bluuebunny/crossref_metadata_2025 huggingface dataset:
Ab initio Study on Spectral Properties of Charge-Compensated Ce3+ in NaF
Authors: Ma Nai-yu , Yang Feng , Shen Xian-chun , Huang Yu-cheng , Ning Li-xin
Published: November 2014

We report an ab initio study of spectral properties of Ce3+ doped at Na+ site of the NaF crystal, with the charge imbalance compensated by two oxygen substitutions for fluoride (OF′) in the first coordination shell or two sodium vacancies (VNa′) in the second coordination sphere. Density functional theory calculations within the supercell model are first performed to optimize the local structures of the charge-compensated Ce3+, based on which Ce-centered embedded clusters are constructed and wave function-based CASSCF/CASPT2/RASSI-SO calculations are carried out to obtain the energies of 4f1 and 5d1 levels. By comparing the calculated 4f→5d transition energies with experimental excitation spectra at low temperatures, the lowest 4f→5d transition band peaked at 390 nm is assigned to the Ce3+ with charge compensation by two coordinating OF′ substitutions, rather than to the Ce3+ with compensation by two VNa′ vacancies, as proposed earlier. The electronic reason for the large redshift (by ∼8000 cm−1) of the lowest 4f→d transition as induced by the two nearby OF′ substitutions is analyzed in terms of the changes in the centroid shift and crystal-field splitting.
Density Functional Theory Calculations of Charge-Induced Spin Polarization in Pentacene
Authors: Ren Jun-feng , Zhang Yan-ru , Yuan Xiao-bo , Hu Gui-chao
Published: November 2014

Based on density functional theory (DFT) calculations, we investigate the spin-related properties of spinless-hole injected organic molecule pentacene (Pc). DFT calculations reveal that there is spontaneous spin polarization in Pc when spinless-hole is injected. The charge-induced magnetic moment of Pc increases linearly with the increasing of the extra hole charge amount and its maximum can be up to 1 μB per injected spinless-hole per Pc molecule. The magnetic moment is expected due to the injected unpaired charge. The injected hole will preferably fill the spin-splitted carbon pz orbitals, which makes the Pc molecule spin polarize.
Cu-Co Composite Oxides Supported on Multi-walled Carbon Nanotubes for Catalytic Removal of CO in a H2-rich Stream
Authors: Liu Ning , Gao Yu-xian , Wang Wen-dong , Huang Wei-xin
Published: November 2014

Multi-walled carbon nanotubes (MWCNT) supported Cu-Co composite oxides catalysts were prepared by an ultrasonication treatment-aided impregnation method. The structure properties of the catalysts were characterized by XRD, TEM, H2-TPR, XPS and Raman spectra, indicating the strong interactions between Cu and Co mixed oxides as well as between metal oxides and MWCNT support. The catalytic performance of CO removal in a H2-rich stream was examined. In contrast to the single Cu and Co catalyst, the unique performance was observed for Cu-Co composite catalysts, which features an unusual reaction pathway through the combination of CO preferential oxidation and CO methanation especially at high reaction temperature. The optimal catalyst with Cu/Co ratio of 1/8 can achieve the complete CO conversion in a wider temperature range of 150–250 °C under the space velocity as high as 120 L/(h·g), which demonstrates a promising catalyst for the effective CO removal in a H2-rich stream.
pH Influence on Performance of Phytic Acid Conversion Coatings on AZ31 Magnesium Alloy in Simulated Body Fluid
Authors: Zheng Jia , Zhang Sheng-tao , Guo Lei , Lv Tang-man , Zhou Yang , Luo Xiao-fang
Published: November 2014

Phytic acid (PA) conversion coating on AZ31 magnesium alloy is prepared by a deposition method. pH influences on the formation process, microstructure and properties of the conversion coating are investigated. Electrochemical tests including polarization curve and electrochemical impedance spectroscopy are used to examine the corrosion resistance, and scanning electron microscopy is used to observe the microstructure. The chemical nature of conversion coating is investigated by energy dispersive spectroscopy. And thermodynamic method is used to analyze the optimum pH. The results show that PA conversion coating can improve the corrosion resistance of AZ31 Mg alloy. The maximum efficiency achieves 89.19% when the AZ31 Mg alloy is treated by PA solution with pH=5. It makes the corrosion potential of sample shift positively about 156 mV and corrosion current density is nearly an order of magnitude less than that of the untreated sample. The thermodynamic analysis shows that the corrosion resistance of PA coatings is affected by not only the concentration of PA ion and Mg2+ but also the release rate of hydrogen.
Fabrication and Growth Mechanism of Bamboo-structured Boron Nitride Nanotubes with Thorn-Like Morphology
Authors: Zhang Jiang , Chen Xi
Published: November 2014

Bamboo-structured boron nitride (BN) nanotubes with thorn-like morphology were synthesized by thermal chemical reaction using amorphous boron powders and NiO nanoparticles as precursors under the flow of NH3 at 1100 °C. The structural and morphological characteristics of BN nanotubes were investigated by X-ray diffraction and transmission electron microscopy. The results showed that the thorn-like nanostructures attaching to the stems of bamboo-structured BN nanotubes were the hexagonal BN nanoflakes. Based on the diffusion of solid B and vapor B2O2, a possible growth mechanism of these novel thorn-like BN nanotubes was primarily proposed.
Mesh-Like Bi2MoO6 with Enhanced and Stable Visible Light Photocatalytic Activity
Authors: Wang Qing-wei , Guo Xiao-yu , Lin Xue , Liu Chun-bo , Zhai Hong-ju
Published: November 2014

Mesh-like Bi2MoO6 product was successfully synthesized by a hydrothermal method without using any surfactant or template. The pH value played an important role in the formation of this morphology. The as-prepared mesh-like Bi2MoO6 sample exhibited excellent visiblelight-driven photocatalytic efficiency. The photocatalytic activity of the mesh-like Bi2MoO6 sample was much higher than that of bulk Bi2MoO6 sample prepared by solid-state reaction. Difference in the photocatalytic activities of the mesh-like Bi2MoO6 sample and bulk Bi2MoO6 sample was further investigated.
Probe the Effects of Surface Adsorbates on ZnO Nanowire Conductivity using Dielectric Force Microscopy
Authors: Chen Qi , Lu Wei , Wu Yu-kun , Ding Huai-yi , Wang Bing , Chen Liwei
Published: November 2014

Characterization of electric properties of nanomaterials usually involves fabricating field effect transistors (FET) and deriving materials properties from device performances. However, the quality of electrode contacts in FET devices heavily influences the device performance, which makes it difficult to obtain the intrinsic electric properties of nanomaterials. Dielectric force microscopy (DFM), a contactless method developed recently, can detect the low-frequency dielectric responses of nanomaterials without electric contact, which avoids the influence of electric contact and can be used to study the intrinsic conductivity of nanomaterials. Here we study the influences of surface adsorbates on the conductivity of ZnO nanowires (NWs) by using FET and DFM methods. The conductivity of ZnO NW is much larger in N2 atmosphere than that in ambient environment as measured by FET device, which is further proven by DFM measurement that the ZnO NW exhibits larger dielectric response in N2 environment, and the influence of electrode contacts on measurement can be ruled out. Based on these results, it can be concluded that the adsorbates on ZnO NW surface highly influence the conductivity of ZnO NW rather than the electrode contact. This work also verifies the capability of DFM in measuring electric properties of nanomaterials.
Synthesis of an Amphiphilic Dendrimer-Like Block Copolymer and Its Application on Drug Delivery
Authors: Wang Shuai-peng , Song Xiao-wan , Feng Xiao-shuang , Chen Peng , Qian Jia-sheng , Xia Ru , Miao Ji-bin
Published: November 2014

Dendrimer-like amphiphilic copolymer is a kind of three-dimensional spherical structure polymer. An amphiphilic dendrimer-like diblock copolymer, PEEGE-G2-b-PEO(OH)12, constituted of a hydrophobic poly(ethoxyethyl glycidol ether) inner core and a hydrophilic poly(ethylene oxide) outer layer, has been successfully synthesized by the living anionic ring-opening polymerization method. The intermediates and targeted products were characterized with 1H NMR spectroscopy and gel permeation chromatography. The application on drug delivery of dendrimer-like diblock copolymer PEEGE-G2-b-PEO(OH)12 using DOX as a model drug was also studied. The drug loading content and encapsulation efficiency were found at 13.07% and 45.75%, respectively. In vitro release experiment results indicated that the drug-loaded micelles exhibited a sustained release behavior under acidic media.
Significant Enhancement in Built-in Potential and Charge Carrier Collection of Organic Solar Cells using 4-(5-hexylthiophene-2-yl)-2,6-bis(5-trifluoromethyl)thiophen-2-yl)pyridine as a Cathode Buffer Layer
Authors: Zang Yue , Cao Kang-li , Huang Jiang , Zhang Qing , Yu Jun-sheng
Published: November 2014

An electron transporting material of TFTTP (4-(5-hexylthiophene-2-yl)-2,6-bis(5-trifluoromethyl)thiophen-2-yl)pyridine) was investigated as a cathode buffer layer to enhance the power efficiency of organic solar cells (OSCs) based on subphthalocyanine and C60. The overall power conversion efficiency was increased by a factor of 1.31 by inserting the TFTTP interfacial layer between the active layer and metallic cathode. The inner mechanism responsible for the performance enhancement of OSCs was systematically studied with the simulation of dark diode behavior and optical field distribution inside the devices as well as the characterization of device photocurrent. The results showed that the TFTTP layer could significantly increase the built-in potential in the devices, leading to the enhanced dissociation of charge transfer excitons. In addition, by using TFTTP as the buffer layer, a better Ohmic contact at C60/metal interface was formed, facilitating more efficient free charge carrier collection.
Microencapsulation of UV-Curable Self-healing Agent for Smart Anticorrosive Coating
Authors: Zhao Dong , Wang Mo-zhen , Wu Qi-chao , Zhou Xiao , Ge Xue-wu
Published: November 2014

UV-curable polyurethane prepolymer and photoinitiator 1173 were facilely encapsulated in a poly(urea-formaldehyde) shell, which was in situ formed by the polymerization of formaldehyde and urea in an oil-in-water emulsion. The diameters of the microcapsules ranged from 118 µm to 663 µm depending on agitation speed, and were obtained via optical microscopy and scanning electron microscopy analyses. The encapsulation percent and the yield of microcapsules prepared at the agitation speed of 600 r/min can reach 97.52wt% and 65.23wt%, respectively. When the water-borne polyurethane (WPU) coating embedded with the prepared microcapsules were scratched, the healing agent could be released from ruptured microcapsules and filled the scribed region. The excellent anticorrosion properties of the WPU coating embedded with the prepared microcapsules were confirmed by the results obtained from both electrochemical impedance spectroscopy and Tafel curves.
Supramolecular Fixation of Three Amines using Cobalt Tetraphenylporphyrin for SO2 Removal
Authors: Lan Gong-jia , Zhang Jian-bin , Zhao Tian-xiang , Xu Qiu-xia , Wei Xiong-hui
Published: November 2014

In this work, supramolecular fixation of three amines, including aniline, ethylenediamine, and diethylamine, using cobalt tetraphenylporphyrin (CoTPP) for SO2 removal was studied using UV-Vis and fluorescence measurements. The UV-Vis spectra showed that increasing amines concentrations resulted in bathochromic shift for CoTPP Soret absorption band (B band). Once SO2 was introduced, it competed with CoTPP for aniline, ethylenediamine, and diethylamine, which eventually led to the release of CoTPP and the change of solution colour/absorption band. After that, the CoTPP was regenerated and got back to the first state. The fluorescence spectra offered that CoTPP interacted with aniline, ethylenediamine, and diethylamine to form 1:1 molecular adducts. The interactions of CoTPP with aniline, ethylenediamine, and diethylamine were entropy-driven. The interaction of CoTPP with aniline and diethylamine was endothermic, and that with ethylenediamine was exothermic. Ethylenediamine presented a stronger binding constant value for CoTPP, so it was considered as a potential agent for SO2 removal.
How the Desert got a Past: A History of Quaternary Research in Australia’s Deserts
Authors: Smith Mike
Published: November 2014

This paper examines how the past of desert landscapes has been interpreted since European explorers and scientists first encountered them. It charts the research that created the conceptual space within which archaeologists and Quaternarists now work. Studies from the 1840s–1960s created the notion of a ‘Great Australian Arid Period'. The 1960s studies of Lake Mungo and the Willandra Lakes by Jim Bowler revealed the cyclical nature of palaeolakes, that changed with climate changes in the Pleistocene, and the complexity of desert pasts. SLEADS and other researchers in the 1980s used thermoluminescence techniques that showed further complexities in desert lands beyond the Willandra particularly through new studies in the Strzelecki and Simpson Dunefields, Lake Eyre, Lake Woods and Lake Gregory. Australian deserts are varied and have very different histories. Far from ‘timeless lands', they have carried detailed information about long-term climate changes on continental scales.
David James Kemp 1945–2013
Authors: Sriprakash Kadaba S. , Good Michael F.
Published: November 2014

David Kemp's seminal contributions to molecular parasitology of malaria and scabies have placed Australian science at the forefront of research on these important human pathogens. Immunoscreening of expression clones led to the identification of several vaccine candidates against malaria. His contributions to scabies research are pivotal to our understanding of bacteria–parasite–human interactions. Other notable achievements are: the discovery of one of the earliest known multi-gene families; the first cloning of linked variable-region genes in the immunoglobulin heavy-chain locus; the invention of highly cited molecular biology methods, namely Northern blotting and inverted-PCR; and contributions to ‘molecular public health' by his work on various bacterial infections relevant to the health of Indigenous Australians. Kemp's manifest enthusiasm for science was highly infectious. He mentored many high-achieving scientists. In addition to his exemplary career as a scientist, he was a musician at heart and a passionate rock fossicker.
Interference-mediated synaptonemal complex formation with embedded crossover designation
Authors: Zhang Liangran , Espagne Eric , de Muyt Arnaud , Zickler Denise , Kleckner Nancy E.
Published: November 2014

Significance

Spatial patterns occur in biological and nonbiological systems. A paradigmatic example occurs during meiosis. As shown a century ago, crossover recombination events occur at different positions in different meiotic nuclei; nonetheless, occurrence of a cross-over at one position decreases the probability that another will occur nearby. As a result, crossovers tend to be evenly spaced. This study suggests that this classical cross-over interference is part of a broader program that concomitantly specifies even spacing of nucleation sites for formation of synaptonemal complex, a prominent meiotic chromosome structure. A model emerges for how the observed patterns could occur. This model provides an explanation for the formation of complex, multilayered patterns that is generally applicable to biological and nonbiological systems.
Subjectivity in modality, and beyond
Authors: Nuyts Jan
Published: November 2014

This conceptual paper reflects on the role of ‘subjectivity’ in the analysis of the semantic domain of modality. It offers a critical review of the traditional notions of subjectivity vs. objectivity (including Lyons’ 1977), and it elaborates further on an alternative notion, labeled (inter)subjectivity, as proposed in earlier work (Nuyts 2001b; 2012). The paper spends particular attention to the question of the precise range of applicability of the category of (inter)subjectivity (which extends beyond the modal categories), and to the question of its status in a cognitive semantic theory.
Certainty and uncertainty in assertive speech acts
Authors: Labinaz Paolo , Sbisà Marina
Published: November 2014

We begin by considering three main philosophical accounts of assertion, showing that each emphasizes specific aspects of it while leaving others aside, and then proceed to offering a more comprehensive speech-act theoretic account of assertion, which owes much to Austin’s approach to illocutionary acts. On the basis of this account, we investigate how assertion and other members of the assertive speech act family serve the aim of communicating, not merely pieces of information, but also the speaker’s attitude of certainty or uncertainty about them. In so doing, we make use of examples from a corpus of texts in Italian and English, drawn from newspapers, scientific journals and web sites, concerning the so-called Stamina case.
Ideal and deviant interlocutors in a formal interpretation system
Authors: Alberti Gábor , Vadász Noémi , Kleiber Judit
Published: November 2014

Conversational partners’ “ideal” information states – their knowledge (about the world and each other), their beliefs (with different degrees of certainty), their desires and intentions (of different degrees of intensity) – can be specified at any point in the conversation. The various elements making up an information state are sometimes standard-like, but often they serve as basis for various possible deviations from the standard. Some verbs which express particular deviations are discussed, including the extreme case of lying while saying the truth. Our analyses are presented in a formal interpretation system, which allows us to demonstrate how different meanings emerge while only changing polarity parameters from case to case. We thus intend to build a bridge between pragmatics and hardcore formal semantics.
On being certain whether
Authors: Hölker Klaus
Published: November 2014

This contribution deals with the question of why certain predicates, in particular be certain, that normally cannot embed interrogative clauses nevertheless do so when they occur in special contexts. A satisfactory answer to this question requires specifying the general conditions under which predicates can combine with interrogatives. Since, as is well known, such a specification is hard to come by, the larger part of the article is devoted to this question. It will be argued that, counter to the factivity hypothesis, it is reasonable to assume that the restrictions on the combinability of predicates with interrogatives are not rooted in general semantic properties of the predicates, but ultimately in the typical properties of question situations and the knowledge we have of these properties.
Uncertainty as integrated part of meaning and understanding
Authors: Feller Sebastian
Published: November 2014

In this chapter, we discuss the issue of uncertainty in language and communication. The starting point for the discussion is Weigand’s (2010) Mixed Game Model, a theory of dialogic language use. Feller’s (2010) meaning-in-use, which conceptualizes meaning construction as a dialogic process, puts the focus on meaning and understanding in dialog. Against this theoretical background, we discuss the roles of uncertainty in dialog, especially in the context of speaker interests, cross-cultural communication, and inner dialog. We will therefore look into the different knowledge types that are integrated in language use and which are used by the dialog partners to construct meaning and interpret utterances. The main argument is that these knowledge types are veined with blind spots for the dialog partners, which they fill in with their expectations along measures of probability. Uncertainty is thus an integrated part of dialogic language use.
Epistemic stance
Authors: Zuczkowski Andrzej , Bongelli Ramona , Vincze Laura , Riccioni Ilaria
Published: November 2014

In this study, we compare three approaches to epistemic stance: Akio Kamio’s Theory of Territories of Information (intended as a bridge between evidentiality and politeness) and his distinction between direct and indirect forms of utterances; John Heritage’s differentiation between epistemic status and epistemic stance and between speakers’ more knowledgeable and less knowledgeable positions; our theoretical model, which includes three epistemic positions : knowing, unknowing, believing (not knowing whether). Similarities and differences among these three approaches and their applicability to the analysis of naturally occurring conversations are discussed.
Diagnostic news delivery
Authors: Plastina Anna Franca , Del Vecchio Fabrizia
Published: November 2014

This paper focuses on the issue of diagnostic news delivery by addressing the research questions of how doctors shield language when breaking bad news to patients and how shields are positioned within the sequential order of these interactions. Empirical research was conducted on a collected corpus of authentic interactions through microanalysis of their epistemic organisation. Findings showed that when doctors were uncomfortable in giving bad news they mainly used verbs and verb phrases to shield the seriousness of the news. Different categories of shields were also used according to varying levels of distress. Following the biomedical SPIKES Protocol, different degrees of certainty were found in the step of Knowledge, whereas mitigating devices occurred in the steps of Empathy and Strategy.
Epistemic struggles in addiction Therapeutic Community meetings
Authors: Pino Marco
Published: November 2014

In this study I analyse Therapeutic Community (TC) group meetings for persons with drug addiction problems. Using the method of Conversation Analysis, I specifically focus on practices of knowledge management and sharing between the educators and clients of a TC in Italy. As part of their institutional remit, the educators encourage the clients to report information on their activities and to disclose aspects of their inner experience. This can lead to epistemic struggles, in which the clients resist providing information and the educators seek to overcome such resistance by making claims of pre-existing knowledge about the clients’ experience. After describing the design and sequential positioning of such claims, I argue that their use is functional to manage one of the dilemmas that characterise the educators’ professional practice.
The fabric of certainty
Authors: Caronia Letizia
Published: November 2014

This chapter concerns the tactic of “ignoring uncertainty” that takes place during research interviewing. Drawing on extent research on research interviews as an interactive phenomenon, we contend that most micro-actions implied in scientific practices are purifying activities aimed to clean discursive data from uncertainty-marks and relativization cues. By analysing a collection of question/answer sequences from a telephone survey, we shows how the interviewer-in-the-field and the analyst-at-the-desk ignore these uncertainty markers as much as possible and turn almost every utterance into a declarative statement. We contend that these techniques of knowledge produce one of the culturally relevant traits of scientific knowledge: certainty. They therefore serve the purpose of nourishing our enduring positivistic vision of (scientific) knowledge as a mirror of reality.
Hedging and attitude markers in Spanish and English scientific medical writing
Authors: Oliver del Olmo Sonia
Published: November 2014

Hedging, a sociopragmatic phenomenon that allows authors to maintain their presence in discourse, is a rather difficult strategy for non-natives scholars. In this paper, we present two studies: the first analyses hedging from cross-linguistic (Spanish and English L2) and cross-generic (Research Paper and Case Report) approaches in a corpus of 30 Medical full-texts from highly indexed research journals. Our results indicate that Spanish authors hedge more when writing in English L2 but less than an English native. The second focus on attitude markers (Affect, Judgement and Appreciation) following Appraisal Theory (Martin and White 2005) to detect cross-cultural differences in 60 Medical Book Reviews. The outcome shows that Spanish reviewers blend categories and seem more positive and direct in their assessments.
A theoretical contribution to tackling certainty and uncertainty in scientific writing
Authors: Graça Pinto Maria da , Osório Paulo , Martins Fernanda
Published: November 2014

Our theoretical contribution to tackling certainty and uncertainty in scientific writing is based on a study of four research articles from the journal Brain collected at random (from 1997 to 2012), to determine whether any differences in writing, design and analysis with modality implications arise over that interval. We hypothesize that, according to the sections of a research article, considered as a multi-modal genre, several types of linguistic modality are used to convey contextual, evidential and interpreted truths. The study aims to show that methodological approaches, the type of analysis (qualitative/quantitative) and statistical tools, together with other means of translating modality, will affect the final product of scientific research articles regarding linguistic and non-linguistic devices used to convey certainty/uncertainty.
BioUncertainty
Authors: Bongelli Ramona , Riccioni Ilaria , Canestrari Carla , Pietrobon Ricardo , Zuczkowski Andrzej
Published: November 2014

The communication of the uncertainty of a scientific finding largely determines whether that information will be translated to practice. Unfortunately, however, our ability to study these phenomena is restrained since existing uncertainty corpora are limited in their number of full text articles and in their provision of a historical perspective. We describe a historical corpus evaluating uncertainty markers through a random sample of 167 years (1840–2007) of articles published in the British Medical Journal. Randomization was stratified from four distinct time periods, namely 1840–1880, 1881–1920, 1921–1960, and 1961–2007. Each full-text article was tagged by a group of analysts associated with a physician. We describe extensive data on the distribution of each of these linguistic markers. Contrary to our initial hypothesis, the rates of  uncertainty markers have remained surprisingly stable over the period studied in this project, except for the modal verbs in the simple present, which occur with a minor frequency in the first time period compared to the other three.
Uncertainty markers in a corpus of German biomedical papers from Spektrum der Wissenschaft (1993-2012)
Authors: Bucciarelli Paola , Bongelli Ramona , Zuczkowski Andrzej , Cantarini Sibilla , Berthold Christine
Published: November 2014

In this paper we present the analysis of uncertainty markers in a corpus of 60 articles randomly selected from the German popular science magazine
Spektrum der Wissenschaft since 1993 until 2012. In addition to identifying which and how many uncertainty lexical and morphosyntactic markers were used by scientific writers, our aims were to detect their trends over time and single out their scope, in order to test if the ratio between the amount of certainty and uncertainty remained constant in all the papers or if, on the contrary, it changed over time. The results show that there were no significant changes.
Questioning certainty in research articles and popular science articles
Authors: Pic Elsa , Furmaniak Gregory
Published: November 2014

This paper is a comparative study of the use of direct and indirect modalized wh-questions in research articles and popular science articles. The corpus analysis reveals that these questions are often interpreted as rhetorical questions and that they are often used to question a proposition that has been previously presented as certain or almost certain. We first suggest that rhetorical questions of this form fall into three semantic types (non-polyphonic, polemic and pseudo-polemic). Their distribution and/or function are then shown to vary across genres – they tend to serve argumentative purposes in research articles and explicative purposes in popular science articles. Finally we examine the parameters which affect the strength with which the presupposition is questioned.
Self-repairs and certainty in Romanian academic meetings
Authors: Velea Adina I.
Published: November 2014

This paper investigates the connection between self-repairs, conversation analytical mechanisms, and the concept of certainty in Romanian academic meetings. The focus is on the design of turn(s) in which the chair and the other participants provide feedback on a piece of writing. The data reveal that at the turn design level, through self-repairs (namely replacing, deleting, reformatting, inserting), the speakers employ several lexical and grammatical items in order to communicate different degrees of certainty.
Joint amalgamation of most parsimonious reconciled gene trees
Authors: Scornavacca Celine , Jacox Edwin , Szöllősi Gergely J.
Published: November 2014

Motivation: Traditionally, gene phylogenies have been reconstructed solely on the basis of molecular sequences; this, however, often does not provide enough information to distinguish between statistically equivalent relationships. To address this problem, several recent methods have incorporated information on the species phylogeny in gene tree reconstruction, leading to dramatic improvements in accuracy. Although probabilistic methods are able to estimate all model parameters but are computationally expensive, parsimony methods—generally computationally more efficient—require a prior estimate of parameters and of the statistical support.

Results: Here, we present the Tree Estimation using Reconciliation (TERA) algorithm, a parsimony based, species tree aware method for gene tree reconstruction based on a scoring scheme combining duplication, transfer and loss costs with an estimate of the sequence likelihood. TERA explores all reconciled gene trees that can be amalgamated from a sample of gene trees. Using a large scale simulated dataset, we demonstrate that TERA achieves the same accuracy as the corresponding probabilistic method while being faster, and outperforms other parsimony-based methods in both accuracy and speed. Running TERA on a set of 1099 homologous gene families from complete cyanobacterial genomes, we find that incorporating knowledge of the species tree results in a two thirds reduction in the number of apparent transfer events.

Availability and implementation: The algorithm is implemented in our program TERA, which is freely available from http://mbb.univ-montp2.fr/MBB/download_sources/16__TERA.

Contact:  celine.scornavacca@univ-montp2.fr, ssolo@angel.elte.hu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries
Authors: Gillet-Markowska Alexandre , Richard Hugues , Fischer Gilles , Lafontaine Ingrid
Published: November 2014

Motivation: The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging.

Results: Here, we present Ulysses, a tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high specificity over the complete spectrum of variants by assessing, in a principled manner, the statistical significance of each possible variant (duplications, deletions, translocations, insertions and inversions) against an explicit model for the generation of experimental noise. This statistical model proves particularly useful for the detection of low frequency variants. SV detection performed on a large insert Mate-Pair library from a breast cancer sample revealed a high level of somatic duplications in the tumor and, to a lesser extent, in the blood sample as well. Altogether, these results show that Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes.

Availability and implementation: Ulysses is available at http://www.lcqb.upmc.fr/ulysses.

Contact:  ingrid.lafontaine@upmc.fr or gilles.fischer@upmc.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks
Authors: Moni Mohammad Ali , Xu Haoming , Liò Pietro
Published: November 2014

Summary: CytoCom is an interactive plugin for Cytoscape that can be used to search, explore, analyse and visualize human disease comorbidity network. It represents disease–disease associations in terms of bipartite graphs and provides International Classification of Diseases, Ninth Revision (ICD9)-centric and disease name centric views of disease information. It allows users to find associations between diseases based on the two measures: Relative Risk (RR) and ϕ-correlation values. In the disease network, the size of each node is based on the prevalence of that disease. CytoCom is capable of clustering disease network based on the ICD9 disease category. It provides user-friendly access that facilitates exploration of human diseases, and finds additional associated diseases by double-clicking a node in the existing network. Additional comorbid diseases are then connected to the existing network. It is able to assist users for interpretation and exploration of the human diseases by a variety of built-in functions. Moreover, CytoCom permits multi-colouring of disease nodes according to standard disease classification for expedient visualization.

Availability and implementation: CytoCom is compatible with CytoScape 3.1.0 or later version. Please visit http://www.cl.cam.ac.uk/∼mam211/ for user tutorial and download.

Contact:  Mohammad.Moni@cl.cam.ac.uk
TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm
Authors: Pey Jon , Villar Juan A. , Tobalina Luis , Rezola Alberto , García José Manuel , Beasley John E. , Planes Francisco J.
Published: November 2014

Motivation: Elementary flux modes (EFMs) analysis constitutes a fundamental tool in systems biology. However, the efficient calculation of EFMs in genome-scale metabolic networks (GSMNs) is still a challenge. We present a novel algorithm that uses a linear programming-based tree search and efficiently enumerates a subset of EFMs in GSMNs.

Results: Our approach is compared with the EFMEvolver approach, demonstrating a significant improvement in computation time. We also validate the usefulness of our new approach by studying the acetate overflow metabolism in the Escherichia coli bacteria. To do so, we computed 1 million EFMs for each energetic amino acid and then analysed the relevance of each energetic amino acid based on gene/protein expression data and the obtained EFMs. We found good agreement between previous experiments and the conclusions reached using EFMs. Finally, we also analysed the performance of our approach when applied to large GSMNs.

Availability and implementation: The stand-alone software TreeEFM is implemented in C++ and interacts with the open-source linear solver COIN-OR Linear program Solver (CLP).

Contact: fplanes@ceit.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments
Authors: Bläßle Alexander , Müller Patrick
Published: November 2014

Summary: We developed the graphical user interface PyFDAP for the fitting of linear and non-linear decay functions to data from fluorescence decay after photoconversion (FDAP) experiments. PyFDAP structures and analyses large FDAP datasets and features multiple fitting and plotting options.

Availability and implementation: PyFDAP was written in Python and runs on Ubuntu Linux, Mac OS X and Microsoft Windows operating systems. The software, a user guide and a test FDAP dataset are freely available for download from http://people.tuebingen.mpg.de/mueller-lab.

Contact:  pmueller@tue.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Perceptual Training Restores Impaired Cortical Temporal Processing Due to Lead Exposure
Authors: Zhu Xiaoqing , Liu Xia , Wei Fanfan , Wang Fang , Merzenich Michael M. , Schreiner Christoph E. , Sun Xinde , Zhou Xiaoming
Published: November 2014

Low-level lead exposure is a risk factor for cognitive and learning disabilities in children and has been specifically associated with deficits in auditory temporal processing that impair aural language and reading abilities. Here, we show that rats exposed to low levels of lead in early life display a significant behavioral impairment in an auditory temporal rate discrimination task. Lead exposure also results in a degradation of the neuronal repetition-rate following capacity and response synchronization in primary auditory cortex. A modified go/no-go repetition-rate discrimination task applied in adult animals for ∼50 days nearly restores to normal these lead-induced deficits in cortical temporal fidelity. Cortical expressions of parvalbumin, brain-derived neurotrophic factor, and NMDA receptor subunits NR2a and NR2b, which are down-regulated in lead-exposed animals, are also partially reversed with training. These studies in an animal model identify the primary auditory cortex as a novel target for low-level lead exposure and demonstrate that perceptual training can ameliorate lead-induced deficits in cortical discrimination between sound sequences.
An intraplate slow earthquake observed by a dense GPS network in Hokkaido, northernmost Japan
Authors: Ohzono Mako , Takahashi Hiroaki , Ichiyanagi Masayoshi
Published: November 2014

An intraplate slow earthquake was detected in northernmost Hokkaido, Japan, by a dense network of the global navigation satellite system. Transient abnormal acceleration of <12 mm was observed during the period 2012 July to 2013 January (∼5.5 months) at several sites. The spatial displacement distribution suggests that a localized tectonic event caused localized deformation. Estimated fault parameter indicates very shallow-dip reverse faulting in the uppermost crust, with a total seismic moment of 1.75E + 17 N m (Mw 5.4). This fault geometry is probably consistent with detachment structure indicated by geological studies. A simultaneous earthquake swarm with the maximum magnitude M4.1 suggests a possibility that the slow slip triggered the seismic activity for unknown reasons. This slow earthquake is slower than its moment would indicate, with a duration–magnitude scaling relationship unlike either regular earthquakes or subduction slow slip events. This result indicates that even if the area is under different physical property from subduction zones, slow earthquake can occur by some causes. Slow earthquakes exist in remote regions away from subduction zones and might play an important role in strain release and tectonic activity.
Offensive Expression and the Workplace
Authors: Pearson Megan
Published: November 2014

In this article I argue that freedom of expression is an important right even within the employment context. I contend that there should be a presumption in favour of free expression even if the expression is offensive, particularly if it involves a matter of public debate. However, the interests of colleagues and employers should be taken into account and may be decisive. Where expression takes place outside work, employees should only be subject to disciplinary action if there is a clear link between their employment and the expression. I consider the law relating to these issues in the contexts of harassment, unfair dismissal and discrimination on the grounds of religion and belief.
Members, Partners, Employees, Workers? Partnership Law and Employment Status revisited. Clyde & Co LLP v Bates van Winkelhof
Authors: Prassl Jeremias
Published: November 2014

The recent Supreme Court decision in Clyde & Co v Bates van Winkelhof1 at first sight addresses no more than a rather technical point at the intersection of employment and partnership law, brought about as the result of questionable statutory drafting in section 4(4) of the Limited Liability Partnerships Act of 2004. Upon closer inspection, however, the case brings to the forefront a tension underpinning discussions of the personal scope of employment law, between an inclusive approach encompassing all relationships of employment or akin thereto, and the view that ‘private law’ or primarily commercial relationships should fall outside the scope of employment regulation. It will therefore have far-reaching implications for the employment status of partners in all forms of partnership arrangements, as explored in Section 2 of this note. The decision furthermore has the potential significantly to change our understanding of the interrelationship between the notions of employees and workers, by challenging a strand of previous decisions which seemed narrowly to interpret statutory extensions of employment status (Section 3). A brief third section, finally, explores the changing role of ECHR jurisprudence in UK employment law.
Bemovi, software for extracting Behaviour and Morphology from Videos
Authors: Pennekamp Frank , Schtickzelle Nicolas , Petchey Owen L.
Published: November 2014

Microbes are critical components of ecosystems and vital to the services they provide. The essential role of microbes is due to high levels of functional diversity, which are, however, not always mirrored in morphological differentiation hampering their taxonomic identification. In addition, the small size of microbes hinders the measurement of morphological and behavioural traits at the individual level, as well as interactions between individuals.

Recent advances in microbial community genetics and genomics, flow cytometry and digital image analysis are promising approaches, however they miss out on a very important aspect of populations and communities: the behaviour of individuals. Video analysis complements these methods by providing in addition to abundance and trait measurements, detailed behavioural information, capturing dynamic processes such as movement, and hence has the potential to describe the interactions between individuals.

We introduce bemovi, a package using R - the statistical computing environment - and the free image analysis software ImageJ. Bemovi is an automated digital video processing and analysis work flow to extract abundance and morphological and movement data for numerous individuals on a video, hence characterizing a population or community by multiple traits. Through a set of functions, bemovi identifies individuals present in a video and reconstruct their movement trajectories through space and time, merges measurements from all treated videos into a single database to which information on experimental conditions is added, readily available for further analysis in R.

We illustrate the validity, precision and accuracy of the method for experimental multi-species communities of protists in aquatic microcosms. We show the high correspondence between manual and automatic counts of individuals and illustrate how simultaneous time series of abundance, morphology and behaviour are constructed. We demonstrate how the data from videos can be used in combination with supervised machine learning algorithms to automatically classify individuals according to the species they belong to, and that information on movement behaviour can substantially improve the predictive ability and helps to distinguish morphologically similar species. In principle, bemovi should be able to extract from videos information about other types of organism, including “microbes”, so long as the individuals move relatively fast compared to their background.
Tools and Methods from the Anopheles 16 Genome Project
Authors: Steele Aaron , Fontaine Michael C. , Martin Andres , Emrich Scott J.
Published: November 2014

The dramatic reduction in sequencing costs has resulted in many initiatives to sequence certain organisms and populations. These initiatives aim to not only sequence and assemble genomes but also to perform a more broader analysis of the population structure. As part of the Anopheline Genome Consortium, which has a vested interest in studying anpopheline mosquitoes, we developed novel methods and tools to further the communities goals. We provide a brief description of these methods and tools as well as assess the contributions that each offers to the broader study of comparative genomics.
What to compare and how: comparative transcriptomics for Evo-Devo
Authors: Roux Julien , Rosikiewicz Marta , Robinson-Rechavi Marc
Published: November 2014

Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org).
WASP: allele-specific software for robust discovery of molecular quantitative trait loci
Authors: van de Geijn Bryce , McVicker Graham , Gilad Yoav , Pritchard Jonathan K.
Published: November 2014

Allele-specific sequencing reads provide a powerful signal for identifying molecular quantitative trait loci (QTLs), however they are challenging to analyze and prone to technical artefacts. Here we describe WASP, a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs. Using simulated reads, RNA-seq reads and ChIP-seq reads, we demonstrate that our approach has a low error rate and is far more powerful than existing QTL mapping approaches.