bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrasound-guided tissue fractionation by high intensity focused ultrasound in an in vivo porcine liver model
Authors: Khokhlova Tatiana D. , Wang Yak-Nam , Simon Julianna C. , Cunitz Bryan W. , Starr Frank , Paun Marla , Crum Lawrence A. , Bailey Michael R. , Khokhlova Vera A.
Published: May 2014

Significance

High intensity focused ultrasound (HIFU) therapy is a promising, clinically adopted method of noninvasive tissue ablation used to treat both benign and malignant conditions. This work presents, to our knowledge, the first in vivo validation of a previously developed HIFU-based method that allows for noninvasive fractionation of targeted tissue into subcellular debris—boiling histotripsy—in a large animal model. While fractionating the targeted soft tissue, boiling histotripsy is shown to spare the adjacent connective tissue structures such as blood vessels. The process can be readily targeted and monitored by B-mode ultrasound. The resulting tissue debris are liquid, which provides a potential clinical benefit over thermal ablation in the treatment of tumors that exert uncomfortable pressure on surrounding tissues.
Spatially robust estimates of biological nitrogen (N) fixation imply substantial human alteration of the tropical N cycle
Authors: Sullivan Benjamin W. , Smith W. Kolby , Townsend Alan R. , Nasto Megan K. , Reed Sasha C. , Chazdon Robin L. , Cleveland Cory C.
Published: May 2014

Significance

Biological nitrogen fixation (BNF) is the largest natural source of new nitrogen (N) to terrestrial ecosystems. Tropical forest ecosystems are a putative global hotspot of BNF, but direct, spatially explicit measurements in the biome are virtually nonexistent. Nonetheless, robust estimates of tropical forest BNF are critical for understanding how these important ecosystems may respond to global change and assessing human perturbations to the N cycle. Here, we introduce a spatial sampling method to assess BNF and present evidence that tropical forest BNF is much lower than previously assumed. Our results imply that humans have roughly doubled N inputs to the tropical forest biome relative to N inputs through BNF.
Hierarchical expression of genes controlled by theBacillus subtilisglobal regulatory protein CodY
Authors: Brinsmade Shaun R. , Alexander Elizabeth L. , Livny Jonathan , Stettner Arion I. , Segrè Daniel , Rhee Kyu Y. , Sonenshein Abraham L.
Published: May 2014

Significance

This report reveals that the more than 200 genes controlled byBacillus subtilisglobal regulatory protein CodY are controlled in a hierarchical manner that reflects the extent of activation of CodY by its ligands. The results suggest thatB. subtilisuses hierarchical regulation by CodY to achieve strategic goals.
Hydrodynamic starvation in first-feeding larval fishes
Authors: China Victor , Holzman Roi
Published: May 2014

Significance

A century ago, Johan Hjort described extreme mortality rates (>99%) of marine fish larvae within days of hatching and termed it the “critical period.” Although multiple hypotheses were raised to explain this mass mortality, the mechanisms behind it remained unresolved. Here, we show that first-feeding larvae experience “hydrodynamic starvation,” in which their hydrodynamic environment mechanistically limits their feeding performance. Our study offers an experimentally supported mechanism of starvation in larval fishes, focusing on the physics of suction feeding in low Reynolds numbers, rather than on prey concentrations and encounter. We believe our findings can help to better understand the early life history of marine fish and the selective forces they experience during the pelagic larval phase.
Exploring the collaboration between antibiotics and the immune response in the treatment of acute, self-limiting infections
Authors: Ankomah Peter , Levin Bruce R.
Published: May 2014

Significance

We use a mathematical model and computer simulations to explore the design and evaluation of antibiotic treatment protocols for an acute, self-limiting bacterial infection. We consider the effect of dose, dosing frequency, and term of treatment on the time before clearance of the infection and the likelihood of resistance emerging and ascending during therapy. Our analysis supports high-dose, full-term antimicrobial chemotherapy as the most effective strategy for maximizing the rate of cure and minimizing the de novo evolution of resistance during the course of therapy. We discuss the current status of data in support of and against the predictions of this study and identify potential ways of testing the hypotheses derived from our analysis.
The small GTPase RAB-11 directs polarized exocytosis of the intracellular pathogen
N. parisii
for fecal-oral transmission from
C. elegans
Authors: Szumowski Suzannah C. , Botts Michael R. , Popovich John J. , Smelkinson Margery G. , Troemel Emily R.
Published: May 2014

Significance

Microbial pathogens cause food and water-borne disease through infection of the intestine. Many of these pathogens invade intestinal cells to replicate, but they ultimately need to exit out of these cells to spread to new hosts. We use the transparent nematode
Caenorhabditis elegans
to show that a natural intracellular pathogen called
Nematocida parisii
escapes from intestinal cells by using host trafficking pathways and a host small GTPase protein called RAB-11 for directional exocytosis into the lumen.
N. parisii
belongs to a large phylum of pathogens called microsporidia that can infect all animals, including humans, so our findings may be broadly applicable to understanding how agriculturally and medically relevant diseases are spread.
Iron chaperones PCBP1 and PCBP2 mediate the metallation of the dinuclear iron enzyme deoxyhypusine hydroxylase
Authors: Frey Avery G. , Nandal Anjali , Park Jong Hwan , Smith Pamela M. , Yabe Toshiki , Ryu Moon-Suhn , Ghosh Manik C. , Lee Jaekwon , Rouault Tracey A. , Park Myung Hee , Philpott Caroline C.
Published: May 2014

Significance

One-third of the proteins expressed in eukaryotic and prokaryotic cells may require bound metal ions or metal cofactors for activity. In human cells, the processes by which proteins acquire their native cofactors and avoid mismetallation are largely unknown. The multifunctional adaptor proteins poly(rC)-binding protein (PCBP)1 and PCBP2 are iron chaperones that deliver ferrous iron via a metal-mediated, protein–protein interaction. Three PCBP targets have been identified: ferritin, an iron storage protein; and prolyl and asparagyl hydroxylase, two mononuclear iron enzymes. Here, we show that PCBP1 and PCBP2 deliver iron to deoxyhypusine hydroxylase, a dinuclear iron enzyme representing a major class of nonheme iron enzymes. PCBPs may generally function to maintain nonheme iron cofactors in cytosolic enzymes, especially when iron becomes scarce.
Chapter 6. Graphics and invention in academic engineers’ writing for publication
Authors: Curry Mary Jane
Published: May 2014

This chapter explores how academic engineers write for publication, focusing on “invention” – that is, moments when writers identify the research results they want to present and decide on the arguments they want to make in an article. A key finding presented is that beyond the well-documented role of graphics in displaying research results, graphics also play a crucial heuristic role in invention. This finding emerged from an ethnographic study of three engineering research groups, which entailed the analysis of a range of qualitative data to offer perspectives on the experiences of academic engineers writing for publication. Drawing on this research, the chapter documents that in developing texts for publication, engineers often begin with the graphic results of data analysis to identify findings and begin to craft arguments. Further, in research group and informal meetings, engineers invoke the notion of storytelling through graphics as they socialize their group members into the practices of research dissemination via posters and articles.
Subjectivity, intersubjectivity and Japanese grammar
Authors: Shinzato Rumiko
Published: May 2014

This survey study intends to show the benefits of adopting the functional linguistic perspectives of emphasizing the non-referential and emotive/subjective aspects of language, which are largely neglected in mainstream formalist linguistics. Specifically, this paper will first point out the fact that both Japanese linguist Haga and French linguist Benveniste independently proposed very similar dichotomies, juttei vs. dentatsu (Haga 1954) and subjectivity vs. intersubjectivity (Benveniste 1971[1958]) for their analyses of the non-propositional parts of language. Subsequently, drawing upon published studies, this paper will point out the relevance of these two dichotomies to syntactic organization (predicate order in particular), soliloquy and dialogue (or mental and speech act) dyad, and diachronic change (namely, the unidirectionality in grammaticalization from subjectification > intersubjectification (Traugott 2003).
Consumer Markets' Trust Regimes across Europe
Authors: Berg Lisbet
Published: May 2014

Given the importance of trust and confidence for the individual consumer's well-being and societies' overall consumer conditions, this paper intends to conceptualize, investigate and map European consumer markets' trust regimes. Based on statistics from DG Sanco's Consumer Condition Scoreboard 2012, trust dimensions in 29 European countries (EU27 + Norway and Iceland) are reanalyzed and compared. The material reveals large differences in consumer markets' trust regime levels across Europe. This paper suggests that one way people evaluate consumer market institutions, is by their perceptions of food and product safety. The concluding discussion gives attention to possible discrepancies between consumer markets' trust regimes and consumer institutions' trustworthiness.
History of Arab cinema (introduction to understanding and interpretation)
Authors: Messnaoui Mostafa
Published: May 2014

Since the inception of cinema, historians have totally ignored or only briefly mentioned Arab productions and achievements in their depictions of the history of cinema. Therefore, some Arab writers, such as Jalal Sharqawi, broke an Arab ‘tradition’ of confining works on cinema to narrating stories about movie stars and ‘subject inventories’ to talk about this cinema and its history. Another concern was that technical cinematic terms translated into Arabic were frequently inaccurate and included some major mistakes which made the Arab reader misunderstand this history. Aside from that, though, the general lack of interest of Arab readers in all cognitive fields and their lack of awareness of history and the need for it may be the core of the problem. The main focus of historians of Arab cinema is Egypt, thus relegating all other countries to the margins, although many Arab cinemas have proved themselves internationally in the field of production, including Morocco, Tunisia and Lebanon, while the United Arab Emirates have been pioneering in the field of film festivals, keeping pace with the modernization witnessed in Dubai and Abu Dhabi. The main problem, however, resides in the allocation of public or private funding for film production, while overlooking other significant cinema-related issues, such as the availability of cinema halls and training institutes.
Islamists between revolution and the state: an epilogue
Authors: Imad Abdul Ghani
Published: May 2014

The problematic addressed in this article is the challenge initiated by the Arab revolutions to reform the Arab political system in such a way as to facilitate the incorporation of ‘democracy’ at the core of its structure. Given the profound repercussions, this issue has become the most serious matter facing the forces of change in the Arab world today; meanwhile, it forms the most prominent challenge and the most difficult test confronting Islamists. The Islamist phenomenon is not an alien implant that descended upon us from another planet beyond the social context or manifestations of history. Thus it cannot but be an expression of political, cultural, and social needs and crises. Over the years this phenomenon has presented, through its discourse, an ideological logic that falls within the context of ‘advocacy’; however, today Islamists find themselves in office, and in a new context that requires them to produce a new type of discourse that pertains to the context of a ‘state’. Political participation ‘tames’ ideology and pushes political actors to rationalize their discourse in the face of daily political realities and the necessity of achievement. The logic of advocacy differs from that of the state: in the case of advocacy, ideology represents an enriching asset, whereas in the case of the state, it constitutes a heavy burden. This is one reason why so much discourse exists within religious jurisprudence related to interest or necessity or balancing outcomes. This article forms an epilogue to the series of articles on religion and the state published in previous issues of this journal. It adopts the methodologies of ‘discourse analysis’ and ‘case studies’ in an attempt to examine the arguments presented by Islamists under pressure from the opposition. It analyses the experiences, and the constraints, that inhibit the production of a ‘model’, and monitors the development of the discourse, its structure, and transformations between advocacy, revolution and the state.
An image-based RNAi screen identifies SH3BP1 as a key effector of Semaphorin 3E–PlexinD1 signaling
Authors: Tata Aleksandra , Stoppel David C. , Hong Shangyu , Ben-Zvi Ayal , Xie Tiao , Gu Chenghua
Published: May 2014

Extracellular signals have to be precisely interpreted intracellularly and translated into diverse cellular behaviors often mediated by cytoskeletal changes. Semaphorins are one of the largest families of guidance cues and play a critical role in many systems. However, how different cell types translate extracellular semaphorin binding into intracellular signaling remains unclear. Here we developed and performed a novel image-based genome-wide functional RNAi screen for downstream signaling molecules that convert the interaction between Semaphorin 3E (Sema3E) and PlexinD1 into cellular behaviors. One of the genes identified in this screen is a RhoGAP protein, SH3-domain binding protein 1 (SH3BP1). We demonstrate that SH3BP1 mediates Sema3E-induced cell collapse through interaction with PlexinD1 and regulation of Ras-related C3 botulinum toxin substrate 1 (Rac1) activity. The identification and characterization of SH3BP1 as a novel downstream effector of Sema3E-PlexinD1 provides an explanation for how extracellular signals are translated into cytoskeletal changes and unique cell behavior, but also lays the foundation for characterizing other genes identified from our screen to obtain a more complete picture of plexin signaling.
Assembly factors monitor sequential hemylation of cytochrome b to regulate mitochondrial translation
Authors: Hildenbeutel Markus , Hegg Eric L. , Stephan Katharina , Gruschke Steffi , Meunier Brigitte , Ott Martin
Published: May 2014

Mitochondrial respiratory chain complexes convert chemical energy into a membrane potential by connecting electron transport with charge separation. Electron transport relies on redox cofactors that occupy strategic positions in the complexes. How these redox cofactors are assembled into the complexes is not known. Cytochrome b, a central catalytic subunit of complex III, contains two heme bs. Here, we unravel the sequence of events in the mitochondrial inner membrane by which cytochrome b is hemylated. Heme incorporation occurs in a strict sequential process that involves interactions of the newly synthesized cytochrome b with assembly factors and structural complex III subunits. These interactions are functionally connected to cofactor acquisition that triggers the progression of cytochrome b through successive assembly intermediates. Failure to hemylate cytochrome b sequesters the Cbp3–Cbp6 complex in early assembly intermediates, thereby causing a reduction in cytochrome b synthesis via a feedback loop that senses hemylation of cytochrome b.
In vivo imaging reveals PKA regulation of ERK activity during neutrophil recruitment to inflamed intestines
Authors: Mizuno Rei , Kamioka Yuji , Kabashima Kenji , Imajo Masamichi , Sumiyama Kenta , Nakasho Eiji , Ito Takeshi , Hamazaki Yoko , Okuchi Yoshihisa , Sakai Yoshiharu , Kiyokawa Etsuko , Matsuda Michiyuki
Published: May 2014

Many chemical mediators regulate neutrophil recruitment to inflammatory sites. Although the actions of each chemical mediator have been demonstrated with neutrophils in vitro, how such chemical mediators act cooperatively or counteractively in vivo remains largely unknown. Here, by in vivo two-photon excitation microscopy with transgenic mice expressing biosensors based on Förster resonance energy transfer, we time-lapse–imaged the activities of extracellular signal–regulated kinase (ERK) and protein kinase A (PKA) in neutrophils in inflamed intestinal tissue. ERK activity in neutrophils rapidly increased during spreading on the endothelial cells and showed positive correlation with the migration velocity on endothelial cells or in interstitial tissue. Meanwhile, in the neutrophils migrating in the interstitial tissue, high PKA activity correlated negatively with migration velocity. In contradiction to previous in vitro studies that showed ERK activation by prostaglandin E2 (PGE2) engagement with prostaglandin receptor EP4, intravenous administration of EP4 agonist activated PKA, inhibited ERK, and suppressed migration of neutrophils. The opposite results were obtained using nonsteroidal antiinflammatory drugs (NSAIDs). Therefore, NSAID-induced enteritis may be caused at least partially by the inhibition of EP4 receptor signaling of neutrophils. Our results demonstrate that ERK positively regulates the neutrophil recruitment cascade by promoting adhesion and migration steps.
MicroRNAs in Right Ventricular (dys)function (2013 Grover Conference Series)
Authors: Thum Thomas , Batkai Sandor
Published: May 2014

MicroRNAs (miRNAs) are molecules increasingly investigated for both diagnostic and therapeutic strategies. Whereas information about their role in the left ventricle has been studied for many years, there is scarce information about the right ventricle. We thus here review known details about the expression, regulation, and function of miRNAs in right heart diseases. Current identified therapeutic strategies using miRNA modulators to treat pulmonary hypertension and thus also having beneficial effects on the right ventricle are also discussed. Finally, the current knowledge about the diagnostic and predictive use of circulating miRNAs in patients with pulmonary hypertension and right ventricular failure is presented. There is strong hope that the increasing knowledge about miRNAs in the right heart will finally help to improve the treatment of patients with pulmonary and right ventricular heart diseases.
Lower volume growth estimates for self-shrinkers of mean curvature flow
Authors: Li Haizhong , Wei Yong
Published: May 2014

We obtain a Calabi-Yau type volume growth estimate for complete noncompact self-shrinkers of the mean curvature flow. More precisely, every complete noncompact properly immersed self-shrinker has at least linear volume growth.
Yang–Baxter deformations and rack cohomology
Authors: Eisermann Michael
Published: May 2014

In his study of quantum groups, Drinfeld suggested considering set-theoretic solutions of the Yang–Baxter equation as a discrete analogon. As a typical example, every conjugacy class in a group or, more generally, every rack

Q
Q

provides such a Yang–Baxter operator

c
Q

:
x
⊗
y
↦
y
⊗

x
y

c_Q \colon x \otimes y \mapsto y \otimes x^y

. In this article we study deformations of

c
Q

c_Q

within the space of Yang–Baxter operators over some complete ring. Infinitesimally these deformations are classified by Yang–Baxter cohomology. We show that the Yang–Baxter cochain complex of

c
Q

c_Q

homotopy-retracts to a much smaller subcomplex, called quasi-diagonal. This greatly simplifies the deformation theory of

c
Q

c_Q

, including the modular case which had previously been left in suspense, by establishing that every deformation of

c
Q

c_Q

is gauge equivalent to a quasi-diagonal one. In a quasi-diagonal deformation only behaviourally equivalent elements of

Q
Q

interact; if all elements of

Q
Q

are behaviourally distinct, then the Yang–Baxter cohomology of

c
Q

c_Q

collapses to its diagonal part, which we identify with rack cohomology. This establishes a strong relationship between the classical deformation theory following Gerstenhaber and the more recent cohomology theory of racks, both of which have numerous applications in knot theory.
An 𝐿^{𝑝} regularity theory for harmonic maps
Authors: Moser Roger
Published: May 2014

Motivated by the harmonic map heat flow, we consider maps between Riemannian manifolds such that the tension field belongs to an

L
p

L^p

-space. Under an appropriate smallness condition, a certain degree of regularity follows. For suitable solutions of the harmonic map heat flow, we have a partial regularity result as a consequence.
Les Enjeux des animaux (humains) chez Michel Houellebecq, du darwinisme au post-humanisme
Authors: Posthumus Stephanie
Published: May 2014

Le présent article se propose d'analyser la représentation des êtres humains et non-humains dans deux romans de l'auteur français contemporain Michel Houellebecq:
Les Particules élémentaires
(1998) et
La Possibilité d'une île
(2005). Dans un premier temps, il sera question d'examiner le cadre darwiniste tel que mis en évidence dans
Les Particules élémentaires
, où le lien entre humains et animaux est affirmé, mais où les animaux ne sont qu'un miroir de la cruauté humaine. Dans un deuxième temps, il s'agira d'analyser le cadre post-humain dans
La Possibilité d'une île
, où l'on trouve un portrait plus complet du monde après la fin de la civilisation humaine, mais où la promesse de l'être post-humain comme dépassement de l'être humain ne se réalise pas. Tout en maintenant la thèse de la lutte du plus fort, le deuxième roman n'embrasse pas la fin de l'espèce humaine comme le premier; il cherche plutôt à redéfinir ce qu'est l'humain, non pas comme animal darwiniste, mais comme
homo literatus
, c'est-à-dire comme être capable de raconter sa vie. Ainsi, la littérature s'avère le lieu où et par lequel l'être humain se définit continuellement et indéfiniment.
The Arecibo Galaxy Environment Survey – VIII. Discovery of an isolated dwarf galaxy in the Local Volume
Authors: Taylor R. , Minchin R. F. , Herbst H. , Smith R.
Published: May 2014

The Arecibo Galaxy Environment Survey has detected a nearby H i source at a heliocentric velocity of +363 km s−1. The object was detected through its neutral hydrogen emission and has an obvious possible optical counterpart in Sloan Digital Sky Survey data (though it does not have an optical redshift measurement). We discuss three possible scenarios for the object: (1) it is within the Local Group, in which case its H i properties are comparable with recently discovered ultracompact high-velocity clouds; (2) it is just behind the Local Group, in which case its optical characteristics are similar to the newly discovered Leo P galaxy; (3) it is a blue compact dwarf galaxy within the local volume but not associated with the Local Group. We find the third possibility to be the most likely, based on distance estimates from the Tully–Fisher relation and its velocity relative to the Local Group.
Very high energy γ-ray emission from RBS 0970
Authors: Brown Anthony M.
Published: May 2014

In this Letter I report the Fermi Large Area Telescope (LAT) detection of very high energy (VHE; E > 100 GeV) γ-ray emission from the BL Lac object RBS 0970. 5.3 years of LAT observations revealed the presence of three VHE photon events within 0$_{.}^{\circ}$1 of RBS 0970, with a subsequent unbinned likelihood analysis finding RBS 0970 to be a source of VHE photons at the 6.5σ level of confidence. The ≥1 GeV flux, binned in monthly periods, did not indicate any flux brightening of RBS 0970 accompanying the emission of the VHE photons. However, a likelihood analysis of the 0.1-100 GeV flux, binned in 28 d periods centred on detection of the VHE photons, revealed that the emission of the lowest energy VHE photons coincided with a hardening of the γ-ray spectrum. Interestingly, the same analysis did not find any significant γ-ray emission from RBS 0970 during the emission of the highest energy VHE event. The discovery of RBS 0970 as a VHE emitter, combined with the spectral variability, suggest RBS 0970 to be a good candidate for follow-up observations with ground-based γ-ray observatories.
Broad-band spectroscopy of Hercules X-1 with Suzaku
Authors: Asami Fumi , Enoto Teruaki , Iwakiri Wataru , Yamada Shin’ya , Tamagawa Toru , Mihara Tatehiro , Nagase Fumiaki
Published: May 2014

Hercules X-1 was observed with Suzaku in the main-on state from 2005 to 2010. The 0.4–100 keV wide-band spectra obtained in four observations showed a broad hump around 4–9 keV in addition to narrow Fe lines at 6.4 and 6.7 keV. The hump was seen in all the four observations regardless of the selection of the continuum models. Thus it is considered a stable and intrinsic spectral feature in Her X-1. The broad hump lacked a sharp structure like an absorption edge. Thus it was represented by two different spectral models: an ionized partial covering or an additional broad line at 6.5 keV. The former required a persistently existing ionized absorber, whose origin was unclear. In the latter case, the Gaussian fitting of the 6.5-keV line needs a large width of σ = 1.0–1.5 keV and a large equivalent width of 400–900 eV. If the broad line originates from Fe fluorescence of accreting matter, its large width may be explained by the Doppler broadening in the accretion flow. However, the large equivalent width may be inconsistent with a simple accretion geometry.
Influence of shear motion on evolution of molecular clouds in the spiral galaxy M 51
Authors: Miyamoto Yusuke , Nakai Naomasa , Kuno Nario
Published: May 2014

We have investigated the dynamics of the molecular gas and the evolution of giant molecular associations (GMAs) in the spiral galaxy M 51 with the Nobeyama Radio Observatory 45-m telescope. The velocity components of the molecular gas perpendicular and parallel to the spiral arms are derived at each spiral phase from the distribution of the line-of-sight velocity of the CO gas. In addition, the shear motion in the galactic disk is determined from the velocity vectors at each spiral phase. It is revealed that the distributions of the shear strength and of GMAs are anti-correlated. GMAs exist only in the area of the weak shear strength and further on the upstream side of the high shear strength. GMAs and most giant molecular clouds (GMCs) exist in the regions where the shear critical surface density is smaller than the gravitational critical surface density, indicating that they can stably grow by self-gravity and the collisional agglomeration of small clouds without being destroyed by shear motion. These factors indicate that the shear motion is an important factor in evolution of GMCs and GMAs.
X-ray development of the classical nova V2672 Ophiuchi with Suzaku
Authors: Takei Dai , Tsujimoto Masahiro , Drake Jeremy J. , Kitamoto Shunji
Published: May 2014

We report on the Suzaku detection of a rapid flare-like X-ray flux amplification early in the development of the classical nova V2672 Ophiuchi. Two target-of-opportunity ∼ 25 ks X-ray observations were made 12 and 22 d after the outburst. The flux amplification was found in the latter half of day 12. Time-sliced spectra are characterized by a growing supersoft excess with edge-like structures and a relatively stable optically-thin thermal component with Kα emission lines from highly ionized Si. The observed spectral evolution is consistent with a model that has a time development of circumstellar absorption, for which we obtained a decline rate of ∼ 10%–40% on a time scale of 0.2 d on day 12. Such a rapid drop of absorption and short-term flux variability on day 12 suggests inhomogeneous ejecta with dense blobs/holes in the line-of-sight. Then on day 22 the fluxes of both supersoft and thin-thermal plasma components became significantly fainter. Based on the serendipitous results we discuss the nature of this source in the context of both short- and long-term X-ray behavior.
Markov chain algorithms: a template for building future robust low-power systems
Authors: Deka Biplab , Birklykke Alex A. , Duwe Henry , Mansinghka Vikash K. , Kumar Rakesh
Published: May 2014

Although computational systems are looking towards post CMOS devices in the pursuit of lower power, the expected inherent unreliability of such devices makes it difficult to design robust systems without additional power overheads for guaranteeing robustness. As such, algorithmic structures with inherent ability to tolerate computational errors are of significant interest. We propose to cast applications as stochastic algorithms based on Markov chains (MCs) as such algorithms are both sufficiently general and tolerant to transition errors. We show with four example applications—Boolean satisfiability, sorting, low-density parity-check decoding and clustering—how applications can be cast as MC algorithms. Using algorithmic fault injection techniques, we demonstrate the robustness of these implementations to transition errors with high error rates. Based on these results, we make a case for using MCs as an algorithmic template for future robust low-power systems.
Inexactness and a future of computing
Authors: Palem Krishna V.
Published: May 2014

As pressures, notably from energy consumption, start impeding the growth and scale of computing systems, inevitably, designers and users are increasingly considering the prospect of trading accuracy or
exactness
. This paper is a perspective on the progress in embracing this somewhat unusual philosophy of innovating computing systems that are designed to be
inexact
or
approximate
, in the interests of realizing extreme efficiencies. With our own experience in designing inexact physical systems including hardware as a backdrop, we speculate on the rich potential for considering inexactness as a broad emerging theme if not an entire domain for investigation for exciting research and innovation. If this emerging trend to pursuing inexactness persists and grows, then we anticipate an increasing need to consider system co-design where application domain characteristics and technology features interplay in an active manner. A noteworthy early example of this approach is our own excursion into tailoring and hence co-designing floating point arithmetic units guided by the needs of stochastic climate models. This approach requires a unified effort between software and hardware designers that does away with the normal clean abstraction layers between the two.
Influence of stochastic sea ice parametrization on climate and the role of atmosphere–sea ice–ocean interaction
Authors: Juricke Stephan , Jung Thomas
Published: May 2014

The influence of a stochastic sea ice strength parametrization on the mean climate is investigated in a coupled atmosphere–sea ice–ocean model. The results are compared with an uncoupled simulation with a prescribed atmosphere. It is found that the stochastic sea ice parametrization causes an effective weakening of the sea ice. In the uncoupled model this leads to an Arctic sea ice volume increase of about 10–20% after an accumulation period of approximately 20–30 years. In the coupled model, no such increase is found. Rather, the stochastic perturbations lead to a spatial redistribution of the Arctic sea ice thickness field. A mechanism involving a slightly negative atmospheric feedback is proposed that can explain the different responses in the coupled and uncoupled system. Changes in integrated Antarctic sea ice quantities caused by the stochastic parametrization are generally small, as memory is lost during the melting season because of an almost complete loss of sea ice. However, stochastic sea ice perturbations affect regional sea ice characteristics in the Southern Hemisphere, both in the uncoupled and coupled model. Remote impacts of the stochastic sea ice parametrization on the mean climate of non-polar regions were found to be small.
Assessing parametrization uncertainty associated with horizontal resolution in numerical weather prediction models
Authors: Shutts Glenn , Pallarès Alfons Callado
Published: May 2014

The need to represent uncertainty resulting from model error in ensemble weather prediction systems has spawned a variety of
ad hoc
stochastic algorithms based on plausible assumptions about sub-grid-scale variability. Currently, few studies have been carried out to prove the veracity of such schemes and it seems likely that some implementations of stochastic parametrization are misrepresentations of the true source of model uncertainty. This paper describes an attempt to quantify the uncertainty in physical parametrization tendencies in the European Centre for Medium-Range Weather Forecasts (ECMWF) Integrated Forecasting System with respect to horizontal resolution deficiency. High-resolution
truth
forecasts are compared with matching
target
forecasts at much lower resolution after coarse-graining to a common spatial and temporal resolution. In this way, model error is defined and its probability distribution function is examined as a function of tendency magnitude. It is found that the temperature tendency error associated with convection parametrization and explicit water phase changes behaves like a Poisson process for which the variance grows in proportion to the mean, which suggests that the assumptions underpinning the Craig and Cohen statistical model of convection might also apply to parametrized convection. By contrast, radiation temperature tendency errors have a very different relationship to their mean value. These findings suggest that the ECMWF stochastic perturbed parametrization tendency scheme could be improved since it assumes that the standard deviation of the tendency error is proportional to the mean. Using our finding that the variance error is proportional to the mean, a prototype stochastic parametrization scheme is devised for convective and large-scale condensation temperature tendencies and tested within the ECMWF Ensemble Prediction System. Significant impact on forecast skill is shown, implying its potential for further development.
Increasing horizontal resolution in numerical weather prediction and climate simulations: illusion or panacea?
Authors: Wedi Nils P.
Published: May 2014

The steady path of doubling the global horizontal resolution approximately every 8 years in numerical weather prediction (NWP) at the European Centre for Medium Range Weather Forecasts may be substan- tially altered with emerging novel computing architectures. It coincides with the need to appropriately address and determine forecast uncertainty with increasing resolution, in particular, when convective-scale motions start to be resolved. Blunt increases in the model resolution will quickly become unaffordable and may not lead to improved NWP forecasts. Consequently, there is a need to accordingly adjust proven numerical techniques. An informed decision on the modelling strategy for harnessing exascale, massively parallel computing power thus also requires a deeper understanding of the sensitivity to uncertainty—for each part of the model—and ultimately a deeper understanding of multi-scale interactions in the atmosphere and their numerical realization in ultra-high-resolution NWP and climate simulations. This paper explores opportunities for substantial increases in the forecast efficiency by judicious adjustment of the formal accuracy or relative resolution in the spectral and physical space. One path is to reduce the formal accuracy by which the spectral transforms are computed. The other pathway explores the importance of the ratio used for the horizontal resolution in gridpoint space versus wavenumbers in spectral space. This is relevant for both high-resolution simulations as well as ensemble-based uncertainty estimation.
Control of morphogenesis, protease secretion and gene expression in Candida albicans by the preferred nitrogen source ammonium
Authors: Dunkel Nico , Biswas Kajal , Hiller Ekkehard , Fellenberg Kurt , Satheesh Somisetty V. , Rupp Steffen , Morschhäuser Joachim
Published: May 2014

Micro-organisms sense the availability of nutrients in their environment to control cellular behaviour and the expression of transporters and enzymes that are required for the utilization of these nutrients. In the pathogenic yeastCandida albicans, the preferred nitrogen source ammonium suppresses the switch from yeast to filamentous growth in response to certain stimuli, and it also represses the secretion of proteases, which are required for the utilization of proteins as an alternative nitrogen source. To investigate whetherC. albicanssenses the availability of ammonium in the extracellular environment or if ammonium uptake into the cell is required to regulate morphogenesis and gene expression, we compared the behaviour of wild-type cells and ammonium uptake-deficient mutants in the presence and absence of extracellular ammonium. Arginine-induced filamentous growth was suppressed by ammonium in the wild-type, but not in mutants lacking the ammonium permeases Mep1 and Mep2. Similarly, ammonium suppressed protease secretion and extracellular protein degradation in the wild-type, but not in mutants lacking the ammonium transporters. By comparing the gene expression profiles ofC. albicansgrown in the presence of low or high ammonium concentrations, we identified a set of genes whose expression is controlled by nitrogen availability. The repression of genes involved in the utilization of alternative nitrogen sources, which occurred under ammonium-replete conditions in the wild-type, was abrogated inmep1Δmep2Δ mutants. These results demonstrate thatC. albicansdoes not respond to the presence of sufficient amounts of the preferred nitrogen source ammonium by sensing its availability in the environment. Instead, ammonium has to be taken up into the cell to control morphogenesis, protease secretion and gene expression.
Automation and Evaluation of the SOWH Test with SOWHAT
Authors: Church Samuel H. , Ryan Joseph F. , Dunn Casey W.
Published: May 2014

The Swofford-Olsen-Waddell-Hillis (SOWH) test evaluates statistical support for incongruent phylogenetic topologies. It is commonly applied to determine if the maximum likelihood tree in a phylogenetic analysis is significantly different than an alternative hypothesis. The SOWH test compares the observed difference in likelihood between two topologies to a null distribution of differences in likelihood generated by parametric resampling. The test is a well-established phylogenetic method for topology testing, but is is sensitive to model misspecification, it is computationally burdensome to perform, and its implementation requires the investigator to make multiple decisions that each have the potential to affect the outcome of the test. We analyzed the effects of multiple factors using seven datasets to which the SOWH test was previously applied. These factors include bootstrap sample size, likelihood software, the introduction of gaps to simulated data, the use of distinct models of evolution for data simulation and likelihood inference, and a suggested test correction wherein an unresolved “zero-constrained” tree is used to simulate sequence data. In order to facilitate these analyses and future applications of the SOWH test, we wrote SOWHAT, a program that automates the SOWH test. We find that inadequate bootstrap sampling can change the outcome of the SOWH test. The results also show that using a zero-constrained tree for data simulation can result in a wider null distribution and higher p-values, but does not change the outcome of the SOWH test for most datasets. These results will help others implement and evaluate the SOWH test and allow us to provide recommendation for future applications of the SOWH test. SOWHAT is available for download fromhttps://github.com/josephryan/SOWHAT.
Phylogenetic confidence intervals for the optimal trait value
Authors: Bartoszek Krzysztof , Sagitov Serik
Published: May 2014

We consider a stochastic evolutionary model for a phenotype developing amongstnrelated species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned onncontemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein-Uhlenbeck process. As a result, the trait values of thenspecies form a sample with dependent observations. We establish three limit theorems for the sample mean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean is approximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.
Cytochrome P450 93G1 Is a Flavone Synthase II That Channels Flavanones to the Biosynthesis of Tricin O-Linked Conjugates in Rice
Authors: Lam Pui Ying , Zhu Fu-Yuan , Chan Wai Lung , Liu Hongjia , Lo Clive
Published: May 2014

Flavones are a major class of flavonoids with a wide range of physiological functions in plants. They are constitutively accumulated as C-glycosides and O-linked conjugates in vegetative tissues of grasses. It has long been presumed that the two structural modifications of flavones occur through independent metabolic routes. Previously, we reported that cytochrome P450 93G2 (CYP93G2) functions as a flavanone 2-hydroxylase (F2H) that provides 2-hydroxyflavanones for C-glycosylation in rice (Oryza sativa). Flavone C-glycosides are subsequently formed by dehydratase activity on 2-hydroxyflavanone C-glycosides. On the other hand, O-linked modifications were proposed to proceed after the flavone nucleus is generated. In this study, we demonstrate that CYP93G1, the closest homolog of CYP93G2 in rice, is a bona fide flavone synthase II (FNSII) that catalyzes the direct conversion of flavanones to flavones. In recombinant enzyme assays, CYP93G1 desaturated naringenin and eriodictyol to apigenin and luteolin, respectively. Consistently, transgenic expression of CYP93G1 in Arabidopsis (Arabidopsis thaliana) resulted in the accumulation of different flavone O-glycosides, which are not naturally present in cruciferous plants. Metabolite analysis of a rice CYP93G1 insertion mutant further demonstrated the preferential depletion of tricin O-linked flavanolignans and glycosides. By contrast, redirection of metabolic flow to the biosynthesis of flavone C-glycosides was observed. Our findings established that CYP93G1 is a key branch point enzyme channeling flavanones to the biosynthesis of tricin O-linked conjugates in rice. Functional diversification of F2H and FNSII in the cytochrome P450 CYP93G subfamily may represent a lineage-specific event leading to the prevalent cooccurrence of flavone C- and O-linked derivatives in grasses today.
3-(4-Bromophenyl)cyclopent-2-en-1-one
Authors: Shurdha Endrit , Dees Kelsey , Miller Hannah A. , Iacono Scott T. , Balaich Gary J.
Published: May 2014

In the title compound, C11H9BrO, the cyclopentenone ring is almost planar with an r.m.s. deviation of 0.0097 Å. The largest inter-ring torsion angles [2.4 (3), 1.3 (3) and 3.53 (2)°] reveal only a very small twist between the rings, and suggest that the two rings are conjugated. The molecule is slightly bowed, as shown by the small dihedral angle between the rings [5.3 (1)°]. The crystal packing pattern consists of parallel sheets that stack parallel to theacplane. Each sheet consists of molecules that pack side-to-side with the same relative orientation of phenyl and cyclopentenone rings along thea- andc-axis directions. Slipped side-to-side, face-to-face and edge-to-face interactions exist between pairs of sheets with edge-to-edge and edge-to-face O...H—C(sp2) weak hydrogen-bond contacts. A relatively short edge-to-face contact (2.77 Å) also exists between pairs of sheets.
2,4,6-Trinitrophenyl 3-bromobenzoate
Authors: Moreno-Fuquen Rodolfo , Mosquera Fabricio , Ellena Javier , Tenorio Juan C.
Published: May 2014

In the title picryl-substituted ester, C13H6BrN3O8, the mean plane of the central ester C–O–C(=O)–C fragment (r.m.s. deviation= 0.0186 Å) is rotated by 84.73 (7)° and 19.92 (12)° to the picryl and phenyl rings, respectively. In the crystal, the molecules are linked by C—H...O interactions, forming centrosymmetric dimers enclosingR22(10) andR22(22) ring motifs along [001] and further helical chains of dimers enclosingR22(10) ring motifs along [010].
REVIEW: Can retention forestry help conserve biodiversity? A meta‐analysis
Authors: Fedrowitz Katja , Koricheva Julia , Baker Susan C. , Lindenmayer David B. , Palik Brian , Rosenvald Raul , Beese William , Franklin Jerry F. , Kouki Jari , Macdonald Ellen , Messier Christian , Sverdrup‐Thygeson Anne , Gustafsson Lena
Published: May 2014

Industrial forestry typically leads to a simplified forest structure and altered species composition. Retention of trees at harvest was introduced about 25 years ago to mitigate negative impacts on biodiversity, mainly from clearcutting, and is now widely practiced in boreal and temperate regions. Despite numerous studies on response of flora and fauna to retention, no comprehensive review has summarized its effects on biodiversity in comparison to clearcuts as well as un‐harvested forests.

Using a systematic review protocol, we completed a meta‐analysis of 78 studies including 944 comparisons of biodiversity between retention cuts and either clearcuts or un‐harvested forests, with the main objective of assessing whether retention forestry helps, at least in the short term, to moderate the negative effects of clearcutting on flora and fauna.

Retention cuts supported higher richness and a greater abundance of forest species than clearcuts as well as higher richness and abundance of open‐habitat species than un‐harvested forests. For all species taken together (i.e. forest species, open‐habitat species, generalist species and unclassified species), richness was higher in retention cuts than in clearcuts.

Retention cuts had negative impacts on some species compared to un‐harvested forest, indicating that certain forest‐interior species may not survive in retention cuts. Similarly, retention cuts were less suitable for some open‐habitat species compared with clearcuts.

Positive effects of retention cuts on richness of forest species increased with proportion of retained trees and time since harvest, but there were not enough data to analyse possible threshold effects, that is, levels at which effects on biodiversity diminish. Spatial arrangement of the trees (aggregated vs. dispersed) had no effect on either forest species or open‐habitat species, although limited data may have hindered our capacity to identify responses. Results for different comparisons were largely consistent among taxonomic groups for forest and open‐habitat species, respectively.

Synthesis and applications. Our meta‐analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention. Nevertheless, retention forestry will not substitute for conservation actions targeting certain highly specialized species associated with forest‐interior or open‐habitat conditions.