bluuebunny/crossref_metadata_2025 huggingface dataset:
Glycogen synthase kinase 3 inhibitors induce the canonical WNT/β-catenin pathway to suppress growth and self-renewal in embryonal rhabdomyosarcoma
Authors: Chen Eleanor Y. , DeRan Michael T. , Ignatius Myron S. , Grandinetti Kathryn Brooke , Clagg Ryan , McCarthy Karin M. , Lobbardi Riadh M. , Brockmann Jillian , Keller Charles , Wu Xu , Langenau David M.
Published: March 2014

Significance

Embryonal rhabdomyosarcoma (ERMS) is a cancer of skeletal muscle and is one of the most common pediatric cancers of soft tissue. There is no effective treatment for patients with relapsed ERMS, with less than 50% surviving the disease. The self-renewing and molecularly defined tumor propagating cells (TPCs) drive continued tumor growth and relapse. Yet to date, drugs targeting ERMS self-renewal and differentiation of TPCs have not been identified. Our study describes a large-scale chemical screen to identify targetable pathways essential for modulating self-renewal and differentiation of ERMS and demonstrates the feasibility of inducing differentiation of TPCs in ERMS by small molecules.
Small cationic antimicrobial peptides delocalize peripheral membrane proteins
Authors: Wenzel Michaela , Chiriac Alina Iulia , Otto Andreas , Zweytick Dagmar , May Caroline , Schumacher Catherine , Gust Ronald , Albada H. Bauke , Penkova Maya , Krämer Ute , Erdmann Ralf , Metzler-Nolte Nils , Straus Suzana K. , Bremer Erhard , Becher Dörte , Brötz-Oesterhelt Heike , Sahl Hans-Georg , Bandow Julia Elisabeth
Published: March 2014

Significance

Multidrug-resistant bacteria present an acute problem to medicine, generating interest in novel antimicrobial strategies. Antimicrobial peptides currently are being investigated, both as antibiotics and as immunomodulatory agents. Many antimicrobial peptides interact with the bacterial membrane, a previously underexplored antibiotic target. We present a system-based study of the mode of action of small cationic peptides and the mechanisms that bacteria use to defend against them. We show that peptide integration into the membrane causes delocalization of essential peripheral membrane proteins. This delocalization impacts on two cellular processes, namely respiration and cell-wall biosynthesis. We describe a bacterial survival strategy in which mechanosensitive channels in the bacterial membrane establish osmoprotection against membrane-targeting bacteriolytic peptides. Understanding the peptides' mode of action and bacterial survival strategies opens up new avenues for devising peptide-based antibacterial strategies.
Salt stress-induced Ca
2+
waves are associated with rapid, long-distance root-to-shoot signaling in plants
Authors: Choi Won-Gyu , Toyota Masatsugu , Kim Su-Hwa , Hilleary Richard , Gilroy Simon
Published: March 2014

Significance

This work documents a previously unreported plant-wide signaling system based on the rapid, long-distance transmission of Ca
2+
waves. In the root these waves move through the cortical and endodermal cell layers at speeds of up to 400 µm/s, i.e., traversing several cells per second. This Ca
2+
wave system correlates with the triggering of molecular responses in distant parts of the plant upon perception of localized (salt) stress. Such propagating Ca
2+
waves provide a new mechanism for the rapid integration of activities throughout the plant body.
Optogenetic control of selective neural activity in multiple freely moving
Drosophila
adults
Authors: Wu Ming-Chin , Chu Li-An , Hsiao Po-Yen , Lin Yen-Yin , Chi Chen-Chieh , Liu Tsung-Ho , Fu Chien-Chung , Chiang Ann-Shyn
Published: March 2014

Significance

We present an automated laser tracking and optogenetic manipulation system (ALTOMS) for studying social memory in
Drosophila
. Based on behavioral interactions computed with a high-speed image analysis system, ALTOMS can target two lasers (a 473-nm blue laser and a 593.5-nm yellow laser) independently on any specified body parts of two freely moving
Drosophila
adults in real time. We performed an operant conditioning assay in which a courting male quickly learned and formed a long-lasting memory to stay away from a freely moving virgin female. Given its capacity for optogenetic manipulation to transiently and independently activate/inactivate selective neurons, ALTOMS offers opportunities to systematically map brain circuits that orchestrate specific
Drosophila
behaviors.
‘Land’ and life
Authors: Duvall Chris
Published: March 2014

Understanding how people classify physical geographic features is necessary for identifying cross-cultural geographic concepts necessary for successful communication of landscape knowledge. Identifying cross-cultural geographic concepts will require development of the field of ethnogeography, which employs ethnographic methods to analyze geographic knowledge. This chapter analyzes physical geographic knowledge in the Maninka language of southwestern Mali, and compares Maninka knowledge to that of other culturalgroups. The results suggest that broad physical geographic concepts may be shared pan-environmentally, but that most physical geographic knowledge is contained in culturally specific classifications within a broad cross-cultural framework. Academic geographers should expect only broad correspondence between their categories of physical geographic variation and those of people who classify biophysical features according to local knowledge systems.
Perspectives on the ethical conduct of landscape in language research
Authors: Turk Andrew G. , Mark David M.
Published: March 2014

This chapter provides a transcript of the panel session held late in the Landscape in Language Workshop to discuss ethical issues, especially in the context of research by, or with, Indigenous peoples. The session was chaired by David Stea and the panel members were Renee Louis, Carmelita Topaha, Andrew Turk and Renée Sieber. Eight other workshop participants also contributed to the discussion. The transcript of the panel session has been slightly edited to remove comments about the process and to improve the coherence and flow of the dialogue. No significant content was removed.
Syncretic speech, linguistic ideology, and intertextuality
Authors: Messing Jacqueline , Rosales Flores Ramos
Published: March 2014

“Syncretism” describes the structural incorporation of indigenous languages like Mexicano (Nahuatl) from Central Mexico with majority languages like Spanish. Building on research of Hill and Hill (1986), and collaborations with local scholars including teacher Ramos Rosales Flores, We analyze a 1999 public linguistic event celebrating the Spanish publication of “Speaking Mexicano” in Tlaxcala. Syncretic Mexicano, so-called “mixed speech,” exists within a local ideological landscape in which legítimo Mexicano – true Mexicano – is an idealized, largely not-spoken form of the native language, free of Spanish. We analyze multiple ideologies and metadiscursive practices at this event. I (Messing) further explore interpretation of syncretism by locals, resident-scholars and outsider-scholars, adding intertextual complexity to the academic and local interpretations of purism.
Textsetting as constraint conflict
Authors: Hayes Bruce
Published: March 2014

Halle & Lerdahl (1993) lay out the problem of textsetting: when singers encounter a novel stanza for a song they know, they have consistent intuitions about where the syllables of each line should be aligned in time when the new stanza is sung. In other words, people have a productive ability for setting text to rhythm. Halle & Lerdahl offer the first explicit proposal for modeling this ability. The present paper likewise proposes a formal model of textsetting, but using a different theoretical approach. I argue that many well-formed textsettings represent the best possible resolution between conflicting metrical principles. These involve: (a) matching of stress to rhythmically strong position; (b) avoidance of long lapses (sequences where no syllable is initiated); (c) avoidance of extreme syllable compression; and (d) alignment of phonological phrase boundaries with line boundaries. A good textsetting often must sacrifice perfect realization of one of these goals in order to satisfy another goal that takes higher priority. For instance, many lines place stressed syllables in weaker rhythmic positions, and stressless syllables in stronger positions, in order to avoid a long syllable lapse, thus sacrificing (a) to satisfy (b). I formalize this approach under Optimality Theory (Prince & Smolensky 1993/2004). Using data from Hayes & Kaun (1996), in which native English speakers spontaneously set many lines of verse, I show that an approach based on constraint conflict offers considerable improvement in the accuracy with which the native speakers’ settings are predicted.
Generative linguistics and Arabic metrics
Authors: Paoli Bruno
Published: March 2014

The classical theory of Arabic metrics has been reinterpreted numerous times in a variety of theoretical frameworks, notable among them Metrical Phonology (Prince 1989 & Schuh 1996) and Optimality Theory (Golston & Riad 1991), which we briefly examine to show that they do not permit an adequate account of the structure of Arabic verse-patterns. The analyses that have been proposed, by simply reinterpreting classical analyses, suffer from the same failings as the classical theory, whose descriptive adequacy (or inadequacy) is never discussed. To these failings we can add the problems inherent in the basic presuppositions of these theories (hierarchical organisation of meter, constituency and, above all, binarity), whose relevance (their explanatory power) and universality deserve to be seriously questioned. Finally, it is shown that a detailed descriptive analysis of actual instances of classical verse-patterns in terms of free and fixed metrical positions reveals a system which relies on principles and constraints that consistently depart from the classical framework and should thus serve as the basis for future analyses of Arabic meter.
Grammaticality, interfaces, and UG
Authors: Ott Dennis
Published: March 2014

It is argued that the notions “well-formedness” and “grammaticality,” inspired by formal-language theory, are not necessarily relevant for the study of natural language. The assumption that a [± grammatical] distinction exists, i.e. that I-language generates only certain structures but not others, is empirically questionable and presumably requires a richly structured UG. Some aspects of “crash-proof” models of syntax that assume such a distinction are discussed and contrasted with an alternative proposal (the Minimalist Program as pursued by Chomsky), which dispenses entirely with grammaticality, allowing syntax to generate freely. The latter program aims not at distinguishing “grammatical” from “ungrammatical” sentences, but at providing a true theory of the mechanisms that assign interpretations to structures at the interfaces.
On the mathematical foundations of crash-proof grammars
Authors: Leung Tommi Tsz-Cheung
Published: March 2014

This paper looks at how the particular computational mechanism of Crash-Proof Syntax (CPS) (Frampton & Gutmann 1999, 2002) as an instantiation of the Minimalist Program (Chomsky 1995) can be understood from the point of view of mathematical foundation that captured the spotlight among mathematicians during the nineteenth century. I claim that CPS can be analyzed as an analogy with Classical Peano’s Axioms that generate the theory of natural numbers. Instead of its computational efficiency, CPS is driven by the economization of axioms of formal systems. Further comparisons between syntax and natural numbers reveal that the central tenets of CPS can be defined mathematically on one hand, and highlight the significance of the ‘third factor’ as the design feature of language (Chomsky 2005) on the other hand.
Crash-free syntax and crash phenomena in model-theoretic grammar
Authors: Chaves Rui P.
Published: March 2014

The problem of obtaining a ‘crash-proof syntax’ has proved a difficult one for the Minimalist Program (Chomsky, 1995). This paper argues that this difficulty stems from the intrinsic enumerative-generative nature of the framework, since model-theoretic frameworks of grammar are crash-proof by definition (Pullum & Scholtz, 2001). The latter do not describe, define or produce derivations, or any kind of linguistic structure for that matter. The production of linguistic structures is left to the performance modules (i.e. comprehension and production), which consult the competence grammar module in order to determine which structures are possible. On the other hand, it is clear that the construction of syntactic structure performed by performance modules can – and often does – go awry during production and comprehension. A proper general theory of language should account for such empirically motivated performance ‘crashes’. Because they lack the notion of derivation, model-theoretic frameworks are better suited to be integrated with theories of how linguistic structure is actually built in production and comprehension. It is unclear what psychological correlate, if any, there is to derivations and crashes in a Minimalist setting. It is known since Fodor et al. (1974) that a derivational theory of complexity has no psycholinguistic grounding. Model-theoretic frameworks do not have this problem precisely because they are process-neutral.
Weak versus strong resumption
Authors: Guilliot Nicolas , Malkawi Nouman
Published: March 2014

This article focuses on the distribution and interpretation of resumption in Jordanian Arabic with respect to a well-known distinction: weak (clitics and doubled pronouns) versus strong (strong pronouns and epithets) resumption. We propose an analysis of resumption and reconstruction that relates two major asymmetries with respect to that distinction, (i) strong resumption banning QP antecedents in non-island contexts, contrary to weak resumption, and (ii) strong resumption banning reconstruction in strong island contexts, contrary to weak resumption. Our main conclusion is that weak (functional) resumptives support two distributive readings, either bound variable or e- type, whereas strong (lexical) resumptives can only get an e-type interpretation. The asymmetries stated above then just follow from further constraints on the two distributive readings.
Categorization and features
Authors: Archangeli Diana , Baker Adam , Mielke Jeff
Published: March 2014

Phonological features allow for formal expression of sound patterns used by speakers of a language. To understand where features come from, it is worth exploring where the patterns themselves come from. In this paper, we argue that the retroflex (tongue tip up) or bunched (tongue tip down) articulation of American English /ɹ/ is speaker- and context-dependent. We provide arguments against two overt sources for these patterns, phonological patterns and perception, as well as against their being purely the result of physiology. The conclusion we come to is that these patterns are spontaneously created by the speakers in order to provide order to their articulations of the sound /ɹ/. We conjecture that if patterns arise spontaneously, so too might features.
Chapter 4. Dylan Thomas’s meters
Authors: Fabb Nigel , Halle Morris
Published: March 2014

This chapter applies to Dylan Thomas’s metrical poetry the theory of meter developed in collaboration with Carlos Piera in Fabb and Halle (2008). We explain the various properties of the strict and loose meters used by Thomas. We also discuss some poems which can be analyzed as simultaneously in two meters at the same time: a strict syllable-counting meter and a loose stress-based meter. These polymetrical poems may reflect the influence, possibly mediated through Gerard Manley Hopkins, of the Welsh poetic tradition.
GPU-accelerated ray-tracing for real-time treatment planning
Authors: Heinrich H , Ziegenhein P , Kamerling C P , Froening H , Oelfke U
Published: March 2014

Dose calculation methods in radiotherapy treatment planning require the radiological depth information of the voxels that represent the patient volume to correct for tissue inhomogeneities. This information is acquired by time consuming ray-tracing-based calculations. For treatment planning scenarios with changing geometries and real-time constraints this is a severe bottleneck. We implemented an algorithm for the graphics processing unit (GPU) which implements a ray-matrix approach to reduce the number of rays to trace. Furthermore, we investigated the impact of different strategies of accessing memory in kernel implementations as well as strategies for rapid data transfers between main memory and memory of the graphics device. Our study included the overlapping of computations and memory transfers to reduce the overall runtime using Hyper-Q. We tested our approach on a prostate case (9 beams, coplanar). The measured execution times for a complete ray-tracing range from 28 msec for the computations on the GPU to 99 msec when considering data transfers to and from the graphics device. Our GPU-based algorithm performed the ray-tracing in real-time. The strategies efficiently reduce the time consumption of memory accesses and data transfer overhead. The achieved runtimes demonstrate the viability of this approach and allow improved real-time performance for dose calculation methods in clinical routine.
𝐿¹ error estimates for difference approximations of degenerate convection-diffusion equations
Authors: Karlsen K. , Risebro N. , Storrøsten E.
Published: March 2014

We analyze monotone finite difference schemes for strongly degenerate convection-diffusion equations in one spatial dimension. These nonlinear equations are well-posed within a class of (discontinuous) entropy solutions. We prove that the

L
1

L^1

error between the approximate and exact solutions is

O

(
Δ

x

1

/

3

)

\mathcal {O}(\Delta x^{1/3})

, where

Δ
x

\Delta x

is the spatial grid parameter. This result should be compared with the classical

O

(
Δ

x

1

/

2

)

\mathcal {O}(\Delta x^{1/2})

error estimate for conservation laws (Kuznecov, 1976), and a recent estimate of

O

(
Δ

x

1

/

11

)

\mathcal {O}(\Delta x^{1/11})

for degenerate convection-diffusion equations (Karlsen, Koley, Risebro 2012).
Coxeter orbits and Brauer trees III
Authors: Dudas Olivier , Rouquier Raphaël
Published: March 2014

This article is the final one of a series of articles on certain blocks of modular representations of finite groups of Lie type and the associated geometry. We prove the conjecture of Broué on derived equivalences induced by the complex of cohomology of Deligne-Lusztig varieties in the case of Coxeter elements. We also prove a conjecture of Hiß, Lübeck, and Malle on the Brauer trees of the corresponding blocks. As a consequence, we determine the Brauer tree (in particular, the decomposition matrix) of the principal

ℓ
\ell

-block of

E
7

(
q
)

E_7(q)

when

ℓ
∣

Φ

18

(
q
)

\ell \mid \Phi _{18}(q)

and

E
8

(
q
)

E_8(q)

when

ℓ
∣

Φ

18

(
q
)

\ell \mid \Phi _{18}(q)

or

ℓ
∣

Φ

30

(
q
)

\ell \mid \Phi _{30}(q)

.
Heat-shock Response Increases Lung Injury Caused by Pseudomonas aeruginosa via an Interleukin-10-dependent Mechanism in Mice
Authors: Carles Michel , Wagener Brant M. , Lafargue Mathieu , Roux Jérémie , Iles Karen , Liu Dong , Rodriguez Cilina Ann , Anjum Naseem , Zmijewski Jaroslaw , Ricci Jean-Ehrland , Pittet Jean-Francois
Published: March 2014

Background:

The heat-shock response (HSR) protects from insults, such as ischemia–reperfusion injury, by inhibiting signaling pathways activated by sterile inflammation. However, the mechanisms by which the HSR activation would modulate lung damage and host response to a bacterial lung infection remain unknown.

Methods:

HSR was activated with whole-body hyperthermia or by intraperitoneal geldanamycin in mice that had their lungs instilled with Pseudomonas aeruginosa 24 h later (at least six mice per experimental group). Four hours after instillation, lung endothelial and epithelial permeability, bacterial counts, protein levels in bronchoalveolar lavage fluid, and lung myeloperoxidase activity were measured. Mortality rate 24 h after P. aeruginosa instillation was recorded. The HSR effect on the release of interleukin-10 and killing of P. aeruginosa bacteria by a mouse alveolar macrophage cell line and on neutrophil phagocytosis was also examined.

Results:

HSR activation worsened lung endothelial (42%) and epithelial permeability (50%) to protein, decreased lung bacterial clearance (71%), and increased mortality (50%) associated with P. aeruginosa pneumonia, an effect that was not observed in heat-shock protein–72-null mice. HSR-mediated decrease in neutrophil phagocytosis (69%) and bacterial killing (38%) by macrophages was interleukin-10 dependent, a mechanism confirmed by increased lung bacterial clearance and decreased mortality (70%) caused by P. aeruginosa pneumonia in heat-shocked interleukin-10-null mice.

Conclusions:

Prior HSR activation worsens lung injury associated with P. aeruginosa pneumonia in mice via heat-shock protein–72- and interleukin-10-dependent mechanisms. These results provide a novel mechanism for the immunosuppression observed after severe trauma that is known to activate HSR in humans.
Phase II Study of Neoadjuvant Chemotherapy With S-1 and CDDP in Patients With Lymph Node Metastatic Stage II or III Gastric Cancer
Authors: Kochi Mitsugu , Fujii Masashi , Kanamori Noriaki , Mihara Yoshiaki , Funada Tomoya , Tamegai Hidenori , Watanabe Megumu , Takayama Yuriko , Suda Hiroshi , Takayama Tadatoshi
Published: March 2014

Objectives:

We conducted a phase II trial to investigate the efficacy and safety of neoadjuvant chemotherapy (NAC) comprising S-1 and cisplatin (CDDP) followed by extensive resection in the management of resectable locally advanced gastric cancer with lymph node (LN) metastases.

Methods:

Patients with LN metastases from stage II or III gastric cancer received S-1 and CDDP, as NAC criteria for LN metastases were the involvement of ≥4 nodes <2 cm or ≥1 nodes ≥2 cm as confirmed by a total body computed tomography scan. All patients underwent extensive resection including D2 gastrectomy. The primary endpoint was complete resection rate and the secondary endpoints were 3-year relapse-free and overall survival.

Results:

Fifty patients were assessable for the analysis. The complete resection rate was 87.8%. Three-year relapse-free survival was 44.9% and 3-year overall survival rate was 48.0%.

Conclusions:

NAC with S-1 and CDDP is safe and may improve the complete resection rate in patients with metastatic LN gastric cancer. This suggests that LN metastases would provide good target lesions in future clinical trials of NAC.
Chemical kinetics on extrasolar planets
Authors: Moses Julianne I.
Published: March 2014

Chemical kinetics plays an important role in controlling the atmospheric composition of all planetary atmospheres, including those of extrasolar planets. For the hottest exoplanets, the composition can closely follow thermochemical-equilibrium predictions, at least in the visible and infrared photosphere at dayside (eclipse) conditions. However, for atmospheric temperatures

, and in the uppermost atmosphere at any temperature, chemical kinetics matters. The two key mechanisms by which kinetic processes drive an exoplanet atmosphere out of equilibrium are photochemistry and transport-induced quenching. I review these disequilibrium processes in detail, discuss observational consequences and examine some of the current evidence for kinetic processes on extrasolar planets.
Galactic planetary science
Authors: Tinetti Giovanna
Published: March 2014

Planetary science beyond the boundaries of our Solar System is today in its infancy. Until a couple of decades ago, the detailed investigation of the planetary properties was restricted to objects orbiting inside the Kuiper Belt. Today, we cannot ignore that the number of known planets has increased by two orders of magnitude nor that these planets resemble anything but the objects present in our own Solar System. Whether this fact is the result of a selection bias induced by the kind of techniques used to discover new planets—mainly radial velocity and transit—or simply the proof that the Solar System is a rarity in the Milky Way, we do not know yet. What is clear, though, is that the Solar System has failed to betheparadigm not only in our Galaxy but even ‘just’ in the solar neighbourhood. This finding, although unsettling, forces us to reconsider our knowledge of planets under a different light and perhaps question a few of the theoretical pillars on which we base our current ‘understanding’. The next decade will be critical to advance in what we should perhaps callGalactic planetary science. In this paper, I review highlights and pitfalls of our current knowledge of this topic and elaborate on how this knowledge might arguably evolve in the next decade. More critically, I identify what should be the mandatory scientific and technical steps to be taken in this fascinating journey of remote exploration of planets in our Galaxy.
Habitable worlds with no signs of life
Authors: Cockell Charles S.
Published: March 2014

‘Most habitable worlds in the cosmos will have no remotely detectable signs of life’ is proposed as a biological hypothesis to be tested in the study of exoplanets. Habitable planets could be discovered elsewhere in the Universe, yet there are many hypothetical scenarios whereby the search for life on them could yield negative results. Scenarios for habitable worlds with no remotely detectable signatures of life include: planets that are habitable, but have no biosphere (Uninhabited Habitable Worlds); planets with life, but lacking any detectable surface signatures of that life (laboratory examples are provided); and planets with life, where the concentrations of atmospheric gases produced or removed by biota are impossible to disentangle from abiotic processes because of the lack of detailed knowledge of planetary conditions (the ‘problem of exoplanet thermodynamic uncertainty’). A rejection of the hypothesis would require that the origin of life usually occurs on habitable planets, that spectrally detectable pigments and/or metabolisms that produce unequivocal biosignature gases (e.g. oxygenic photosynthesis) usually evolve and that the organisms that harbour them usually achieve a sufficient biomass to produce biosignatures detectable to alien astronomers.
Possible climates on terrestrial exoplanets
Authors: Forget F. , Leconte J.
Published: March 2014

What kind of environment may exist on terrestrial planets around other stars? In spite of the lack of direct observations, it may not be premature to speculate on exoplanetary climates, for instance, to optimize future telescopic observations or to assess the probability of habitable worlds. To begin with, climate primarily depends on (i) the atmospheric composition and the volatile inventory; (ii) the incident stellar flux; and (iii) the tidal evolution of the planetary spin, which can notably lock a planet with a permanent night side. The atmospheric composition and mass depends on complex processes, which are difficult to model: origins of volatiles, atmospheric escape, geochemistry, photochemistry, etc. We discuss physical constraints, which can help us to speculate on the possible type of atmosphere, depending on the planet size, its final distance for its star and the star type. Assuming that the atmosphere is known, the possible climates can be explored using global climate models analogous to the ones developed to simulate the Earth as well as the other telluric atmospheres in the solar system. Our experience with Mars, Titan and Venus suggests that realistic climate simulators can be developed by combining components, such as a ‘dynamical core’, a radiative transfer solver, a parametrization of subgrid-scale turbulence and convection, a thermal ground model and a volatile phase change code. On this basis, we can aspire to build reliable climate predictors for exoplanets. However, whatever the accuracy of the models, predicting the actual climate regime on a specific planet will remain challenging because climate systems are affected by strong positive feedbacks. They can drive planets with very similar forcing and volatile inventory to completely different states. For instance, the coupling among temperature, volatile phase changes and radiative properties results in instabilities, such as runaway glaciations and runaway greenhouse effect.
Disentangling degenerate solutions from primary transit and secondary eclipse spectroscopy of exoplanets
Authors: Griffith Caitlin A.
Published: March 2014

Infrared transmission and emission spectroscopy of exoplanets, recorded from primary transit and secondary eclipse measurements, indicate the presence of the most abundant carbon and oxygen molecular species (H
2
O, CH
4
, CO and CO
2
) in a few exoplanets. However, efforts to constrain the molecular abundances to within several orders of magnitude are thwarted by the broad range of degenerate solutions that fit the data. Here, we explore, with radiative transfer models and analytical approximations, the nature of the degenerate solution sets resulting from the sparse measurements of ‘hot Jupiter’ exoplanets. As demonstrated with simple analytical expressions, primary transit measurements probe roughly four atmospheric scale heights at each wavelength band. Derived mixing ratios from these data are highly sensitive to errors in the radius of the planet at a reference pressure. For example, an uncertainty of 1% in the radius of a 1000 K and H
2
-based exoplanet with Jupiter's radius and mass causes an uncertainty of a factor of approximately 100–10 000 in the derived gas mixing ratios. The degree of sensitivity depends on how the line strength increases with the optical depth (i.e. the curve of growth) and the atmospheric scale height. Temperature degeneracies in the solutions of the primary transit data, which manifest their effects through the scale height and absorption coefficients, are smaller. We argue that these challenges can be partially surmounted by a combination of selected wavelength sampling of optical and infrared measurements and, when possible, the joint analysis of transit and secondary eclipse data of exoplanets. However, additional work is needed to constrain other effects, such as those owing to planetary clouds and star spots. Given the current range of open questions in the field, both observations and theory, there is a need for detailed measurements with space-based large mirror platforms (e.g. James web space telescope) and smaller broad survey telescopes as well as ground-based efforts.
Radial velocity studies of cool stars
Authors: Jones Hugh R. A. , Barnes John , Tuomi Mikko , Jenkins James S. , Anglada-Escude Guillem
Published: March 2014

Our current view of exoplanets is one derived primarily from solar-like stars with a strong focus on understanding our Solar System. Our knowledge about the properties of exoplanets around the dominant stellar population by number, the so-called low-mass stars or M dwarfs, is much more cursory. Based on radial velocity discoveries, we find that the semi-major axis distribution of M dwarf planets appears to be broadly similar to those around more massive stars and thus formation and migration processes might be similar to heavier stars. However, we find that the mass of M dwarf planets is relatively much lower than the expected mass dependency based on stellar mass and thus infer that planet formation efficiency around low-mass stars is relatively impaired. We consider techniques to overcome the practical issue of obtaining good quality radial velocity data for M dwarfs despite their faintness and sustained activity and emphasize (i) the wavelength sensitivity of radial velocity signals, (ii) the combination of radial velocity data from different experiments for robust detection of small amplitude signals, and (iii) the selection of targets and radial velocity interpretation of late-type M dwarfs should consider H
α
behaviour.
Very high-density planets: a possible remnant of gas giants
Authors: Mocquet A. , Grasset O. , Sotin C.
Published: March 2014

Data extracted from the Extrasolar Planets Encyclo- paedia (see
http://exoplanet.eu
) show the existence of planets that are more massive than iron cores that would have the same size. After meticulous verification of the data, we conclude that the mass of the smallest of these planets is actually not known. However, the three largest planets, Kepler-52b, Kepler-52c and Kepler-57b, which are between 30 and 100 times the mass of the Earth, have indeed density larger than an iron planet of the same size. This observation triggers this study that investigates under which conditions these planets could represent the naked cores of gas giants that would have lost their atmospheres during their migration towards the star. This study shows that for moderate viscosity values (10
25
 Pa s or lower), large values of escape rate and associated unloading stress rate during the atmospheric loss process lead to the explosion of extremely massive planets. However, for moderate escape rate, the bulk viscosity and finite-strain incompressibility of the cores of giant planets can be large enough to retain a very high density during geological time scales. This would make those a new kind of planet, which would help in understanding the interior structure of the gas giants. However, this new family of exoplanets adds some degeneracy for characterizing terrestrial exoplanets.
Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens
Authors: Hung Wei-Chun , Chen Hsiao-Jan , Tsai Jui-Chang , Tseng Sung-Pin , Lee Tai-Fen , Hsueh Po-Ren , Shieh Wung Yang , Teng Lee-Jene
Published: March 2014

Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465T, NTUH_2196, NTUH_4957 and NTUH_5572T, were isolated from human specimens. The four isolates displayed more than 99.6 % 16S rRNA gene sequence similarity with

Gemella haemolysans

ATCC 10379T, and 96.7 to 98.6 % similarity with

Gemella sanguinis

ATCC 700632T,

Gemella morbillorum

ATCC 27824T or

Gemella cuniculi

CCUG 42726T. However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from

G. haemolysans

ATCC 10379T and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572T clustered together and formed a stable monophyletic clade. DNA–DNA hybridization values among strains NTUH_1465T and NTUH_5572T and their phylogenetically related neighbours were all lower than 49 %. The four isolates could be distinguished from

G. haemolysans

and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465T = BCRC 80365T = JCM 18067T) and Gemella taiwanensis sp. nov. (type strain NTUH_5572T = BCRC 80366T = JCM 18066T) are proposed.
Galleria mellonella as an alternative model of Coxiella burnetii infection
Authors: Norville I. H. , Hartley M. G. , Martinez E. , Cantet F. , Bonazzi M. , Atkins T. P.
Published: March 2014

Coxiella burnetii is a Gram-negative intracellular bacterium and is the causative agent of the zoonotic disease Q fever. Several rodent and non-human primate models of virulent phase I C. burnetii [Nine Mile (NM)I] have been developed, and have been used to determine the efficacy of antibiotics and vaccine candidates. However, there are several advantages to using insect models to study host–microbe interactions, such as reduced animal use, lowered cost and ease of manipulation in high containment. In addition, many laboratories use the avirulent phase II C. burnetii clone (NMII) to study cellular interactions and identify novel virulence determinants using genetic manipulation. We report that larvae of the greater wax moth, Galleria mellonella, were susceptible to infection with both C. burnetii NMI and NMII. Following subcutaneous infection, we report that intracellular bacteria were present within haemocytes and that larval death occurred in a dose-dependent manner. Additionally, we have used the model to characterize the role of the type 4 secretion system in C. burnetii NMII and to determine antibiotic efficacy in a non-mammalian model of disease.
(E)-3,4,5-Trimethoxy-N′-[(4-oxo-4H-chromen-3-yl)methylidene]benzohydrazide
Authors: Ishikawa Yoshinobu , Watanabe Kohzoh
Published: March 2014

In the title chromone-tethered benzohydrazide derivative, C20H18N2O6, the atoms of theE-3-(hydrazonomethyl)-4H-chromen-4-one segment are essentially coplanar, the largest deviation being 0.065 (6) Å. The dihedral angle between this segment and the benzene ring of the trimethoxybenzene unit is 40.18 (10) Å. In the crystal, the molecule is linked to its inverse-symmetry equivalent by pairs of N—H...O hydrogen bonds and C—H...π interactions. The –CH=N—NH– segment is stacked on the benzene ring of the chromone unit of a translation-related equivalent molecule [centroid–centroid distance = 3.413 (6) Å].
5-Cyclopentyl-2-methyl-3-(3-methylphenylsulfonyl)-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Lee Uk
Published: March 2014

In the title compound, C21H22O3S, the five-membered ring adopts an envelope conformation with theipsoatom deviating by 0.596 (2) Å from the plane through the rest of the ring atoms. The dihedral angle between the mean planes of the benzofuran andm-tolyl moieties is 78.4 (1)°. In the crystal, molecules related by a glide plane are linkedviaC—H...O hydrogen bonds into chains along thea-axis direction. These chains are in turn connected by C—H...π interactions into layers parallel to theacplane.
The systems approach to the improvement of innovation in Slovenian tourism
Authors: Ropret Marko , Jere Jakulin Tadeja , Likar Borut
Published: March 2014

Purpose

– This paper aims to analyse whether and how the Development Plan and Policies of Slovenian Tourism (SiPlan) could be improved systematically and systemically, enabling more comprehensive management of innovation.

Design/methodology/approach

– The data were obtained within a comprehensive national innovation study. Data analysis was performed in four phases. In the initial phase, a link between the innovation project and SiPlan was established. In the next phase, which of the innovation factors are significantly correlated with the tourism destination development concept was identified. In the third phase, further policy potential for improving the innovation factors was identified. In the last phase, a systems approach was applied to develop a qualitative systems model, a causal loop diagram, taking into consideration the empirically identified strengths and weaknesses of the current SiPlan and other pertinent factors.

Findings

– The results of empirical research indicate that SiPlan represents a valuable, but not optimum development model of Slovene tourism development. Therefore, the authors propose a qualitative tourism development model based on the research results and a systems dynamics methodology.

Originality/value

– The work is important from the scientific point of view, i.e. as a methodology and research results that could be applied in further research activities. In addition, the results could be usefully used by policy makers by way of focusing on the most influential factors: policies that have a potential for the systems (holistic) and socially responsible development of tourism in Slovenia.
Can critical realism enable a journey from description to understanding in operations and supply chain management?
Authors: Rotaru Kristian , Churilov Leonid , Flitman Andrew
Published: March 2014

Purpose

– The current state of theory-building in the field of operations and supply chain management (OSCM) is in a strong need of rigorous, empirically based theories that enhance understanding of the causal relationships between the structural elements and properties of the business processes. In this research note the authors propose the critical realism (CR) philosophy of science as a particularly suitable philosophical position (not to the exclusion of others) to review the mechanisms of OSCM knowledge generation and to provide philosophical grounding and methodological guidance for both OSCM theory building and testing.

Design/methodology/approach

– To demonstrate potential benefits of CR-based structured approach to knowledge generation in OSCM research, this conceptual paper uses a case study that illustrates the adoption of one of the OSCM theories – i.e. the theory of swift, even flow.

Findings

– CR interprets the accumulated empirical information about OSCM phenomena as observable manifestations of the underlying causal mechanisms that cannot be perceived otherwise. CR can provide epistemological support to the choice of performance measures that manifest the underlying causal mechanisms of interest. Extensive accumulation of empirical data from multiple innovative sources will not dramatically add to understanding of the system under investigation, unless and until the underlying causal mechanisms that trigger the observed behaviour are identified and tested. The CR abductive mode of reasoning emphasises the role of uncertainty in complex process behaviours and can facilitate enrichment and refutation of OSCM theories.

Originality/value

– CR has a clear potential to contribute to OSCM research by enabling better understanding of causal relationships underlying complex behaviours of different elements of business process by providing robust and relevant mechanisms of generating knowledge about business processes that explicitly link empirical and causal aspects of theory building and testing.
Within‐species variability is the main driver of community‐level responses of traits of epiphytes across a long‐term chronosequence
Authors: Asplund Johan , Wardle David A.
Published: March 2014

There has been growing recent interest in the relative importance of within‐species trait variation vs. across‐species trait variation in vascular plants in determining total community‐level trait variation across communities and environmental gradients. Recent studies on plant communities have generally found across‐species variation to be more important than within‐species variation, but comparable studies involving other functionally important biota, such as lichens, are largely lacking.

We used a fire‐driven chronosequence involving 30 lake islands in northern Sweden to study how declining soil fertility during retrogression affects the functional traits of each of the dominant epiphytic lichen species growing on the trunks of the tree Betula pubescens. We measured several functional traits for the commonest lichen species on each island and used community‐weighted measures to study the community‐level responses of lichens to the gradient.

We found that as retrogression proceeds and soil fertility declines, thallus N and P concentrations and specific thallus mass (STM) increase, both within species and at the community level. Lichen secondary compounds showed contrasting within‐species responses and were non‐responsive at the whole community level.

By decomposing community‐level measures of these traits across the gradient, we showed that for the three most responsive traits (N, P and STM), within‐species variation was substantially more important than across‐species variation. This emerges in part because lichen species composition was not very responsive to ecosystem retrogression, and because unlike vascular plants, lichens easily absorb elements over their entire surface, meaning that nutrient concentrations within lichen species are likely to more closely reflect nutrient availability.

We found that within‐species variability drove the changes in community‐weighted measures of lichen traits across a strong environmental gradient, which contrasts strongly with what we know from studies of vascular plants where across‐species variation and species turnover is much more important. To understand how lichen functional traits at the community level respond to environmental factors, it is therefore essential to consider the responses of individual species, and the application of traits‐based approaches to lichen communities needs to account for their considerable intraspecific variability.
Evaluating targets and trade‐offs among fisheries and conservation objectives using a multispecies size spectrum model
Authors: Blanchard Julia L. , Andersen Ken H. , Scott Finlay , Hintzen Niels T. , Piet Gerjan , Jennings Simon
Published: March 2014

Marine environmental management policies seek to ensure that fishing impacts on fished populations and other components of the ecosystem are sustainable, to simultaneously meet objectives for fisheries and conservation. For example, in Europe, targets for (i) biodiversity, (ii) food web structure as indicated by the proportion of large fish and (iii) fishing mortality rates for exploited species that lead to maximum sustainable yield, FMSY, are being proposed to support implementation of the Marine Strategy Framework Directive. Efforts to reconcile any trade‐offs among objectives need to be informed by knowledge on the consequences of alternate management actions.

We develop, calibrate and apply a multispecies size spectrum model of the North Sea fish community to assess the response of populations and the community to fishing. The model predicts species' size distributions, abundance, productivity and interactions and therefore provides a single framework for evaluating trade‐offs between population status, community and food web structure, biodiversity and fisheries yield.

We show that the model can replicate realistic fish population and community structure and past responses to fishing. We assess whether meeting management targets for exploited North Sea populations (fishing species at FMSY) will be sufficient to meet proposed targets for biodiversity and food web indicators under two management scenarios (status quo and FMSY).

The recovery in biodiversity indicators is 60% greater when fishing populations at FMSY than if status quo (2010) fishing rates are maintained. The probability of achieving a food web target was 60% under both scenarios in spite of major community restructuring revealed by other indicators of community size structure.

Synthesis and applications. Our model can be applied to evaluate indicator targets and trade‐offs among fisheries and conservation objectives. There is a significant probability that reductions in fishing mortality below FMSY would be needed in Europe if managers make a binding commitment to a proposed large fish indicator target, with concomitant reductions in fisheries yield.
Pedalling the Death of a Life: A Late Victorian Variation on Dealing with Grief
Authors: Cadwallader Alan H.
Published: March 2014

This article seeks to explore how one forgotten, Victorian‐formed individual sought to deal privately with the death of his publicly esteemed father. Through the journey that carried a cyclist and train traveller from the north to the south of England, we discover the conjunction of athleticism and mortality, place and people, pilgrimage and passages, religion and leisure, photography and memorialisation, discipline and dissipation, networks and mourning. It provides a counterpoint to the accent on death‐bed and grave in Victorian England during a time of national readjustment by arguing that the particular method of dealing with a significant death carved by Henry Westcott for himself was novel, cathartic, and yet constantly interacting with and informed by the legacy of a range of Victorian values. Those values are explored through the writings of his father, Brooke Foss Westcott, a famous biblical exegete who provided a distinctive interpretation of the key scriptural text of Victorian death: the Gospel of John, chapter 11. Those values became a legacy that is both reinforced in Henry through the death of his famous father and also subtly interrogated and eroded as Henry pedalled through the complexities of disentanglement from the paterfamilias, a journey that Henry recorded in diary and photograph.