bluuebunny/crossref_metadata_2025 huggingface dataset:
SMS communication as plurilingual communication
Authors: Morel Étienne , Bucher Claudia , Pekarek Doehler Simona , Siebenhaar Beat
Published: June 2014

The use of more than one language in SMS communication is widespread, yet has remained relatively underexplored in the existing research. In this paper we ask: What methodological and conceptual tools are needed for empirically investigating code-switching in large databases of SMS communication? We show that the investigation of SMS communication calls for an adaptation of the conceptual and the methodological apparatus of classical code-switching studies, which have been typically concerned with the analysis of spoken, mostly interactional, data. We argue for a broad understanding of code-switching that comprises switching between natural languages and language varieties along with style shifts as well as switching between language and other semiotic systems (ideographic switching). We also document, as a key feature of SMS communication, hybrid forms of language use that blur the boundaries between what we commonly call languages (e.g. homographs, mixed spellings or allogenisms), and we suggest that these possibly indicate that SMS communication has become one site where the tension between localized and globalized social practices is played out. The study presented here is part of an inter-university research project, entitled “SMS communication in Switzerland: Facets of linguistic variation in a multilingual country”, based on a corpus of 26,000 authentic messages collected between 2009 and 2011.
Negation marking in French text messages
Authors: Stark Elisabeth
Published: June 2014

This study investigates the drop of the first clitic element, ne, of French sentential negation. It is based on 4,628 French text messages taken from the newly established corpus sms4science.ch. It shows that regional or stylistic factors do not play a major role in triggering ne deletion or ne retention, and that the only relevant language-internal factor is subject type, more precisely clitic subjects (also in subject doubling structures) and subject drop, which seem to favour or even trigger categorically ne deletion. Our findings are in keeping with those by R. van Compernolle (2008) on European French in online chats, and thereby indicate partially specific regularities in French computer-mediated communication (CMC). The findings question traditional assumptions on ne drop as a variety marker in French, irrespective of the phonic or graphic nature of the data (cf. P. Koch and W. Oesterreicher 2011). In fact, even in graphically deviant data, ne drop seems to follow the observed robust language-internal regularities. Some data seem to indicate that the graphic nature of SMSes plays a role also in ne-drop (cf. similar conclusions by R. van Compernolle 2008 for chats); this has to be checked by examining a larger number of French text messages.
Introductory chapter
Authors: Hyland Ken
Published: June 2014

The expression of personal opinions and assessments is a ubiquitous feature of

human interaction and, despite its apparently impersonal facade, also central

to academic writing. In scholarly genres argument involves presenting a position

on things that matter to a discipline in ways that disciplinary members are

likely to find familiar and persuasive. Beneath its frozen surface, an academic

text is seeking to build an appropriate relationship between the writer and the

reader by anticipating the audience’s likely interests, knowledge, reactions and

processing needs. We can, then, see academic writing as essentially dialogic as

writers seek to engage and persuade their readers. In this introductory chapter

I explore some of the ways that this is achieved. Based on an analysis of 240

published research papers I show how features of stance and engagement, such

as hedges, self-mention, directives and reader pronouns, are not simply dry

textualisations but elements of persuasive craftsmanship which help construct

a disciplinary view of the world while simultaneously negotiating a credible

persona for writers.
Chapter 4. From ‘Readers may be left wondering’ to I’m genuinely puzzled’
Authors: Gea-Valor Maria-Lluïsa
Published: June 2014

The book review (BR) has recently been the focus of insightful research in

academia, but few studies have explored this genre in a non-academic context,

more specifically in fiction. This paper focuses on how reviewers of fiction

books construct their own identity and that of their readers in the text. Drawing

on a corpus of 46 fiction BRs published in The New York Times and Newsweek,

I explore the use and function of interactional metadiscourse, in particular

attribution and engagement markers. Results indicate that reviewers generally

seek to strike a balance between assessing a novel and engaging with the audience.

Though appraisal is usually carried out implicitly, at certain points writers

choose to make their presence explicit and to open a dialogue with readers,

which greatly enhances the persuasiveness of the discourse.
Chapter 5. Dialogic voices of writers and readers in traveller forums through interpersonality
Authors: Suau-Jiménez Francisca
Published: June 2014

This study explores web-based discourse genres and applies a dialogic framework

to the study of interpersonality in traveller forums. This genre belongs to

the domain of travel and tourism, where the interaction of writers-readers leads

towards its ultimate purpose: to persuade others through positive or negative

opinions. The theory of Dialogic Action Games (Weigand 2008, 2009, 2010)

aids to understand its rationale since these dialogic interactions can be seen as

an application of Weigand’s principles (2010), in this case materialized through

interpersonal markers (Vande Kopple 1985; Crismore et al. 1993). A corpus of

traveller forums (180 threads of conversation) from Trip Advisor was compiled

and analyzed. The quantitative and qualitative analyses draw on the notion

of voice (White 2003; Hyland 2008), divided into writer’s stance and reader’s

engagement. This research shows that they are encoded in a number of interpersonal

markers which participate in the genre’s rhetorical characterization.
Chapter 6. A corpus-based study of the discursive creation of a child consumer identity in official tourist information websites vs. opinion forums
Authors: Dolón Rosana
Published: June 2014

Starting from an understanding of forums in terms of dialogic action games,

as put forward by Weigand (see e.g. Weigand 2008, 2009, 2010), I look into the

dialogic behaviour that unfolds in forums as an action game that conforms to a

specific cultural unit. Largely based on previous research (Dolón 2012), where

I studied the socio-semantic discursive construction of a consumer identity

for the child as a social actor in official tourist information websites, this paper

addresses the question of whether tourist opinion forums construct similar

or differentiated identity profiles in comparison with official tourist websites.

Behind this question lies the assumption that both genres often recreate identical

rhetorical patterns where the discursive identity construction of the child as

a consumer may be rarely questioned or contested, and therefore fail to express

real consumer choices and, more specifically, identity traits. The study is corpusdriven,

applying concordancing tools to allow for the scrutiny of a large specialized

corpus, and relies on the methodological framework of Critical Discourse

Analysis.
Chapter 7. Interactions with readers through online specialised genres
Authors: Yus Francisco
Published: June 2014

Success in written academic communication depends on the presence of elements

related to author-reader interactions which supplement propositional

information in the text, help readers reach the intended interpretation and

shape the author’s identity. But is this claim equally valid for online genres?

This new environment demands an adaptation of the role of authors, texts, and

readers concerning (a) a re-structuring of texts to fit the margins of the screen;

(b) a new type of non-linear structure, with no specific reading sequence, which

often blurs authorial intention; (c) a new type of reader that does not read in

a linear way, but often engages in multi-tasking, is used to processing small

chunks of text and often browses without a predictable reading sequence; and

(d) a new context of text processing. This chapter addresses these qualities of

electronic genres and their implications. For that purpose, 4 different academic

texts will be analysed: (1) an academic printed journal uploaded online without

variations, Computers in Human Behavior; (2) an online journal, First Monday;

(3) several entries of a specialised native discourse on the Internet: Second Life

New World Notes; and (4) a popular native online discourse, the technology blog

by The Guardian.
Phraseological Substitutions in Newspaper Headlines
Authors: Jaki Sylvia
Published: June 2014

The major purpose of newspaper headlines is to trigger the reader’s interest. A popular way to achieve this goal is the use of phraseological modifications. Based on previous findings from various linguistic disciplines, this book provides an interdisciplinary approach to shed light on the reception of substitutions like More than Meats the Eye. It develops an empirical methodology for investigating the complex cognitive processes involved, using a large sample of authentic examples for illustration. Along these lines, this volume not only shows what associations readers make when they encounter a lexical substitution and what factors facilitate the recognition of the canonical form. It also addresses the question of how meaning is constructed in terms of Conceptual Integration Theory and establishes an experimentally supported model of interpretation. This multifaceted perspective renders Phraseological Substitutions in Newspaper Headlines: "More than Meats the Eye" relevant to scholars and advanced students from a wide range of linguistic areas, such as phraseology, cognitive linguistics, psycholinguistics, and humour research, but also to interested journalists.
Geminate representation in Arabic
Authors: Davis Stuart , Ragheb Marwa
Published: June 2014

Arabic dialects are characterized by the occurrence of geminate consonants in word-medial and word-final position. This article relates the patterning of Arabic geminates to the on-going controversy in phonological theory concerning the representation of geminate consonants. Two views are contrasted: the prosodic length analysis of geminates whereby a geminate is underlyingly a single consonant phoneme linked to two C-slots, and the moraic weight representation where a geminate is underlyingly a single consonant linked to a mora. We specifically argue that the patterning of geminate consonants in Arabic dialects largely supports the moraic weight representation. Evidence comes from phenomena such as the patterning of word-final geminates, the behavior of geminates with respect to stress, geminates in loanwords, and geminates in first language acquisition. We show that each of these phenomena supports the moraic weight representation of geminates.
The Morpheme /-in(n)-/ in central  Asian Arabic
Authors: Miller Kerith
Published: June 2014

Linguists have observed a morpheme /-in(n)-/ which occurs in certain dialects of Arabic from Nigeria to Uzbekistan. The development of this feature may be one key toward understanding internal language development processes on one hand, and morphological borrowing due to language contact on the other. The aim of this paper is to classify the functions of this morpheme and its homomorphs as they appear in the folktales collected by the linguist G. Tsereteli and the ethnographer I. Vinnikov between the years 1935 and 1940, narrated by Arabs of the Bukhara region of Uzbekistan, and analyze them against the theories of development of the /-in(n)-/ morpheme as it appears more broadly across the Arabic dialects. The analysis is in relation to the claims of Uzbek Turkic influence and Tajik Persian influence in a search for consistency.
On the distribution and licensing of polarity-sensitive items in Egyptian Arabic:
Authors: Soltan Usama
Published: June 2014

The goal of this paper is twofold: First, to provide a descriptive account of the grammatical distribution and behavior of the two Egyptian Arabic (ea) polarity-sensitive items (psis) ʔayy (= ‘any’) and walaa (a negative element used in negative concord structures); second, to discuss the implications that these ea facts have for two approaches to the licensing of psis in natural language: The monotonicity-based approach, first proposed in Ladusaw (1979), and the veridicality-based approach, first articulated in Giannakidou (1997, 1998). I conclude that the empirical facts related to the grammatical distribution and contrastive behavior of ʔayy and walaa in ea are more in line with (non)veridicality as the licensing grammatical property regulating the occurrence of psis.
Does innovation need reanalysis?
Authors: De Smet Hendrik
Published: June 2014

Syntactic reanalysis has been claimed to be the only mechanism capable of explaining syntactic change. However, the concept of syntactic reanalysis is flawed. It insufficiently accommodates gradience in synchronic grammar and in language change, and depends too heavily on ambiguity as a cause of change. Alternative mechanisms exist to account for innovation that do not suffer from these problems. At the same time, the problem of explaining syntactic innovations is partly tied to models of language that overstate the role of syntax. Part of the problem therefore disappears under different theoretical starting assumptions.
Constructional change, paradigmatic structure and the orientation of usage processes
Authors: Heltoft Lars
Published: June 2014

This article presents a model analysis of the interplay between structure and usage in the semantic change of constructions, with a focus on the role of content structure in the sense of paradigmatically organised semantic structure. The case at hand is the development of the Danish indirect object construction from the 18th century to the present, a specialisation process parallel to the one described for English by Colleman & De Clerck (2011), though not identical to it. The semantics of constructions is described in terms of linguistic content, as distinct from conceptual structure, and the linguistic content of constructions is organised to a great extent in paradigmatic oppositions, similar to those found in classical morphology (Nørgård-Sørensen, Heltoft & Schøsler 2011). This organisation principle implies that the semantic description must uncover the boundaries of the construction’s content, a strategy different from a description in terms of prototypicality, but compatible with it.The identification of changes in the paradigmatic organisation of constructions is a precondition for identifying and interpreting the changes we observe in usage. In a concluding example, the reanalyses of the verbs bebrejde ‘reproach’ and gifte sig ‘marry’ are compared, and two kinds of usage processes (actualisation processes) are identified: (1) actualisation processes that are a consequence of structural change in the sense of reanalysis, and (2) processes of redistribution which, in the present case, move verb stems from one already existing construction type to another. Thus, structural descriptions allow us to orient and interpret usage processes.
Ethics of War and Peace in theShahnamehof Ferdowsi
Authors: Mahallati Mohammad Jafar Amir
Published: June 2014

This article provides an overview of the ethics of war and peace in the most important and normatively influential work of epic literature known in the eastern lands of Islam, namely theShahnamehof Ferdowsi (d. 1020 CE). As one of the greatest sources of the Iranian cultural identity for over a millennium, Shahnameh (lit. The book of kings) defines normative ideals in the ethics of war and peace within narratives that connect the ancient history of Iran to its mythical eras and in effect to both the medieval time of the epic's authorship and modern Iranian identity. By identifying limits, standards and legitimacy for war and peace in Shahnameh, this article aims to facilitate an Iranian contribution to the global literature and practice on peacemaking that has deep roots in the Islamo-Persian tradition.
Piecewise versus Total Support: How to Deal with Background Information in Likelihood Arguments
Authors: Jantzen Benjamin C.
Published: June 2014

The use of the Law of Likelihood (LL) as a general tool for assessing rival hypotheses has been criticized for its ambiguous treatment of background information. The LL endorses radically different answers depending on what information is designated as background versus evidence. I argue that once one distinguishes between two questions about evidentiary support, the ambiguity vanishes. I demonstrate this resolution by applying it to a debate over the status of the ‘fine-tuning argument’.
Unity for Kant’s Natural Philosophy
Authors: Stan Marius
Published: June 2014

I uncover here a conflict in Kant’s natural philosophy. His matter theory and laws of mechanics are in tension. Kant’s laws are fit for particles but are too narrow to handle continuous bodies, which his doctrine of matter demands. To fix this defect, Kant ultimately must ground the Torque Law; that is, the impressed torque equals the change in angular momentum. But that grounding requires a premise—the symmetry of the stress tensor—that Kant denies himself. I argue that his problem would not arise if he had kept his early theory of matter as made of mass points, or “physical monads.”
Grades of Inductive Skepticism
Authors: Skyrms Brian
Published: June 2014

There is not a unique inductive skeptical position; there are grades of inductive skepticism. There is nothing much to say about complete skepticism, but some more restricted skeptical positions may be profitably analyzed.
Causal Theories of Explanation and the Challenge of Explanatory Disagreement
Authors: Jansson Lina
Published: June 2014

When evaluating the success of causal theories of explanation the focus has typically been on the legitimacy of causal relations and on putative examples of explanations that we cannot capture in causal terms. Here I motivate the existence of a third kind of problem: the difficulty of accounting for explanatory disputes. Moreover, I argue that this problem remains even if the first two are settled and that it threatens to undercut one of the central motivations for causal accounts of explanation, namely, the causal account of the directionality of scientific explanation.
Effectiveness of Screening Hospital Admissions to Detect Asymptomatic Carriers of Clostridium difficile: A Modeling Evaluation
Authors: Lanzas Cristina , Dubberke Erik R.
Published: June 2014

Objective

Both asymptomatic and symptomatic Clostridium difficile carriers contribute to new colonizations and infections within a hospital, but current control strategies focus only on preventing transmission from symptomatic carriers. Our objective was to evaluate the potential effectiveness of methods targeting asymptomatic carriers to control C. difficile colonization and infection (CDI) rates in a hospital ward: screening patients at admission to detect asymptomatic C. difficile carriers and placing positive patients into contact precautions.

Methods

We developed an agent-based transmission model for C. difficile that incorporates screening and contact precautions for asymptomatic carriers in a hospital ward. We simulated scenarios that vary according to screening test characteristics, colonization prevalence, and type of strain present at admission.

Results

In our baseline scenario, on average, 42% of CDI cases were community-onset cases. Within the hospital-onset (HO) cases, approximately half were patients admitted as asymptomatic carriers who became symptomatic in the ward. On average, testing for asymptomatic carriers reduced the number of new colonizations and HO-CDI cases by 40%–50% and 10%–25%, respectively, compared with the baseline scenario. Test sensitivity, turnaround time, colonization prevalence at admission, and strain type had significant effects on testing efficacy.

Conclusions

Testing for asymptomatic carriers at admission may reduce both the number of new colonizations and HO-CDI cases. Additional reductions could be achieved by preventing disease in patients who are admitted as asymptomatic carriers and developed CDI during the hospital stay.
The curse of dimensionality for numerical integration of smooth functions
Authors: Hinrichs A. , Novak E. , Ullrich M. , Woźniakowski H.
Published: June 2014

We prove the curse of dimensionality for multivariate integration of

C
r

C^r

functions: The number of needed function values to achieve an error

ϵ
\epsilon

is larger than

c
r

(
1
+
γ

)
d

c_r (1+\gamma )^d

for

ϵ
≤

ϵ
0

\epsilon \le \epsilon _0

, where

c
r

,
γ
>
0

c_r,\gamma >0

. The proofs are based on volume estimates for

r
=
1

r=1

together with smoothing by convolution. This allows us to obtain smooth fooling functions for

r
>
1

r>1

.
Correcting for link loss in causal network inference caused by regulator interference
Authors: Wang Ying , Penfold Christopher A. , Hodgson David A. , Gifford Miriam L. , Burroughs Nigel J.
Published: June 2014

Motivation: There are a number of algorithms to infer causal regulatory networks from time series (gene expression) data. Here we analyse the phenomena of regulator interference, where regulators with similar dynamics mutually suppress both the probability of regulating a target and the associated link strength; for instance, interference between two identical strong regulators reduces link probabilities by ∼50%.

Results: We construct a robust method to define an interference-corrected causal network based on an analysis of the conditional link probabilities that recovers links lost through interference. On a large real network ( Streptomyces coelicolor , phosphate depletion), we demonstrate that significant interference can occur between regulators with a correlation as low as 0.865, losing an estimated 34% of links by interference. However, levels of interference cannot be predicted from the correlation between regulators alone and are data specific. Validating against known networks, we show that high numbers of functional links are lost by regulator interference. Performance against other methods on DREAM4 data is excellent.

Availability and implementation : The method is implemented in R and is publicly available as the NIACS package at http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software .

Contact:  N.J.Burroughs@warwick.ac.uk

Supplementary information:  Supplementary materials are available at Bioinformatics online.
Benthos distribution modelling and its relevance for marine ecosystem management
Authors: Reiss Henning , Birchenough Silvana , Borja Angel , Buhl-Mortensen Lene , Craeymeersch Johan , Dannheim Jennifer , Darr Alexander , Galparsoro Ibon , Gogina Mayya , Neumann Hermann , Populus Jacques , Rengstorf Anna M. , Valle Mireia , van Hoey Gert , Zettler Michael L. , Degraer Steven
Published: June 2014

Marine benthic ecosystems are difficult to monitor and assess, which is in contrast to modern ecosystem-based management requiring detailed information at all important ecological and anthropogenic impact levels. Ecosystem management needs to ensure a sustainable exploitation of marine resources as well as the protection of sensitive habitats, taking account of potential multiple-use conﬂicts and impacts over large spatial scales. The urgent need for large-scale spatial data on benthic species and communities resulted in an increasing application of distribution modelling (DM). The use of DM techniques enables to employ full spatial coverage data of environmental variables to predict benthic spatial distribution patterns. Especially, statistical DMs have opened new possibilities for ecosystem management applications, since they are straightforward and the outputs are easy to interpret and communicate. Mechanistic modelling techniques, targeting the fundamental niche of species, and Bayesian belief networks are the most promising to further improve DM performance in the marine realm. There are many actual and potential management applications of DMs in the marine benthic environment, these are (i) early warning systems for species invasion and pest control, (ii) to assess distribution probabilities of species to be protected, (iii) uses in monitoring design and spatial management frameworks (e.g. MPA designations), and (iv) establishing long-term ecosystem management measures (accounting for future climate-driven changes in the ecosystem). It is important to acknowledge also the limitations associated with DM applications in a marine management context as well as considering new areas for future DM developments. The knowledge of explanatory variables, for example, setting the basis for DM, will continue to be further developed: this includes both the abiotic (natural and anthropogenic) and the more pressing biotic (e.g. species interactions) aspects of the ecosystem. While the response variables on the other hand are often focused on species presence and some work undertaken on species abundances, it is equally important to consider, e.g. biological traits or benthic ecosystem functions in DM applications. Tools such as DMs are suitable to forecast the possible effects of climate change on benthic species distribution patterns and hence could help to steer present-day ecosystem management.
Visible-wavelength spectroscopy of subkilometer-sized near-Earth asteroids with a low delta-v
Authors: Kuroda Daisuke , Ishiguro Masateru , Takato Naruhisa , Hasegawa Sunao , Abe Masanao , Tsuda Yuichi , Sugita Seiji , Usui Fumihiko , Hattori Takashi , Iwata Ikuru , Imanishi Masatoshi , Terada Hiroshi , Choi Young-Jun , Watanabe Sei-ichiro , Yoshikawa Makoto
Published: June 2014

This paper provides a unique data set representing the taxonomic type of near-Earth asteroids (NEAs) accessible by available spacecraft. The research on NEAs has entered upon a new phase, thanks to sample-return space explorations together with state-of-the-art large ground-based telescopes. We made observations of 13 asteroids with the Subaru, GEMINI-North, GEMINI-South, and Okayama 188 cm telescopes. Twelve of them have low delta-v orbits with the potential to be investigated by manned/unmanned spacecraft. Also, ten subkilometer-sized bodies are included among them, and are one of remarkable characteristics in terms of their evolutionary scenario. We have found that eleven asteroids are classified as S-complex, and one asteroid as the V-type. Most S-complex asteroids (eight out of eleven, ∼ 70%) have spectra similar to subgroups of Q- or Sq-type, suggesting that these objects are less matured by space weathering. We discuss the dominance of S-complex asteroids based on previous research.
Critical transitions in a game theoretic model of tumour metabolism
Authors: Kianercy Ardeshir , Veltri Robert , Pienta Kenneth J.
Published: June 2014

Tumour proliferation is promoted by an intratumoral metabolic symbiosis in which lactate from stromal cells fuels energy generation in the oxygenated domain of the tumour. Furthermore, empirical data show that tumour cells adopt an intermediate metabolic state between lactate respiration and glycolysis. This study models the metabolic symbiosis in the tumour through the formalism of evolutionary game theory. Our game model of metabolic symbiosis in cancer considers two types of tumour cells, hypoxic and oxygenated, while glucose and lactate are considered as the two main sources of energy within the tumour. The model confirms the presence of multiple intermediate stable states and hybrid energy strategies in the tumour. It predicts that nonlinear interaction between two subpopulations leads to tumour metabolic critical transitions and that tumours can obtain different intermediate states between glycolysis and respiration which can be regulated by the genomic mutation rate. The model can apply in the epithelial–stromal metabolic decoupling therapy.
The ecology of cancer from an evolutionary game theory perspective
Authors: Pacheco Jorge M. , Santos Francisco C. , Dingli David
Published: June 2014

The accumulation of somatic mutations, to which the cellular genome is permanently exposed, often leads to cancer. Analysis of any tumour shows that, besides the malignant cells, one finds other ‘supporting’ cells such as fibroblasts, immune cells of various types and even blood vessels. Together, these cells generate the microenvironment that enables the malignant cell population to grow and ultimately lead to disease. Therefore, understanding the dynamics of tumour growth and response to therapy is incomplete unless the interactions between the malignant cells and normal cells are investigated in the environment in which they take place. The complex interactions between cells in such an ecosystem result from the exchange of information in the form of cytokines- and adhesion-dependent interactions. Such processes impose costs and benefits to the participating cells that may be conveniently recast in the form of a game pay-off matrix. As a result, tumour progression and dynamics can be described in terms of evolutionary game theory (EGT), which provides a convenient framework in which to capture the frequency-dependent nature of ecosystem dynamics. Here, we provide a tutorial review of the central aspects of EGT, establishing a relation with the problem of cancer. Along the way, we also digress on fitness and of ways to compute it. Subsequently, we show how EGT can be applied to the study of the various manifestations and dynamics of multiple myeloma bone disease and its preceding condition known as monoclonal gammopathy of undetermined significance. We translate the complex biochemical signals into costs and benefits of different cell types, thus defining a game pay-off matrix. Then we use the well-known properties of the EGT equations to reduce the number of core parameters that characterize disease evolution. Finally, we provide an interpretation of these core parameters in terms of what their function is in the ecosystem we are describing and generate predictions on the type and timing of interventions that can alter the natural history of these two conditions.
Bacteria and game theory: the rise and fall of cooperation in spatially heterogeneous environments
Authors: Lambert Guillaume , Vyawahare Saurabh , Austin Robert H.
Published: June 2014

One of the predictions of game theory is that cooperative behaviours are vulnerable to exploitation by selfish individuals, but this result seemingly contradicts the survival of cooperation observed in nature. In this review, we will introduce game theoretical concepts that lead to this conclusion and show how the spatial competition dynamics between microorganisms can be used to model the survival and maintenance of cooperation. In particular, we focus on howEscherichia colibacteria with a growth advantage in stationary phase (GASP) phenotype maintain a proliferative phenotype when faced with overcrowding to gain a fitness advantage over wild-type populations. We review recent experimental approaches studying the growth dynamics of competing GASP and wild-type strains ofE. coliinside interconnected microfabricated habitats and use a game theoretical approach to analyse the observed inter-species interactions. We describe how the use of evolutionary game theory and the ideal free distribution accurately models the spatial distribution of cooperative and selfish individuals in spatially heterogeneous environments. Using bacteria as a model system of cooperative and selfish behaviours may lead to a better understanding of the competition dynamics of other organisms—including tumour–host interactions during cancer development and metastasis.
Evolutionary game theory for physical and biological scientists. II. Population dynamics equations can be associated with interpretations
Authors: Liao David , Tlsty Thea D.
Published: June 2014

The use of mathematical equations to analyse population dynamics measurements is being increasingly applied to elucidate complex dynamic processes in biological systems, including cancer. Purely ‘empirical’ equations may provide sufficient accuracy to support predictions and therapy design. Nevertheless, interpretation of fitting equations in terms of physical and biological propositions can provide additional insights that can be used both to refine models that prove inconsistent with data and to understand the scope of applicability of models that validate. The purpose of this tutorial is to assist readers in mathematically associating interpretations with equations and to provide guidance in choosing interpretations and experimental systems to investigate based on currently available biological knowledge, techniques in mathematical and computational analysis and methods forin vitroandin vivoexperiments.
Production of a neutralizing antibody against envelope protein of dengue virus type 2 using the linear array epitope technique
Authors: Lai Peng-Yeh , Hsu Chia-Tse , Wang Shao-Hung , Lee Jin-Ching , Tseng Min-Jen , Hwang Jaulang , Ji Wen-Tsai , Chen Hau-Ren
Published: June 2014

Dengue virus (DENV; genus Flavivirus) contains a positive-stranded RNA genome. Binding of DENV to host cells is mediated through domain III of the viral envelope protein. Many therapeutic mAbs against domain III have been generated and characterized because of its high antigenicity. We have previously established a novel PCR method named the linear array epitope (LAE) technique for producing monoclone-like polyclonal antibodies. To prove this method could be utilized to produce antibody against epitopes with low antigenicity, a region of 10 aa (V365NIEAEPPFG374) from domain III of the envelope protein in DENV serotype 2 (DENV2) was selected to design the primers for the LAE technique. A DNA fragment encoding 10 directed repeats of these 10 aa for producing the tandem-repeated peptides was obtained and fused with glutathione S-transferase (GST)-containing vector. This fusion protein (GST-Den EIII10-His6) was purified from Escherichia coli and used as antigen for immunizing rabbits to obtain the polyclonal antibody. Furthermore, the EIII antibody could recognize envelope proteins either ectopically overexpressed or synthesized by DENV2 infection using Western blot and immunofluorescence assays. Most importantly, this antibody was also able to detect DENV2 virions by ELISA, and could block viral entry into BHK-21 cells as shown by immunofluorescence and quantitative real-time PCR assays. Taken together, the LAE technique could be applied successfully for the production of antibodies against antigens with low antigenicity, and shows high potential to produce antibodies with good quality for academic research, diagnosis and even therapeutic applications in the future.
The natverse: a versatile computational toolbox to combine and analyse neuroanatomical data
Authors: Bates Alexander S. , Manton James D. , Jagannathan Sridhar R. , Costa Marta , Schlegel Philipp , Rohlfing Torsten , Jefferis Gregory S. X. E.
Published: June 2014

To analyse neuron data at scale, neuroscientists expend substantial effort reading documentation, installing dependencies and moving between analysis and visualisation environments. To facilitate this, we have developed a suite of interoperable open-source R packages called the natverse. The natverse allows users to read local and remote data, perform popular analyses including visualisation, clustering and graph-theoretic analysis of neuronal branching. Unlike most tools, the natverse enables comparison of morphology and connectivity across many neurons after imaging or co-registration within a common template space. The natverse also enables transformations between different template spaces and imaging modalities. We demonstrate tools that integrate the vast majority of Drosophila neuroanatomical light microscopy and electron microscopy connectomic datasets. The natverse is an easy-to-use environment for neuroscientists to solve complex, large-scale analysis challenges as well as an open platform to create new code and packages to share with the community.
Beyond library size: a field guide to NGS normalization
Authors: Aleksic Jelena , Carl Sarah , Frye Michaela
Published: June 2014

Background:

Next generation sequencing (NGS) is a widely used technology in both basic research and clinical settings and it will continue to have a major impact on biomedical sciences. However, the use of incorrect normalization methods can lead to systematic biases and spurious results, making the selection of an appropriate normalization strategy a crucial and often overlooked part of NGS analysis.

Results:

We present a basic introduction to the currently available normalization methods for differential expression and ChIP-seq applications, along with best use recommendations for different experimental techniques and datasets.

We demonstrate that the choice of normalization technique can have a significant impact on the number of genes called as differentially expressed in an RNA-seq experiment or peaks called in a ChIP-seq experiment.

Conclusions:

The choice of the most adequate normalization method depends on both the distribution of signal in the dataset and the intended downstream applications. Depending on the design and purpose of the study, appropriate bias correction should also be considered.
The Cellulase KORRIGAN Is Part of the Cellulose Synthase Complex
Authors: Vain Thomas , Crowell Elizabeth Faris , Timpano Hélène , Biot Eric , Desprez Thierry , Mansoori Nasim , Trindade Luisa M. , Pagant Silvère , Robert Stéphanie , Höfte Herman , Gonneau Martine , Vernhettes Samantha
Published: June 2014

Plant growth and organ formation depend on the oriented deposition of load-bearing cellulose microfibrils in the cell wall. Cellulose is synthesized by a large relative molecular weight cellulose synthase complex (CSC), which comprises at least three distinct cellulose synthases. Cellulose synthesis in plants or bacteria also requires the activity of an endo-1,4-β-d-glucanase, the exact function of which in the synthesis process is not known. Here, we show, to our knowledge for the first time, that a leaky mutation in the Arabidopsis (Arabidopsis thaliana) membrane-bound endo-1,4-β-d-glucanase KORRIGAN1 (KOR1) not only caused reduced CSC movement in the plasma membrane but also a reduced cellulose synthesis inhibitor-induced accumulation of CSCs in intracellular compartments. This suggests a role for KOR1 both in the synthesis of cellulose microfibrils and in the intracellular trafficking of CSCs. Next, we used a multidisciplinary approach, including live cell imaging, gel filtration chromatography analysis, split ubiquitin assays in yeast (Saccharomyces cerevisiae NMY51), and bimolecular fluorescence complementation, to show that, in contrast to previous observations, KOR1 is an integral part of the primary cell wall CSC in the plasma membrane.
MYB5 and MYB14 Play Pivotal Roles in Seed Coat Polymer Biosynthesis in Medicago truncatula
Authors: Liu Chenggang , Jun Ji Hyung , Dixon Richard A.
Published: June 2014

In Arabidopsis (Arabidopsis thaliana), the major MYB protein regulating proanthocyanidin (PA) biosynthesis is TT2, named for the transparent testa phenotype of tt2 mutant seeds that lack PAs in their coats. In contrast, the MYB5 transcription factor mainly regulates seed mucilage biosynthesis and trichome branching, with only a minor role in PA biosynthesis. We here characterize MYB5 and MYB14 (a TT2 homolog) in the model legume Medicago truncatula. Overexpression of MtMYB5 or MtMYB14 strongly induces PA accumulation in M. truncatula hairy roots, and both myb5 and myb14 mutants of M. truncatula exhibit darker seed coat color than wild-type plants, with myb5 also showing deficiency in mucilage biosynthesis. myb5 mutant seeds have a much stronger seed color phenotype than myb14. The myb5 and myb14 mutants accumulate, respectively, about 30% and 50% of the PA content of wild-type plants, and PA levels are reduced further in myb5 myb14 double mutants. Transcriptome analyses of overexpressing hairy roots and knockout mutants of MtMYB5 and MtMYB14 indicate that MtMYB5 regulates a broader set of genes than MtMYB14. Moreover, we demonstrate that MtMYB5 and MtMYB14 physically interact and synergistically activate the promoters of anthocyanidin reductase and leucoanthocyanidin reductase, the key structural genes leading to PA biosynthesis, in the presence of MtTT8 and MtWD40-1. Our results provide new insights into the complex regulation of PA and mucilage biosynthesis in M. truncatula.
6-Bromo-N-(6-bromopyridin-2-yl)-N-[4-(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)phenyl]pyridin-2-amine
Authors: Mitchell Lauren A. , Holliday Bradley J.
Published: June 2014

In the title molecule, C22H15Br2N3O2S, the central benzene ring forms dihedral angles of 12.39 (17), 56.66 (17) and 74.71 (19)°, respectively, with the mean planes of the thiophene and two pyridine rings. The dioxane ring is in a half-chair conformation. An intramolecular C—H...O hydrogen forms anS(6) ring. The amine N atom issp2-hybridized.
2-{4-[Bis(4-bromophenyl)amino]benzylidene}malononitrile
Authors: Zhang Yu-Jian , Ni Sheng-Liang
Published: June 2014

In the crystal structure of the title compound, C22H13Br2N3, the two bromophenyl rings are rotated out of the plane of the central benzylidene ring by 68.7 (1) and 69.3 (1)°. Both cyano substituents are located nearly in the plane of the benzylidene ring, with the mean plane of the methylmalononitrile group being inclined to this ring by 5.8 (1)°. In the crystal, the molecules are linked by weak C—H...N hydrogen bonds into layers parallel to thebcplane.
Poly[[(μ4-benzene-1,3,5-tricarboxylato-κ4O1:O1′:O2:O3)bis(2,2-bipyridine-κ2N,N′)(μ2-hydroxido)dicopper(II)] trihydrate]
Authors: El-kaheli Mohamed N. , El-mehdawi Ramadan M. , Abuhmaiera Ramadan G. , Ben Younes Mufida M. , Treish Fathia A. , Guerri Annalisa , Bazzicalupi Carla
Published: June 2014

In the title two-dimensional coordination polymer, {[Cu2(C9H3O6)(OH)(C10H8N2)2]·3H2O}n, each of the two independent CuIIatoms is coordinated by a bridging OH group, two O atoms from two benzene-1,3,5-tricarboxylate (L) ligands and two N atoms from a 2,2- bipyridine (bipy) ligand in a distorted square-pyramidal geometry. EachLligand coordinates four CuIIatoms, thus forming a polymeric layer parallel to thebcplane with bipy molecules protruding up and down. The lattice water molecules involved in O—H...· O hydrogen bonding are situated in the inner part of each layer. The crystal packing is consolidated by π–π interactions between the aromatic rings of bipy ligands from neigbouring layers [intercentroid distance = 3.762 (3) Å].
4-Chloro-3-ethylphenol
Authors: Majer Sean H. , Tanski Joseph M.
Published: June 2014

The title compound, C8H9ClO, packs with two independent molecules in the asymmetric unit, without significant differences in corresponding bond lengths and angles, with the ethyl group in each oriented nearly perpendicular to the aromatic ring having ring-to-side chain torsion angles of 81.14 (18) and −81.06 (19)°. In the crystal, molecules form an O—H...O hydrogen-bonded chain extending along theb-axis direction, through the phenol groups in which the H atoms are disordered. These chains pack together in the solid state, giving a sheet lying parallel to (001),viaan offset face-to-face π-stacking interaction characterized by a centroid–centroid distance of 3.580 (1) Å, together with a short intermolecular Cl...Cl contact [3.412 (1) Å].
catena-Poly[[trans-bis(1,3-benzothiazole-κN)manganese(II)]-di-μ-chlorido]
Authors: Bouchareb Hasna , Benmebarek Sabrina , Bouacida Sofiane , Merazig Hocine , Boudraa Mhamed
Published: June 2014

In the title coordination polymer, [MnCl2(C7H5NS)2]n, the MnIIion is located on the intersection of a twofold rotation axis and a mirror plane and adopts an octahedral coordination geometry defined by two mutuallytransN atoms from benzothiazole ligands which occupy the axial positions, and four Cl atoms which form the equatorial sites. The MnIIions are connected by two bridging Cl atoms, forming chains parallel to thecaxis. The crystal packing can be descibed as alternating layers parallel to (001) featuring π–π stacking interactions with a centroid–centroid distance of 3.6029 (15) Å.
6-Chloro-7-methyl-4-oxo-4H-chromene-3-carbaldehyde
Authors: Ishikawa Yoshinobu
Published: June 2014

In the title compound, C11H7ClO3, a chlorinated and methylated 3-formylchromone derivative, the non-H atoms are essentially coplanar (r.m.s. deviation = 0.0670 Å), with the largest deviation from the least-squares plane [0.2349 (17) Å] being for the pyran carbonyl O atom. In the crystal, molecules are linked through π–π stacking interactions along theaaxis [centroid–centroid distance between the pyran rings = 3.824 (6) Å] and two stacks are connected by type I halogen–halogen interactions between the Cl atoms [Cl...Cl = 3.397 (3) Å].
Effect of ethical ideologies on ethical judgment of future accountants: Malaysian evidence
Authors: Ismail Suhaiza
Published: June 2014

Purpose

– The purpose of this paper is to investigate the effect of ethical ideologies on ethical judgments of future Malaysian accountants in general situations and based on the legality of the situations. The examination covers the relationships of both the specific ethical dimension (i.e. idealism and relativism) and the specific categories of ideology (i.e. absolutist and subjectivist) on ethical judgments.

Design/methodology/approach

– Using a questionnaire survey that comprises Ethical Position Questionnaire and ethical dilemma vignettes, 396 usable responses were received. In achieving the objectives, multivariate analysis of variance, correlations and univariate analysis of variance were performed.

Findings

– The study discovered a significant impact of ethical ideology on judgments regardless of the legality of the cases. In addition, the study found a significant positive and negative impact of idealism and relativism, respectively, on ethical judgment. Moreover, the study reported that absolutists are stricter whilst situationists are more lenient in making ethical judgments compared to other ideologies.

Originality/value

– The present study investigated the effect of ethical ideologies on ethical judgment, in general, as well as the effect on ethical judgment based on the legality of the ethical dilemma. This study also considered the effect of the two dimensions of ethical ideology – idealism and relativism – on ethical judgment and captured the four categories of ideology based on the taxonomy of ethical ideologies.