bluuebunny/crossref_metadata_2025 huggingface dataset:
Inverse halftoning using super‐resolution image processing
Authors: Minami Yuki , Azuma Shun‐ichi , Sugie Toshiharu
Published: December 2011

This paper focuses on the inverse halftoning problem, that is, the problem of reconstructing continuous‐tone images from halftone images of white and black pixels. In general, the problem does not have a unique solution, since halftoning is a many‐to‐one map from continuous‐tone images to binary ones. To this problem, we provide a simple and useful inverse halftoning method, composed of two steps. The first step is to generate several grayscale images from the original halftone image and low‐pass filters. The next step is to reconstruct a continuous‐tone image from the multiple grayscale images by using super‐resolution image processing. This method allows us to obtain good continuous‐tone images which are comparable to the results of the existing methods. The validity of the proposed method is demonstrated by several experiments. © 2011 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
A wireless sensor network for precision agriculture and its performance
Authors: Sahota Herman , Kumar Ratnesh , Kamal Ahmed
Published: December 2011

The use of wireless sensor networks is essential for implementation of information and control technologies in precision agriculture. We present our design of network stack for such an application where sensor nodes periodically collect data from fixed locations in a field. Our design of the physical layer consists of multiple power modes in both the receive and transmit operations for the purpose of achieving energy savings. In addition, we design our MAC layer to use these multiple power modes to improve the energy efficiency of wake‐up synchronization phase. Our MAC protocol also organizes all the sender nodes to be synchronized with the receiver simultaneously and transmit their data in a time scheduled manner. Next, we design our energy aware routing strategy that balances the energy consumption over the nodes in the entire field and minimizes the number of wake‐up synchronization overheads by scheduling the nodes for transmission in accordance with the structure of the routing tree. We develop analytical models and simulation studies to compare the energy consumption of our MAC protocol with that of the popular S‐MAC protocol for a typical network topology used in our application under our routing strategy. Our MAC protocol is shown to have better energy efficiency as well as latency in a periodic data collection application. We also show the improvements resulting from the use of our routing strategy, in simulations, compared with the case when the next hop is chosen randomly from the set of neighbors that are closer to the sink node. Copyright © 2011 John Wiley & Sons, Ltd.
Proposed new simple scoring system to identify indications for urgent ERCP in acute cholangitis based on the Tokyo Guidelines
Authors: Nishino Takayoshi , Onizawa Shunsuke , Hamano Mie , Shirato Izumi , Shirato Miho , Hamano Tetsuya , Tagata Tomoko , Araida Tatsuo , Mitsunaga Atsushi
Published: December 2011

Background/purpose

The Tokyo Guidelines (TG) have enabled more accurate diagnosis of acute cholangitis (AC). This study was undertaken to develop a new prognostic scoring system to predict the need for urgent endoscopic retrograde cholangiopancreatography (ERCP) based on the clinical findings on admission.

Methods

We prospectively reviewed 40 consecutive cases of AC and divided them into an urgent‐ERCP group and an elective‐ERCP group.

Results

Univariate analysis identified four factors that predicted the need for urgent ERCP: serum albumin level below 3.0 g/dl, blood urea nitrogen level above 20 mg/dl, platelet count below 120,000/μl, and the presence of systemic inflammatory response syndrome. These four predictors plus four predictors of organ dysfunction in the TG: shock, consciousness disturbance, respiratory failure, and prothrombin time/international normalized ratio >1.5, were used to devise a scoring system in which 1 point was assigned for the first four predictors and 2 points were assigned for the latter four predictors (maximum score possible: 12 points). The receiver‐operator characteristic curve of the scores showed good test performance for predicting the need for urgent ERCP and for predicting a positive blood culture, and the areas under the concentration curves (AUCs) were 0.96 and 0.97, respectively. The optimal cut‐off value for urgent ERCP was 2 points.

Conclusions

This new simple scoring system allows identification of high‐risk AC patients soon after admission to hospital.
Numerical experiment of cyclic layering in a solidified binary eutectic melt
Authors: Toramaru Atsushi , Matsumoto Mitsuo
Published: December 2011

In shallow magmatic intrusions, a characteristic layering structure (hereafter referred to as cyclic layering) can sometimes be observed. This cyclic layering is caused by double diffusion and crystallization kinetics, and different from what is observed as rhythmic layering caused by gravity. The cyclic layering is visualized as differential weathering in response to the differential stiffness caused by textural variations such as those in the volume fraction, number density, and size of vesicles or crystals. The spacing of layers seems to increase according to a geometric progression, like as in Liesegang bands of a diffusion‐precipitation system. In order to understand the development condition for cyclic layering and the characteristics of textural variations, such as the spacing of layering in crystallized multi‐component melts by conductive cooling, we carried out a numerical experiment on the 1D crystallization process of a binary eutectic melt. This simulation took into account the cooling from contact with country rock as well as the compositional and thermal diffusion and the kinetics of diffusion‐limited crystallization. The governing equations include dimensionless control parameters describing the relative importance of thermal diffusion or compositional diffusion (Lewis number, Le) and the effective latent heat release (Stefan number, St). From the results of the numerical experiments, it was found that the layering develops through eutectic oscillation (compositional and thermal oscillation below the eutectic point), suggesting that the bi‐activating condition, whereby both phases cooperatively activate their crystallization rates, is essential for the development of layering. No layering is observed at the margin, and the length of the region with no layering increases exponentially with decreasing St. The amplitude of textural oscillation decreases with decreasing St. Thus, practically no layering develops at small latent heat release. Three types of layering structure or oscillatory profiles of texture are observed (short, long and multiple types), depending mainly on Le. Realistic values of Le and St suggest that natural cyclic layering is the multiple or long type of layering. The common ratios of geometric progressions converge with increasing Le to constants in the range of approximately 1.02–1.05, which is similar to the range of the natural observations. Experiments with no latent heat release by the second‐phase simulating vesicles show similar oscillatory behaviors, suggesting that the latent heat release of the first crystallizing phase is an essential factor for the development of vesicle layering.
A case study of observations of volcanic ash from the Eyjafjallajökull eruption: 1. In situ airborne observations
Authors: Turnbull Kate , Johnson Ben , Marenco Franco , Haywood Jim , Minikin Andreas , Weinzierl Bernadett , Schlager Hans , Schumann Ulrich , Leadbetter Susan , Woolley Alan
Published: December 2011

On 17 May 2010, the FAAM BAe‐146 aircraft made remote and in situ measurements of the volcanic ash cloud from Eyjafjallajökull over the southern North Sea. The Falcon 20E aircraft operated by Deutsches Zentrum für Luft‐ und Raumfahrt (DLR) also sampled the ash cloud on the same day. While no “wingtip‐to‐wingtip” co‐ordination was performed, the proximity of the two aircraft allows worthwhile comparisons. Despite the high degree of inhomogeneity (e.g., column ash loadings varied by a factor of three over ∼100 km) the range of ash mass concentrations and the ratios between volcanic ash mass and concentrations of SO2, O3 and CO were consistent between the two aircraft and within expected instrumental uncertainties. The data show strong correlations between ash mass, SO2concentration and aerosol scattering with the FAAM BAe‐146 data providing a specific extinction coefficient of 0.6–0.8 m2 g−1. There were significant differences in the observed ash size distribution with FAAM BAe‐146 data showing a peak in the mass at ∼3.5μm (volume‐equivalent diameter) and DLR data peaking at ∼10μm. Differences could not be accounted for by refractive index and shape assumptions alone. The aircraft in situ and lidar data suggest peak ash concentrations of 500–800 μg m−3with a factor of two uncertainty. Comparing the location of ash observations with the ash dispersion model output highlights differences that demonstrate the difficulties in forecasting such events and the essential nature of validating models using high quality observational data from platforms such as the FAAM BAe‐146 and the DLR Falcon.
A method to calculate heterogeneous evapotranspiration using submeter thermal infrared imagery coupled to a stomatal resistance submodel
Authors: Moffett Kevan B. , Gorelick Steven M.
Published: December 2011

Thermal infrared (TIR) remote sensing of vegetation temperature, combined with surface energy balance modeling, allows efficient estimation of spatially distributed evapotranspiration (ET). Many ET models are sensitive to the parameterization of stomatal control; yet, modelers often employ spatially uniform stomatal resistance values, even in distributed applications. Unfortunately, assuming uniform resistance across a canopy with large temperature variance is physically unrealistic and may produce artifacts in ET magnitude. To account for spatial variations in stomatal control that likely accompany temperature variations, we propose nesting a new submodel within some well‐established ET models. The submodel derives, for the canopy patch of interest, a concave‐downward relationship between stomatal conductance and temperature, as expected from plant biology. Using the submodel, each pixel's contribution to the total canopy patch ET is influenced both by its observed temperature and by its location‐specific estimated stomatal resistance. The submodel requires only one more parameter than the unmodified ET models, which can be obtained from the literature; it conserves energy between the pixel and image scales, unlike single‐valued resistance approaches; it produces realistic ET values at extreme temperature locations; and provides a remote sensing‐based way to estimate the in situ canopy stomatal conductance‐temperature relationship, which otherwise must be measured under controlled conditions. Since very high‐resolution TIR data provide one means to observe large temperature variance, the submodel was tested using data with cm‐scale pixels collected over 1.5 m2 patches of two vegetation types. The biophysical relationships derived by the submodel were successfully verified against laboratory data.
Nanohertz frequency determination for the gravity probe B high frequency superconducting quantum interference device signal
Authors: Salomon M. , Conklin J. W. , Kozaczuk J. , Berberian J. E. , Keiser G. M. , Silbergleit A. S. , Worden P. , Santiago D. I.
Published: December 2011

In this paper, we present a method to measure the frequency and the frequency change rate of a digital signal. This method consists of three consecutive algorithms: frequency interpolation, phase differencing, and a third algorithm specifically designed and tested by the authors. The succession of these three algorithms allowed a 5 parts in 1010 resolution in frequency determination. The algorithm developed by the authors can be applied to a sampled scalar signal such that a model linking the harmonics of its main frequency to the underlying physical phenomenon is available. This method was developed in the framework of the gravity probe B (GP-B) mission. It was applied to the high frequency (HF) component of GP-B’s superconducting quantum interference device signal, whose main frequency fz is close to the spin frequency of the gyroscopes used in the experiment. A 30 nHz resolution in signal frequency and a 0.1 pHz/s resolution in its decay rate were achieved out of a succession of 1.86 s-long stretches of signal sampled at 2200 Hz. This paper describes the underlying theory of the frequency measurement method as well as its application to GP-B’s HF science signal.
Synthesis of zinc fulleride (ZnxC60) thin films with ultra-low thermal conductivity
Authors: Check Michael H. , Dudis Douglas S. , Ferguson John B. , Gengler Jamie J. , Seibel Harry A. , Elliott Bevan C. , Votaw Zachary S. , Voevodin Andrey A.
Published: December 2011

The structure and physical properties of doped fullerene materials were investigated for their interesting thermal properties. The synthesis and thermal properties of ZnxC60 thin films are reported. Thin films of ZnxC60 were found to have an exceedingly low thermal conductivity of 0.13 Wm−1 K−1. Differential scanning calorimetry results suggested that a temperature of 357 °C is needed in order to fully intercalate the Zn with the C60. Both charge transfer and covalent bonding (between Zn and C60) should be considered when attempting to understand the Raman spectra observed. Moreover, the ZnxC60 thin films created represent an interesting class of materials that could find use in several thermal applications. Furthermore, in the present case, the exceptionally low thermal conductivity is accompanied by a substantial increase in the electrical conductivity, suggesting interesting thermal and electrical transport.
Mapping the magnetic field vector in a fountain clock
Authors: Gertsvolf Marina , Marmet Louis
Published: December 2011

We show how the mapping of the magnetic field vector components can be achieved in a fountain clock by measuring the Larmor transition frequency in atoms that are used as a spatial probe. We control two vector components of the magnetic field and apply audio frequency magnetic pulses to localize and measure the field vector through Zeeman spectroscopy.
Wave and transport studies utilizing dense plasma filaments generated with a lanthanum hexaboride cathode
Authors: Van Compernolle B. , Gekelman W. , Pribyl P. , Cooper C. M.
Published: December 2011

A portable lanthanum hexaboride (LaB6) cathode has been developed for use in the LArge Plasma Device (LAPD) at UCLA. The LaB6 cathode can be used as a tool for many different studies in experimental plasma physics. To date, the cathode has been used as a source of a plasma with a hot dense core for transport studies and diagnostics development, as a source of gradient driven modes, as a source of shear Alfvén waves, and as a source of interacting current channels in reconnection experiments. The LaB6 cathode is capable of higher discharge current densities than the main barium oxide coated LAPD cathode and is therefore able to produce plasmas of higher densities and higher electron temperatures. The 8.25 cm diameter cathode can be introduced into the LAPD at different axial locations without the need to break vacuum. The cathode can be scaled up or down for use as a portable secondary plasma source in other machines.
Bounce-free spherical hydrodynamic implosion
Authors: Kagan Grigory , Tang Xian-Zhu , Hsu Scott C. , Awe Thomas J.
Published: December 2011

In a bounce-free spherical hydrodynamic implosion, the post-stagnation hot core plasma does not expand against the imploding flow. Such an implosion scheme has the advantage of improving the dwell time of the burning fuel, resulting in a higher fusion burn-up fraction. The existence of bounce-free spherical implosions is demonstrated by explicitly constructing a family of self-similar solutions to the spherically symmetric ideal hydrodynamic equations. When applied to a specific example of plasma liner driven magneto-inertial fusion, the bounce-free solution is found to produce at least a factor of four improvement in dwell time and fusion energy gain.
Dependence of recombination mechanisms and strength on processing conditions in polymer solar cells
Authors: Nalwa Kanwar S. , Kodali Hari K. , Ganapathysubramanian Baskar , Chaudhary Sumit
Published: December 2011

Charge carrier recombination due to carrier trapping is not often considered in polymer based solar cells, except in those using non-fullerene acceptors or new donor polymers with limited short-range order. However, we show that even for the canonical poly(3-hexylthiophene): phenyl-C61-butyric acid methyl ester (P3HT:PCBM) system, relative strengths of bimolecular and trap-assisted recombination are strongly dependent on processing conditions. For slow-grown active-layers, bimolecular recombination is indeed the major loss mechanism under one sun illumination. However, for fast-grown active-layers, trap-assisted recombination dominates over bimolecular recombination by an order of magnitude, and recombination strength at short-circuit condition is 3-4 times higher, leading to loss of photocurrent and lowering of fill factor.
Fabrication of sub-10 nm gap arrays over large areas for plasmonic sensors
Authors: Siegfried T. , Ekinci Y. , Solak H. H. , Martin O. J. F. , Sigg H.
Published: December 2011

We report a high-throughput method for the fabrication of metallic nanogap arrays with high-accuracy over large areas. This method, based on shadow evaporation and interference lithography, achieves sub-10 nm gap sizes with a high accuracy of ±1.5 nm. Controlled fabrication is demonstrated over mm2 areas and for periods of 250 nm. Experiments complemented with numerical simulations indicate that the formation of nanogaps is a robust, self-limiting process that can be applied to wafer-scale substrates. Surface-enhanced Raman scattering (SERS) experiments illustrate the potential for plasmonic sensing with an exceptionally low standard-deviation of the SERS signal below 3% and average enhancement factors exceeding 1 × 106.
Realization of tightly confined channel plasmon polaritons at low frequencies
Authors: Jiang Tao , Shen Linfang , Wu Jin-Jei , Yang Tzong-Jer , Ruan Zhichao , Ran Lixin
Published: December 2011

Subwavelength guiding of channel plasmon polaritons (CPPs) is realized by a properly structured metallic groove at frequencies far below the plasma frequency of metal. Compared with CPPs at visible frequencies, more versatile physical mechanisms can be introduced in these CPPs by surface patterning, so that they can exhibit superior features as visible CPPs, while eliminating the potential drawbacks of the latter. Such designer CPPs are explained physically with the effective-index method and verified experimentally in the microwave regime.
Distribution of electronic reconstruction at the n-type LaAlO3/SrTiO3 interface revealed by hard x-ray photoemission spectroscopy
Authors: Chu Y. Y. , Liao Y. F. , Tra V. T. , Yang J. C. , Liu W. Z. , Chu Y. H. , Lin J. Y. , Huang J. H. , Weinen J. , Agrestini S. , Tsuei K.-D. , Huang D. J.
Published: December 2011

We investigated the electronic reconstruction at the n-type LaAlO3/SrTiO3 interface with hard x-ray photoelectron spectroscopy (HAXPES) under grazing incidence. By exploiting the collapse of evanescent x-ray waves and the abrupt increase of x-ray absorption at the critical incidence angle, our HAXPES study reveals a 2% electronic reconstruction from Ti4+ to Ti3+ occurring near the interface. Such an electronic reconstruction also extends from the interface into SrTiO3 with a depth of about 48 Å (∼12 unit cells) and an estimated total charge transfer of ∼0.24 electrons per two-dimensional unit cell.
Comparative study on aging effect in BiFeO3 thin films substituted at A- and B-sites
Authors: Wang Xi , Hu Guangda , Cheng Ling , Yang Changhong , Wu Weibing
Published: December 2011

Typical characteristics of aging effect, double hysteresis loops, were observed in (100)pseudocubic-oriented Bi0.95Ca0.05FeO3 (BCFO) and BiFe0.95Ni0.05O3 (BFNO) films grown on LaNiO3(100)/Si substrates. The double hysteresis loops for BCFO film become less “constrained” with increasing applied voltage compared to that for BFNO, indicating that the aging effect is more severe in the latter. This can be demonstrated by the lower leakage current and smaller dielectric constant for BFNO. These phenomena are explained based on the crystal structure and defect chemistry.
Tunable fringe magnetic fields induced by converse magnetoelectric coupling in a FeGa/PMN-PT multiferroic heterostructure
Authors: Fitchorov Trifon , Chen Yajie , Hu Bolin , Gillette Scott M. , Geiler Anton , Vittoria Carmine , Harris Vincent G.
Published: December 2011

The fringe magnetic field, induced by magnetoelectric coupling in a bilayer Fe-Ga/Pb(Mg1/3Nb2/3)O3_PbTiO3 (PMN-PT) multifunctional composite, was investigated. The induced external field is characterized as having a butterfly hysteresis loop when tuned by an applied electric field. A tuning coefficient of the electrically induced fringe magnetic field is derived from the piezoelectric and magnetostrictive properties of the composite. A measured maximum tuning coefficient, 4.5 Oe/(kV cm−1), is found to agree well with theoretical prediction. This work establishes a foundation in the design of transducers based on the magnetoelectric effect.
Three-dimensional simulation of electron beam induced current collected by a nano-contact: Diffusion and collection analysis
Authors: Doan Q. T. , El Hdiy A. , Troyon M.
Published: December 2011

Three-dimensional simulation is used to study the electron beam induced current collected by a nano-contact forming a nano-junction. For the calculation the surface recombination velocity is supposed to be either infinite or zero. The influence of the bulk diffusion length, energy of the incident electron beam, shape and size of the depletion zone beneath the nano-contact on the induced current collected by the nano-junction is studied. From the fit of the simulated data, the minority carrier effective diffusion length is extracted, and its variation with the electron beam energy is compared with experimental measurements obtained with the nano-EBIC (electron beam induced current) technique that we have developed by combining scanning probe microscopy and scanning electron microscopy. The effective diffusion length is an increasing function with electron beam energy up to a certain value beyond which it decreases. The simulation shows that the same behavior also occurs in the case of the conventional detection by a semi-infinite Schottky contact perpendicular to the electron beam. This is the first time, to our knowledge, that this behavior is pointed out.
What can co-speech gestures in aphasia tell us about the relationship between language and gesture?
Authors: Dipper Lucy , Cocks Naomi , Rowe Melanie , Morgan Gary
Published: December 2011

Cross-linguistic evidence suggests that language typology influences how people gesture when using ‘manner-of-motion’ verbs (Kita 2000; Kita & Özyürek 2003) and that this is due to ‘online’ lexical and syntactic choices made at the time of speaking (Kita, Özyürek, Allen, Brown, Furman & Ishizuka, 2007). This paper attempts to relate these findings to the co-speech iconic gesture used by an English speaker with conduction aphasia (LT) and five controls describing a Sylvester and Tweety1 cartoon. LT produced co-speech gesture which showed distinct patterns which we relate to different aspects of her language impairment, and the lexical and syntactic choices she made during her narrative.
Gesture production and language development
Authors: Zampini Laura , D'Odorico Laura
Published: December 2011

The present study aimed to describe language development in children with Down syndrome, focussing on the relationships between gestural and vocal communication. The individual developmental trajectories of gesture production and its predictive role on later language development were analysed in a group of children with Down syndrome. Eight two-year-old children were followed for a two-year period until they reached the age of four years old. With regard to the developmental trends, two distinct patterns were found. Some children showed an increasing profile of gesture production, whereas others showed an inverted U-shaped profile or a stable production of gestures. Only the children in the second group showed a remarkable growth in their lexical abilities. Moreover, gesture production was identified as a reliable predictor of later vocabulary size when children were both 24 and 36 months old, and the production of crossmodal transitional forms (i.e., gesture-word associations) appeared to be a significant predictive index of their later two-word production.
Amangama amathathu ‘The three letters’
Authors: Brookes Heather J.
Published: December 2011

This paper describes the emergence of a quotable gesture for HIV/AIDS in South Africa. The gesture has its origin in the Zulu phrase amangama amathathu ‘the three letters’, an expression South Africans began to use from the mid-1990s to refer to the acronym HIV. This phrase generated a plethora of words and phrases for HIV using the concept of ‘three’. With these spoken references, speakers would sometimes use a manual expression for ‘three’ by showing three extended fingers. With repeated use, the manual expression by itself came to be established as a quotable gesture for HIV. The gesture became independent of speech as a noticeable increase in the number of deaths from HIV occurred. From observations of use in every day situations, speakers use the gesture primarily to mitigate the crude or indelicate effect of directly saying a person has HIV in speech. Use of the gesture also demonstrates sensitivity and empathy on the part of the speaker and lessens the speaker’s commitment to, and consequently their responsibility for suggesting a person has the disease. Whether for secret communication or openly displayed for dramatic effect, speakers use this gesture in conjunction with speech in nuanced ways to avoid breaking the spoken taboo and flouting social norms. The emergence of this gesture suggests that speech taboos are a key reason for gestures becoming quotable; hence the large number of quotable gestures that represent socially awkward and potentially offensive words and speech acts. The adaptation of a counting gesture demonstrates that one source for new quotable gestures may be the re-semanticization of an existing gesture through spoken semantic links. In the case of the HIV gesture, spoken language played a key role in disseminating the metonym of ‘three’ and establishing a common ground for a quotable gesture to emerge across many communities in South Africa.
The role of onomastics for diachronic sociolinguistics
Authors: Korhonen Kalle
Published: December 2011

The article focuses on the roles of Greek, Latin/Romance and Arabic in the onomastics of Northeastern Sicily between the 11th and 13th centuries. The first part deals with landless peasants from four villages at the turn of the 11th and 12th centuries. I argue that the role played by Arabic in the nomenclature of these communities was more important than has previously been suggested and the role of Romance speakers may have been minimal. The important role of Arabic is interpreted as a consequence of a situation of linguistic dominance and borrowing of word-forms. In the second part, I analyze the onomastics of the free population of northeastern Sicily attested in charters during the 12th and 13th centuries. I argue that the 13th century was the crucial period when Greek lost its initially high prestige. This is visible in both first names and second name elements. In first names, Greek speakers started to accommodate their nomenclature to their surroundings, dominated by Romance languages and the church of Rome, which meant that both language shift and religious conversion played a role. The second name elements in Greek were seldom transferred to the name stock of the Romance-speaking population. I argue that the role of the city of Messina, in which monolingual Romance communities were evidently formed, was important in this process. When such a community was formed in Messina, the Greek language was marginalized fairly rapidly even in northeastern Sicily, where it had had an important position. However, some surnames with a Greek or Arabic etymology survived in the local name stock until the present. I explain this by referring to the role of the de-semanticization of such name elements. This consists both of the semantic bleaching of the original significance of the names and of the neutralization of their linguistic connotations.
States of reason and reasons of state
Authors: Bhaya Nair Rukmini
Published: December 2011

Over the past half-century, Noam Chomsky has established a powerful intellectual presence in two apparently unrelated domains of discourse — the field of theoretical linguistics and the arena of anti-establishment politics. This paper examines Chomsky’s use of metaphor across these domains, arguing that in Chomsky’s work metaphor enables an undercover, perhaps even classically ‘anarchic’ dialogue between disciplines. Organizationally as well as psychologically, the two major inquiries into human nature undertaken by him are, the paper suggests, structured and unified in relation to each other via the seemingly innocuous agency of metaphor. The paper also traces Chomsky’s innovative production of metaphors to engage in dialogue with both the past and the future. To reconstruct Chomsky through his metaphors is to attempt to read him not as a doctrinaire Cartesian but as someone who has responded with extreme ‘context-sensitivity’ to changing circumstances in both his fields. Finally, the paper contends that a study of Chomsky’s metaphorical practice could, inter alia, offer unprecedented insights into the creative and essentially unified thought processes of a major 20th century thinker.
Majority and minority language planning in Brunei Darussalam
Authors: Coluzzi Paolo
Published: December 2011

This paper is an overview of language planning as carried out in Brunei Darussalam for Malay, its official language, English, its de facto other official language, and for the other eleven minority languages spoken in the country. After a general introduction to the country and its sociolinguistic situation, the paper outlines the main language planning activities carried out in Brunei through corpus, status and acquisition planning. The overview of status planning includes a brief description of the linguistic landscape of Brunei. The second part of the paper discusses the advantages of education using the students’ first language, something that is not happening in Brunei, and the future of education in the country after the introduction of the new education reform (SPN21). The paper closes with some general remarks on the importance of maintaining minority languages and some suggestions on how this can be achieved.
Motivated word meanings and vocabulary learning
Authors: Piquer-Píriz Ana María
Published: December 2011

The introduction of English as a foreign language in many countries at ever younger ages poses new challenges for teachers, material designers and researchers in terms of finding out and dealing with the needs of such young children when learning a foreign language. This paper focuses on vocabulary learning at early ages, arguing for the inclusion of figurative language in young learners’ English input for two main reasons: firstly, some figurative uses are very frequent in general language and suitable for young learners’ communicative needs and, secondly, research (Piquer-Píriz, 2005) has shown that children as young as 5 years old are able to work out figurative extensions of words whose literal meanings they know, through associative (metonymic) and analogical (metaphoric) reasoning. The specific case of hand is explored, drawing on some of the findings mentioned above, to discuss the potential of cognitive linguistic-inspired approaches in the young learner classroom.
Recognition of personifications in fiction by non-expert readers
Authors: Dorst Aletta G. , Mulder Gerben , Steen Gerard J.
Published: December 2011

This paper offers an integrated typology for the classification of personifications in discourse, based on existing methods for linguistic metaphor identification such as MIP (Pragglejaz Group, 2007) and MIPVU (Steen et al., 2010). The psychological relevance of the proposed typology is explored in an empirical study that examines the recognition of personifications in fiction by non-expert readers. A selection of structural properties of personifications is discussed and predictions are formulated regarding which values of which variables are deemed to boost the recognition of personifications. The results suggest that the different types of personification differ in recognizability and that their recognition may be more strongly determined by inherent properties (such as conventionality) than by external factors (such as the presence of a prime). Though the results cannot be unambiguously interpreted, they do indicate some tendencies in the behaviour of non-expert readers and their perceptions of the forms and functions of personification in fiction.
Attending to the disembodied character in research on professional narratives
Authors: Scott Julie-Ann
Published: December 2011

This essay provides a rationale of how Performance Analysis and Narrative Positioning within research on Physically Disabled Professionals’ Personal Narratives can provide insight into the role of the body in the analysis of professional narratives. Through analyzing the participants’ open-ended narratives as performances in which the narrators draw upon performativities to reconcile the absurdity associated with their deemed ‘unprofessional’ bodies legitimately occupying a professional space, the author traces the emergence of embodied professional heroes in four variations: the Super Hero, Warrior Hero, Tragic Hero, and Rogue Hero, each which illuminates the importance of the body in the construction of personal narratives of professionalism. In conclusion, the author calls for attention to the potential performance of the Anti Hero across personal narratives that emerge in unmarked bodies in order to attend the underlying performativities and discourses of power within all narratives of professionalism.
Autobiographical memory and autobiographical narrative
Authors: Smorti Andrea
Published: December 2011

In this contribution I discuss the link existing between autobiographical memory and autobiographical narrative and, in this context, the concept of coherence. Starting from the Bruner’s seminal concept of autobiographical self, I firstly analyze how autobiographical memories and autobiographical narrative influence each other and, somehow, mirror reciprocally and then I present some results of my previous studies using a methodology consisting in “narrating-transcribing-reading-narrating.” The results show that self narratives can have positive effects on the narrators if they are provided with a tool to reflect on their memories. Moreover these results show that autobiography in its double sides — that of memory and that of narrative — is a process of continuous construction but also that this construction is deeply linked to social interactions.
Identity in life narratives
Authors: Gregg Gary S.
Published: December 2011

In the spirit of Jerome Bruner’s call for the study of individuals’ appropriation of cultural meanings, this paper outlines a “generative” theory of identity based on study-of-lives interviews conducted with young adult Americans and Moroccans. This theory holds that multiple self-representations tend to be integrated by structurally-ambiguous key symbols and metaphors whose meanings can change via figure-ground like shifts in the salience of their features — and that identity-formation employs some of the same cognitive structures as tonal music to organize personal meanings. This “generative” theory of multiple identities complements McAdams’ story structure model and Hermans’ dialogical model.
Virtuous selves in vicious times
Authors: Ritivoi Andreea Deciu
Published: December 2011

In this paper I review some of the key elements of Alasdair MacIntyre’s conception of narrative identity. I focus on his notions of tradition and unified self, which have been interpreted by some critics as signs of a political conservatism and elitism. My argument proceeds by reviewing the critiques offered by Galen Strawson and Hilde Lindemann Nelson, both concerned with the conflict between tradition and choice. While Strawson and Nelson believe that traditions are oppressive at least to some individuals, MacIntyre offers a more complex understanding of tradition, emphasizing that traditions embody conflicts. In proposing a different reading of these concepts, one I claim is more accurate, I suggest that MacIntyre’s concept of narrative selfhood can serve as foundation of a political theory that is utopian in a standard liberal way.
Narratives of the interactive moment
Authors: Lannamann John W. , McNamee Sheila
Published: December 2011

In this article, we identify the contributions to narrative approaches that emerge from a communication perspective. We elaborate on an approach to narrative that centers on the joint, interactive aspects of narrative construction and discuss why it is useful for navigating around two pitfalls encountered by narrative scholars: (1) the psychologist’s fallacy and (2) the problems of finalization in narrative.
Fábulas de origen oriental en la Península Ibérica
Authors: Martín Llúcia
Published: December 2011

En este trabajo pretendemos dar a conocer algunos testimonios de fábulas y colecciones de ejemplos que tuvieron un gran auge durante el medievo en la Península Ibérica, con especial interés por los ejemplos de origen oriental. En este sentido, nos adentraremos en los indicios que encontramos en la literatura catalana medieval, por tratarse de textos menos conocidos y por su vinculación posiblemente derivada de las traducciones castellanas.
La mise en recueil des traités de fauconnerie médiévaux en latin et en langue vernaculaire (français et espagnol)
Authors: Smets An
Published: December 2011

Les traités de fauconnerie circulent souvent sous forme de recueils. Cette contribution se base sur un corpus de 245 manuscrits, contenant des traités de fauconnerie en latin, en français et/ou en espagnol. Différents éléments sont pris en compte, comme le nombre de traités (cynégétiques) par recueil, la langue des traités et la nature d’éventuels autres textes contenus dans les recueils. C’est entre autres une différence de taille qui explique les divergences entre les traités latins et ceux dans les langues vernaculaires.
Dual marking and kinship terms in Afitti
Authors: Voogt Alex de
Published: December 2011

Afitti is part of the Eastern Sudanic branch of the Nilo-Saharan language family. It features dual and plural forms as part of its kinship terminology that have not been attested elsewhere in the language family. Kinship terminology in which possessive pronouns have merged with kinship terms is also known for a series of Eastern Sudanic languages. Nyimang, Afitti’s closest linguistic neighbor, features a dual form but it is limited to its verbal system. The dual in Nyimang supports the suggestion that Afitti’s kinship terminology with a dual form has a historical basis, since a regional influence of the Arabic system of duals can be largely ruled out. Morphological data on Afitti should further the analysis of its kinship terms in future studies.
Rong Li: Tipping the balance in cell biology
Authors: Sedwick Caitlin
Published: December 2011

Li takes multiple approaches to understand how signaling pathways really work.
Mechanism of inhibition of connexin channels by the quinine derivative N-benzylquininium
Authors: Rubinos Clio , Sánchez Helmuth A. , Verselis Vytas K. , Srinivas Miduturu
Published: December 2011

The anti-malarial drug quinine and its quaternary derivative N-benzylquininium (BQ+) have been shown to inhibit gap junction (GJ) channels with specificity for Cx50 over its closely related homologue Cx46. Here, we examined the mechanism of BQ+ action using undocked Cx46 and Cx50 hemichannels, which are more amenable to analyses at the single-channel level. We found that BQ+ (300 µM–1 mM) robustly inhibited Cx50, but not Cx46, hemichannel currents, indicating that the Cx selectivity of BQ+ is preserved in both hemichannel and GJ channel configurations. BQ+ reduced Cx50 hemichannel open probability (Po) without appreciably altering unitary conductance of the fully open state and was effective when added from either extracellular or cytoplasmic sides. The reductions in Po were dependent on BQ+ concentration with a Hill coefficient of 1.8, suggesting binding of at least two BQ+ molecules. Inhibition by BQ+ was voltage dependent, promoted by hyperpolarization from the extracellular side and conversely by depolarization from the cytoplasmic side. These results are consistent with binding of BQ+ in the pore. Substitution of the N-terminal (NT) domain of Cx46 into Cx50 significantly impaired inhibition by BQ+. The NT domain contributes to the formation of the wide cytoplasmic vestibule of the pore and, thus, may contribute to the binding of BQ+. Single-channel analyses showed that BQ+ induced transitions that did not resemble pore block, but rather transitions indistinguishable from the intrinsic gating events ascribed to loop gating, one of two mechanisms that gate Cx channels. Moreover, BQ+ decreased mean open time and increased mean closed time, indicating that inhibition consists of an increase in hemichannel closing rate as well as a stabilization of the closed state. Collectively, these data suggest a mechanism of action for BQ+ that involves modulation loop gating rather than channel block as a result of binding in the NT domain.
Light inactivation of water transport and protein–protein interactions of aquaporin–Killer Red chimeras
Authors: Baumgart Florian , Rossi Andrea , Verkman A.S.
Published: December 2011

Aquaporins (AQPs) have a broad range of cellular and organ functions; however, nontoxic inhibitors of AQP water transport are not available. Here, we applied chromophore-assisted light inactivation (CALI) to inhibit the water permeability of AQP1, and of two AQP4 isoforms (M1 and M23), one of which (M23) forms aggregates at the cell plasma membrane. Chimeras containing Killer Red (KR) and AQPs were generated with linkers of different lengths. Osmotic water permeability of cells expressing KR/AQP chimeras was measured from osmotic swelling–induced dilution of cytoplasmic chloride, which was detected using a genetically encoded chloride-sensing fluorescent protein. KR-AQP1 red fluorescence was bleached rapidly (∼10% per second) by wide-field epifluorescence microscopy. After KR bleaching, KR-AQP1 water permeability was reduced by up to 80% for the chimera with the shortest linker. Remarkably, CALI-induced reduction in AQP4-KR water permeability was approximately twice as efficient for the aggregate-forming M23 isoform; this suggests intermolecular CALI, which was confirmed by native gel electrophoresis on cells coexpressing M23-AQP4-KR and myc-tagged M23-AQP4. CALI also disrupted the interaction of AQP4 with a neuromyelitis optica autoantibody directed against an extracellular epitope on AQP4. CALI thus permits rapid, spatially targeted and irreversible reduction in AQP water permeability and interactions in live cells. Our data also support the utility of CALI to study protein–protein interactions as well as other membrane transporters and receptors.
Measuring the distance between multiple sequence alignments
Authors: Blackburne Benjamin P. , Whelan Simon
Published: December 2011

Motivation: Multiple sequence alignment (MSA) is a core method in bioinformatics. The accuracy of such alignments may influence the success of downstream analyses such as phylogenetic inference, protein structure prediction, and functional prediction. The importance of MSA has lead to the proliferation of MSA methods, with different objective functions and heuristics to search for the optimal MSA. Different methods of inferring MSAs produce different results in all but the most trivial cases. By measuring the differences between inferred alignments, we may be able to develop an understanding of how these differences (i) relate to the objective functions and heuristics used in MSA methods, and (ii) affect downstream analyses.

Results: We introduce four metrics to compare MSAs, which include the position in a sequence where a gap occurs or the location on a phylogenetic tree where an insertion or deletion (indel) event occurs. We use both real and synthetic data to explore the information given by these metrics and demonstrate how the different metrics in combination can yield more information about MSA methods and the differences between them.

Availability:  MetAl is a free software implementation of these metrics in Haskell. Source and binaries for Windows, Linux and Mac OS X are available from http://kumiho.smith.man.ac.uk/whelan/software/metal/.

Contact:  simon.whelan@manchester.ac.uk
Read count approach for DNA copy number variants detection
Authors: Magi Alberto , Tattini Lorenzo , Pippucci Tommaso , Torricelli Francesca , Benelli Matteo
Published: December 2011

Motivation: The advent of high-throughput sequencing technologies is revolutionizing our ability in discovering and genotyping DNA copy number variants (CNVs). Read count-based approaches are able to detect CNV regions with an unprecedented resolution. Although this computational strategy has been recently introduced in literature, much work has been already done for the preparation, normalization and analysis of this kind of data.

Results: Here we face the many aspects that cover the detection of CNVs by using read count approach. We first study the characteristics and systematic biases of read count distributions, focusing on the normalization methods designed for removing these biases. Subsequently, we compare the algorithms designed to detect the boundaries of CNVs and we investigate the ability of read count data to predict the exact number of DNA copy. Finally, we review the tools publicly available for analysing read count data. To better understand the state of the art of read count approaches, we compare the performance of the three most widely used sequencing technologies (Illumina Genome Analyzer, Roche 454 and Life Technologies SOLiD) in all the analyses that we perform.

Contact:  albertomagi@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
ART: a next-generation sequencing read simulator
Authors: Huang Weichun , Li Leping , Myers Jason R. , Marth Gabor T.
Published: December 2011

Summary: ART is a set of simulation tools that generate synthetic next-generation sequencing reads. This functionality is essential for testing and benchmarking tools for next-generation sequencing data analysis including read alignment, de novo assembly and genetic variation discovery. ART generates simulated sequencing reads by emulating the sequencing process with built-in, technology-specific read error models and base quality value profiles parameterized empirically in large sequencing datasets. We currently support all three major commercial next-generation sequencing platforms: Roche's 454, Illumina's Solexa and Applied Biosystems' SOLiD. ART also allows the flexibility to use customized read error model parameters and quality profiles.

Availability: Both source and binary software packages are available at http://www.niehs.nih.gov/research/resources/software/art

Contact:  weichun.huang@nih.gov; gabor.marth@bc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.