphase have been obscured by its prior functions in metaphase. Here we identify a missense allele of Drosophila Survivin that allows CPC localization and function during metaphase but not cytokinesis. Analysis of mutant cells showed that Survivin is essential to target the CPC and the mitotic kinesin-like protein 1 orthologue Pavarotti (Pav) to the central spindle and equatorial cell cortex during anaphase in both larval neuroblasts and spermatocytes. Survivin also enabled localization of Polo kinase and Rho at the equatorial cortex in spermatocytes, critical for contractile ring assembly. In neuroblasts, in contrast, Survivin function was not required for localization of Rho, Polo, or Myosin II to a broad equatorial cortical band but was required for Myosin II to transition to a compact, fully constricted ring. Analysis of this “separation-of-function” allele demonstrates the direct role of Survivin and the CPC in cytokinesis and highlights striking differences in regulation of cytokinesis in different cell systems.
Consumer Response to Commodity‐Specific and Broad‐Based Promotion Programs for Fruits and Vegetables
Authors: Rickard Bradley J. , Liaukonyte Jura , Kaiser Harry M. , Richards Timothy J.
Published: August 2011

Generic promotion activities have traditionally been used for individual agricultural commodities, yet there is renewed interest in implementing a mandatory “broad‐based” promotion program for all fruits and vegetables. Here we use data from an experiment that introduce subjects to various promotional efforts for fruits and vegetables to estimate the shift and rotational effects of advertising. Econometric results indicate that commodity‐specific promotional efforts may not be effective at increasing demand for fruits and vegetables. After controlling for various demographic differences among treatments, our results show that consumers’ valuation of fruits and vegetables was highest among subjects exposed to broad‐based advertisements.
Comparative analysis of algorithms for next-generation sequencing read alignment
Authors: Ruffalo Matthew , LaFramboise Thomas , Koyutürk Mehmet
Published: August 2011

Motivation: The advent of next-generation sequencing (NGS) techniques presents many novel opportunities for many applications in life sciences. The vast number of short reads produced by these techniques, however, pose significant computational challenges. The first step in many types of genomic analysis is the mapping of short reads to a reference genome, and several groups have developed dedicated algorithms and software packages to perform this function. As the developers of these packages optimize their algorithms with respect to various considerations, the relative merits of different software packages remain unclear. However, for scientists who generate and use NGS data for their specific research projects, an important consideration is choosing the software that is most suitable for their application.

Results: With a view to comparing existing short read alignment software, we develop a simulation and evaluation suite, Seal, which simulates NGS runs for different configurations of various factors, including sequencing error, indels and coverage. We also develop criteria to compare the performances of software with disparate output structure (e.g. some packages return a single alignment while some return multiple possible alignments). Using these criteria, we comprehensively evaluate the performances of Bowtie, BWA, mr- and mrsFAST, Novoalign, SHRiMP and SOAPv2, with regard to accuracy and runtime.

Conclusion: We expect that the results presented here will be useful to investigators in choosing the alignment software that is most suitable for their specific research aims. Our results also provide insights into the factors that should be considered to use alignment results effectively. Seal can also be used to evaluate the performance of algorithms that use deep sequencing data for various purposes (e.g. identification of genomic variants).

Availability:  Seal is available as open source at http://compbio.case.edu/seal/.

Contact:  matthew.ruffalo@case.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Detecting biological network organization and functional gene orthologs
Authors: Cui Jike , DeLuca Todd F. , Jung Jae-Yoon , Wall Dennis P.
Published: August 2011

SUMMARY: We developed a package TripletSearch to compute relationships within triplets of genes based on Roundup, an orthologous gene database containing >1500 genomes. These relationships, derived from the coevolution of genes, provide valuable information in the detection of biological network organization from the local to the system level, in the inference of protein functions and in the identification of functional orthologs. To run the computation, users need to provide the GI IDs of the genes of interest.

Availability:  http://wall.hms.harvard.edu/sites/default/files/tripletSearch.tar.gz

Contact:  dpwall@hms.harvard.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Melghirimyces algeriensis gen. nov., sp. nov., a member of the family

Thermoactinomycetaceae

, isolated from a salt lake
Authors: Addou Ammara Nariman , Schumann Peter , Spröer Cathrin , Hacene Hocine , Cayol Jean-Luc , Fardeau Marie-Laure
Published: August 2011

A novel filamentous bacterium, designated NariEXT, was isolated from soil collected from Chott Melghir salt lake, which is located in the south-east of Algeria. The strain was an aerobic, halotolerant, thermotolerant, Gram-positive bacterium that was able to grow in NaCl concentrations up to 21 % (w/v), at 37–60 °C and at pH 5.0–9.5. The major fatty acids were iso- and anteiso-C15 : 0. The DNA G+C content was 47.3 mol%. The major menaquinone was MK-7, but MK-6 and MK-8 were also present. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine (methyl-PE). Results of molecular and phenotypic analysis led to the description of the strain as a new member of the family

Thermoactinomycetaceae

. The isolate was distinct from members of recognized genera of this family by morphological, biochemical and chemotaxonomic characteristics. Strain NariEXT showed 16S rRNA gene sequence similarities of 95.38 and 94.28 % with the type strains of

Desmospora activa

and

Kroppenstedtia eburnea

, respectively, but differed from both type strains in its sugars, polar lipids and in the presence of methyl-PE. On the basis of physiological and phylogenetic data, strain NariEXT represents a novel species of a new genus of the family

Thermoactinomycetaceae

for which the name Melghirimyces algeriensis gen. nov., sp. nov. is proposed. The type strain of Melghirimyces algeriensis, the type species of the genus, is NariEXT ( = DSM 45474T = CCUG 59620T).
Taxonomic revision of the genus

Geobacillus

: emendation of

Geobacillus

,

G. stearothermophilus

,

G. jurassicus

,

G. toebii

,

G. thermodenitrificans

and G. thermoglucosidans (nom. corrig., formerly ‘thermoglucosidasius’); transfer of

Bacillus thermantarcticus

to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of

G. tepidamans

to

Anoxybacillus

as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov.
Authors: Coorevits An , Dinsdale Anna E. , Halket Gillian , Lebbe Liesbeth , De Vos Paul , Van Landschoot Anita , Logan Niall A.
Published: August 2011

Sixty-two strains of thermophilic aerobic endospore-forming bacteria were subjected to polyphasic taxonomic study including 16S rRNA gene sequence analysis, polar lipid and fatty acid analysis, phenotypic characterization, and DNA–DNA hybridization experiments. Distinct clusters of the species

Geobacillus stearothermophilus

,

Geobacillus thermodenitrificans

,

Geobacillus toebii

and

Geobacillus thermoglucosidasius

were formed, allowing their descriptions to be emended, and the distinctiveness of the poorly represented species

Geobacillus jurassicus

,

Geobacillus subterraneus

and

Geobacillus caldoxylosilyticus

was confirmed. It is proposed that the name

Geobacillus thermoglucosidasius

be corrected to Geobacillus thermoglucosidans nom. corrig.

Bacillus thermantarcticus

clustered between

Geobacillus

species on the basis of 16S rRNA gene sequence analysis, and its transfer to the genus

Geobacillus

as Geobacillus thermantarcticus comb. nov. (type strain LMG 23032T = DSM 9572T = strain M1T = R-35644T) is proposed. The above-mentioned species, together with

Geobacillus thermoleovorans

and

Geobacillus thermocatenulatus

, form a monophyletic cluster representing the genus

Geobacillus

. The distinctiveness of ‘Geobacillus caldoproteolyticus’ was confirmed and it is proposed that it be accommodated, along with

Geobacillus tepidamans

, in the genus

Anoxybacillus

as Anoxybacillus caldiproteolyticus sp. nov. (type strain DSM 15730T = ATCC BAA-818T = LMG 26209T = R-35652T) and Anoxybacillus tepidamans comb. nov. (type strain LMG 26208T = ATCC BAA-942T = DSM 16325T = R-35643T), respectively. The type strain of

Geobacillus debilis

was not closely related to any members of the genera

Anoxybacillus

and

Geobacillus

, and it is proposed that this species be placed in the new genus Caldibacillus as Caldibacillus debilis gen. nov. comb. nov. The type strain of the type species, Caldibacillus debilis, is LMG 23386T ( = DSM 16016T = NCIMB 13995T = TfT = R-35653T).
Thermus composti sp. nov., isolated from oyster mushroom compost
Authors: Vajna Balázs , Kanizsai Szilvia , Kéki Zsuzsa , Márialigeti Károly , Schumann Peter , Tóth Erika M.
Published: August 2011

A Gram-stain-negative, rod-shaped bacterium (strain K-39T) was isolated from the thermophilic phase of the composting process for oyster mushroom substrate preparation. The strain grew at 40–80 °C (optimum, 65–75 °C), at pH 5–9 (optimum, pH 7), in media containing up to 1.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain K-39T formed a distinct lineage within the genus

Thermus

. Its closest cultivated relative was

Thermus islandicus

PRI 3838T (96.8 % similarity). The DNA G+C content of strain K-39T was 71.3 mol%. The new strain could be differentiated from the related taxa by not being able to hydrolyse starch. The predominant fatty acids of strain K-39T were iso-C17 : 0 and anteiso-C17 : 0. Strain K-39T contained a lower amount of the fatty acid iso-C15 : 0 as compared to related species of the genus

Thermus

. The predominant respiratory quinone of the new isolate was menaquinone MK-8. On the basis of a taxonomic study using a polyphasic approach, strain K-39T is considered to represent a novel species of the genus

Thermus

, for which the name Thermus composti sp. nov. is proposed. The type strain is K-39T ( = DSM 21686T = NCAIM B 02340T).
Postechiella marina gen. nov., sp. nov., isolated from seawater
Authors: Lee Dong-Heon , Cho Sun Ja , Kim Suk Min , Lee Sun Bok
Published: August 2011

A Gram-staining-negative, strictly aerobic, non-motile, yellow-pigmented bacterium, designated strain M091T, was isolated from seawater at Damupo beach in Pohang, Republic of Korea, and investigated using a polyphasic taxonomic approach. The novel strain grew optimally at 25 °C, pH 7.0–8.0, and in the presence of 3 % (w/v) NaCl. In a phylogenetic analysis based on 16S rRNA gene sequences, strain M091T formed a lineage within the family

Flavobacteriaceae

that was distinct from the most closely related genera of

Flaviramulus

(95.1 % sequence similarity),

Algibacter

(94.9–93.9 %),

Mariniflexile

(94.8–94.2 %),

Winogradskyella

(94.8–93.2 %),

Lacinutrix

(94.7–93.8 %) and

Tamlana

(94.7–92.9 %). The polar lipid profile of the novel strain comprised phosphatidylethanolamine, two unidentified aminolipids, one unidentified phospholipid and seven unidentified lipids. The predominant cellular fatty acids were iso-C15 : 0 (20.5 %), iso-C17 : 0 3-OH (15.4 %), iso-C15 : 0 3-OH (12.4 %), C15 : 0 (10.9 %) and iso-C15 : 1 G (9.9 %). The genomic DNA G+C content of strain M091T was 34.4 mol% and the major respiratory quinone was MK-6. Based on phenotypic and genotypic data, strain M091T represents a new genus and novel species in the family

Flavobacteriaceae

, for which the name Postechiella
marina gen. nov., sp. nov. is proposed. The type strain of the type species is M091T ( = KCTC 23537T = JCM 17630T).
Salinibacter iranicus sp. nov. and Salinibacter luteus sp. nov., isolated from a salt lake, and emended descriptions of the genus

Salinibacter

and of

Salinibacter ruber
Authors: Makhdoumi-Kakhki Ali , Amoozegar Mohammad Ali , Ventosa Antonio
Published: August 2011

Two Gram-staining-negative, red- and orange-pigmented, non-motile, rod-shaped, extremely halophilic bacteria, designated strains CB7T and DGOT, were isolated from Aran-Bidgol salt lake, Iran. Growth occurred at NaCl concentrations of between 2 and 5 M NaCl and the isolates grew optimally with 3 M NaCl. The optimum pH and temperature for growth of the two strains were pH 7.5 and 37 °C, and they were able to grow over pH and temperature ranges of pH 6–8 and 25–50 °C. The predominant fatty acids of the two isolates were C18 : 1ω7c, iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipid pattern of the two isolates consisted of diphosphatidylglycerol, phosphatidylcholine, three unidentified lipids, one unidentified aminolipid and three unidentified glycolipids. The only quinone present was menaquinone 7 (MK-7). The G+C contents of the genomic DNA of strains CB7T and DGOT were 64.8 and 65.6 mol%, respectively. 16S rRNA gene sequence analysis indicated that strains CB7T and DGOT were related to

Salinibacter ruber

in the phylum

Bacteroidetes

. Levels of 16S rRNA gene sequence similarity between strains CB7T and DGOT and

Salinibacter ruber

DSM 13855T were 93.2 and 93.6 %, respectively. The two novel strains shared 98.9 % 16S rRNA gene sequence similarity. DNA–DNA hybridization experiments between strains CB7T and DGOT and

Salinibacter ruber

DSM 13855T indicated levels of relatedness of 44 and 52 %, respectively, while the level of relatedness between the two new isolates was 53 %. Chemotaxonomic data supported the placement of strains CB7T and DGOT in the genus

Salinibacter

. DNA–DNA hybridization studies and biochemical and physiological characterization allowed strains CB7T and DGOT to be differentiated from

Salinibacter ruber

and from each other. They are therefore considered to represent two novel species of the genus

Salinibacter

, for which the names Salinibacter iranicus sp. nov. (type strain CB7T = IBRC-M 10036T = CGMCC 1.11003T) and Salinibacter luteus sp. nov. (type strain DGOT = IBRC-M 10423T = CGMCC 1.11002T) are proposed. Emended descriptions of the genus

Salinibacter

and of

Salinibacter ruber

are also presented.
Caloribacterium cisternae gen. nov., sp. nov., an anaerobic thermophilic bacterium from an underground gas storage reservoir
Authors: Slobodkina G. B. , Kolganova T. V. , Kostrikina N. A. , Bonch-Osmolovskaya E. A. , Slobodkin A. I.
Published: August 2011

A novel anaerobic, moderately thermophilic bacterium (strain SGL43T) was isolated from Severo-Stavropolskoye underground gas storage reservoir (Russia). Cells of strain SGL43Twere motile straight rods, 0.4 µm in diameter and 2.0–3.0 µm in length. The temperature range for growth was 28–65 °C, with optimum growth at 50 °C. The pH range for growth was 5.5–8.0, with optimum growth at pH 7.0–7.5. Growth of strain SGL43Twas observed at NaCl concentrations of 0–4.0 % (w/v) with optimum growth at 1.0 % (w/v) NaCl. Substrates utilized by strain SGL43Tincluded peptone, yeast extract, glucose, fructose, maltose, galactose, pyruvate and citrate. Products of glucose or citrate fermentation were acetate, hydrogen and CO2. Thiosulfate was reduced to sulfide. The DNA G+C content of strain SGL43Twas 43.1 mol%. 16S rRNA gene sequence analysis revealed that strain SGL43Tbelongs to the orderThermoanaerobacterales(phylum ‘Firmicutes’). The closest relative of strain SGL43TwasThermoanaerobacterium saccharolyticum(86.2 % 16S rRNA gene sequence similarity with the type strain). Based on the data presented here, strain SGL43Tis considered to represent a novel species of a new genus, for which the nameCaloribacterium cisternaegen. nov., sp. nov. is proposed. The type strain ofCaloribacterium cisternae, the type species of the genus, is SGL43T( = DSM 23830T = VKM B-2670T).
Enterococcus plantarum sp. nov., isolated from plants
Authors: Švec Pavel , Vandamme Peter , Bryndová Hana , Holochová Pavla , Kosina Marcel , Mašlaňová Ivana , Sedláček Ivo
Published: August 2011

Eight Gram-positive, catalase-negative bacterial strains were isolated during screening of enterococcal populations on plants. rep-PCR fingerprinting using the (GTG)5 primer showed that the isolates constituted a single cluster that was separate from all known enterococcal species. 16S rRNA gene sequence phylogenetic analysis of three representative strains showed that the isolates belonged to the genus

Enterococcus

and that they clustered with the

Enterococcus faecalis

species group. Sequencing of the genes for the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) also revealed the isolates’ separate taxonomic position. Application of whole-cell protein fingerprinting, automated ribotyping and extensive phenotyping demonstrated the genetic and phenotypic homogeneity of the isolates and confirmed their separate position within the

E. faecalis

species group. The isolates represent a novel species of the genus

Enterococcus

, for which the name Enterococcus plantarum sp. nov. is proposed; the type strain is CCM 7889T ( = LMG 26214T = C27T).