bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti-HIV therapy: pipeline approaches and future directions
Authors: Dwivedi Lavkush , Shrivastava Mansi
Published: January 2011

Human immunodeficiency virus (HIV), with about 30 million deaths and double infections (in developing countries), is an open challenge today for global scientists. Developing safe and effective measurements against it has become the prime need of hour. Though, putting it at health priority, various efforts like chemotherapy, vaccines and others are attempted globally over last decade. Consequently, highly active antiretroviral therapy was introduced but fails to completely block the viral replication due to drug resistance and various other severe side effects. The antigenic variability and lack of appropriate experimental models is the major obstacle in the development of an ever effective treatment against HIV. However, to overcome the present hurdles and to emerge a preventive HIV vaccine efforts at various platforms are done. A renewed, coordinated research, preclinical studies, clinical trials together with sufficient long term scientific and commercial commitments are made. Few of the therapeutic efforts viz. RNA interference (RNAi) based replication arrest of HIV, viral enzymes’ inhibitors, nanotechnology based HIV control and various preclinically trialed vaccines are reviewed in this paper. Also, the observed toxicity of existing therapeutic regimen, key challenges and future prospects for the development of better tolerated prophylactic HIV-1 vaccine are discussed.
Effects of sowing date and cultivar on radiation use efficiency in durum wheat
Authors: Bassu Simona , Giunta Francesco , Motzo Rosella
Published: January 2011

Field studies were conducted on durum wheat to assess the effects of three sowing dates and three cultivars with different flowering times on the stability of the biomass accumulated per unit of solar radiation intercepted that is usually considered constant in crop-simulation models. Aboveground dry matter varied widely, with minimum values ranging from 292 g m–2 at booting to 384 g m–2 at maturity and maximum values ranging from 1452 g m–2 at booting to 2565 g m–2 at maturity. The cumulative intercepted radiation at each phenological stage decreased as sowing was delayed. The leaf area index (LAI) ranged from 1.5 to 7.6 at booting and from 0.1 to 4.6 at the beginning of grain filling across treatments. Sowing dates and cultivars did not differ significantly in extinction coefficient values (0.38 ± 0.015). The estimated radiation use efficiency (eRUE) differed significantly between the two seasons (1.16 ± 0.09 g MJ–1 in 2000 and 1.61 ± 0.08 g MJ–1 in 2001) due to waterlogging in 2000 but did not differ among sowing dates and cultivars within each season. Under optimal growing conditions, eRUE of different cultivars of durum wheat were relatively stable across sowing dates, confirming their reliability for crop modelling in durum wheat as well as in bread wheat. Although eRUE was constant over the whole crop cycle regardless of the sowing date, it was lower at pre-anthesis in the latest sowing, in parallel with the variation in LAI. This study indicates that pre-anthesis eRUE may vary with sowing date under some conditions, depending on the variation in LAI in the period before anthesis.
Effects of missing-row sowing supplemented with row spacing and nitrogen on weed competition and growth and yield of wheat
Authors: Das T. K. , Yaduraju N. T.
Published: January 2011

Crop husbandry practices, i.e. sowing method, row spacing, and nitrogen (N) fertilisation, influence weed competition in a crop and play a role in ecological weed management. Missing-row sowing is a novel method of sowing wheat, with one row left unsown after several rows of continuous sowing. It affects density and spatial uniformity of wheat, which may influence the wheat plants’ competitiveness and weed suppression. It may have interactions with row spacing and N, which may further improve crop–weed balance, but is rarely studied in India or elsewhere. We undertook this study to optimise the method of missing-row sowing of wheat in combination with row spacing and N application. The results revealed that leaving 20% of rows unsown significantly reduced weed populations and dry weights, and increased the competitiveness of wheat plants through greater leaf area, numbers of ear-bearing tillers, and uptake of N. Leaving 20% of rows unsown increased wheat yield by 10.9%, 17.3%, and 8.2%, respectively, during the first, second, and third year compared with conventional sowing (no missing rows). An 18.5-cm row spacing resulted in a more weed suppression than 22.5-cm row spacing, but the latter gave higher yield. Application of N at 120 kg/ha resulted in higher yield than N at 60 kg/ha, due to a significant reduction in weed growth. A practice that combines 20% of rows unsown, 22.5-cm row spacing, and 120 kg N/ha will yield more through better suppression of a moderate weed infestation.
Application of physiological understanding in soybean improvement. I. Understanding phenological constraints to adaptation and yield potential
Authors: Lawn R. J. , James A. T.
Published: January 2011

The purpose of this paper and its companion1 is to describe how, in eastern Australia, soybean improvement, in terms of both breeding and agronomy, has been informed and influenced over the past four decades by physiological understanding of the environmental control of phenology. This first paper describes how initial attempts to grow soybean in eastern Australia, using varieties and production practices from the southern USA, met with limited success due to large variety × environment interaction effects on seed yield. In particular, there were large variety × location, variety × sowing date, and variety × sowing date × density effects. These various interaction effects were ultimately explained in terms of the effects of photo-thermal environment on the phenology of different varieties, and the consequences for radiation interception, dry matter production, harvest index, and seed yield. This knowledge enabled the formulation of agronomic practices to optimise sowing date and planting arrangement to suit particular varieties, and underpinned the establishment of commercial production in south-eastern Queensland in the early 1970s. It also influenced the establishment and operation over the next three decades of several separate breeding programs, each targeting phenological adaptation to specific latitudinal regions of eastern Australia. This paper also describes how physiological developments internationally, particularly the discovery of the long juvenile trait and to a lesser extent the semi-dwarf ideotype, subsequently enabled an approach to be conceived for broadening the phenological adaptation of soybeans across latitudes and sowing dates. The application of this approach, and its outcomes in terms of varietal improvement, agronomic management, and the structure of the breeding program, are described in the companion paper.
Colloidal quasicrystals with 12-fold and 18-fold diffraction symmetry
Authors: Fischer Steffen , Exner Alexander , Zielske Kathrin , Perlich Jan , Deloudi Sofia , Steurer Walter , Lindner Peter , Förster Stephan
Published: January 2011

Micelles are the simplest example of self-assembly found in nature. As many other colloids, they can self-assemble in aqueous solution to form ordered periodic structures. These structures so far all exhibited classical crystallographic symmetries. Here we report that micelles in solution can self-assemble into quasicrystalline phases. We observe phases with 12-fold and 18-fold diffraction symmetry. Colloidal water-based quasicrystals are physically and chemically very simple systems. Macroscopic monodomain samples of centimeter dimension can be easily prepared. Phase transitions between the fcc phase and the two quasicrystalline phases can be easily followed in situ by time-resolved diffraction experiments. The discovery of quasicrystalline colloidal solutions advances the theoretical understanding of quasicrystals considerably, as for these systems the stability of quasicrystalline states has been theoretically predicted for the concentration and temperature range, where they are experimentally observed. Also for the use of quasicrystals in advanced materials this discovery is of particular importance, as it opens the route to quasicrystalline photonic band gap materials via established water-based colloidal self-assembly techniques.
Roller Coaster Scanning reveals spontaneous triggering of dendritic spikes in CA1 interneurons
Authors: Katona Gergely , Kaszás Attila , Turi Gergely F. , Hájos Norbert , Tamás Gábor , Vizi E. Sylvester , Rózsa Balázs
Published: January 2011

Inhibitory interneurons are considered to be the controlling units of neural networks, despite their sparse number and unique morphological characteristics compared with excitatory pyramidal cells. Although pyramidal cell dendrites have been shown to display local regenerative events—dendritic spikes (dSpikes)—evoked by artificially patterned stimulation of synaptic inputs, no such studies exist for interneurons or for spontaneous events. In addition, imaging techniques have yet to attain the required spatial and temporal resolution for the detection of spontaneously occurring events that trigger dSpikes. Here we describe a high-resolution 3D two-photon laser scanning method (Roller Coaster Scanning) capable of imaging long dendritic segments resolving individual spines and inputs with a temporal resolution of a few milliseconds. By using this technique, we found that local, NMDA receptor-dependent dSpikes can be observed in hippocampal CA1 stratum radiatum interneurons during spontaneous network activities in vitro. These NMDA spikes appear when approximately 10 spatially clustered inputs arrive synchronously and trigger supralinear integration in dynamic interaction zones. In contrast to the one-to-one relationship between computational subunits and dendritic branches described in pyramidal cells, here we show that interneurons have relatively small (∼14 μm) sliding interaction zones. Our data suggest a unique principle as to how interneurons integrate synaptic information by local dSpikes.
Importance of single molecular determinants in the fidelity of expanded genetic codes
Authors: Antonczak Alicja K. , Simova Zuzana , Yonemoto Isaac T. , Bochtler Matthias , Piasecka Anna , Czapińska Honorata , Brancale Andrea , Tippmann Eric M.
Published: January 2011

The site-selective encoding of noncanonical amino acids (NAAs) is a powerful technique for the installation of novel chemical functional groups in proteins. This is often achieved by recoding a stop codon and requires two additional components: an evolved aminoacyl tRNA synthetase (AARS) and a cognate tRNA. Analysis of the most successful AARSs reveals common characteristics. The highest fidelity NAA systems derived from the
Methanocaldococcus jannaschii
tyrosyl AARS feature specific mutations to two residues reported to interact with the hydroxyl group of the substrate tyrosine. We demonstrate that the restoration of just one of these determinants for amino acid specificity results in the loss of fidelity as the evolved AARSs become noticeably promiscuous. These results offer a partial explanation of a recently retracted strategy for the synthesis of glycoproteins. Similarly, we reinvestigated a tryptophanyl AARS reported to allow the site-selective incorporation of 5-hydroxy tryptophan within mammalian cells. In multiple experiments, the enzyme displayed elements of promiscuity despite its previous characterization as a high fidelity enzyme. Given the many similarities of the TyrRSs and TrpRSs reevaluated here, our findings can be largely combined, and in doing so they reinforce the long-established central dogma regarding the molecular basis by which these enzymes contribute to the fidelity of translation. Thus, our view is that the central claims of fidelity reported in several NAA systems remain unproven and unprecedented.
Cortical representation of the constituent structure of sentences
Authors: Pallier Christophe , Devauchelle Anne-Dominique , Dehaene Stanislas
Published: January 2011

Linguistic analyses suggest that sentences are not mere strings of words but possess a hierarchical structure with constituents nested inside each other. We used functional magnetic resonance imaging (fMRI) to search for the cerebral mechanisms of this theoretical construct. We hypothesized that the neural assembly that encodes a constituent grows with its size, which can be approximately indexed by the number of words it encompasses. We therefore searched for brain regions where activation increased parametrically with the size of linguistic constituents, in response to a visual stream always comprising 12 written words or pseudowords. The results isolated a network of left-hemispheric regions that could be dissociated into two major subsets. Inferior frontal and posterior temporal regions showed constituent size effects regardless of whether actual content words were present or were replaced by pseudowords (jabberwocky stimuli). This observation suggests that these areas operate autonomously of other language areas and can extract abstract syntactic frames based on function words and morphological information alone. On the other hand, regions in the temporal pole, anterior superior temporal sulcus and temporo-parietal junction showed constituent size effect only in the presence of lexico-semantic information, suggesting that they may encode semantic constituents. In several inferior frontal and superior temporal regions, activation was delayed in response to the largest constituent structures, suggesting that nested linguistic structures take increasingly longer time to be computed and that these delays can be measured with fMRI.
RA-inducible gene-I induction augments STAT1 activation to inhibit leukemia cell proliferation
Authors: Jiang Lin-Jia , Zhang Nan-Nan , Ding Fei , Li Xian-Yang , Chen Lei , Zhang Hong-Xin , Zhang Wu , Chen Sai-Juan , Wang Zhu-Gang , Li Jun-Min , Chen Zhu , Zhu Jiang
Published: January 2011

RA-inducible gene I (RIG-I/DDX58) has been shown to activate IFN-β promoter stimulator 1 (IPS-1) on recognizing cytoplasmic viral RNAs. It is unclear how RIG-I functions within the IFN and/or RA signaling process in acute myeloid leukemia (AML) cells, however, where obvious RIG-I induction is observed. Here, we show that the RIG-I induction functionally contributes to IFN-α plus RA-triggered growth inhibition of AML cells. Interestingly, although RIG-I induction itself is under the regulation of STAT1, a major IFN intracellular signal mediator, under circumstances in which it does not stimulate IPS-1, it conversely augments STAT1 activation to induce IFN-stimulatory gene expression and inhibit leukemia cell proliferation. Thus, our results unveil a previously undescribed RIG-I activity in regulating the cellular proliferation of leukemia cells via STAT1, which is independent of its classic role of sensing viral invasion to trigger type I IFN transcription.
Language acquisition as a side effect of language processing
Authors: Sharwood Smith Michael
Published: January 2011

Researchers in the field of language acquisition may adopt various particular theoretical approaches to the description and explanation of linguistic phenomena. They need this theory to describe the nature of what is or is not undergoing change over time. However linguistic theory normally makes no reference to the time dimension, a dimension crucial to any study of development. Psycholinguists, on the other hand, focus on temporal phenomena but these are normally measured in milliseconds. At the same time, they still need a coherent model of linguistic structure to carry out their investigations. The logic of this suggests that a framework is needed that integrates linguistic theories about the properties of language, i.e., linguistic knowledge, with theories about on-line processing. The need to integrate these two ways of looking at language is also crucial for researchers who study linguistic development in the individual. One such approach is Modular Growth and Use of Language (MOGUL), a theoretical framework based on a close examination of research in several disciplines and within which utterance processing plays a vital role in explaining development. In fact, in that part of MOGUL which is devoted to explaining acquisition, the claim is that development is a side-effect of making sense of language to which we are exposed. No special learning mechanisms are involved.
Parsing the L2 input, an overview
Authors: Roberts Leah
Published: January 2011

The acquisition of second language (L2) syntax has been central to the study of L2 acquisition, but recently there has been an interest in how learners apply their L2 syntactic knowledge to the input in real-time comprehension. Investigating L2 learners’ moment-by-moment syntactic analysis during listening or reading of sentence as it unfolds — their parsing of the input — is important, because language learning involves both the acquisition of knowledge and the ability to use it in real time. Using methods employed in monolingual processing research, investigations often focus on the processing of temporary syntactic ambiguities and structural dependencies. Investigating ambiguities involves examining parsing decisions at points in a sentence where there is a syntactic choice and this can offer insights into the nature of the parsing mechanism, and in particular, its processing preferences. Studying the establishment of syntactic dependencies at the critical point in the input allows for an investigation of how and when different kinds of information (e.g., syntactic, semantic, pragmatic) are put to use in real-time interpretation. Within an L2 context, further questions are of interest and familiar from traditional L2 acquisition research. Specifically, how native-like are the parsing procedures that L2 learners apply when processing the L2 input? What is the role of the learner’s first language (L1)? And, what are the effects of individual factors such as age, proficiency/dominance and working memory on L2 parsing? In the current paper I will provide an overview of the findings of some experimental research designed to investigate these questions.
Linguistic input factors in native and L2 processing of inflectional morphology
Authors: Frenck-Mestre Cheryl , Carrasco-Ortiz Haydee , McLaughlin Judith , Osterhout Lee , Foucart Alice
Published: January 2011

Numerous studies have examined the processing of inflectional morphology by second language learners, with the underlying aim of determining whether native-like processing can ever be attained. Indeed, this is an area where L2 speakers show notorious deficits, in contrast to the achievement of “target-like” grammar in other areas. The present paper reviews a series of experiments performed using online measures, notably ERPs and the recording of eye-movements, to address this question. The novelty of the present work lies in its emphasis on the properties of the L2 itself, i.e., “input factors” and how they may affect learning rate.
L’influence des langues non maternelles dans l’acquisition du SN en espagnol L3
Authors: Bono Mariana
Published: January 2011

This article investigates the role of second or non-native languages (L2) in the acquisition of an additional language (L3). We study the impact of cross-linguistic influence on the placement of the adjective in the Noun Phrase. The analysis of oral data from learners of Spanish L3 shows that the position of adjectives departs from the canonical word order of both Spanish L3 and French L1, reflecting the word order that characterizes the other languages known by the speakers, English and German. We will attempt to identify the psycholinguistic factors underlying this phenomenon. Particular attention will be placed on the ‘foreign language effect,’ which can transform non-native languages into a default grammatical model for the processing of L3 linguistic input.
Interactional feedback as instructional input
Authors: Lyster Roy , Saito Kazuya
Published: January 2011

This article reports on an increasing number of SLA studies showing that interactional feedback plays a significant role in improving classroom learners’ use of the target language. Whereas the provision of feedback has proven more effective than no feedback, there are still many variables that mediate the effectiveness of interactional feedback. This article synthesizes a set of classroom studies about interactional feedback taking into account four mediating variables: (a) feedback types, (b) instructional setting, (c) learners’ age, and (d) linguistic targets. The synthesis leads to the conclusion that prescriptions to use only “implicit negative feedback” at the expense of other more overt types of interactional feedback are not supported by classroom research. The article closes with a recommendation for teachers to adopt a wide variety of interactional feedback techniques in accordance with a range of contextual, individual, and linguistic variables.
La structuration de l’input dans le cadre des interactions multimodales de la classe de langue étrangère
Authors: Griggs Peter
Published: January 2011

Starting from the notion of input as it is used in second language acquisition research, this study explores the conditions and forms of
input processing specific to the foreign language class. The ecological analysis of a filmed corpus of two English classes at beginner and
intermediate level focuses particularly on the articulation between different verbal and non verbal components of pedagogical interactions.
The study highlights the multifunctional nature of these multimodal interactions and the synergy that emerges from their functioning. It
also shows how the nature of non verbal behaviour and its role in structuring linguistic data depends on conditions that were specific to
the language class and varies according to the level and content of learning. Within a sociocognitive perspective, the study aims to
contribute to the modelisation of learning processes in the foreign language class.
Interference and the Representation of Order within Associations
Authors: Rehani Mayank , Caplan Jeremy B.
Published: January 2011

In the presence of interference, recall of pairs can critically depend on the diagnostic power of memory of the order of items within the pair. Models of pair memory make different assumptions about whether and how such order information is stored, from convolution-based models, which assume no explicit storage of order, to matrix models and several models that assume a pair is learned by concatenating the representations of the constituent items, which lead to perfect within-pair order memory (given retrieval of the pair). Here we investigate memory for associations and within-pair order by examining the relationship between forward and backward probes of pairs subject to order-dependent associative interference in a double-function list paradigm. Associative interference disrupted the high correlation between forward and backward recall accuracy that is typically observed in standard paired-associate learning, challenging matrix and concatenation-based models. However, participants could overcome some interference due to within-pair order ambiguity, challenging directionally ambiguous convolution-based models. Unexpectedly, the test–retest correlation was reduced for pairs under the influence of interference compared to control pairs. This finding is incompatible with all existing implementations of the model classes we consider. Any model must include an assumption that order encoding (but not retrieval) is unreliable, and the form of this additional mechanism may depend intimately on how a given model is designed. In sum, our findings suggest that within-pair order memory is neither poor nor perfect, pointing to a fallible mechanism for within-pair order learning in verbal association-memory tasks.
Top-illuminated dye-sensitized solar cells with a room-temperature-processed ZnO photoanode on metal substrates and a Pt-coated Ga-doped ZnO counter electrode
Authors: Kyaw A K K , Sun X W , Zhao J L , Wang J X , Zhao D W , Wei X F , Liu X W , Demir H V , Wu T
Published: January 2011

We report on top-illuminated, fluorine tin oxide/indium tin oxide-free (FTO/ITO-free), dye-sensitized solar cells (DSCs) using room-temperature-processed ZnO layers on metal substrates as the working electrodes and Pt-coated Ga-doped ZnO layers (GZO) as the counter electrodes. These top-illuminated DSCs with GZO render comparable efficiency to those employing commercial FTO counter electrodes. Despite a lower current density, the top-illuminated DSCs result in a higher fill factor than conventional DSCs due to a low ohmic loss at the electrode/semiconductor interface. The effect of metal substrate on the performance of the resulting top-illuminated DSCs is also studied by employing various metals with different work functions. Ti is shown to be a suitable metal to be used as the working electrode in the top-illuminated device architecture owing to its low ohmic loss at the electrode/semiconductor interface, minimum catalytic activity on redox reactions and high resistance to corrosion by liquid electrolytes.
A new structure to increase the photostability of CdTe quantum dot sensitized solar cells
Authors: Samadpour M , Irajizad A , Taghavinia N , Molaei M
Published: January 2011

In this paper a new cell structure is introduced to reduce the rate of CdTe corrosion in quantum dot sensitized solar cells (QDSSCs) using
electrolyte. In this cell, one electrode is a titania nanorod that was sensitized with CdTe quantum dots as the working electrode. A thin gold layer is sputtered on the electrode to act as a protective layer against the
corrosive electrolyte and to passivate the CdTe surface traps which are the main recombination centres in a QDSSC. In addition, a Schottky barrier formed at the interface of Au and CdTe prevents direct electron recombination from the CdTe conduction band with
ions. The mechanism of charge transfer and quantum dot regeneration in the presence of gold layer is discussed and our results show that the solar cells made of TiO2/CdTe/Au photoanode have more photostability and a higher fill factor relative to the TiO2/CdTe photoanodes.
Three-dimensional structural engineering of nanoporous alumina by controlled sprinkling of an electrolyte on a porous anodic alumina (PAA) template
Authors: Moradi M , Noormohammadi M , Behzadi F
Published: January 2011

The significant effect of anodization current on the morphology of nanopores encourages us to consider a novel method for engineering these nanostructures. In this paper we study a controlled anodization process using controlled electrolyte stirring. This is done using an electrical pump with variable speed for sprinkling an electrolyte on a membrane. The variable voltage applied to the pump can control the temperature gradient and diffusion of the ions which produce the anodization current. Here we show the significant role of pumping and how this effect can be used in the engineering of nanopores as a three-dimensional nanostructure. These experiments are carried out for a variety of anodization voltages and various electrolyte concentrations, and thus we investigate how these parameters in the vicinity of pumping can control the porosity of the template in three dimensions.
Buckling patterns of thin films on compliant substrates: the effect of plasticity
Authors: Yin Jie , Chen Xi
Published: January 2011

Most previous studies on spontaneous buckling pattern formations in thin films on compliant substrates were limited to elastic deformation, where the herringbone mode is the most often observed under equi-biaxial compression. In practice, plastic deformation is often encountered in ductile metal and polymer films. The effect of plasticity on buckling patterns is explored in this paper using extensive finite element simulations, where the film is assumed to be elastic–perfectly plastic. It is found that upon equi-biaxial compression, depending on the competition among the yield strain, critical buckling strain and applied strain, three new types of patterns may emerge: the plastic diamond-like pattern, the elastoplastic square lattice pattern and the elastoplastic sharp herringbone pattern, and their characteristics are compared with the elastic herringbone mode. Moreover, unique features including the asymmetry in crests and troughs, the sharp saw-like undulation profile and varying wavelengths with applied strain are observed for some types of the new patterns. The study may find its potential applications in the design of stretchable electronics, fabrication of micro/nanofluid channels or channel networks, and morphogenesis of tissues and plants, among others.
Acoustic band gaps of the woodpile sonic crystal with the simple cubic lattice
Authors: Wu Liang-Yu , Chen Lien-Wen
Published: January 2011

This study theoretically and experimentally investigates the acoustic band gap of a three-dimensional woodpile sonic crystal. Such crystals are built by blocks or rods that are orthogonally stacked together. The adjacent layers are perpendicular to each other. The woodpile structure is embedded in air background. Their band structures and transmission spectra are calculated using the finite element method with a periodic boundary condition. The dependence of the band gap on the width of the stacked rods is discussed. The deaf bands in the band structure are observed by comparing with the calculated transmission spectra. The experimental transmission spectra for the Γ–X and Γ–X′ directions are also presented. The calculated results are compared with the experimental results.
Mechanism of photostructural changes in mixed-chalcogen As–S–Se glasses investigated by Raman spectroscopy
Authors: Lin Fang-Yin , Gulbiten Ozgur , Yang Zhiyong , Calvez Laurent , Lucas Pierre
Published: January 2011

The structure and photosensitivity of chalcogen-rich As–S–Se glasses are investigated ex situ and in situ. The Raman spectra of these glasses exhibit three well-defined bands associated with Se-based, S-based and mixed Se–S based structural units. The deconvolutions of these bands show a coherent correlation between intensity and composition. It is then shown that the magnitude of photoexpansion and photorefraction measured ex situ increases continuously with Se content therefore indicating a central role of Se atoms in the mechanism of photostructural changes. The key role of Se is indeed directly observed and confirmed using in situ Raman characterization. It is shown that the band associated with Se–Se oscillators decays continuously during photostructural changes. Furthermore, it is shown that the kinetics of Raman decay closely matches the kinetics of photoexpansion when measured simultaneously. Overall these results demonstrate the central contribution of Se–Se fragment during sub-bandgap irradiation which is consistent with the presence of Se lone pair states at the top of the valence band.
Forming microstructures by controlling the accumulation and discharge of Al atoms by electromigration
Authors: Lu Y , Tohmyoh H , Saka M
Published: January 2011

We present a mechanism for controlling the accumulation and discharge of Al atoms using electromigration, by which long thin Al wires of lengths up to 336 µm and diameters ranging from 0.8 to 4 µm were fabricated. The experimental samples were Al lines formed on a TiN layer and covered with a SiO2 passivation layer. A slit in the Al film and a hole through the oxide or through the oxide and the Al film at the anode end of the line were used to control the accumulation and discharge processes. It was found that the position of the bottom of the hole, which was either at the SiO2/Al or Al/TiN interface, significantly affected these processes. A hole introduced down to the Al/TiN interface prevented cracks from forming in the line by relieving the compressive stress caused by accumulating atoms, and helped to extend the lifetime of the line. Guidelines for effectively controlling the accumulation and discharge of Al atoms were drawn, and based on these guidelines, other Al microstructures requiring the accumulation of a large number of atoms were fabricated after several tens of minutes of current supply.
GPU accelerated biochemical network simulation
Authors: Zhou Yanxiang , Liepe Juliane , Sheng Xia , Stumpf Michael P. H. , Barnes Chris
Published: January 2011

Motivation: Mathematical modelling is central to systems and synthetic biology. Using simulations to calculate statistics or to explore parameter space is a common means for analysing these models and can be computationally intensive. However, in many cases, the simulations are easily parallelizable. Graphics processing units (GPUs) are capable of efficiently running highly parallel programs and outperform CPUs in terms of raw computing power. Despite their computational advantages, their adoption by the systems biology community is relatively slow, since differences in hardware architecture between GPUs and CPUs complicate the porting of existing code.

Results: We present a Python package, cuda-sim, that provides highly parallelized algorithms for the repeated simulation of biochemical network models on NVIDIA CUDA GPUs. Algorithms are implemented for the three popular types of model formalisms: the LSODA algorithm for ODE integration, the Euler–Maruyama algorithm for SDE simulation and the Gillespie algorithm for MJP simulation. No knowledge of GPU computing is required from the user. Models can be specified in SBML format or provided as CUDA code. For running a large number of simulations in parallel, up to 360-fold decrease in simulation runtime is attained when compared to single CPU implementations.

Availability:  http://cuda-sim.sourceforge.net/

Contact:  christopher.barnes@imperial.ac.uk; m.stumpf@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
A k-mer scheme to predict piRNAs and characterize locust piRNAs
Authors: Zhang Yi , Wang Xianhui , Kang Le
Published: January 2011

Motivation: Identifying piwi-interacting RNAs (piRNAs) of non-model organisms is a difficult and unsolved problem because piRNAs lack conservative secondary structure motifs and sequence homology in different species.

Results: In this article, a k-mer scheme is proposed to identify piRNA sequences, relying on the training sets from non-piRNA and piRNA sequences of five model species sequenced: rat, mouse, human, fruit fly and nematode. Compared with the existing ‘static’ scheme based on the position-specific base usage, our novel ‘dynamic’ algorithm performs much better with a precision of over 90% and a sensitivity of over 60%, and the precision is verified by 5-fold cross-validation in these species. To test its validity, we use the algorithm to identify piRNAs of the migratory locust based on 603 607 deep-sequenced small RNA sequences. Totally, 87 536 piRNAs of the locust are predicted, and 4426 of them matched with existing locust transposons. The transcriptional difference between solitary and gregarious locusts was described. We also revisit the position-specific base usage of piRNAs and find the conservation in the end of piRNAs. Therefore, the method we developed can be used to identify piRNAs of non-model organisms without complete genome sequences.

Availability: The web server for implementing the algorithm and the software code are freely available to the academic community at http://59.79.168.90/piRNA/index.php.

Contact:  lkang@ioz.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Aerosol optical thickness and spatial variability along coastal and offshore waters of the eastern Arabian Sea
Authors: Menon Harilal B. , Sangekar Nutan , Lotliker Aneesh , Krishna Moorthy Krishnaswamy , Vethamony Ponnumani
Published: January 2011

Menon, H. B., Sangekar, N., Lotliker, A., Krishna Moorthy, K., and Vethamony, P. 2011. Aerosol optical thickness and spatial variability along coastal and offshore waters of the eastern Arabian Sea. – ICES Journal of Marine Science, 68: 745–750. Data from the ocean-colour monitor (OCM) on board the Indian Remote Sensing Satellite P4 were used to analyse the spatial and temporal distribution of aerosol optical thickness (AOT) over the coastal and offshore waters of the eastern Arabian Sea. Zero water-leaving radiance from the near infrared (NIR) region was assumed for oceanic (open ocean) waters, because of the absorption of long-wave radiation by water molecules. As this assumption fails in coastal waters, it was necessary to correct for water-leaving radiance and sun glint to the NIR bands. The aerosol size-distribution parameter (α) was derived from a relationship between two NIR bands. The Ångström turbidity parameter (β) was obtained using an algorithm relating in situ hand-held, sun-photometer measurements and aerosol radiance (La) at 490 nm. The relationship between β and La (490) was derived with a sensitivity analysis, using a calibrated radiative transfer model. AOTs were retrieved for each pixel of 500 nm. The algorithm's performance was tested by comparing OCM-derived AOT values with in situ AOT and MODIS-derived values. Aerosol maps thus generated from January to December 2005 demonstrate the potential of this new retrieval method for producing AOT climatology from OCM data over coastal waters.
A trade-off between embryonic development rate and immune function of avian offspring is revealed by considering embryonic temperature
Authors: Martin Thomas E. , Arriero Elena , Majewska Ania
Published: January 2011

Long embryonic periods are assumed to reflect slower intrinsic development that are thought to trade off to allow enhanced physiological systems, such as immune function. Yet, the relatively rare studies of this trade-off in avian offspring have not found the expected trade-off. Theory and tests have not taken into account the strong extrinsic effects of temperature on embryonic periods of birds. Here, we show that length of the embryonic period did not explain variation in two measures of immune function when temperature was ignored, based on studies of 34 Passerine species in tropical Venezuela (23 species) and north temperate Arizona (11 species). Variation in immune function was explained when embryonic periods were corrected for average embryonic temperature, in order to better estimate intrinsic rates of development. Immune function of offspring trades off with intrinsic rates of embryonic development once the extrinsic effects of embryonic temperatures are taken into account.
Competition between high- and higher-mutating strains ofEscherichia coli
Authors: Gentile Christopher F. , Yu Szi-Chieh , Serrano Sebastian Akle , Gerrish Philip J. , Sniegowski Paul D.
Published: January 2011

Experimental studies have shown that a mutator allele can readily hitchhike to fixation with beneficial mutations in an asexual population having a low, wild-type mutation rate. Here, we show that a genotype bearing two mutator alleles can supplant a population already fixed for one mutator allele. Our results provide experimental support for recent theory predicting that mutator alleles will tend to accumulate in asexual populations by hitchhiking with beneficial mutations, causing an ever-higher genomic mutation rate.
Evidence of social learning in black-and-white ruffed lemurs (
Varecia variegata
)
Authors: Stoinski T. S. , Drayton L. A. , Price E. E.
Published: January 2011

Although many studies have examined social learning capabilities in apes and monkeys, experiments involving prosimians remain largely absent. We investigated the potential for social learning in black-and-white ruffed lemurs using a two-action foraging task. Eight individuals were divided into two experimental groups and exposed to conspecifics using one of two techniques to access food. Subjects were then given access to the apparatus and their retrieval techniques were recorded and compared. All subjects made their first retrieval using the technique they observed being demonstrated, and there were significant differences between the two groups in their overall response patterns. These results suggest that prosimians are capable of social learning and that additional long-term field studies may reveal the presence of behavioural traditions similar to those found in other primates.
Old-growth forest is what giant pandas really need
Authors: Zhang Zejun , Swaisgood Ronald R. , Zhang Shanning , Nordstrom Lisa A. , Wang Hongjia , Gu Xiaodong , Hu Jinchu , Wei Fuwen
Published: January 2011

Giant pandas (
Ailuropoda melanoleuca
) are an iconic conservation species, but despite significant research effort, do we understand what they really need? Estimating and mapping suitable habitat play a critical role in conservation planning and policy. But if assumptions about ecological needs are wrong, maps with misidentified suitable habitat will misguide conservation action. Here, we use an information-theoretic approach to analyse the largest, landscape-level dataset on panda habitat use to date, and challenge the prevailing wisdom about panda habitat needs. We show that pandas are associated with old-growth forest more than with any ecological variable other than bamboo. Other factors traditionally used in panda habitat models, such as topographic slope, are less important. We suggest that our findings are disparate from previous research in part because our research was conducted over a larger ecological scale than previous research conducted over more circumscribed areas within individual reserves. Thus, extrapolating from habitat studies on small scales to conservation planning on large scales may entail some risk. As the Chinese government is considering the renewal of its logging ban, it should take heed of the panda's dependency on old growth.
Directional preference may enhance hunting accuracy in foraging foxes
Authors: Červený Jaroslav , Begall Sabine , Koubek Petr , Nováková Petra , Burda Hynek
Published: January 2011

Red foxes hunting small animals show a specific behaviour known as ‘mousing’. The fox jumps high, so that it surprises its prey from above. Hearing seems to be the primary sense for precise prey location in high vegetation or under snow where it cannot be detected with visual cues. A fox preparing for the jump displays a high degree of auditory attention. Foxes on the prowl tend to direct their jumps in a roughly north-eastern compass direction. When foxes are hunting in high vegetation and under snow cover, successful attacks are tightly clustered to the north, while attacks in other directions are largely unsuccessful. The direction of attacks was independent of time of day, season of the year, cloud cover and wind direction. We suggest that this directional preference represents a case of magnetic alignment and enhances the precision of hunting attacks.
The effect of aspect ratio on adhesion and stiffness for soft elastic fibres
Authors: Aksak Burak , Hui Chung-Yuen , Sitti Metin
Published: January 2011

The effect of aspect ratio on the pull-off stress and stiffness of soft elastic fibres is studied using elasticity and numerical analysis. The adhesive interface between a soft fibre and a smooth rigid surface is modelled using the Dugdale–Barenblatt model. Numerical simulations show that, while pull-off stress increases with decreasing aspect ratio, fibres get stiffer. Also, for sufficiently low aspect ratio fibres, failure occurs via the growth of internal cracks and pull-off stress approaches the intrinsic adhesive strength. Experiments carried out with various aspect ratio polyurethane elastomer fibres are consistent with the numerical simulations.
Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs
Authors: Wan Shunzhou , Coveney Peter V.
Published: January 2011

The epidermal growth factor receptor (EGFR) is a major target for drugs in treating lung carcinoma. Mutations in the tyrosine kinase domain of EGFR commonly arise in human cancers, which can cause drug sensitivity or resistance by influencing the relative strengths of drug and ATP-binding. In this study, we investigate the binding affinities of two tyrosine kinase inhibitors—AEE788 and Gefitinib—to EGFR using molecular dynamics simulation. The interactions between these inhibitors and the EGFR kinase domain are analysed using multiple short (ensemble) simulations and the molecular mechanics/Poisson–Boltzmann solvent area (MM/PBSA) method. Here, we show that ensemble simulations correctly rank the binding affinities for these systems: we report the successful ranking of each drug binding to a variety of EGFR sequences and of the two drugs binding to a given sequence, using petascale computing resources, within a few days.
Interpretation of the human skin biotribological behaviour after tape stripping
Authors: Pailler-Mattei C. , Guerret-Piécourt C. , Zahouani H. , Nicoli S.
Published: January 2011

The present study deals with the modification of the human skin biotribological behaviour after tape stripping. The tape-stripping procedure consists in the sequential application and removal of adhesive tapes on the skin surface in order to remove stratum corneum (SC) layers, which electrically charges the skin surface. The skin electric charges generated by tape stripping highly change the skin friction behaviour by increasing the adhesion component of the skin friction coefficient. It has been proposed to rewrite the friction adhesion component as the sum of two terms: the first classical adhesion term depending on the intrinsic shear strength,
τ
0
, and the second term depending on the electric shear strength,
τ
elec
. The experimental results allowed to estimate a numerical value of the electric shear strength
τ
elec
. Moreover, a plan capacitor model with a dielectric material inside was used to modelize the experimental system. This physical model permitted to evaluate the friction electric force and the electric shear strength values to calculate the skin friction coefficient after the tape stripping. The comparison between the experimental and the theoretical value of the skin friction coefficient after the tape stripping has shown the importance of the electric charges on skin biotribological behaviour. The static electric charges produced by tape stripping on the skin surface are probably able to highly modify the interaction of formulations with the skin surface and their spreading properties. This phenomenon, generally overlooked, should be taken into consideration as it could be involved in alteration of drug absorption.
The Royal Society and the decline of magic
Authors: Hunter Michael
Published: January 2011

Whereas some have asserted that the early Royal Society actively sought to discredit magical beliefs, others have seen ideas of this kind as integral to the Society's ‘nature’ in its early years. This paper argues that, whatever the magical commitments of individual Fellows, the Society's corporate policy simply sidelined such pursuits. Yet, insofar as the result was that magic was excluded by default from the proper realm of scientific enquiry, this attitude was to prove paradoxically influential (although its roots have been retrospectively misconstrued to an extent that is significant in itself).
‘Explaining’ themselves: The Barrington papers, the board of longitude, and the fate of John Harrison
Authors: Barrett Katy
Published: January 2011

In 2003 the National Maritime Museum acquired a group of documents compiled by Viscount Barrington while he was a commissioner on the Board of Longitude. These focus on the year 1765, when the Board sought two Acts from Parliament to explain its decisions and to extend its powers. Since its establishment in 1714, the Board had considered two main solutions to the problem of finding longitude at sea: the clocks of John Harrison and the lunar distance method of Tobias Meyer. Trials of both had shown that the Board needed to clarify what constituted a real solution. Barrington's papers revolve around a speech that he gave to the House of Commons during the passage of the Acts, and include accounts, correspondence and notes. These not only reveal the internal workings of the Board but also make clear for the first time the extent to which the commissioners were explaining their decisions and their existence to a sceptical Parliament.