bluuebunny/crossref_metadata_2025 huggingface dataset:
Sloshing-induced slamming in screen-equipped rectangular tanks in shallow-water conditions
Authors: Wei Zhi-Jun , Faltinsen Odd Magnus , Lugni Claudio , Yue Qian-Jin
Published: March 2015

Sloshing-induced slamming in a rectangular tank with centralized slat-screens with high solidity ratios was experimentally studied under nearly two-dimensional shallow-water conditions with large-amplitude harmonic lateral excitation. The main objective was to identify the solidity ratio that provides an optimal suppressing function on the free-surface elevation and slamming pressure on the vertical tank walls with a frequency domain containing the three lowest natural sloshing frequencies in a clean tank with a water depth-to-tank length ratio of h/l = 0.125 and a high forced sway amplitude. The experiments show that the optimal solidity ratio among four considered slat-screens is approximately 0.6-0.7 for the applied filling level and excitation amplitude in the examined forced frequency range. The results have potential applications in areas such as swash bulkhead design and liquefied-cargo tank design in ship and offshore engineering.
Magnetic modification at sub-surface of FeRh bulk by energetic ion beam irradiation
Authors: Koide T. , Uno H. , Sakane H. , Sakamaki M. , Amemiya K. , Iwase A. , Matsui T.
Published: March 2015

Ferromagnetic layered structure has been made at sub-surface of the antiferromagnetic FeRh bulk samples by high energy He ion beam irradiation. In accordance with the Transport of Ions in Matter simulation, such ion beam can effectively deposit the elastic collision energy in several μm regions in the depth from the surface. Measurement with a superconducting quantum interference device reveals the irradiated samples to be ferromagnetic. Assuming that only the part the energy deposited can be modified to be ferromagnetic, the corresponding irradiation induced magnetization is consistent with the data that we previously reported. On the other hand, the X-ray magnetic circular dichroism (XMCD) spectra for the irradiated samples are totally unchanged as those for the unirradiated samples. Since XMCD signal in total emission yield method is considered to be surface sensitive with a typical probing depth of several nm, the surface magnetic state is maintained to be antiferromagnetic. By utilizing these phenomena, three-dimensional magnetic patterning of FeRh can be realized, which may potentially be used for future magnetic exchange device application such as nano-scale sensors and memories.
High-resolution electron microscopy in spin pumping NiFe/Pt interfaces
Authors: Ley Domínguez D. , Sáenz-Hernández R. J. , Faudoa Arzate A. , Arteaga Duran A. I. , Ornelas Gutiérrez C. E. , Solís Canto O. , Botello-Zubiate M. E. , Rivera-Gómez F. J. , Azevedo A. , da Silva G. L. , Rezende S. M. , Matutes-Aquino J. A.
Published: March 2015

In order to understand the effect of the interface on the spin pumping and magnetic proximity effects, high resolution transmission electron microscopy and ferromagnetic resonance (FMR) were used to analyze Py/Pt bilayer and Pt/Py/Pt trilayer systems. The samples were deposited by dc magnetron sputtering at room temperature on Si (001) substrates. The Py layer thickness was fixed at 12 nm in all the samples and the Pt thickness was varied in a range of 0–23 nm. A diffusion zone of approximately 8 nm was found in the Py/Pt interfaces and confirmed by energy dispersive X-ray microanalysis. The FMR measurements show an increase in the linewidth and a shift in the ferromagnetic resonance field, which reach saturation.
Dispersion of flagellated swimming microorganisms in planar Poiseuille flow
Authors: Chilukuri Sandeep , Collins Cynthia H. , Underhill Patrick T.
Published: March 2015

The presence of an external fluid flow significantly impacts the properties of swimming microorganisms between two surfaces. By performing computer simulations of dilute populations of flagellated swimming microorganisms, we calculate the dispersivity of the microorganisms at different flow rates by tracking each individual organism in the direction of the flow. Our results show how the dispersion of swimming microorganisms is different from passive particles. For low flow rates, the dispersivity is higher than that of non-motile organisms because of their swimming motion. As the flow rate increases, the dispersivity drops, reaching a minimum before increasing at high flow rates. The minimum occurs approximately when the swimming speed of the organism equals the mean velocity of the external flow. A scaling analysis is used to qualitatively capture the dispersion at both low and high flow rates. Closed-form expressions for the dispersivity were derived at low and high flow rates using an analytical theory. This analysis showed that at low flow rates, the alignment of the organisms by the flow is responsible for the reduction of the dispersion in comparison to the dispersion without any external flow. At high flow rates, the distribution and dynamics across the channel produce a dispersivity that is lower than that of passive particles.
Modeling of fluctuation processes on the biochemically sensorial surface of silicon nanowire field-effect transistors
Authors: Georgakopoulou K. , Birbas A. , Spathis C.
Published: March 2015

Affinity-type silicon-based nanowire biosensors rely on the biochemical interaction between target molecules and their molecular complements (recognition probes), located on the SiO2 insulator layer. This biochemical reaction is associated with twofold fluctuations through the mechanisms of binding/unbinding and regular charge thermal equilibrium processes. These fluctuations have a direct implication on the surface potential fluctuations which in turn affect, through the field effect transduction process, the electrical characteristics of the sensor device. The resulting noise could potentially contain detectable information, which can be extracted through the time constants (characteristic frequencies) related to the kinetics of the molecules under detection and their charge fluctuations. In this work, we present a comprehensive model for the fluctuations on the surface of the biosensor and attribute them to the two physical mechanisms. The spectral densities corresponding to these types of fluctuations add on the overall device noise spectrum and are directly detectable if they lie above the inherent noise level of the sensor device.
Considerations on double porosity structure for micropolar bodies
Authors: Marin M. , Vlase S. , Paun M.
Published: March 2015

In this study we want to extend the results of B. Straughan, which quite recently addressed the issue of double porosity structure for classical elastic bodies. In this case, the double porosity structure of the body is not influenced by the displacement field, which is not consistent with reality. For the mixed initial boundary value problem in the context of micropolar bodies with double porosity, we prove the existence of the solution, its uniqueness as well as some considerations on stability of solution.
Living Absence: The Strange Geographies of Missing People
Authors: Parr Hester , Stevenson Olivia , Fyfe Nick , Woolnough Penny
Published: March 2015

In this paper ‘missing people’ gain an unstable presence through their (restaged) testimonies recounting individual occupations of material urban public space during the lived practice of absence. We explore ‘missing experience’ with reference to homeless geographies, and as constituted by paradoxical spatialities in which people are both absent and present. We seek to understand such urban geographies of absence through diverse voices of missing people, who discuss their embodiment of unusual rhythmic occupations of the city. We conclude by considering how a new politics of missing people might take account of such voices in ways to think further about rights-to-be-absent in the city.
Wet Ontologies, Fluid Spaces: Giving Depth to Volume through Oceanic Thinking
Authors: Steinberg Philip , Peters Kimberley
Published: March 2015

This paper expands on recent attempts to destabilise the static, bordered, and linear framings that typify human geographical studies of place, territory, and time. In a world conceptualised as open, immanent, and ever-becoming, scholars have turned away from notions of fixity towards fluidity and flow, and, in so doing, have developed networked, ‘flat’ ontologies. Recent attempts have gone further, challenging the horizontalism inherent in such approaches by opening up a vertical world of volume. In this paper we contend that such approaches are still somewhat lacking. The vertical element of volume is all too often abstract and dematerialised; the emphasis on materiality that is typically used to rectify this excess of abstraction tends to reproduce a sense of matter as fixed and grounded; and the temporality that is employed to reintroduce ‘motion’ to matter has the unintended effect of signalling a periodised sense of time that minimises the chaotic underpinnings and experiences of place. We argue that the ocean is an ideal spatial foundation for addressing these challenges since it is indisputably voluminous, stubbornly material, and unmistakably undergoing continual reformation, and that a ‘wet ontology’ can reinvigorate, redirect, and reshape debates that are all too often restricted by terrestrial limits.
Signal Detection Measures Cannot Distinguish Perceptual Biases from Response Biases
Authors: Witt Jessica K , Taylor J Eric T , Sugovic Mila , Wixted John T
Published: March 2015

A common conceptualization of signal detection theory (SDT) holds that if the effect of an experimental manipulation is truly perceptual, then it will necessarily be reflected in a change in d' rather than a change in the measure of response bias. Thus, if an experimental manipulation affects the measure of bias, but not d', then it is safe to conclude that the manipulation in question did not affect perception but instead affected the placement of the internal decision criterion. However, the opposite may be true: an effect on perception may affect measured bias while having no effect on d'. To illustrate this point, we expound how signal detection measures are calculated and show how all biases—including perceptual biases—can exert their effects on the criterion measure rather than on d'. While d' can provide evidence for a perceptual effect, an effect solely on the criterion measure can also arise from a perceptual effect. We further support this conclusion using simulations to demonstrate that the Müller-Lyer illusion, which is a classic visual illusion that creates a powerful perceptual effect on the apparent length of a line, influences the criterion measure without influencing d'. For discrimination experiments, SDT is effective at discriminating between sensitivity and bias but cannot by itself determine the underlying source of the bias, be it perceptual or response based.
Temporal dynamics of allochthonous coarse particulate organic matter in a subtropical Atlantic rainforest Brazilian stream
Authors: Kleba Lisboa Leonardo , Lemes da Silva Aurea Luiza , Siegloch Ana Emilia , Gonçalves Júnior José Francisco , Mello Petrucio Mauricio
Published: March 2015

Allochthonous organic matter is a major energy source for headwater stream ecosystems. Therefore, examinations of how energy flows throughout these streams requires knowledge of mechanisms driving leaf input, retention and export. In this study we quantified the major input pathways and retention dynamics of coarse particulate organic matter (CPOM) in an Atlantic Rainforest stream in southern Brazil. We hypothesised that much of the temporal variability in the CPOM budget would be driven by precipitation, and thus we focus especially on the importance of vertical v. lateral input pathways, precipitation-driven inputs v. stocks, and composition of CPOM throughout 1 year. Most leaf litter entered the stream by the lateral input pathway (70.5gm–2month–1±108s.d.) compared with the vertical (32.4gm–2 month–1 ±17.5s.d.), and lateral input was correlated with precipitation and bank slope. In addition, torrential rainfall caused a net decrease in CPOM by reduction in the benthic stocks. Finally, six species represented 52.9% of total leaf input, where the most important (~25% of total input) was Schizolobium parahyba. Overall, this research confirms our prediction that the CPOM budget of this Atlantic Rainforest stream is driven in large part by precipitation.
Barriers and facilitators of sexually transmissible infection testing in remote Australian Aboriginal communities: results from the Sexually Transmitted Infections in Remote Communities, Improved and Enhanced Primary Health Care (STRIVE) Study
Authors: Hengel Belinda , Guy Rebecca , Garton Linda , Ward James , Rumbold Alice , Taylor-Thomson Debbie , Silver Bronwyn , McGregor Skye , Dyda Amalie , Knox Janet , Kaldor John , Maher Lisa
Published: March 2015

Background Remote Australian Aboriginal communities experience high rates of bacterial sexually transmissible infections (STI). A key strategy to reduce STIs is to increase testing in primary health care centres. The current study aimed to explore barriers to offering and conducting STI testing in this setting. Methods: A qualitative study was undertaken as part of the STI in Remote communities, Improved and Enhanced Primary Health Care (STRIVE) project; a large cluster randomised controlled trial of a sexual health quality improvement program. We conducted 36 in-depth interviews in 22 participating health centres across four regions in northern and central Australia. Results: Participants identified barriers including Aboriginal cultural norms that require the separation of genders and traditional kinship systems that prevent some staff and patients from interacting, both of which were exacerbated by a lack of male staff. Other common barriers were concerns about client confidentiality (lack of private consulting space and living in small communities), staff capacity to offer testing impacted by the competing demands for staff time, and high staff turnover resulting in poor understanding of clinic systems. Many participants also expressed concerns about managing positive test results. To address some of these barriers, participants revealed informal strategies, such as team work, testing outside the clinic and using adult health checks. Conclusions: Results identify cultural, structural and health system issues as barriers to offering STI testing in remote communities, some of which were overcome through the creativity and enthusiasm of individuals rather than formal systems. Many of these barriers can be readily addressed through strengthening existing systems of cultural and clinical orientation and educating staff to view STI in a population health framework. However others, particularly issues in relation to culture, kinship ties and living in small communities, may require testing modalities that do not rely on direct contact with health staff or the clinic environment.
Words matter: radio misunderstandings in wildland firefighting
Authors: Gabor Elena
Published: March 2015

Unclear, ambiguous communication during a wildland fire can have serious consequences for firefighters' safety. This paper grounds its observations in media richness theory and the theory of communicative action. Radio is a less rich medium than video or face-to-face communication because it relies on hearing only and it requires a longer time to convey understanding. The theory of communicative action explains that effective messages should be true (content-wise), appropriate and truthful (expressive). This paper uses data from the investigation reports of the Cramer fire in Idaho, 2003, the Dutch Creek incident in California, 2008, and the Panther fire in California, 2008, to show that ambiguous, shortened and information-poor messages can impact decision-making and the safety of firefighters. Although previous research has pointed to technical and cultural barriers to effective radio communication, this paper draws attention to the actual wording of messages.
Children’s knowledge of bushfire emergency response
Authors: Towers Briony
Published: March 2015

In the aftermath of the Black Saturday bushfire disaster, the Victorian Bushfires Royal Commission recommended that bushfire education be made a formal part of the Australian national curriculum. Crucially, the success of any hazards education program depends on the degree to which the learner’s existing knowledge and experience is accommodated in the education process. Yet accommodating children’s knowledge in bushfire education is hampered by a lack of research on how children conceptualise bushfire hazards. To address this gap, this paper presents a detailed qualitative analysis of children’s knowledge of bushfire hazards with a specific focus on emergency response. Across four bushfire-prone locations in south-eastern Australia, 26 focus group interviews were conducted with 87 children aged between 8 and 12 years. To better understand the construction of children’s knowledge, individual interviews were also conducted with 37 parents. Through their engagement in the research process, children demonstrated a capacity for engaging in serious discussions about bushfire hazards and although their knowledge was often characterised by gaps and misconceptions, they also demonstrated a capacity for understanding the fundamental principles of emergency response, particularly when they had been involved in bushfire planning within their household.
Differences in land ownership, fire management objectives and source data matter: a reply to Hanson and Odion (2014)
Authors: Safford Hugh D. , Miller Jay D. , Collins Brandon M.
Published: March 2015

We respond to Hanson and Odion (2014), who claim in this journal (vol. 23, no. 1, pp. 1–8) that their reanalysis of fire severity patterns in and around the Sierra Nevada refutes earlier work showing increases in fire severity in certain forest types over the last 3 decades. Hanson and Odion base their reanalysis on a highly inaccurate, very coarse-scale, and geographically misregistered vegetation map. Also, in contrast to the previous work, which was restricted to wildfires on Forest Service lands in forest types differentiated by their fire regimes, Hanson and Odion combine all types of fires on lands of all jurisdictions and stratify by very broad, unorthodox vegetation types that conjoin very different fire regimes. As such, their work does not constitute a test of the previous work. We present analyses that demonstrate sources of error associated with Hanson and Odion’s data and the analyses they perform, and explore how that error might confound their results. Fundamental and compounded problems in Hanson and Odion (2014) cast strong doubt on their conclusions.
Solar electricity supply isolines of generation capacity and storage
Authors: Grossmann Wolf , Grossmann Iris , Steininger Karl W.
Published: March 2015

Significance

The recent sharp drop in the cost of photovoltaic (PV) electricity generation accompanied by globally rapidly increasing investment in PV plants calls for new planning and management tools for large-scale distributed solar networks. We found that pairs of electricity generation capacity
G
and storage
S
, such that
S
is minimal to provide a given dispatchable electricity capacity for a given
G
, exhibit a smooth relationship of mutual substitutability between
G
and
S
. These
G
−
S
isolines support the solution of several tasks. This includes optimizing the size of
G
and
S
for dispatchable electricity, optimizing connections between solar parks across time zones for minimizing intermittency, and management of storage in situations of far below average insolation.
Emergence of coherence and the dynamics of quantum phase transitions
Authors: Braun Simon , Friesdorf Mathis , Hodgman Sean S. , Schreiber Michael , Ronzheimer Jens Philipp , Riera Arnau , del Rey Marco , Bloch Immanuel , Eisert Jens , Schneider Ulrich
Published: March 2015

Significance

Quantum phase transitions are characterized by a dramatic change of the ground-state behavior; famous examples include the appearance of magnetic order or superconductivity as a function of doping in cuprates. In this work, we explore how a system dynamically crosses such a transition and in particular, investigate in detail how coherence emerges when an initially incoherent Mott insulating system enters the superfluid regime. We present results from an experimental study using ultracold atoms in an optical lattice as well as numerical simulations and find a rich behavior beyond the scope of any existing theory. This quantum simulation of a complex many-body system is an important stepping stone for a deeper understanding of the intricate dynamics of quantum phase transitions.
Plant-derived antifungal agent poacic acid targets β-1,3-glucan
Authors: Piotrowski Jeff S. , Okada Hiroki , Lu Fachuang , Li Sheena C. , Hinchman Li , Ranjan Ashish , Smith Damon L. , Higbee Alan J. , Ulbrich Arne , Coon Joshua J. , Deshpande Raamesh , Bukhman Yury V. , McIlwain Sean , Ong Irene M. , Myers Chad L. , Boone Charles , Landick Robert , Ralph John , Kabbage Mehdi , Ohya Yoshikazu
Published: March 2015

Significance

The search for new antifungal compounds is struggling to keep pace with emerging fungicide resistance. Through chemoprospecting of an untapped reservoir of inhibitory compounds, lignocellulosic hydrolysates, we have identified a previously undescribed antifungal agent, poacic acid. Using both chemical genomics and morphological analysis together for the first time, to our knowledge, we identified the cellular target of poacic acid as β-1,3-glucan. Through its action on the glucan layer of fungal cell walls, poacic acid is a natural antifungal agent against economically significant fungi and oomycete plant pathogens. This work highlights the chemical diversity within lignocellulosic hydrolysates as a source of potentially valuable chemicals.
Differentiation of antiinflammatory and antitumorigenic properties of stabilized enantiomers of thalidomide analogs
Authors: Jacques Vincent , Czarnik Anthony W. , Judge Thomas M. , Van der Ploeg Lex H. T. , DeWitt Sheila H.
Published: March 2015

Significance

Despite dramatically improved therapeutic properties of single enantiomer drugs over the racemic mixtures, numerous drugs and drug candidates are still being developed and sold as racemates, including the class of immunomodulatory drugs derived from thalidomide. The chiral center of these thalidomide analogs is chemically unstable, resulting in interconversion of the enantiomers both in vitro and in vivo. Through stabilization of the chiral center with deuterium, we show for the first time, to our knowledge, that the in vitro antiinflammatory and in vivo antitumorigenic activities of a thalidomide analog currently in clinical development (CC-122) are caused exclusively by one enantiomer. Our findings enable the development of improved thalidomide analogs as therapeutics following stated regulatory guidance for the development of single enantiomers.
Reverse switching of surface roughness in a self-organized polydomain liquid crystal coating
Authors: Liu Danqing , Liu Ling , Onck Patrick R. , Broer Dirk J.
Published: March 2015

Significance

Switching surface topographic patterns in a dynamic way controls properties such as friction, sticking–release, light reflection, aero- and hydrodynamics, self-cleaning, and touch experience. We present a method to make coatings which are initially flat but form a spiked surface structure under light exposure. The surface turns flat again immediately as the light switches off. The polydomain liquid crystal provides a convenient method that makes fabrication of responsive coatings significantly easier than previous methods. The polydomain texture is simulated by finite elements and the topographic deformation can be understood in terms of director-dependent absorption and related changes in local order. Moreover, the dynamic creation of free volume further enhances the surface modulation to the record value of 24% of the film thickness.
Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4
Authors: Cedervall Peder , Aulabaugh Ann , Geoghegan Kieran F. , McLellan Thomas J. , Pandit Jayvardhan
Published: March 2015

Significance

Phosphodiesterase 4 (PDE4) is an essential contributor to intracellular signaling and an important drug target. We have used protein engineering, biochemistry, and X-ray crystallography to elucidate how its conserved N-terminal regions regulate its activity. Our results show that a helical segment in the regulatory domain of one subunit crosses over to occlude the catalytic site of the other subunit of the homodimer. The structure suggests a strategy for the design of inhibitors that target specific splice variants of this enzyme. By mapping onto our structure all the mutations in PDE4D that underlie the rare human genetic disorder of acrodysostosis, we present a rationale for why they could lead to a dysregulation of PDE4D activity.
Vaccine composition formulated with a novel TLR7-dependent adjuvant induces high and broad protection against
Staphylococcus aureus
Authors: Bagnoli Fabio , Fontana Maria Rita , Soldaini Elisabetta , Mishra Ravi P. N. , Fiaschi Luigi , Cartocci Elena , Nardi-Dei Vincenzo , Ruggiero Paolo , Nosari Sarah , De Falco Maria Grazia , Lofano Giuseppe , Marchi Sara , Galletti Bruno , Mariotti Paolo , Bacconi Marta , Torre Antonina , Maccari Silvia , Scarselli Maria , Rinaudo C. Daniela , Inoshima Naoko , Savino Silvana , Mori Elena , Rossi-Paccani Silvia , Baudner Barbara , Pallaoro Michele , Swennen Erwin , Petracca Roberto , Brettoni Cecilia , Liberatori Sabrina , Norais Nathalie , Monaci Elisabetta , Bubeck Wardenburg Juliane , Schneewind Olaf , O’Hagan Derek T. , Valiante Nicholas M. , Bensi Giuliano , Bertholet Sylvie , De Gregorio Ennio , Rappuoli Rino , Grandi Guido
Published: March 2015

Significance

Staphylococcus aureus
is a human pathogen causing life-threatening infections. The high incidence of methicillin-resistant
S. aureus
isolates resistant to all antibiotics makes the development of anti
-S. aureus
vaccines an urgent medical need. However, the unique ability of
S. aureus
to produce virulent factors, which counteract virtually all pathways of innate and adaptive immunity, has hampered all vaccine discovery efforts. Starting from the assumption that to be effective a vaccine should induce highly functional antibodies and potentiate the killing capacity of phagocytic cells, we selected a cocktail of five conserved antigens involved in different mechanisms of pathogenesis, and we formulated them with a potent adjuvant. This vaccine provides an unprecedented protective efficacy against
S. aureus
infection in animal models.
Adding insult to inquiry
Authors: Wee Lionel
Published: March 2015

While compliments are usually intended to give credit and insults offense, the latter cannot simply be treated as opposites of the former. For example, a speaker can give credit to others as well as himself/herself. But while a speaker can offend others, it is less clear that a speaker can offend himself/herself. Understanding why this should be so provides us with a key insight into the nature of insults, namely, that it is predicated on the presumption that some dissimilarity exists between the speaker and the target of the insult. Various interesting implications follow from this insight, allowing us to (i) understand why competitive ritualized exchanges of insults are more commonly attested than are analogous competitions involving compliments; (ii) better appreciate the ideological bases of politically correct speech; and (iii) adjudicate on the relative merits of various theories of politeness, in particular, on claims concerning the relationship between politeness and face.
Patterns of discourse semantics
Authors: Schröter Melani , Storjohann Petra
Published: March 2015

Corpus-assisted analyses of public discourse often focus on the lexical level. This article argues in favour of corpus-assisted analyses of discourse, but also in favour of conceptualising salient lexical items in public discourse in a more determined way. It draws partly on non-Anglophone academic traditions in order to promote a conceptualisation of discourse keywords, thereby highlighting how their meaning is determined by their use in discourse contexts. It also argues in favour of emphasising the cognitive and epistemic dimensions of discourse-determined semantic structures. These points will be exemplified by means of a corpus-assisted, as well as a frame-based analysis of the discourse keyword financial crisis in British newspaper articles from 2009. Collocations of financial crisis are assigned to a generic matrix frame for ‘event’ which contains slots that specify possible statements about events. By looking at which slots are more, respectively less filled with collocates of financial crisis, we will trace semantic presence as well as absence, and thereby highlight the pragmatic dimensions of lexical semantics in public discourse. The article also advocates the suitability of discourse keyword analyses for systematic contrastive analyses of public/political discourse and for lexicographical projects that could serve to extend the insights drawn from corpus-guided approaches to discourse analysis.
The Death of Kings: Group Identity and the Tragedy of Nezhād in Ferdowsi's Shahnameh
Authors: Hayes Edmund
Published: March 2015

Ferdowsi's Shahnameh was not conceived as a national epic, but it does encapsulate another kind of group identity: it provides context and meaning for the glorious pedigree of the Iranian aristocracy. Ferdowsi himself was a member of the Khorasani dehqān gentry whose collective effort in the tenth century CE was turned towards preserving and reshaping their own history and literary heritage in the terms of the new era. This article analyzes the final section of the Shahnameh, dealing with the reign and death of the last Sasanian king, Yazdegerd III. As such, this section provides crucial clues for the function of the Shahnameh as a means to construct meaning for Ferdowsi's own group in his own time. The description of this crucial moment in history, pivoting between the era of Iranian kingship and the Islamic era, suggested possible modes for interpreting the present. The study reads this section of the Shahnameh with close attention to the use of the word nezhād (“lineage”), which circumscribes the identity of both the aristocrats of Ferdowsi's present, and the kings and heroes of the mythic past. In doing so, the transition between eras appears as a tragedy of nezhād, as the Sasanian dynasty is extinguished, raising permanent existential ambiguities for the entire class of Iranian gentry whose genealogies were associated with it.
Vote for me. Don’t vote for the other one
Authors: Arnold Edward , Labbe Dominique
Published: March 2015

The French presidential election takes place in two ballots. The second round opposes the two leading candidates at the end of the first. Between the two ballots, since 1974, the two finalists take part in a TV debate along the lines of the US presidential debates. This presentation analyses the texts of these six debates (136,000 words). A library of more than 6000 political texts – and nearly 13 million words – provides some benchmarks.

This paper presents the statistical indices proposed for the analysis of the communication within a situation of interaction. These indices are derived from theories concerning the presentation of actants in the speech, the expression of the speaker’s subjectivity and the speech modalization. The application of these indices allows to bring a new perspective on these debates and it defines, for each of these indices, its scope, limitations and possible improvements.

The first part analyses the tendency of the speakers to personalize. These indices are broken down into the following dimensions: the relative importance given to the speaker, to the other and to the real message recipients (the listeners). The second part measures the fundamental choice in favour of the verb and, within this part of speech, between the accomplished ones (verbs to be and to have) and modal verbs (possible, desirable, obligation, knowledge). Finally, the greater or lesser density of the negation highlights the real scope of discourse.

The study leads to interesting conclusions about electoral discourse and the evolution of French political discourse over the last 40 years. Finally, it emphasizes the usefulness of vast corpuses of texts and of lexicometry for language studying and teaching.
Sufficiency of simplex inequalities
Authors: Izumi Shuzo
Published: March 2015

Let

z
0

,
…
,

z
n

z_0,\dots ,z_n

be the

(
n
−
1
)

(n-1)

-dimensional volumes of facets of an

n
n

-simplex. Then we have the simplex inequalities:

z
p

>

z
0

+
⋯
+

z
ˇ

p

+
⋯
+

z
n

z_p > z_0+\dots +\check {z}_p+\dots +z_n

(
0
≤
p
≤
n
)

(0\le p\le n)

, generalizations of the triangle inequalities. Conversely, suppose that numbers

z
0

,
…
,

z
n

>
0

z_0,\dots ,z_n>0

satisfy these inequalities. Does there exist an

n
n

-simplex the volumes of whose facets are them? Kakeya solved this problem affirmatively in the case

n
=
3

n=3

and conjectured the assertion for all

n
≥
4

n\ge 4

. We prove that his conjecture is affirmative.
Integrability of unitary representations on reproducing kernel spaces
Authors: Merigon Stéphane , Neeb Karl-Hermann , Ólafsson Gestur
Published: March 2015

Let

g

\mathfrak {g}

be a Banach–Lie algebra and

τ
:

g

→

g

\tau : \mathfrak {g} \to \mathfrak {g}

an involution. Write

g

=

h

⊕

q

\mathfrak {g}=\mathfrak {h}\oplus \mathfrak {q}

for the eigenspace decomposition of

g

\mathfrak {g}

with respect to

τ
\tau

and

g

c

:=

h

⊕
i

q

\mathfrak {g}^c := \mathfrak {h}\oplus i\mathfrak {q}

for the dual Lie algebra. In this article we show the integrability of two types of infinitesimally unitary representations of

g

c

\mathfrak {g}^c

. The first class of representation is determined by a smooth positive definite kernel

K
K

on a locally convex manifold

M
M

. The kernel is assumed to satisfy a natural invariance condition with respect to an infinitesimal action

β
:

g

→

V

(
M
)

\beta \colon \mathfrak {g} \to \mathcal {V}(M)

by locally integrable vector fields that is compatible with a smooth action of a connected Lie group

H
H

with Lie algebra

h

\mathfrak {h}

. The second class is constructed from a positive definite kernel corresponding to a positive definite distribution

K
∈

C

−
∞

(
M
×
M
)

K \in C^{-\infty }(M \times M)

on a finite dimensional smooth manifold

M
M

which satisfies a similar invariance condition with respect to a homomorphism

β
:

g

→

V

(
M
)

\beta \colon \mathfrak {g} \to \mathcal {V}(M)

. As a consequence, we get a generalization of the Lüscher–Mack Theorem which applies to a class of semigroups that need not have a polar decomposition. Our integrability results also apply naturally to local representations and representations arising in the context of reflection positivity.
BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method
Authors: Shi Xu , Barnes Robert O. , Chen Li , Shajahan-Haq Ayesha N. , Hilakivi-Clarke Leena , Clarke Robert , Wang Yue , Xuan Jianhua
Published: March 2015

Summary: Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and C++, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein–protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic user interface is developed as a Cytoscape plugin for the BMRF-Net software to deal with the input/output interface. The detailed structure of the identified networks can be visualized in Cytoscape conveniently. The BMRF-Net package has been applied to breast cancer data to identify significant subnetworks related to breast cancer recurrence.

Availability and implementation: The BMRF-Net package is available at http://sourceforge.net/projects/bmrfcjava/. The package is tested under Ubuntu 12.04 (64-bit), Java 7, glibc 2.15 and Cytoscape 3.1.0.

Contact:  xuan@vt.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Quantifying the projected impact of the South African sardine fishery on the Robben Island penguin colony
Authors: Robinson William M. L. , Butterworth Douglas S. , Plagányi Éva E.
Published: March 2015

Quantitative methods are needed to evaluate the ecological effects of fishing forage species upon which predators depend. African penguin Spheniscus demersus numbers at the Robben Island colony rose during the 1990s co-incidental with a marked increase in sardine Sardinops sagax and anchovy Engraulis encrasicolus abundances, but decreased appreciably during the 2000s as sardine suffered a series of poor recruitments. A population dynamics model is developed which relates penguin adult annual mortality to local sardine biomass, and is fit to penguin moult counts and re-sightings of tagged penguins. The predator–prey interaction is best explained by a sardine–penguin mortality relationship with average penguin survival decreasing only when the local sardine biomass is less than approximately one-quarter of the maximum observed. Results suggest that the rapid growth of the colony during the 1990s was driven primarily by immigration. Penguin projections are generated by linking to future sardine abundances predicted under the operational management procedure used to set catch limits for these sardine and anchovy fisheries, and compared with equivalent scenarios without fishing. Results indicate that fishing is likely to have a relatively small impact on penguins, especially when compared with uncertainties that arise from the variable spatial distribution of the sardine population.
Surveillance of antibiotic susceptibility of urinary tract pathogens for a population of 5.6 million over 4 years
Authors: Ironmonger Dean , Edeghere Obaghe , Bains Amardeep , Loy Richard , Woodford Neil , Hawkey Peter M.
Published: March 2015

Objectives

To retrospectively analyse routine susceptibility testing data to describe antimicrobial non-susceptibility trends in isolates of Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa from urine samples in a population of 5.6 million people over a 4 year period.

Methods

De-duplicated laboratory data submitted to the AmSurv surveillance system from the West Midlands region of England and results of submissions to the Antimicrobial Resistance and Healthcare Associated Infections Reference Unit were extracted for the period 2010–13. Descriptive analysis of the non-susceptibility of selected Gram-negative organisms to key antibiotics, as recommended for monitoring in the UK Five Year Antimicrobial Resistance Strategy, was undertaken.

Results

During the study period, there were 431 461 reports for E. coli, 23 786 for K. pneumoniae and 6985 for P. aeruginosa from urine specimens. These represented 61%, 3% and 1%, respectively, of all organisms isolated from urine specimens. There was a linear increase in non-susceptibility to third-generation cephalosporins for E. coli and K. pneumoniae, and to ciprofloxacin for E. coli, in specimens from both hospital and community settings (P < 0.001). The proportions of E. coli and K. pneumoniae reported non-susceptible to meropenem and/or imipenem remained low during the study period, with no evidence of linear trend (P ≥ 0.05).

Conclusions

Automated antimicrobial resistance surveillance enabled, for the first time in England, the systematic monitoring of resistance in bacteria responsible for urinary tract infections in a defined population, and thereby provided a representative indication of the burden of resistance in Gram-negative bacteria in hospital and community settings.
Highly frequent HIV-1 minority resistant variants at baseline of the ANRS 139 TRIO trial had a limited impact on virological response
Authors: Charpentier Charlotte , Lee Guinevere Q. , Rodriguez Christophe , Visseaux Benoit , Storto Alexandre , Fagard Catherine , Molina Jean-Michel , Katlama Christine , Yazdanpanah Yazdan , Harrigan P. Richard , Descamps Diane
Published: March 2015

Objectives

To assess the prevalence of minority resistant variants (MRVs) at baseline and their impact on the virological response. The ANRS 139 TRIO trial evaluated the combination of raltegravir, etravirine and darunavir, plus an optimized background therapy, in 87% of cases. Patients were highly experienced and harboured multiresistant viruses, but were naive to the three drugs, and showed a high level of virological suppression.

Methods

Ultra-deep sequencing of reverse transcriptase, protease and integrase regions was performed at the trial baseline, and sequences were interpreted according to the ANRS algorithm. MRVs were assessed using MiSeq and 454 technologies (limit of detection 1%).

Results

At baseline, minority variants with at least one NRTI, one NNRTI, one PI, one major PI or an integrase inhibitor resistance-associated mutation were present in 46%, 45%, 68%, 24% and 13% of patients, respectively. When minority variants are taken into account, the prevalence of resistance to etravirine, darunavir and raltegravir at baseline was 29%, 40% and 9%, respectively. No difference was observed in the prevalence of MRVs between patients with virological failure and those with virological success, except a trend for patients exhibiting baseline etravirine MRVs (50% versus 26%, P = 0.09).

Conclusions

We have shown a high level of MRVs at baseline in highly pre-treated patients harbouring multiresistant viruses. However, these MRVs were not associated with an increased risk of virological failure, except for a trend for etravirine MRVs.
Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features
Authors: Nikfarjam Azadeh , Sarker Abeed , O’Connor Karen , Ginn Rachel , Gonzalez Graciela
Published: March 2015

Objective Social media is becoming increasingly popular as a platform for sharing personal health-related information. This information can be utilized for public health monitoring tasks, particularly for pharmacovigilance, via the use of natural language processing (NLP) techniques. However, the language in social media is highly informal, and user-expressed medical concepts are often nontechnical, descriptive, and challenging to extract. There has been limited progress in addressing these challenges, and thus far, advanced machine learning-based NLP techniques have been underutilized. Our objective is to design a machine learning-based approach to extract mentions of adverse drug reactions (ADRs) from highly informal text in social media.

Methods We introduce ADRMine, a machine learning-based concept extraction system that uses conditional random fields (CRFs). ADRMine utilizes a variety of features, including a novel feature for modeling words’ semantic similarities. The similarities are modeled by clustering words based on unsupervised, pretrained word representation vectors (embeddings) generated from unlabeled user posts in social media using a deep learning technique.

Results ADRMine outperforms several strong baseline systems in the ADR extraction task by achieving an F-measure of 0.82. Feature analysis demonstrates that the proposed word cluster features significantly improve extraction performance.

Conclusion It is possible to extract complex medical concepts, with relatively high performance, from informal, user-generated content. Our approach is particularly scalable, suitable for social media mining, as it relies on large volumes of unlabeled data, thus diminishing the need for large, annotated training data sets.
Electronic health records and health care quality over time in a federally qualified health center
Authors: Kern Lisa M. , Edwards Alison M. , Pichardo Michelle , Kaushal Rainu
Published: March 2015

The longitudinal effects of electronic health records (EHRs) on ambulatory quality are not clear. It is not known whether adoption and meaningful use of EHRs result in a brief period of quality improvement that then plateaus, or whether with ongoing use quality improvement continues. We studied health care quality at six sites of a Federally Qualified Health Center in New York State over 3 years (2008–2010) for 25 290 unique patients. Patients were twice as likely to receive recommended care on a set of 12 quality measures (11 of which are included in Stage 1 Meaningful Use) 3 years post-EHR implementation, compared to 1-year post-implementation (odds ratio 1.97; 95% confidence interval, 1.91–2.03). The magnitude of absolute improvement ranged from 5% to 20% per measure. EHRs were associated with continuing improvement in health care quality for at least 3 years post-implementation in the safety-net setting of a Federally Qualified Health Center.
Predicted properties of multiple images of the strongly lensed supernova SN Refsdal
Authors: Oguri Masamune
Published: March 2015

We construct a mass model of the cluster MACS J1149.6+2223 to study the expected properties of multiple images of SN Refsdal, the first example of a gravitationally lensed supernova with resolved multiple images recently reported by Kelly et al. We find that the best-fitting model predicts six supernova images in total, i.e. two extra images in addition to the observed four Einstein cross supernova images S1–S4. One extra image is predicted to have appeared about 17 years ago, whereas the other extra image is predicted to appear in about one year from the appearance of S1–S4, which is a testable prediction with near-future observations. The predicted magnification factors of individual supernova images range from ∼18 for the brightest image to ∼4 for the faint extra images. Confronting these predictions with future observations should provide an unprecedented opportunity to improve our understanding of cluster mass distributions.
Activation of Latent Human Immunodeficiency Virus by the Histone Deacetylase Inhibitor Panobinostat: A Pilot Study to Assess Effects on the Central Nervous System
Authors: Rasmussen Thomas A. , Tolstrup Martin , Møller Holger Jon , Brinkmann Christel R. , Olesen Rikke , Erikstrup Christian , Laursen Alex L. , Østergaard Lars , Søgaard Ole S.
Published: March 2015

In a substudy of a clinical trial, we assessed whether activation of latent human immunodeficiency virus (HIV) by the histone deacetylase inhibitor panobinostat had detrimental effects on the central nervous system (CNS). Adults infected with HIV received oral panobinostat 20 mg 3 times per week every other week for 8 weeks. In cerebrospinal fluid (CSF), we assayed panobinostat concentration, HIV RNA, and the level of neuroinflammatory or degenerative biomarkers in 11 individuals before and during study therapy. Neither panobinostat nor HIV RNA was detected in CSF. In addition, there was no change from baseline in CSF biomarkers. Thus, panobinostat administration was not associated with CNS adverse effects as assessed by CSF biomarkers.