bluuebunny/crossref_metadata_2025 huggingface dataset:
Travels in Arabia
Authors: Burckhardt John Lewis
Published: November 2011

John Lewis Burckhardt (1784–1817) was a Swiss explorer who is best remembered for his rediscovery of the ancient city of Petra in modern Jordan. In 1809 he was commissioned by the African Association to discover the source of the River Niger. In preparation for this journey, for which he needed to pass as a Muslim, Burckhardt spent two years exploring and studying Arabic and Islamic law in Aleppo, before travelling widely in Arabia and Egypt. These volumes, first published by the African Association in 1829, contain his account of the time he spent in Mecca and Medina: he was the first westerner to give an account of the Hajj pilgrimage. The work provides important and fascinating descriptions of the social, economic and political situation in Mecca and Medina during this period. Volume 2 describes the city of Medina.
Women Modernists and Fascism
Authors: Zox-Weaver Annalisa
Published: November 2011

Modernism both influenced and was fascinated by the rhetorical and aesthetic manifestations of fascism. In examining how four artists and writers represented fascist leaders, Annalisa Zox-Weaver aims to achieve a more complex understanding of the modernist political imagination. She examines how photographer Lee Miller, filmmaker Leni Riefenstahl, writer Gertrude Stein and journalist Janet Flanner interpret, dramatize and exploit Hitler, Göring and Pétain. Within their own artistic medium, each of these modernists explore confrontations between private and public identity, and historical narrative and the construction of myth. This study makes use of extensive archival material, such as letters, photographs, journals, unpublished manuscripts and ephemera and includes ten illustrations. This interdisciplinary perspective opens up wider discussions of the relationship between artists and dictators, modernism and fascism, and authority and representation.
Game Theory in Wireless and Communication Networks
Authors: Han Zhu , Niyato Dusit , Saad Walid , Başar Tamer , Hjørungnes Are
Published: November 2011

This unified treatment of game theory focuses on finding state-of-the-art solutions to issues surrounding the next generation of wireless and communications networks. Future networks will rely on autonomous and distributed architectures to improve the efficiency and flexibility of mobile applications, and game theory provides the ideal framework for designing efficient and robust distributed algorithms. This book enables readers to develop a solid understanding of game theory, its applications and its use as an effective tool for addressing wireless communication and networking problems. The key results and tools of game theory are covered, as are various real-world technologies including 3G networks, wireless LANs, sensor networks, dynamic spectrum access and cognitive networks. The book also covers a wide range of techniques for modeling, designing and analysing communication networks using game theory, as well as state-of-the-art distributed design techniques. This is an ideal resource for communications engineers, researchers, and graduate and undergraduate students.
Muslim Endowments and Society in British India
Authors: Kozlowski Gregory C.
Published: November 2011

Dr Kozlowski's important study pioneers a fresh approach to the study of a critical Muslim institution: the endowments or awqaf which almost everywhere in the Islamic world provide support for mosques, schools and shrines. The wealthier Muslims who establish endowments inevitably have an eye on social, political and economic conditions and have traditionally used awqaf as part of an effort to preserve their wealth and influence, especially in periods of change and uncertainty. The book focuses on the use of endowments by Muslims suffering the dislocations caused by the imposition of British rule in India and examines in detail the social and political implications of the controversy over endowments that took place in the imperial courts and councils. The author's observations and insights can be applied to many periods and places in the Muslim world and his novel approach will attract all those interested in the study of Islam.
Theosophy, Religion and Occult Science
Authors: Olcott Henry Steel
Published: November 2011

The renowned lawyer and journalist Henry Steel Olcott (1832–1907) published this work in 1885. In this work Olcott carefully lays out his arguments for the basis of theosophy, arguing for the truth of all religions because they share the same ancient roots or 'ur-religion'. As a founding member and the first president of the Theosophical Society, Olcott uses the work to set out the aims and objectives of the Society and attempts to reconcile his spiritual beliefs with science, reason and modernity. The work also includes accounts of his attempted empirical investigations into hypnotism, mesmerism and other spiritualist activities. The final chapters include discussions of India, Buddhism and Zoroastrian religion. The work was deeply influenced by Helena Blavatsky (1831–1891), then Olcott's close friend but later his opponent. It is a key text of the nineteenth-century theosophical movement and is an indispensable source for research into Victorian occult philosophy.
The Lithosphere
Authors: Artemieva Irina
Published: November 2011

Presenting a coherent synthesis of lithosphere studies, this book covers a range of geophysical methods (seismic reflection, refraction, and receiver function methods; elastic and anelastic seismic tomography; electromagnetic and magnetotelluric methods; thermal, gravity and rheological models), complemented by petrologic and laboratory data on rock properties. It also provides a critical discussion of the uncertainties, assumptions, and resolution issues that are inherent in the different methods and models of the lithosphere. Multidisciplinary in scope, global in geographical extent, and covering a wide variety of tectonics settings across 3.5 billion years of Earth history, this book presents a comprehensive overview of lithospheric structure and evolution. It is a core reference for researchers and advanced students in geophysics, geodynamics, tectonics, petrology, and geochemistry, and for petroleum and mining industry professionals.
Migration, Refugee Policy, and State Building in Postcommunist Europe
Authors: Shevel Oxana
Published: November 2011

Why do similar postcommunist states respond differently to refugees? Why do some states privilege certain refugee groups, while other states do not? This book presents a theory to account for this puzzle, and it centers on the role of the politics of nation-building and of the office of the UN High Commissioner for Refugees (UNHCR). A key finding of the book is that when the boundaries of a nation are contested (and thus there is no consensus on which group should receive preferential treatment in state policies), a political space for a receptive and nondiscriminatory refugee policy opens up. The book speaks to the broader questions of how nationalism matters after communism and under what conditions and through what mechanisms international actors can influence domestic polices. The analysis is based on extensive primary research the author conducted in four languages in the Czech Republic, Poland, Russia and Ukraine.
Travel and Adventure in South-East Africa
Authors: Selous Frederick Courteney
Published: November 2011

Frederick Courteney Selous (1851–1917) was a British explorer, officer, hunter, and conservationist, famous for his work in south-east Africa. In early 1882 he embarked on an eleven-year expedition to record species that, to his great sadness, were becoming endangered. First published in 1893, these revealing memoirs document the wildlife, landscapes and people that characterised his journey. Through vivid descriptions and extensive illustrations, he recalls exhilarating adventures with lions, leopards, hyenas and crocodiles, recounts challenging treks across lakes and mountains, and describes hostile - and at times barbaric - encounters with native peoples. Detailed accounts of hunting endeavours, colonial institutions, and commercial enterprises such as gold mining, also feature in this study, which provides a unique and diverse perspective on Africa in the late nineteenth century. Insightful and revealing, Selous' experiences remain of enduring interest to geographers, anthropologists, zoologists, and all those interested in African history and culture.
Two Trips to Gorilla Land and the Cataracts of the Congo
Authors: Burton Richard Francis
Published: November 2011

Sir Richard Burton (1821–90) is well known for his colourful career, recorded in numerous books and articles, as a diplomat, explorer and ethnographer. In 1861 he was appointed consul to Fernando Po (now Bioko) in Equatorial Guinea, remaining there for four years until he was transferred to Brazil. These volumes collate the expeditions and ethnographic observations made during his time there. In his preface, Burton writes that the 'plain truth' about the African has not been told in Britain, declaring that English occupation of West Africa has proved 'a remarkable failure'. First published in 1876, Volume 1 records Burton's landing at the Gaboon River and includes geographical details, information about local tribes, and reports of journeys to Sanga Tanga and up the Gaboon River to its source. Burton also writes about a 'specimen day' with the reputed Fán cannibals and includes a chapter on gorillas.
The Influence of Anticipated Emotions on Consumer Decisions
Authors: Pollai Maria , Hoelzl Erik , Hahn Luise , Hahn Alexandra
Published: November 2011

The present research examined variables moderating the influence of anticipated consumption-related emotions on consumer decisions. Two studies indicated that the intention to purchase a product and the intention to take out a loan were influenced by anticipated emotions. The influence of anticipated emotions was similar for hedonic and utilitarian products. However, the influence was reduced when a belief in adaptation to products was cued. Examining the specific circumstances under which consumers base their decisions on anticipated emotions is relevant for marketing and consumer advisory service.
Modeling of the vapor release from the LCROSS impact: 2. Observations from LAMP
Authors: Hurley Dana M. , Gladstone G. Randall , Stern S. Alan , Retherford Kurt D. , Feldman Paul D. , Pryor Wayne , Egan Anthony F. , Greathouse Thomas K. , Kaufmann David E. , Steffl Andrew J. , Parker Joel William , Miles Paul F. , Horvath David , Davis Michael W. , Versteeg Maarten H. , Slater David C. , Hendrix Amanda R. , Hibbitts Charles A. , Ernst Carolyn M. , Vervack Ronald J. , Grieves Gregory A.
Published: November 2011

Using a Monte Carlo model, we analyze the evolution of the vapor plume emanating from the Lunar Crater Observation and Sensing Satellite (LCROSS) impact into Cabeus as seen by the Lyman Alpha Mapping Project (LAMP), a far‐ultraviolet (FUV) imaging spectrograph onboard the Lunar Reconnaissance Orbiter. The best fit to the data utilizes a bulk velocity between 3.0 and 4.0 km/s. The fits to the light curve comprised of Hg, Ca, and Mg are not strongly dependent on the temperature. In contrast, the best fit to the light curve from H2 and CO corresponds to a 500 K thermal velocity distribution. The LAMP field of view primarily encounters particles released at low angles to the horizontal and misses fast moving particles released at more vertical angles. The isotropic model suggests that 117 ± 16 kg H2, 41 ± 3 kg CO, 16 ± 1 kg Ca, 12.4 ± 0.8 kg Hg, and 3.8 ± 0.3 kg Mg are released by the LCROSS impact. Additional errors could arise from an anisotropic plume, which cannot be distinguished with LAMP data. Mg and Ca are likely incompletely volatilized owing to their high vapor temperatures. The highly volatile components (H2 and CO) might derive from a greater mass of material. To agree with predicted abundances by weight of 0.047%, 0.023%, 11%, 0.28% and 3.4% for H2, CO, Ca, Hg, and Mg, respectively, the species would be released from 250,000 kg, 180,000 kg, 140 kg, 4400 kg, and 110 kg of regolith, respectively. This is consistent with the relative volatility of these species.
Mild Hypoxemia during Initial Reperfusion Alleviates the Severity of Secondary Energy Failure and Protects Brain in Neonatal Mice with Hypoxic-Ischemic Injury
Authors: Niatsetskaya Zoya V , Charlagorla Pradeep , Matsukevich Dzmitry A , Sosunov Sergey A , Mayurasakorn Korapat , Ratner Veniamin I , Polin Richard A , Starkov Anatoly A , Ten Vadim S
Published: November 2011

Reperfusion triggers an oxidative stress. We hypothesized that mild hypoxemia in reperfusion attenuates oxidative brain injury following hypoxia-ischemia (HI). In neonatal HI-mice, the reperfusion was initiated by reoxygenation with room air (RA) followed by the exposure to 100%, 21%, 18%, 15% oxygen for 60 minutes. Systemic oxygen saturation (SaO2), cerebral blood flow (CBF), brain mitochondrial respiration and permeability transition pore (mPTP) opening, markers of oxidative injury, and cerebral infarcts were assessed. Compared with RA-littermates, HI-mice exposed to 18% oxygen exhibited significantly decreased infarct volume, oxidative injury in the brain mitochondria and tissue. This was coupled with improved mitochondrial tolerance to mPTP opening. Oxygen saturation maintained during reperfusion at 85% to 95% was associated ( r=0.57) with the best neurologic outcome. Exposure to 100% or 15% oxygen significantly exacerbated brain injury and oxidative stress. Compared with RA-mice, hyperoxia dramatically increased reperfusion CBF, but exposure to 15% oxygen significantly reduced CBF to values observed during the HI-insult. Mild hypoxemia during initial reperfusion alleviates the severity of HI-brain injury by limiting the reperfusion-driven oxidative stress to the mitochondria and mPTP opening. This suggests that at the initial stage of reperfusion, a slightly decreased systemic oxygenation (SaO2 85% to 95%) may be beneficial for infants with birth asphyxia.
Vascular Changes in Rat Hippocampus following a High Saturated Fat and Cholesterol Diet
Authors: Freeman Linnea R , Granholm Ann-Charlotte E
Published: November 2011

The long-term effects of a diet rich in saturated fat and cholesterol on the hippocampus were evaluated in this study. It has previously been shown that this type of diet is detrimental to health, particularly affecting peripheral organs such as the heart and liver. However, effects on the brain have not been fully evaluated. This study focused on the hippocampus, a brain region instrumental for learning and memory and vulnerable to ischemic damage. Reduced blood—brain barrier (BBB) integrity and increased microgliosis were observed in the hippocampus of rats fed a high-saturated-fat and cholesterol (HFHC) diet for 6 months. Interestingly, an increase in hippocampal protein levels of occludin, a tight junction protein, was found in HFHC-treated rats as well. Further investigation revealed decreased expression of the occludin protein in blood vessels and increased expression in the dentate gyrus hilar neurons and mossy fibers of the hippocampal cornus ammonis 3 in HFHC-treated rats. Our results show alterations in BBB integrity and expression of tight junction proteins after long-term exposure to HFHC diet in rats. These findings may suggest a biologic mechanism for previously observed behavioral deficits occurring in rats fed this diet.
CaMKII-γ mediates phosphorylation of BAD at Ser170 to regulate cytokine-dependent survival and proliferation
Authors: Hojabrpour Payman , Waissbluth Ivan , Ghaffari Mazyar , Cox Michael E. , Duronio Vincent
Published: November 2011

Phosphorylation of the BH3 (Bcl-2 homology domain 3)-only protein BAD (Bcl-2/Bcl-XL-antagonist, causing cell death) can either directly disrupt its association with the pro-survival proteins Bcl-XL and/or Bcl-2, or cause association of BAD with 14-3-3 proteins. In the present study, we further characterize phosphorylation of BAD at Ser170, a unique site with unclear function. We provide further evidence that mutation of Ser170 to a phospho-mimetic aspartic acid residue (S170D) can have a profound inhibitory effect on the pro-apoptosis function of BAD. Furthermore, mutated BAD with an alanine substitution inhibited cell proliferation, slowing progression specifically through S-phase. We identify the kinase responsible for phosphorylation at this site as CaMKII-γ (γ isoform of Ca2+/calmodulin-dependent kinase II), but not the other three isoforms of CaMKII, revealing an extraordinary specificity among these closely related kinases. Furthermore, cytokine treatment increased BAD-Ser170-directed CaMKII-γ activity and phosphorylation of CaMKII-γ at an activating site, and CaMKII activity directed to the BAD-Ser170 site was elevated during S-phase. Treating cells with a selective inhibitor of CaMKII caused apoptosis in cells expressing BAD, but not in cells expressing the BAD-S170D mutant. The present study provides support for BAD-Ser170 phosphorylation playing a key role not only in regulating BAD's pro-apoptotic activity, but also in cell proliferation.
A molecular dynamics study of diamond and graphite under tritium bombardment
Authors: Dunn A. R. , Duffy D. M.
Published: November 2011

Carbon has proven to be a promising plasma facing material in tokamak reactors because of its high thermal conductivity and limited radiative cooling as a plasma contaminant. It is used in a range of forms, mostly graphitic or amorphous. Diamond, however, has superior thermal properties to other forms of carbon but has been largely overlooked due to fears of graphitisation. Tritium retention is, perhaps, the major disadvantage of using carbon as a plasma facing material in a deuterium-tritium fusion reactor. Here, we use molecular dynamics to study the relative performance of diamond and graphite on exposure to tritium bombardment. We model the cumulative bombarded of diamond and graphitic surfaces with a high flux (1029 m−2 s−1) of low energy 15 eV tritium atoms. This was done for substrate temperatures in the range 300–2100 K. Below temperatures of graphitisation (∼1000 K) the diamond structure confined tritium to the upper surface, this inhibited further structural damage and resulted in lower total retention. The graphitic surface allowed for deeper tritium penetration and therefore greater retention. These results corroborate with recent experimental evidence.
Comment on “Cosmic ray diffusion: Detailed investigation of a recent model” [Phys. Plasmas 18, 082305 (2011)]
Authors: Shalchi A.
Published: November 2011

An improved theory for diffusion of energetic particles across the mean magnetic field has been developed recently. Lerche and Tautz [Phys. Plasmas 18, 082305 (2011)] have revisited the latter theory. They have proposed a different set of mathematical steps and derived a nonlinear integral equation which, according to them, deviates considerably from previous expressions. It is the purpose of the present paper to demonstrate that the latter statement is incorrect. The equation of Lerche and Tautz is very close to the original equation. Furthermore, it is shown that the original equation is even more accurate.
Magnetoacoustic shock waves in dissipative degenerate plasmas
Authors: Hussain S. , Mahmood S.
Published: November 2011

Quantum magnetoacoustic shock waves are studied in homogenous, magnetized, dissipative dense electron-ion plasma by using two fluid quantum magneto-hydrodynamic (QMHD) model. The weak dissipation effects in the system are taken into account through kinematic viscosity of the ions. The reductive perturbation method is employed to derive Korteweg-de Vries Burgers (KdVB) equation for magnetoacoustic wave propagating in the perpendicular direction to the external magnetic field in dense plasmas. The strength of magnetoacoustic shock is investigated with the variations in plasma density, magnetic field intensity, and ion kinematic viscosity of dense plasma system. The necessary condition for the existence of monotonic and oscillatory shock waves is also discussed. The numerical results are presented for illustration by using the data of astrophysical dense plasma situations such as neutron stars exist in the literature.
Carbon nanowalls as platinum support for fuel cells
Authors: Chul Shin Seog , Yoshimura Akihiko , Matsuo Takahiro , Mori Manami , Tanimura Makoto , Ishihara Akimitsu , Ota Ken-ichiro , Tachibana Masaru
Published: November 2011

Platinum catalysts supported on carbon nanowalls (Pt/CNW) were prepared by a solution-reduction method. It is shown that Pt nanoparticles with a mean diameter of 3.5 nm are well dispersed along domain boundaries in each CNW. In addition, it is shown that the Pt/CNW has high electrochemical active surface area and utilization, comparable to those for commercially available T–Pt/CB with good performance. Such high electrocatalytic activity could be attributed to the high electric conductivity of CNW and the improvement of electronic properties of Pt nanoparticles on the domain boundaries, in addition to the high dispersion of Pt particles.
Extracting elements of molecular structure from the all-particle wave function
Authors: Mátyus Edit , Hutter Jürg , Müller-Herold Ulrich , Reiher Markus
Published: November 2011

Structural information is extracted from the all-particle (non-Born–Oppenheimer) wave function by calculating radial and angular densities derived from n-particle densities. As a result, one- and two-dimensional motifs of classical molecular structure can be recognized in quantum mechanics. Numerical examples are presented for three- (H−, Ps−, ${\rm H}_2^+$H2+), four- (Ps2, H2), and five-particle (H2D+) systems.
Fabrication of sharp tungsten-coated tip for atomic force microscopy by ion-beam sputter deposition
Authors: Kinoshita Yukinori , Naitoh Yoshitaka , Li Yan Jun , Sugawara Yasuhiro
Published: November 2011

Tungsten (W) is significantly suitable as a tip material for atomic force microscopy (AFM) because its high mechanical stiffness enables the stable detection of tip-sample interaction forces. We have developed W sputter-coating equipment to compensate the drawbacks of conventional Si cantilever tips used in AFM measurements. By employing an ion gun commonly used for sputter cleaning of a cantilever tip, the equipment is capable of depositing conductive W films in the preparation chamber of a general ultrahigh vacuum (UHV)-AFM system without the need for an additional chamber or transfer system. This enables W coating of a cantilever tip immediately after sputter cleaning of the tip apex and just before the use in AFM observations. The W film consists of grain structures, which prevent tip dulling and provide sharpness (<3 nm in radius of curvature at the apex) comparable to that of the original Si tip apex. We demonstrate that in non-contact (NC)-AFM measurement, a W-coated Si tip can clearly resolve the atomic structures of a Ge(001) surface without any artifacts, indicating that, as a force sensor, the fabricated W-coated Si tip is superior to a bare Si tip.
Molecular diffusion and slip boundary conditions at smooth surfaces with periodic and random nanoscale textures
Authors: Priezjev Nikolai V.
Published: November 2011

The influence of periodic and random surface textures on the flow structure and effective slip length in Newtonian fluids is investigated by molecular dynamics (MD) simulations. We consider a situation where the typical pattern size is smaller than the channel height and the local boundary conditions at wetting and nonwetting regions are characterized by finite slip lengths. In the case of anisotropic patterns, transverse flow profiles are reported for flows over alternating stripes of different wettability when the shear flow direction is misaligned with respect to the stripe orientation. The angular dependence of the effective slip length obtained from MD simulations is in good agreement with hydrodynamic predictions provided that the stripe width is larger than several molecular diameters. We found that the longitudinal component of the slip velocity along the shear flow direction is proportional to the interfacial diffusion coefficient of fluid monomers in that direction at equilibrium. In case of random textures, the effective slip length and the diffusion coefficient of fluid monomers in the first layer near the heterogeneous surface depend sensitively on the total area of wetting regions.
Kinetic and relativistic effects on the surface alloy formation of submonolayer Au adsorbed on Si(111)-3×3-Pb surface
Authors: Li Chong , Wu Fengmin , Li Jingbo
Published: November 2011

Experiment reveals that the two-dimensional ordered phase of 3 × 3-Au/Pb alloy formed on Si(111)-3×3-Pb surface is dominated by Au parallelogram tetramers (4P). However, theoretical results indicate that three-dimensional tetrahedral tetramers (4T) grown on such surface is more energetically favorable. Using first-principles methods, we show that the discrepancy originates from a lower potential energy barrier of formation of the metastable 4P phase than that of the formation of stable 4T phase in nucleation and subsequent growth processes from triangular trimers (3T) islands and from stronger competition between Au s and d states caused by spin-orbit coupling effects.
Angular response of dye solar cells to solar and spectrally resolved light
Authors: D’Ercole Daniele , Dominici Lorenzo , Brown Thomas M. , Michelotti Francesco , Reale Andrea , Di Carlo Aldo
Published: November 2011

The power conversion efficiency (η) of a dye solar cell (DSC) with a 13 μm thick TiO2 layer increases with solar AM1.5 light’s angle of incidence by 10% at 55° ± 5° and then decreases at higher angles due to Fresnel reflection at the front air/glass interface. For cells with thin TiO2 (3 μm), the enhancement in η is substantially larger (16%). We show, also through spectral quantum efficiency measurements, that the angular enhancement for thin cells is mainly due to optical path lengthening, quantifying the relevant parameters useful for photon management strategies and for understanding the productivity of DSC modules outdoors.
Scaling of losses with size and wavelength in nanoplasmonics and metamaterials
Authors: Khurgin Jacob B. , Sun Greg
Published: November 2011

We show that, for the resonant metal-dielectric structures with sub-wavelength confinement of light in all three dimensions, the loss cannot be reduced considerably below the loss of the metal itself unless one operates in the far IR and THz regions of the spectrum or below. Such high losses cannot be compensated by introducing gain due to Purcell-induced shortening of recombination times. The only way low loss optical meta-materials can be engineered is with, as yet unknown, low loss materials with negative permittivity.
Spatial distribution of species richness and endemism of the genus Acacia in Australia
Authors: González-Orozco Carlos E. , Laffan Shawn W. , Miller Joseph T.
Published: November 2011

The aim of this study is to identify and map the spatial distribution of species richness and endemism of the genus Acacia in Australia. A database of 171 758 geo-referenced herbarium records representing 1020 Acacia species was assembled and aggregated to a 0.25° grid cell resolution. A neighbourhood analysis of one-cell radius was applied to each of the grid cells to map the spatial patterns of species richness and endemism. The primary centres of species richness are in accordance with previous results, occurring in the South-West Botanical Province in Western Australia, the MacPherson-Macleay overlap and the Central Coast of the Sydney Sandstone region. We identify 21 centres of endemism, of which six were previously unrecognised. The primary centres of endemism are located in South-West Western Australia, the Kimberley District and the Wet Tropics in Queensland. The South-West Botanical Province in Western Australia contained the greatest number of regions with the highest number of endemic species of Acacia. A randomisation test showed that our 21 centres of endemism were significantly different from random. The majority of centres of Acacia endemism were incongruent with the centres of species richness, with only three grid cells in the top 1% for both measures. We also confirm that South-West Western Australia is a region of very high species richness and endemism, in accordance with its status as a global hotspot of biodiversity.
Topological transitions for lattice bosons in a magnetic field
Authors: Huber Sebastian D. , Lindner Netanel H.
Published: November 2011

The Hall response provides an important characterization of strongly correlated phases of matter. We study the Hall conductivity of interacting bosons on a lattice subjected to a magnetic field. We show that for any density or interaction strength, the Hall conductivity is characterized by an integer. We find that the phase diagram is intersected by topological transitions between different values of this integer. These transitions lead to surprising effects, including sign reversal of the Hall conductivity and extensive regions in the phase diagram where it acquires a negative sign, which implies that flux flow is reversed in these regions—vortices there flow upstream. Our findings have immediate applications to a wide range of phenomena in condensed matter physics, which are effectively described in terms of lattice bosons.
Subcategories of extension modules by Serre subcategories
Authors: Yoshizawa Takeshi
Published: November 2011

In 1962, P. Gabriel showed the existence of a lattice isomorphism between the set of Serre subcategories of the category consisting of finitely generated modules and the set of specialization closed subsets of the set of prime ideals. In this paper, we consider subcategories consisting of the extensions of modules in two given Serre subcategories to find a method of constructing Serre subcategories of the category of modules. We shall give a criterion for this subcategory to be a Serre subcategory.
MetalionRNA: computational predictor of metal-binding sites in RNA structures
Authors: Philips Anna , Milanowska Kaja , Lach Grzegorz , Boniecki Michal , Rother Kristian , Bujnicki Janusz M.
Published: November 2011

Motivation: Metal ions are essential for the folding of RNA molecules into stable tertiary structures and are often involved in the catalytic activity of ribozymes. However, the positions of metal ions in RNA 3D structures are difficult to determine experimentally. This motivated us to develop a computational predictor of metal ion sites for RNA structures.

Results: We developed a statistical potential for predicting positions of metal ions (magnesium, sodium and potassium), based on the analysis of binding sites in experimentally solved RNA structures. The MetalionRNA program is available as a web server that predicts metal ions for RNA structures submitted by the user.

Availability: The MetalionRNA web server is accessible at http://metalionrna.genesilico.pl/.

Contact:  iamb@genesilico.pl

Supplementary information:  Supplementary data are available at Bioinformatics online.
FSR: feature set reduction for scalable and accurate multi-class cancer subtype classification based on copy number
Authors: Wong Gerard , Leckie Christopher , Kowalczyk Adam
Published: November 2011

Motivation: Feature selection is a key concept in machine learning for microarray datasets, where features represented by probesets are typically several orders of magnitude larger than the available sample size. Computational tractability is a key challenge for feature selection algorithms in handling very high-dimensional datasets beyond a hundred thousand features, such as in datasets produced on single nucleotide polymorphism microarrays. In this article, we present a novel feature set reduction approach that enables scalable feature selection on datasets with hundreds of thousands of features and beyond. Our approach enables more efficient handling of higher resolution datasets to achieve better disease subtype classification of samples for potentially more accurate diagnosis and prognosis, which allows clinicians to make more informed decisions in regards to patient treatment options.

Results: We applied our feature set reduction approach to several publicly available cancer single nucleotide polymorphism (SNP) array datasets and evaluated its performance in terms of its multiclass predictive classification accuracy over different cancer subtypes, its speedup in execution as well as its scalability with respect to sample size and array resolution. Feature Set Reduction (FSR) was able to reduce the dimensions of an SNP array dataset by more than two orders of magnitude while achieving at least equal, and in most cases superior predictive classification performance over that achieved on features selected by existing feature selection methods alone. An examination of the biological relevance of frequently selected features from FSR-reduced feature sets revealed strong enrichment in association with cancer.

Availability:  FSR was implemented in MATLAB R2010b and is available at http://ww2.cs.mu.oz.au/~gwong/FSR

Contact:  gwong@csse.unimelb.edu.au

Supplementary information:  Supplementary data are available from Bioinformatics online.
Avirulence Proteins AvrBs7 from Xanthomonas gardneri and AvrBs1.1 from Xanthomonas euvesicatoria Contribute to a Novel Gene-for-Gene Interaction in Pepper
Authors: Potnis Neha , Minsavage Gerald , Smith J. Kennon , Hurlbert Jason C. , Norman David , Rodrigues Rosana , Stall Robert E. , Jones Jeffrey B.
Published: November 2011

A novel hypersensitive resistance (HR) in Capsicum baccatum var. pendulum against the bacterial spot of pepper pathogen, Xanthomonas gardneri, was introgressed into C. annuum cv. Early Calwonder (ECW) to create the near-isogenic line designated as ECW-70R. A corresponding avirulence gene avrBs7, in X. gardneri elicited a strong HR in ECW-70R. A homolog of avrBs7, avrBs1.1, was found in X. euvesicatoria 85-10, which showed delayed HR on ECW-70R leaves. Genetic analysis confirmed the presence of a single dominant resistance gene, Bs7, corresponding to the two avr genes. Both AvrBs7 and AvrBs1.1 share a consensus protein tyrosine phosphatase (PTP) active site domain and can dephosphorylate para-nitrophenyl phosphate. Mutation of Cys(265) to Ser in the PTP domain and subsequent loss of enzymatic activity and HR activity indicated the importance of the PTP domain in the recognition of the Avr protein by the Bs7 gene transcripts. Superpositioning of AvrBs7 and AvrBs1.1 homology models indicated variation in the geometry of the loops adjacent to the active sites. These predicted structural differences might be responsible for the differences in HR timing due to differential activation of the resistance gene. Mutating the PTP domain of AvrBs1.1 to match that of AvrBs7 failed to activate HR on ECW-70R, indicating the possibility of differential substrate specificities between AvrBs1.1 and AvrBs7.
Characterization and Pathogenicity of Rhizoctonia solani Isolates Affecting Pisum sativum in North Dakota
Authors: Mathew F. M. , Lamppa R. S. , Chittem K. , Chang Y. W. , Botschner M. , Kinzer K. , Goswami R. S. , Markell S. G.
Published: November 2011

Acreage of dry field pea (Pisum sativum) in North Dakota has increased approximately eightfold from the late 1990s to the late 2000s to over 200,000 ha annually. A coincidental increase in losses to root rots has also been observed. Root rot in dry field pea is commonly caused by a complex of pathogens which included Fusarium spp. and Rhizoctonia solani. R. solani isolates were obtained from roots sampled at the three- to five-node growth stage from North Dakota pea fields and from symptomatic samples received at the Plant Diagnostic Lab at North Dakota State University in 2008 and 2009. Using Bayesian inference and maximum likelihood analysis of the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA), 17 R. solani pea isolates were determined to belong to anastomosis group (AG)-4 homogenous group (HG)-II and two isolates to AG-5. Pathogenicity of select pea isolates was determined on field pea and two rotation hosts, soybean and dry bean. All isolates caused disease on all hosts; however, the median disease ratings were higher on green pea, dry bean, and soybean cultivars when inoculated with pea isolate AG-4 HG-II. Identification of R. solani AGs and subgroups on field pea and determination of relative pathogenicity on rotational hosts is important for effective resistance breeding and appropriate rotation strategies.
Influence of network dynamics on the spread of sexually transmitted diseases
Authors: Risau-Gusman Sebastián
Published: November 2011

Network epidemiology often assumes that the relationships defining the social network of a population are static. The dynamics of relationships is only taken indirectly into account by assuming that the relevant information to study epidemic spread is encoded in the network obtained, by considering numbers of partners accumulated over periods of time roughly proportional to the infectious period of the disease. On the other hand, models explicitly including social dynamics are often too schematic to provide a reasonable representation of a real population, or so detailed that no general conclusions can be drawn from them. Here, we present a model of social dynamics that is general enough so its parameters can be obtained by fitting data from surveys about sexual behaviour, but that can still be studied analytically, using mean-field techniques. This allows us to obtain some general results about epidemic spreading. We show that using accumulated network data to estimate the static epidemic threshold lead to a significant underestimation of that threshold. We also show that, for a dynamic network, the relative epidemic threshold is an increasing function of the infectious period of the disease, implying that the static value is a lower bound to the real threshold. A practical example is given of how to apply the model to the study of a real population.
Disparity and convergence in bipedal archosaur locomotion
Authors: Bates K. T. , Schachner E. R.
Published: November 2011

This study aims to investigate functional disparity in the locomotor apparatus of bipedal archosaurs. We use reconstructions of hindlimb myology of extant and extinct archosaurs to generate musculoskeletal biomechanical models to test hypothesized convergence between bipedal crocodile-line archosaurs and dinosaurs. Quantitative comparison of muscle leverage supports the inference that bipedal crocodile-line archosaurs and non-avian theropods had highly convergent hindlimb myology, suggesting similar muscular mechanics and neuromuscular control of locomotion. While these groups independently evolved similar musculoskeletal solutions to the challenges of parasagittally erect bipedalism, differences also clearly exist, particularly the distinct hip and crurotarsal ankle morphology characteristic of many pseudosuchian archosaurs. Furthermore, comparative analyses of muscle design in extant archosaurs reveal that muscular parameters such as size and architecture are more highly adapted or optimized for habitual locomotion than moment arms. The importance of these aspects of muscle design, which are not directly retrievable from fossils, warns against over-extrapolating the functional significance of anatomical convergences. Nevertheless, links identified between posture, muscle moments and neural control in archosaur locomotion suggest that functional interpretations of osteological changes in limb anatomy traditionally linked to postural evolution in Late Triassic archosaurs could be constrained through musculoskeletal modelling.
Upper and lower limits on the stability of calving glaciers from the yield strength envelope of ice
Authors: Bassis J. N. , Walker C. C.
Published: November 2011

Observations indicate that substantial changes in the dynamics of marine-terminating ice sheets and glaciers are tightly coupled to calving-induced changes in the terminus position. However, the calving process itself remains poorly understood and is not well parametrized in current numerical ice sheet models. In this study, we address this uncertainty by deriving plausible upper and lower limits for the maximum stable ice thickness at the calving face of marine-terminating glaciers, using two complementary models. The first model assumes that a combination of tensile and shear failure can render the ice cliff near the terminus unstable and/or enable pre-existing crevasses to intersect. A direct consequence of this model is that thick glaciers must terminate in deep water to stabilize the calving front, yielding a predicted maximum ice cliff height that increases with increasing water depth, consistent with observations culled from glaciers in West Greenland, Antarctica, Svalbard and Alaska. The second model considers an analogous lower limit derived by assuming that the ice is already fractured and fractures are lubricated by pore pressure. In this model, a floating ice tongue can only form when the ice entering the terminus region is relatively intact with few pre-existing, deeply penetrating crevasses.
Color Recovery after Photoconversion of H2B::mEosFP Allows Detection of Increased Nuclear DNA Content in Developing Plant Cells
Authors: Wozny Michael , Schattat Martin H. , Mathur Neeta , Barton Kiah , Mathur Jaideep
Published: November 2011

Many higher plants are polysomatic whereby different cells possess variable amounts of nuclear DNA. The conditional triggering of endocycles results in higher nuclear DNA content (C value) that in some cases has been correlated to increased cell size. While numerous multicolored fluorescent protein (FP) probes have revealed the general behavior of the nucleus and intranuclear components, direct visualization and estimation of changes in nuclear-DNA content in live cells during their development has not been possible. Recently, monomeric Eos fluorescent protein (mEosFP) has emerged as a useful photoconvertible protein whose color changes irreversibly from a green to a red fluorescent form upon exposure to violet-blue light. The stability and irreversibility of red fluorescent mEosFP suggests that detection of green color recovery would be possible as fresh mEosFP is produced after photoconversion. Thus a ratiometric evaluation of the red and green forms of mEosFP following photoconversion could be used to estimate production of a core histone such as H2B during its concomitant synthesis with DNA in the synthesis phase of the cell cycle. Here we present proof of concept observations on transgenic tobacco (Nicotiana tabacum) Bright Yellow 2 cells and Arabidopsis (Arabidopsis thaliana) plants stably expressing H2B::mEosFP. In Arabidopsis seedlings an increase in green fluorescence is observed specifically in cells known to undergo endoreduplication. The detection of changes in nuclear DNA content by correlating color recovery of H2B::mEosFP after photoconversion is a novel approach involving a single FP. The method has potential for facilitating detailed investigations on conditions that favor increased cell size and the development of polysomaty in plants.
Conceptualising Listening to Young Children as an Ethic of Care in Early Childhood Education and Care
Authors: Bath Caroline
Published: November 2011

This paper focuses on recent discourses and practices of listening to young children, in order to highlight listening as an ethical practice in early childhood education and care settings. The paper asks how discourses of listening should be viewed in theoretical terms and explores the work of a diverse range of authors who define autonomy and rights issues as relational. Central to the paper is a consideration of feminist critique of Foucault’s ethics of care argument. To contextualise this, the paper discusses examples of recent research in the field of listening to young children and highlights issues facing the status of the early years workforce. In summary, the paper contends that an ethical view of listening can bring adults and children together in democratic care practices which challenge conceptions of childhood and reconnect ideas of care and education.
Re: Oral desensitization as a useful treatment in 2‐year‐old children with cow's milk allergy
Authors: Hulshof L. , Schoemaker A. A. , Petrus N. C. M. , van Aalderen W. M. C. , Sprikkelman A. B.
Published: November 2011

Cite this as: L. Hulshof, A. A. Schoemaker, N. C. M. Petrus, W. M. C. van Aalderen and A. B. Sprikkelman, Clinical & Experimental Allergy, 2011 (41) 1815–1816.
Response to Hulshof et al by Antonio Martorell and Belen de la Hoz, on behalf of the authors
Authors: Martorell A. , de la Hoz B. ,   on behalf of the authors
Published: November 2011

Cite this as: A. Martorell and B. de la Hoz, on behalf of the authors, Clinical & Experimental Allergy, 2011 (41) 1817–1818
Local sex ratio affects the cost of reproduction
Authors: Nicolaus Marion , Michler Stephanie P. M. , Ubels Richard , van der Velde Marco , Bouwman Karen M. , Both Christiaan , Tinbergen Joost M.
Published: November 2011

1. Costs and benefits of reproduction are central to life‐history theory, and the outcome of reproductive trade‐offs may depend greatly on the ecological conditions in which they are estimated. In this study, we propose that costs and benefits of reproduction are modulated by social effects, and consequently that selection on reproductive rates depends on the social environment.

2. We tested this hypothesis in a great titParus majorpopulation. Over 3 years, we altered parental reproductive effort via brood size manipulations (small, intermediate, large) and manipulated the local social environment via changes in the local fledgling density (decreased, increased) and the local sex ratio (female‐biased, control, male‐biased).

3. We found that male‐biased treatment consistently increased the subsequent local breeding densities over the 3‐year study period. We also found that parents rearing small broods in these male‐biased plots had increased survival rates compared with the other experimental groups.

4. We conclude that reproductive costs are the product of an interaction between parental phenotypic quality after reproduction and the social environment: raising a small brood had long‐lasting effects on some phenotypic traits of the parents and that this increased their survival chances in male‐biased environment where habitat quality may have deteriorated (via increased disease/predation risk or intraspecific competition).

5. Our results provide the first experimental evidence that local sex ratio can affect reproductive costs and thus optimal clutch size.
Testing gradual and speciational models of evolution in extant taxa: the example of ratites
Authors: LAURIN M. , GUSSEKLOO S. W. S. , MARJANOVIĆ D. , LEGENDRE L. , CUBO J.
Published: November 2011

Abstract  Ever since Eldredge and Gould proposed their model of punctuated equilibria, evolutionary biologists have debated how often this model is the best description of nature and how important it is compared to the more gradual models of evolution expected from natural selection and the neo‐Darwinian paradigm. Recently, Cubo proposed a method to test whether morphological data in extant ratites are more compatible with a gradual or with a speciational model (close to the punctuated equilibrium model). As shown by our simulations, a new method to test the mode of evolution of characters (involving regression of standardized contrasts on their expected standard deviation) is easier to implement and more powerful than the previously proposed method, but the Mesquite module comet (aimed at investigating evolutionary models using comparative data) performs better still. Uncertainties in branch length estimates are probably the largest source of potential error. Cubo hypothesized that heterochronic mechanisms may underlie morphological changes in bone shape during the evolution of ratites. He predicted that the outcome of these changes may be consistent with a speciational model of character evolution because heterochronic changes can be instantaneous in terms of geological time. Analysis of a more extensive data set confirms his prediction despite branch length uncertainties: evolution in ratites has been mostly speciational for shape‐related characters. However, it has been mostly gradual for size‐related ones.