bluuebunny/crossref_metadata_2025 huggingface dataset:
Proximate topology and shape theory
Authors: Čerin Zvonko
Published: November 2011

Most of the development of shape theory was in the so-called outer shape theory, where the shape of spaces is described with the help of some outside objects.

This paper belongs to the so-called inner shape theory, in which the shape of spaces is described intrinsically without the use of any outside gadgets. We give a description of shape theory that does not need absolute neighbourhood retracts. We prove that the category ℋN whose objects are topological spaces and whose morphisms are proximate homotopy classes of proximate nets is naturally equivalent to the shape category h. The description of the category ℋN for compact metric spaces was given earlier by José M. R. Sanjurjo. We also give three applications of this new approach to shape theory.
Special Freudenthal–Kantor triple systems and Lie algebras with dicyclic symmetry
Authors: Elduque Alberto , Okubo Susumu
Published: November 2011

We study Lie algebras endowed with an action by automorphisms of the dicyclic group of degree 3. The close connections of these algebras with Lie algebras graded over the non-reduced root system BC1, with J-ternary algebras and with Freudenthal–Kantor triple systems are explored.
Using experimental human influenza infections to validate a viral dynamic model and the implications for prediction
Authors: CHEN S. C. , YOU S. H. , LIU C. Y. , CHIO C. P. , LIAO C. M.
Published: November 2011

The aim of this work was to use experimental infection data of human influenza to assess a simple viral dynamics model in epithelial cells and better understand the underlying complex factors governing the infection process. The developed study model expands on previous reports of a target cell-limited model with delayed virus production. Data from 10 published experimental infection studies of human influenza was used to validate the model. Our results elucidate, mechanistically, the associations between epithelial cells, human immune responses, and viral titres and were supported by the experimental infection data. We report that the maximum total number of free virions following infection is 103-fold higher than the initial introduced titre. Our results indicated that the infection rates of unprotected epithelial cells probably play an important role in affecting viral dynamics. By simulating an advanced model of viral dynamics and applying it to experimental infection data of human influenza, we obtained important estimates of the infection rate. This work provides epidemiologically meaningful results, meriting further efforts to understand the causes and consequences of influenza A infection.
The Goods of Human Sexuality: Ethics and Moral Theology
Authors: Wondra Ellen
Published: November 2011

Christian ethics has always taken a complex view of the goods and purposes of human sexuality and its role in human relationships. Sexual desire and behavior have to be seen always within the overarching moral imperatives of love of God and love of neighbor. Such love entails self-giving and other-regard, and in longer-term relationships also some measure of commitment, fidelity, reciprocity or mutuality, truthfulness and generativity. Yet not all relationships with these characteristics do (or should) include sexual behavior. Nor do all sexual relationships include all these characteristics or virtues all the time. So we do better to base our moral evaluations of relationships on the exercise of these virtues than on more obvious criteria of sexual orientation or even status in the eyes of the church. At the same time, it is also possible for faithful and reasonable people to disagree faithfully and reasonably on sexual ethics, as on other things.
Learn about communicating with Congress at Fall Meeting lunch workshop
Authors: Hankin Erik
Published: November 2011

Are you interested in science policy and curious about how you can use your expertise to help inform policy makers? Come to a luncheon event at the AGU Fall Meeting in San Francisco to learn how you can better inform legislators. The “Communicating With Congress” workshop will emphasize that good policy is informed by good science. As a scientist, you have every reason to establish a relationship with your legislators. At the event, AGU's 2009–2010 Congressional Science Fellow, Maeve Boland, will use her experience as a scientist and legislative staff member to teach you how to effectively share your science with local and national policy makers.
First observations of SPEAR‐induced topside and bottomside sporadic E layer heating observed using the EISCAT Svalbard and SuperDARN radars
Authors: Baddeley L. J. , Haggstrøm I. , Yeoman T. K. , Rietveld M.
Published: November 2011

We present the first observations of heater‐induced simultaneous topside and bottomside sporadic E layer enhancements at very high latitudes (78.15°N) using the Space Plasma Exploration by Active Radar (SPEAR) heating facility and the European Incoherent Scatter (EISCAT) Svalbard Radar. During the experiment the SPEAR heating facility was transmitting with O‐mode polarization in a field‐aligned direction with a constant effective radiated power of ∼16 MW. Results show distinct heater‐induced enhancements in both the ion and plasma line spectra. The plasma line enhancements are observed at the SPEAR heater frequency of 4.45 MHz. The plasma line observations represent the highest spatial resolution data (100 m) obtained of such heater‐induced enhancements and indicate simultaneous enhancements at both the topside and bottomside of the layer, respectively (located at ∼107.5 and 109 km altitude, respectively). It is postulated that the results represent evidence of O‐ to Z‐mode conversion of the heater wave occurring at the bottom of the E layer, allowing propagation through the layer resulting in simultaneous topside enhancements. The Z‐mode enhancements are observed outside the Spitze angle, which is thought to be a result of field‐aligned irregularities causing an increase in angular extent of the observations. Additional data from the Super Dual Auroral Radar Network (SuperDARN) HF Finland radar are also shown, which indicate that upon a thinning of the sporadic E layer, the heater beam propagated into the F region, where it induced artificial field‐aligned irregularities.
Methane fluxes to the atmosphere from deepwater hydrocarbon seeps in the northern Gulf of Mexico
Authors: Hu Lei , Yvon‐Lewis Shari A. , Kessler John D. , MacDonald Ian R.
Published: November 2011

Three deepwater hydrocarbon seep sites in the northern Gulf of Mexico that feature near‐seafloor gas hydrates, MC118 (depth = 900 m), GC600 (depth = 1250 m) and GC185 (depth = 550 m), were investigated during the Remote Sensing and Sea‐Truth Measurements of Methane Flux to the Atmosphere (HYFLUX) study in July 2009. Continuous measurements of air and sea surface concentrations of methane were made to obtain high spatial and temporal resolution of the diffusive net sea‐to‐air fluxes. The atmospheric methane fluctuated between 1.70 and 2.40 parts per million (ppm) during the entire cruise except for high concentrations (up to 4.01 ppm) sampled during the end of the occupation of GC600 and the transit between GC600 and GC185. In conjunction with air‐mass back trajectory analysis, these high concentrations are likely from a localized methane source to the atmosphere. Methane concentrations in surface seawater and methane net sea‐to‐air fluxes show high temporal and spatial variability within and between sites. The presence of ethane and propane in the surface seawater indicates a thermogenic source in the plume areas, suggesting the surface methane could be at least partly attributable to transport from the deepwater hydrocarbon seeps. Results from interpolations within the survey areas show the daily methane fluxes to the atmosphere at the three sites range from 0.744 to 300 mol d−1. Extrapolating the highest daily sea‐to‐air flux of methane to other deepwater seeps in the northern Gulf of Mexico suggests that the net diffusive sea‐to‐air flux from deepwater hydrocarbon seeps in this region is an insignificant source to the atmospheric methane.
Shrub encroachment alters sensitivity of soil respiration to temperature and moisture
Authors: Cable Jessica M. , Barron‐Gafford Greg A. , Ogle Kiona , Pavao‐Zuckerman Mitchell , Scott Russell L. , Williams David G. , Huxman Travis E.
Published: November 2011

A greater abundance of shrubs in semiarid grasslands affects the spatial patterns of soil temperature, moisture, and litter, resulting in fertile islands with potentially enhanced soil metabolic activity. The goal of this study was to quantify the microsite specificity of soil respiration in a semiarid riparian ecosystem experiencing shrub encroachment. We quantified the response of soil respiration to different microsite conditions created by big mesquite shrubs (near the trunk and the canopy edge), medium‐sized mesquite, sacaton bunchgrasses, and open spaces. We hypothesized that soil respiration would be more temperature sensitive and less moisture sensitive and have a greater magnitude in shrub microsites compared with grass and open microsites. Field and incubation soil respiration data were simultaneously analyzed in a Bayesian framework to quantify the microsite‐specific temperature and moisture sensitivities and magnitude of respiration. The analysis showed that shrub expansion increases the heterogeneity of respiration. Respiration has greater temperature sensitivity near the shrub canopy edge, and respiration rates are higher overall under big mesquite compared with those of the other microsites. Respiration in the microsites beneath medium‐sized mesquites does not behave like a downscaled version of big mesquite microsites. The grass microsites show more similarity to big mesquite microsites than medium‐sized shrubs. This study shows there can be a great deal of fine‐scale spatial heterogeneity that accompanies shifts in vegetation structure. Such complexity presents a challenge in scaling soil respiration fluxes to the landscape for systems experiencing shrub encroachment, but quantifying this complexity is significantly important in determining overall ecosystem metabolic behavior.
Historical temporal trends in overwinter and spring snowpack for the Okanagan and Similkameen River watersheds in south-central British Columbia, Canada
Authors: Rayne Sierra , Forest Kaya
Published: November 2011

Potential historical temporal trends in the overwinter and spring snowpack were investigated for the Canadian portions of the Okanagan and Similkameen Valleys in south-central British Columbia. Significant evidence is available that the Okanagan and Similkameen River watersheds are exhibiting both spatially and temporally heterogeneous declines in snowpacks over the past several decades, but whether the causes are part of a natural cycle or result from longer term climatic changes is not clear. The variability in the magnitude, timing, and location of any significant time trends in snowpack decline also precludes efforts towards developing reliable hydrologic models that reflect a response to potential future changes in snowpack patterns for these regions of British Columbia.
Identity in research infrastructure and scientific communication: Report from the 1st IRISC workshop, Helsinki Sep 12-13, 2011
Authors: Thorisson Gudmundur , Linden Mikael , Brookes Anthony , Byrne Myles , Muilu Juha , Nyronen Tommi
Published: November 2011

Motivation for the IRISC workshop came from the observation that identity and digital identification are increasingly important factors in modern scientific research, especially with the now near-ubiquitous use of the Internet as a global medium for dissemination and debate of scientific knowledge and data, and as a platform for scientific collaborations and large-scale e-science activities.The 1 1/2 day IRISC2011 workshop sought to explore a series of interrelated topics under two main themes: i) unambiguously identifying authors/creators & attributing their scholarly works, and ii) individual identification and access management in the context of identity federations. Specific aims of the workshop included:• Raising overall awareness of key technical and non-technical challenges, opportunities and developments.• Facilitating a dialogue, cross-pollination of ideas, collaboration and coordination between diverse – and largely unconnected – communities.• Identifying & discussing existing/emerging technologies, best practices and requirements for researcher identification.This report provides background information on key identification-related concepts & projects, describes workshop proceedings and summarizes key workshop findings.
Assessment of Economic and Environmental Cost-benefits of Developed Biorefinery Schemes
Authors: Binns Michael , Vlysidis Anestis , Theodoropoulos* Constantinos
Published: November 2011

In this work modelling and optimisation studies for the evaluation and improvement of several biorefinery schemes were performed. Economic and environmental objectives were considered with the aim to find configurations that maximise profits while minimising the environmental impact. Biorefineries were modelled using a commercial simulator (Aspen Plus) combined with calculations in MatLab. Optimisation studies (including multi-objective optimisation) were carried out using both stochastic (simulated annealing) and deterministic (sequential-quadratic-programming based) approaches. The results show that for a number of schemes improved profits can be found including biodiesel and biogas production in addition to supercritical CO2 extraction from wheat straws. An oil-to-methanol ratio of around 1:13 to 1:14 was found to be optimal for the biodiesel-producing transesterification reaction. The optimum conditions for the biogas case involved recycling most of the digestate, which leads to a high productivity of biogas. Supercritical CO2 extraction was found to be most profitable at around 36,000 tons per year capacity.

Multi-objective optimisation was also performed in order to find how the optimal profits change when different constraints are placed on the emissions from each process. For the biodiesel cases these constraints reduced the profits by up to €10 per ton of feed. For biogas production reducing the emissions meant using more of the digestate as fertiliser. For supercritical CO2 extraction reducing emissions requires reducing the yearly capacity, which in turn reduces the profits by €63 per ton.

Comparisons of the different schemes are performed using calculations of profits and emissions ‘per ton of feed’ in order to give a fair comparison of biorefinery processes operating at different scales. These comparisons showed that the most profitable schemes were those with the lowest capacity. These lower capacity schemes could be very profitable if they can be scaled up and if there is sufficient feedstock available. Comparison of the emissions for these cases showed that the most profitable schemes also have the highest emissions. This is because these cases involve either high-energy usage (usually with larger quantities of electricity) or combustion.
Lubrication mechanism of concentrated polymer brushes in solvents: effect of solvent viscosity
Authors: Nomura Akihiro , Ohno Kohji , Fukuda Takeshi , Sato Takaya , Tsujii Yoshinobu
Published: November 2011

The frictional/lubricational properties of concentrated polymer brushes were investigated in ionic liquids using the colloidal-probe AFM technique, revealing the lubrication mechanism especially from the viewpoint of solvent viscosity.
A preliminary characterization of the cytosolic glutathione transferase proteome from Drosophila melanogaster
Authors: Saisawang Chonticha , Wongsantichon Jantana , Ketterman Albert J.
Published: November 2011

The cytosolic GST (glutathione transferase) superfamily has been annotated in the Drosophila melanogaster genome database. Of 36 genes, four undergo alternative splicing to yield a total of 41 GST proteins. In the present study, we have obtained the 41 transcripts encoding proteins by RT (reverse transcription)–PCR using RNA template from Drosophila S2 cells, an embryonic cell line. This observation suggests that all of the annotated DmGSTs (D. melanogaster GSTs) in the proteome are expressed in the late embryonic stages of D. melanogaster. To avoid confusion in naming these numerous DmGSTs, we have designated them following the universal GST nomenclature as well as previous designations that fit within this classification. Furthermore, in the cell line, we identified an apparent processed pseudogene, gste8, in addition to two isoforms from the Delta class that have been published previously. Only approximately one-third of the expressed DmGSTs could be purified by conventional GSH affinity chromatography. The diverse kinetic properties as well as physiological substrate specificity of the DmGSTs are such that each individual enzyme displayed a unique character even compared with members from the same class.
Characterization of high-current electron beam interaction with metal targets
Authors: An W. , Krasik Ya. E. , Fetzer R. , Bazylev B. , Mueller G. , Weisenburger A. , Bernshtam V.
Published: November 2011

The process of electron beam interaction with metal targets was characterized using electrical and optical diagnostics. Electron beams with current density of 5–10 A/cm2, electron energy up to 120 keV, pulse duration up to 200 μs, and cross-sectional area of 8–30 cm2 at the target surface were generated by GESA I and GESA II facilities. Streak imaging of the target surface specular reflectivity was used to determine the onset of melting and re-solidification of the target surface. Using time- and space-resolved schlieren imaging, the evolution of surface irregularities was studied. Experimental and numerical investigations of the neutral flow evaporated from the target surface showed a neutral density of ∼1019 cm−3 in the vicinity of the target and neutral velocities up to 2 × 105 cm/s. Framing and streak images of visible light emission were used to study the temporal evolution of the target surface plasma and vapors. Time- and space-resolved spectroscopy was applied to determine the surface plasma density and temperature, which were found to be ∼1014 cm−3 and ≤1 eV, respectively. Because of this small plasma density, electric fields in the plasma sheath are not sufficient to cause electrohydrodynamic instability of the liquid target surface. However, hydrodynamic instabilities due to the intense neutral flow observed in experimental and numerical studies are likely to be responsible for the growth of wavelike irregularities.
Tetragonal and hexagonal polymorphs of BaTi1−xFexO3−δ multiferroics using x-ray and Raman analyses
Authors: Nguyen Ha M. , Dang N. V. , Chuang Pei-Yu , Thanh T. D. , Hu Chih-Wei , Chen Tsan-Yao , Lam V. D. , Lee Chih-Hao , Hong L. V.
Published: November 2011

The effect of Fe doping on the crystalline phase transformation and on the local environment around Fe dopant ions is investigated for BaTi1−xFexO3−δ (0.0 ≤ x ≤ 0.5) polycrystalline samples, using x-ray diffraction, x-ray absorption spectroscopy, and Raman scattering spectroscopy. Our experimental results show that the tetragonal-to-hexagonal transformation is gradually taken place when increasing the Fe content in the range 0.02 ≤ x ≤ 0.12. Although both hexagonal and tetragonal polymorphs coexist in this doping range, Fe ions preferably substitute for Ti sites in the hexagonal lattice and exist in both Fe3+ and Fe4+ forms. Our work is of paramount importance to provide a direct evidence to the preferable substitution of transition metal ions for Ti ions.
Effect of mesh bias on the properties of the lateral conductivity of intrinsic microcrystalline silicon films deposited by low-frequency inductively coupled plasma
Authors: Yan W. S. , Xu S. , Sern C. C. , Wei D. Y.
Published: November 2011

A meshgrid is installed to study the effect of mesh bias on the lateral conductivity properties of intrinsic microcrystalline silicon films deposited by low frequency inductively coupled plasma. When a mesh bias is increased from 0 to −15 V, the dark conductivity remarkably decreases by three orders of magnitude, whereas the ratio of the photo and dark conductivity improves by one order. On contrary, the applied substrate bias has only a marginal effect on the lateral conductivity. It is revealed from the measured electron energy distribution functions that the sheath layer induced ion bombardment is responsible for the drastic change.
Corrigendum to: Athelstan L. J. Beckwith and the Flowering of Hex-5-enyl Radical Cyclization Chemistry. The Adelaide Years
Authors: Serelis Algirdas K.
Published: November 2011

Athel Beckwith chose to embark on a career in free radical chemistry at a time when it was largely ignored by all but a small coterie within the broader Organic Chemistry community. Of his many contributions in this area, the mechanistic clarification and exploitation of the cyclization of hex-5-enyl radical-containing systems is undoubtedly the most significant, leading to what is now, in a multitude of variants, a universally-used, powerful, sophisticated, selective, general synthetic methodology. This account revisits and highlights the early studies carried out by the Beckwith group at The University of Adelaide from the late-1960s to 1980, a period when the main breakthroughs in kinetic and mechanistic understanding were made, and the implications for wider synthetic utility in more complex hex-5enyl systems became apparent.
Modulations of Starch Structure with Potential to Influence Health
Authors: Thompson Donald B.
Published: November 2011

Starch is typically a mixture of essentially linear amylose and highly branched amylopectin. The difference is in the nature of the covalent bonding, with multiple branch points emanating from 1–6 glycosidic linkages of amylopectin. Equally important as the chemical structure is the physical structure: single helices and double helices exist and may be the basis for crystallinity. Starch chemical structure has been modulated through breeding: high-amylose maize starch is well studied with respect to its potential to influence health. Its altered chemical structure leads to differences in the physical structure as well. Physical treatments can also lead to altered physical structure. Modulation of chemical and/or physical structures may influence health by altering the rate and extent of starch digestion in the small intestine. Undigested starch (resistant starch) reaches the large intestine where it is fermented to potentially beneficial microbial by-products that are absorbed there.
The Role of Oxygen in Synthesizing Monodisperse Silver Nanocubes
Authors: Gupta Bakul , Rouesnel Will , Gooding J. Justin
Published: November 2011

In this work, we report on silver nanocubes prepared by using the conventional polyol synthesis in the presence of hydrochloric acid and oxygen. We found that by controlling the headspace oxygen concentration in the sample vial at a temperature of 140°C, monodisperse silver nanocubes of 100–115 nm in edge length were produced. A specific headspace oxygen concentration along with the chloride ions promoted the oxidative etching of twinned particles so that only single crystal cubes were produced. At lower oxygen concentrations, nanorods and wires were obtained whereas at very high concentrations all the particles were completely etched away resulting in a solution with no nanoparticles. Electron diffraction and X-ray diffraction analysis was employed to study the structural characterization. Scanning electron microscopy was used to examine the morphology of the silver nanoparticles.
Bovine dominant follicular fluid promotes the in vitro development of goat preantral follicles
Authors: Duarte A. B. G. , Araújo V. R. , Chaves R. N. , Silva G. M. , Magalhães-Padilha D. M. , Satrapa R. A. , Donato M. A. M. , Peixoto C. A. , Campello C. C. , Matos M. H. T. , Barros C. M. , Figueiredo J. R.
Published: November 2011

The aim of this study was to evaluate the effect of follicular fluid collected from bovine dominant follicles (bFF) on the in vitro development of goat preantral follicles and determine the best time to add this supplement to the culture medium. The preantral follicles were isolated and randomly distributed into four treatments in absence (control) or presence of 10% of bFF added on Days 0 (FF0–18), 6 (FF6–18) or 12 (FF12–18) of culture onwards. After 18 days, follicular development was assessed based on follicular survival, antral cavity formation, increased follicular diameter as well as fully grown oocyte (>110 μm) viability and meiosis resumption. The oocytes from the cultured follicles were in vitro-matured and processed for fluorescence or ultrastructural analysis. The results showed that on Day 18 the treatment FF0–18 had a significantly higher (P < 0.05) survival than control and FF12–18, but not FF6–18. The addition of bFF at the beginning of culture (FF0–18 and FF6–18) promoted a high percentage of follicular growth, meiosis resumption and early antrum formation. Moreover, this study described for the first time the ultrastructural analysis of caprine oocytes grown in vitro. This evaluation revealed that in the presence of bFF on (FF0–18) the in vitro-grown oocytes presented normal organelle distribution and well-defined, intact plasma and nuclear membranes. In conclusion, bFF originating from dominant follicles maintain the survival and promote the in vitro growth of goat preantral follicles when added at the beginning of culture.
Continentalism and the invention of traditions in translation studies
Authors: Delabastita Dirk
Published: November 2011

This theoretical case study starts from a brief critical discussion of Eurocentrism in translation studies, underscoring the importance of the efforts toward a more inclusive, truly global and culturally balanced approach to translation which are increasingly being made in our field, often under the banner of “the international turn.” However, the rejection of Eurocentrism leaves open a wide range of alternative models and approaches, and this paper aims to show that the search for alternatives is not without its own difficulties. For example, it might be tempting for non-European scholars to derive an alternative way of thinking about translation from translational practices and discourses in their own continent that appear to be at odds with what is perceived as the “European” model of translation. A post-colonial sensibility would seem to make this an extremely attractive proposition. This is the line of thinking which inspired Edwin Gentzler’s Translation and Identity in the Americas. New Directions in Translation Theory (2008). The paper enters into a critical dialogue with Gentzler’s book in order to argue the general thesis that the replacement of one (perceived) continent-based paradigm by another (perceived) continent-based paradigm is not the best way forward, suffering as it does from a range of methodological problems. The best way to overcome Eurocentrism is not to construct and promote an American continentalism (“translation in the American sense”) as an alternative to it, or any other nationally or continentally defined concept of translation, for that matter.
The representation of agents of translation in (South) Africa
Authors: Marais Kobus
Published: November 2011

This article discusses agency in translation as conceptualized in recent developments in Translation Studies. As a subtext, it poses the representation of its own data as a methodological problem. The article discusses Donald Strachan as a possible agent of translation, probing the implications of his interpreting and translation work in a border setting in South Africa in the late 1800s. It then juxtaposes this perspective with the translation theory of Edwin Gentzler, who claims that translators are creating cultures by way of their work. From this encounter, the author suggests a number of implications for researching translation in Africa. The paper ends by reflecting on its own subtext.
On fictional turns, fictionalizing twists and the invention of the Americas
Authors: Valdeón Roberto A.
Published: November 2011

In his 2008 book, Translation and Identity in the Americas, Edwin Gentzler proposed a “fictional turn” to refer to translation in connection with the construction of identity in the Americas, a highly positive view of the role played by this activity since the arrival of the Europeans. This paper proposes a “fictionalizing twist,” that is, a complementary approach that would attest to the less positive use of translation in the relation between Europe and the Americas on the one hand, and among European nations on the other. Thus, I examine how translation and Translation Studies have contributed to create certain negative images of translators and nations, a tendency that can still be traced nowadays. First, I discuss the views on the indigenous interpreter Malinche and her part in the conquest of Mexico. Then I move on to examine the ideological manipulation of texts to promote antagonistic national identities within the European context at the time. Finally, it is argued that both the fictional turn and the fictionalizing twist need to be considered as an integral part of the identity-construction process in the Americas and in Europe.
The Rap1–Rgl–Ral signaling network regulates neuroblast cortical polarity and spindle orientation
Authors: Carmena Ana , Makarova Aljona , Speicher Stephan
Published: November 2011

A crucial first step in asymmetric cell division is to establish an axis of cell polarity along which the mitotic spindle aligns. Drosophila melanogaster neural stem cells, called neuroblasts (NBs), divide asymmetrically through intrinsic polarity cues, which regulate spindle orientation and cortical polarity. In this paper, we show that the Ras-like small guanosine triphosphatase Rap1 signals through the Ral guanine nucleotide exchange factor Rgl and the PDZ protein Canoe (Cno; AF-6/Afadin in vertebrates) to modulate the NB division axis and its apicobasal cortical polarity. Rap1 is slightly enriched at the apical pole of metaphase/anaphase NBs and was found in a complex with atypical protein kinase C and Par6 in vivo. Loss of function and gain of function of Rap1, Rgl, and Ral proteins disrupt the mitotic axis orientation, the localization of Cno and Mushroom body defect, and the localization of cell fate determinants. We propose that the Rap1–Rgl–Ral signaling network is a novel mechanism that cooperates with other intrinsic polarity cues to modulate asymmetric NB division.
Tensor–vector–scalar-modified gravity: from small scale to cosmology
Authors: Bekenstein Jacob D.
Published: November 2011

The impressive success of the standard cosmological model has suggested to many that its ingredients are all that one needs to explain galaxies and their systems. I summarize a number of known problems with this programme. They might signal the failure of standard gravity theory on galaxy scales. The requisite hints as to the alternative gravity theory may lie with the modified Newtonian dynamics (MOND) paradigm, which has proved to be an effective summary of galaxy phenomenology. A simple nonlinear modified gravity theory does justice to MOND at the non-relativistic level, but cannot be consistently promoted to relativistic status. The obstacles were first side-stepped with the formulation of tensor–vector–scalar theory (T
e
V
e
 S), a covariant-modified gravity theory. I review its structure, its MOND and Newtonian limits, and its performance in the face of galaxy phenomenology. I also summarize features of T
e
V
e
 S cosmology and describe the confrontation with data from strong and weak gravitational lensing.
Modifications of gravity
Authors: Skordis Constantinos
Published: November 2011

General relativity (GR) is a phenomenologically successful theory that rests on firm foundations, but has not been tested on cosmological scales. The deep mystery of dark energy (and possibly even the requirement of cold dark matter (CDM)) has increased the need for testing modifications to GR, as the inference of such otherwise undetected fluids depends crucially on the theory of gravity. Here, I discuss a general scheme for constructing consistent and covariant modifications to the Einstein equations. This framework is such that there is a clear connection between the modification and the underlying field content that produces it. I argue that this is mandatory for distinguishing modifications of gravity from conventional fluids. I give a non-trivial example, a simple metric-based modification of the fluctuation equations for which the background is exact
Λ
CDM, but differs from it in the perturbations. I show how this can be generalized and solved in terms of two arbitrary functions. Finally, I discuss future prospects and directions of research.
Surviving chromosome replication: the many roles of the S-phase checkpoint pathway
Authors: Labib Karim , De Piccoli Giacomo
Published: November 2011

Checkpoints were originally identified as signalling pathways that delay mitosis in response to DNA damage or defects in chromosome replication, allowing time for DNA repair to occur. The ATR (ataxia- and rad-related) and ATM (ataxia-mutated) protein kinases are recruited to defective replication forks or to sites of DNA damage, and are thought to initiate the DNA damage response in all eukaryotes. In addition to delaying cell cycle progression, however, the S-phase checkpoint pathway also controls chromosome replication and DNA repair pathways in a highly complex fashion, in order to preserve genome integrity. Much of our understanding of this regulation has come from studies of yeasts, in which the best-characterized targets are the stimulation of ribonucleotide reductase activity by multiple mechanisms, and the inhibition of new initiation events at later origins of DNA replication. In addition, however, the S-phase checkpoint also plays a more enigmatic and apparently critical role in preserving the functional integrity of defective replication forks, by mechanisms that are still understood poorly. This review considers some of the key experiments that have led to our current understanding of this highly complex pathway.
Spindle assembly checkpoint: the third decade
Authors: Musacchio Andrea
Published: November 2011

The spindle assembly checkpoint controls cell cycle progression during mitosis, synchronizing it with the attachment of chromosomes to spindle microtubules. After the discovery of themitotic arrest deficient(MAD) andbudding uninhibited by benzymidazole(BUB) genes as crucial checkpoint components in 1991, the second decade of checkpoint studies (2001–2010) witnessed crucial advances in the elucidation of the mechanism through which the checkpoint effector, the mitotic checkpoint complex, targets the anaphase-promoting complex (APC/C) to prevent progression into anaphase. Concomitantly, the discovery that the Ndc80 complex and other components of the microtubule-binding interface of kinetochores are essential for the checkpoint response finally asserted that kinetochores are crucial for the checkpoint response. Nevertheless, the relationship between kinetochores and checkpoint control remains poorly understood. Crucial advances in this area in the third decade of checkpoint studies (2011–2020) are likely to be brought about by the characterization of the mechanism of kinetochore recruitment, activation and inactivation of checkpoint proteins, which remains elusive for the majority of checkpoint components. Here, we take a molecular view on the main challenges hampering this task.
Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide
Authors: Teves Sheila S. , Henikoff Steven
Published: November 2011

Heat shock rapidly induces expression of a subset of genes while globally repressing transcription, making it an attractive system to study alterations in the chromatin landscape that accompany changes in gene regulation. We characterized these changes in Drosophila cells by profiling classical low-salt-soluble chromatin, RNA polymerase II (Pol II), and nucleosome turnover dynamics at single-base-pair resolution. With heat shock, low-salt-soluble chromatin and stalled Pol II levels were found to decrease within gene bodies, but no overall changes were detected at transcriptional start sites. Strikingly, nucleosome turnover decreased genome-wide within gene bodies upon heat shock in a pattern similar to that observed with inhibition of Pol II elongation, especially at genes involved in the heat-shock response. Relatively high levels of nucleosome turnover were also observed throughout the bodies of genes with paused Pol II. These observations suggest that down-regulation of transcription during heat shock involves reduced nucleosome mobility and that this process has evolved to promote heat-shock gene regulation. Our ability to precisely map both nucleosomal and subnucleosomal particles directly from low-salt-soluble chromatin extracts to assay changes in the chromatin landscape provides a simple general strategy for epigenome characterization.
A flow-through reaction cell forin situX-ray diffraction and absorption studies of heterogeneous powder–liquid reactions and phase transformations
Authors: Ferrer Pilar , da Silva Iván , Rubio-Zuazo Juan , Alfonso Belén F. , Trobajo Camino , Khainakov Sergei , Garcia Jose R. , Garcia-Granda Santiago , Castro Germán R.
Published: November 2011

A portable powder–liquid high-corrosion-resistant reaction cell has been designed to followin situreactions by X-ray powder diffraction (XRD) and X-ray absorption spectroscopy (XAS) techniques. The cell has been conceived to be mounted on the experimental stations for diffraction and absorption of the Spanish CRG SpLine-BM25 beamline at the European Synchrotron Radiation Facility. Powder reactants and/or products are kept at a fixed position in a vertical geometry in the X-ray pathway by a porous membrane, under forced liquid reflux circulation. Owing to the short pathway of the X-ray beam through the cell, XRD and XAS measurements can be carried out in transmission configuration/mode. In the case of the diffraction technique, data can be collected with either a point detector or a two-dimensional CCD detector, depending on specific experimental requirements in terms of space or time resolution. Crystallization processes, heterogeneous catalytic processes and several varieties of experiments can be followed by these techniques with this cell. Two experiments were carried out to demonstrate the cell feasibility: the phase transformations of layered titanium phosphates in boiling aqueous solutions of phosphoric acid, and the reaction of copper carbonate and L-isoleucine amino acid powders in boiling aqueous solution. In this last case the shrinking of the solid reactants and the formation of Cu(isoleucine)2is observed. The crystallization processes and several phase transitions have been observed during the experiments, as well as an unexpected reaction pathway.
Focusing femtosecond X-ray free-electron laser pulses by refractive lenses
Authors: Kohn V. G.
Published: November 2011

The possibility of using a parabolic refractive lens with initial X-ray free-electron laser (XFEL) pulses,i.e.without a monochromator, is analysed. It is assumed that the measurement time is longer than 0.3 fs, which is the time duration of a coherent pulse (spike). In this case one has to calculate the propagation of a monochromatic wave and then perform an integration of the intensity over the radiation spectrum. Here a general algorithm for calculating the propagation of time-dependent radiation in free space and through various objects is presented. Analytical formulae are derived describing the properties of the monochromatic beam focused by a system of one and two lenses. Computer simulations show that the European XFEL pulses can be focused with maximal efficiency,i.e.as for a monochromatic wave. This occurs even for nanofocusing lenses.
Double‐blind placebo‐controlled evaluation of the PROMETA™ protocol for methamphetamine dependence
Authors: Ling Walter , Shoptaw Steven , Hillhouse Maureen , Bholat Michelle A. , Charuvastra Charles , Heinzerling Keith , Chim David , Annon Jeffrey , Dowling Patrick T. , Doraimani Geetha
Published: November 2011

Aims  To evaluate the efficacy and safety of the PROMETA™ Protocol for treating methamphetamine dependence.

Design  A double‐blind, placebo‐controlled 108‐day study with random assignment to one of two study conditions: active medication with flumazenil (2 mg infusions on days 1, 2, 3, 22, 23), gabapentin (1200 mg to day 40) and hydroxazine (50 mg to day 10) versus placebo medication (with active hydroxazine only).

Setting  Three substance abuse treatment clinics: two in‐patient, one out‐patient.

Participants  Treatment‐seeking, methamphetamine‐dependent adults (n = 120).

Measurements  Primary outcome was percentage of urine samples testing negative for methamphetamine during the trial.

Findings  No statistically significant between‐group differences were detected in urine drug test results, craving, treatment retention or adverse events.

Conclusions  The PROMETA protocol, consisting of flumazenil, gabapentin and hydroxyzine, appears to be no more effective than placebo in reducing methamphetamine use, retaining patients in treatment or reducing methamphetamine craving.
Analysis of very elderly (≥80 years) non‐hodgkin lymphoma: impact of functional status and co‐morbidities on outcome
Authors: Nabhan Chadi , Smith Sonali M. , Helenowski Irene , Ramsdale Erika , Parsons Benjamin , Karmali Reem , Feliciano Josephine , Hanson Britt , Smith Scott , McKoy June , Larsen Annette , Hantel Andrew , Gregory Stephanie , Evens Andrew M.
Published: November 2011

Data on outcome, prognostic factors, and treatment for very elderly non‐Hodgkin lymphomas (NHL) is sparse. We conducted a multicentre retrospective analysis of NHL patients ≥80 years (at diagnosis) treated between 1999 and 2009. Detailed characteristics were obtained including geriatric syndromes, activities of daily living (ADLs), and co‐morbidities using the Cumulative Illness Rating Scale‐Geriatrics (CIRS‐G). We identified 303 patients: 170 aggressive NHL (84% B cell/16% T cell) and 133 indolent NHL (82% B cell/18% T cell). Median age was 84 years (80–95). A geriatric syndrome was present in 26% of patients, 18% had ≥1 grade 4 CIRS‐G, and 14% had loss of ADLs. At 49‐month median follow‐up, 4‐year progression‐free (PFS) and overall survival (OS) for aggressive NHLs were 31% and 44% respectively (stage I/II: PFS 53% and OS 66%; stage III/IV: PFS 20% and OS 32%; P < 0·0001 and 0·0002, respectively). Four‐year PFS and OS for indolent NHL were 44% and 66% respectively, regardless of stage. Multivariate regression analysis identified two key factors that predicted inferior PFS and OS for both NHL groups: lack of CR and loss of ADLs. Prospective studies for very elderly NHL that incorporate geriatric tools, especially ADLs, are warranted.
Parental phase status affects the cold hardiness of progeny eggs in locusts
Authors: Wang Hongsheng , Ma Zongyuan , Cui Feng , Wang Xianhui , Guo Wei , Lin Zhe , Yang Pengcheng , Kang Le
Published: November 2011

1. The capacity to adapt to low temperature is critical for the persistence of insect populations in heterogeneous environments. Locusts show remarkable phenotypic plasticity, termed ‘phase change’, in response to local population density.

2. In this study, the hypothesis that population density, as a social factor, affects the cold hardiness of progeny is validated in the migratory locust, Locusta migratoria, which shows remarkable density‐dependent phase changes between gregarious and solitarious phases.

3. We demonstrated that eggs of gregarious and solitarious migratory locusts significantly differ not only in size and weight, but also in cold hardiness. Eggs of solitarious locusts are more resistant to cold stress compared with those of gregarious locusts, with longer 50% lethal time at different low temperatures and under different acclimation treatments of cooling rates or cold exposure time, lower upper limit of chill injury zone, and lower sum of injurious temperature resulting from temperature–time regression. The lowest cooling rate (0·05 °C min−1) yields the highest survival of cold for eggs.

4. A custom‐made microarray covering 9154 unigenes of the migratory locust demonstrated quite different gene expression profiles in the two phases in response to normal or low temperature. Under cold stress, the gregarious‐phase eggs have higher transcriptional levels of heat‐shock proteins, DOPA decarboxylases and tyrosine hydroxylase, whereas the solitarious‐phase eggs exhibit stimulated lipid metabolism and carboxylic acid transport.

5. Hybridization between the two phases showed that the cold hardiness of eggs from the hybrid with solitarious females is significantly higher than that of the hybrid with gregarious females, and the cold hardiness of eggs from each reciprocal hybrid is close to their maternal origins. These results indicate that the cold hardiness of progeny is affected by the parental phase status.
The foraging tightrope between predation risk and plant toxins: a matter of concentration
Authors: McArthur Clare , Orlando Paul , Banks Peter B. , Brown Joel S.
Published: November 2011

1. Plants defend and predators attack, provoking the foraging dilemma faced by herbivores and frugivores of how to eat enough without being eaten. High toxin concentration in leaves and fruits inhibits consumption, while predation risk reduces feeding opportunities, as prey forage to avoid encountering predators. Thus, both factors vary and define the quality of the landscape. How foraging animals directly quantify, compare and respond to these two costs has rarely been tested.

2. We show that free‐ranging bushbabies – small, frugivorous primates – change their behaviour and use of artificial food patches based on the interplay between toxin concentration in food and patch safety. Using a titration experiment, we demonstrate that bushbabies quantify the relative costs of toxin and fear. We pinpoint where these costs are equivalent and show that animals seek food patches with the lower net cost.

3. We conclude that the ecological effectiveness of plant toxins as defence against consumers needs to be considered in the context of a landscape of fear – and the relative impact of anti‐predator tactics and plant defence is strongly shaped by the concentration of these defences.

4. A corollary is that plants may benefit from fear as a substitute for their own chemical defence, adding a new dimension to the concept of indirect plant defence. Whether, from the plant’s perspective, the benefits derived from fear can be considered evolutionarily adaptive rather than simply ecologically serendipitous remains to be tested.