bluuebunny/crossref_metadata_2025 huggingface dataset:
Dosimetric and deformation effects of image‐guided interventions during stereotactic body radiation therapy of the prostate using an endorectal balloon
Authors: Jones Bernard L. , Gan Gregory , Diot Quentin , Kavanagh Brian , Timmerman Robert D. , Miften Moyed
Published: May 2012

Purpose:

During stereotactic body radiation therapy (SBRT) for the treatment of prostate cancer, an inflatable endorectal balloon (ERB) may be used to reduce motion of the target and reduce the dose to the posterior rectal wall. This work assessed the dosimetric impact of manual interventions on ERB position in patients receiving prostate SBRT and investigated the impact of ERB interventions on prostate shape.

Methods:

The data of seven consecutive patients receiving SBRT for the treatment of clinical stage T1cN0M0 prostate cancer enrolled in a multi‐institutional, IRB‐approved trial were analyzed. The SBRT dose was 50 Gy in five fractions to a planning target volume (PTV) that included the prostate (implanted with three fiducial markers) with a 3–5 mm margin. All plans were based on simulation images that included an ERB inflated with 60 cm3 of air. Daily kilovoltage cone‐beam computed tomography (CBCT) imaging was performed to localize the PTV, and an automated fusion with the planning images yielded displacements required for PTV relocalization. When the ERB volume and/or position were judged to yield inaccurate repositioning, manual adjustment (ERB reinflation and/or repositioning) was performed. Based on all 59 CBCT image sets acquired, a deformable registration algorithm was used to determine the dose received by, displacement of, and deformation of the prostate, bladder (BLA), and anterior rectal wall (ARW). This dose tracking methodology was applied to images taken before and after manual adjustment of the ERB (intervention), and the delivered dose was compared to that which would have been delivered in the absence of intervention.

Results:

Interventions occurred in 24 out of 35 (69%) of the treated fractions. The direct effect of these interventions was an increase in the prostate radiation dose that included 95% of the PTV (D95) from 9.6 ± 1.0 to 10.0 ± 0.2 Gy (p = 0.06) and an increase in prostate coverage from 94.0% ± 8.5% to 97.8% ± 1.9% (p = 0.03). Additionally, ERB interventions reduced prostate deformation in the anterior–posterior (AP) direction, reduced errors in the sagittal rotation of the prostate, and increased the similarity in shape of the prostate to the radiotherapy plan (increased Dice coefficient from 0.76 ± 0.06 to 0.80 ± 0.04, p = 0.01). Postintervention decreases in prostate volume receiving less than the prescribed dose and decreases in the voxel‐wise displacement of the prostate, bladder, and anterior rectal wall were observed, which resulted in improved dose–volume histogram (DVH) characteristics.

Conclusions:

Image‐guided interventions in ERB volume and/or position during prostate SBRT were necessary to ensure the delivery of the dose distribution as planned. ERB interventions resulted in reductions in prostate deformations that would have prevented accurate localization of patient anatomy.
Secreted Kinase Phosphorylates Extracellular Proteins That Regulate Biomineralization
Authors: Tagliabracci Vincent S. , Engel James L. , Wen Jianzhong , Wiley Sandra E. , Worby Carolyn A. , Kinch Lisa N. , Xiao Junyu , Grishin Nick V. , Dixon Jack E.
Published: May 2012

The Real McCoy

Some secreted proteins are phosphorylated, the most prominent example being the milk protein casein, but the enzymes that catalyze such phosphorylation have not been identified. (The proteins known as “casein kinases” are in fact cytosolic proteins and do not mediate physiological phosphorylation of casein.)

Tagliabracci
et al.

(p.
1150
, published online 10 May) searched for a human protein with the characteristics expected of a secretory protein kinase and identified Fam20C. Mutations in the gene encoding Fam20C cause defects in bone formation. Furthermore, the consensus sequence for Fam20C phosphorylation was found in several secreted proteins that function in biomineralization. Thus, Fam20C appears to be the “real” casein kinase and to function in bone physiology.
Genome Sequence of Lactobacillus salivarius SMXD51, a Potential Probiotic Strain Isolated from Chicken Cecum, Showing Anti-Campylobacter Activity
Authors: Kergourlay Gilles , Messaoudi Soumaya , Dousset Xavier , Prévost Hervé
Published: May 2012

We report the draft genome sequence of
Lactobacillus salivarius
SMXD51, isolated from the cecum of healthy chickens showing an activity against
Campylobacter
—the food-borne pathogen that is the most common cause of gastroenteritis in the European Union (EU)—and potentially interesting features for a probiotic strain, explaining our interest in it.
Complete Genome Sequence of the Fruiting Myxobacterium Corallococcus coralloides DSM 2259
Authors: Huntley Stuart , Zhang Ye , Treuner-Lange Anke , Kneip Susanne , Sensen Christoph W. , Søgaard-Andersen Lotte
Published: May 2012

Corallococcus coralloides
, like most other myxobacteria, undergoes a developmental program culminating in the formation of fruiting bodies.
C. coralloides
fruiting bodies are morphologically distinct from those of other fruiting myxobacteria for which full-length genome sequences are available. The genome sequence of the 10.0-Mb
C. coralloides
genome is presented herein.
Complete Genome Sequence of Flavobacterium indicum GPSTA100-9T, Isolated from Warm Spring Water
Authors: Barbier Paul , Houel Armel , Loux Valentin , Poulain Julie , Bernardet Jean-François , Touchon Marie , Duchaud Eric
Published: May 2012

We report here the complete annotated genome sequence of
Flavobacterium indicum
CIP 109464
T
(= GPTSA100-9
T
), isolated from warm spring water in Assam, India. The genome sequence of
F. indicum
revealed a number of interesting features and genes in relation to its environmental lifestyle.
Genome Sequence of Kingella kingae Septic Arthritis Isolate PYKK081
Authors: Kaplan Jeffrey B. , Lo Chienchi , Xie Gary , Johnson Shannon L. , Chain Patrick S. G. , Donnelly Robert , Kachlany Scott C. , Balashova Nataliya V.
Published: May 2012

Kingella kingae
is a human oral bacterium that can cause infections of the skeletal system in children. The bacterium is also a cardiovascular pathogen causing infective endocarditis in children and adults. We report herein the draft genome sequence of septic arthritis
K. kingae
strain PYKK081.
Genome Sequence of Pantoea sp. Strain Sc 1, an Opportunistic Cotton Pathogen
Authors: Medrano Enrique G. , Bell Alois A.
Published: May 2012

Pantoea
is comprised of a broad spectrum of species, including plant pathogens. Here, we provide an annotated genome sequence of
Pantoea
sp. strain Sc 1, which was isolated from a diseased cotton boll. This research provides the first genome sequence of a bona fide
Pantoea
sp. insect-vectored cotton pathogen.
Inpatient care for children with diabetes: are standards being met?: Table 1
Authors: Edge Julie , Ackland Frances M , Payne Susan , McAuley Antoinette , Hind Edward , Burren Christine , Burditt Jan , Sims Debbie
Published: May 2012

Background

Hospital inpatient care is frequently mentioned by parents as unsatisfactory for children with diabetes. Ward staff are now less familiar with diabetes, as admissions are less common and diabetes management is more intensive.

Objective

To compare current practice with Department of Health Children's Diabetes Working Group care standards.

Methods

This audit surveyed the organisation of inpatient care for children with diabetes in three regional networks in southern England, and was funded by the Healthcare Quality Improvement Partnership.

Results

All 27 services completed the questionnaire. Protocols for diabetic ketoacidosis, surgery, new diagnosis and hypoglycaemia were generally available on wards (70% had all four protocols) but less available in emergency departments (EDs) (52%). Trained children's nurses worked on every shift in children's wards (100%) but not necessarily in EDs (33%). Diabetes link nurses were identified on 74% of wards and 61% of high-dependency units (HDUs), and diabetes specialist nurses have inpatient liaison in their job description (89%) and working role (93%). Standards achieved less often were access to dietetic advice on wards (37%), education sessions for ED and ward staff, and informing diabetes team (only 26% within 2 h of admission during the day, and only 11% would contact the diabetes consultant overnight for a child admitted to a paediatric intensive care unit/HDU). Half of centres reported insulin errors.

Conclusions

This first audit of children's diabetes inpatient care organisation demonstrates that some standards can be achieved, but others, such as having children's nurses on every shift in EDs, lack of dietetic advice to ward staff, and liaison with the diabetes team quickly out of hours, are more challenging. Further planned audit outcomes are to produce patient and parent literature for children admitted to hospital and to refine the standards further.
Medical results of preparticipation examination in adolescent athletes
Authors: Mayer Frank , Bonaventura Klaus , Cassel Michael , Mueller Steffen , Weber Josefine , Scharhag-Rosenberger Friederike , Carlsohn Anja , Baur Heiner , Scharhag Juergen
Published: May 2012

Background

Preparticipation examinations (PPE) are frequently used to evaluate eligibility for competitive sports in adolescent athletes. Nevertheless, the effectiveness of these examinations is under debate since costs are high and its validity is discussed controversial.

Purpose

To analyse medical findings and consequences in adolescent athletes prior to admission to a sports school.

Methods

In 733 adolescent athletes (318 girls, 415 boys, age 12.3±0.4, 16 sports disciplines), history and clinical examination (musculoskeletal, cardiovascular, general medicine) was performed to evaluate eligibility. PPE was completed by determination of blood parameters, ECG at rest and during ergometry, echocardiography and x-rays and ultrasonography if indicated. Eligibility was either approved or rated with restriction. Recommendations for therapy and/or prevention were given to the athletes and their parents.

Results

Historical (h) and clinical (c) findings (eg, pain, verified pathologies) were more frequent regarding the musculoskeletal system (h:120, 16.4%; c:247, 33.7%) compared to cardiovascular (h:9, 1.2%; c:23, 3.1%) or general medicine findings (h:116, 15.8%; c:71, 9.7%). ECG at rest was moderately abnormal in 46 (6.3%) and severely abnormal in 25 athletes (3.4%). Exercise ECG was suspicious in 25 athletes (3.4%). Relevant echocardiographic abnormalities were found in 17 athletes (2.3%). In 52 of 358 cases (14.5%), x-rays led to diagnosis (eg, Spondylolisthesis). Eligibility was temporarily restricted in 41 athletes (5.6%). Three athletes (0.4%) had to be excluded from competitive sports. Therapy (eg, physiotherapy, medication) and/or prevention (sensorimotor training, vaccination) recommendations were deduced due to musculoskeletal (t:n=76,10.3%;p: n=71,9.8%) and general medicine findings (t:n=80, 10.9%; p:n=104, 14.1%).

Conclusion

Eligibility for competitive sports is restricted in only 5.5% of adolescent athletes at age 12. Eligibility refusals are rare. However, recommendations for therapy and prevention are frequent, mainly regarding the musculoskeletal system. In spite of time and cost consumption, adolescent preparticipation before entering a career in high-performance sports is supported.
USING STRATEGY IMPROVEMENT TO STAY ALIVE
Authors: BRIM LUBOŠ , CHALOUPKA JAKUB
Published: May 2012

We design a novel algorithm for solving Mean-Payoff Games (MPGs). Besides solving an MPG in the usual sense, our algorithm computes more information about the game, information that is important with respect to applications. The weights of the edges of an MPG can be thought of as a gained/consumed energy – depending on the sign. For each vertex, our algorithm computes the minimum amount of initial energy that is sufficient for player Max to ensure that in a play starting from the vertex, the energy level never goes below zero. Our algorithm is not the first algorithm that computes the minimum sufficient initial energies, but according to our experimental study it is the fastest algorithm that computes them. The reason is that it utilizes the strategy improvement technique which is very efficient in practice.
DISCOUNTING AND AVERAGING IN GAMES ACROSS TIME SCALES
Authors: CHATTERJEE KRISHNENDU , MAJUMDAR RUPAK
Published: May 2012

We introduce two-level discounted and mean-payoff games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted or mean-payoff game and the lower level game is a (undiscounted) reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales.

For both discounted and mean-payoff two-level games, we show the existence of pure memoryless optimal strategies for both players and an ordered field property. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted or mean-payoff games can be decided in NP ∩ coNP . We also give an alternate strategy improvement algorithm to compute the value.
CONFIGURATION MIXING AND DISSIPATION FROM THE TIME-DEPENDENT PAIRING EQUATIONS
Authors: MIREA M.
Published: May 2012

The time-dependent pairing equations are developed to include the Landau–Zener effect and a pair breaking mechanism. The new formalism provide information about the configuration mixing and the dissipation for a dynamical evolution of a nuclear system. A formula for a nonadiabatic cranking inertia is also deduced. Results concerning cluster decay and fission processes are presented.
LINEAR RESPONSE IN INFINITE NUCLEAR MATTER AS A TOOL TO REVEAL FINITE SIZE INSTABILITIES
Authors: PASTORE A. , BENNACEUR K. , DAVESNE D. , MEYER J.
Published: May 2012

Nuclear effective interactions are often modeled by simple analytical expressions such as the Skyrme zero-range force. This effective interaction depends on a limited number of parameters that are usually fitted using experimental data obtained from doubly magic nuclei. It was recently shown that many Skyrme functionals lead to the appearance of instabilities, in particular when symmetries are broken, for example unphysical polarization of odd–even or rotating nuclei. In this paper, we show how the formalism of the linear response in infinite nuclear matter can be used to predict and avoid the regions of parameters that are responsible for these unphysical instabilities.
THE QUEST FOR THE HEAVIEST URANIUM ISOTOPE
Authors: SCHRAMM S. , GRIDNEV D. , TARASOV D. V. , TARASOV V. N. , GREINER W.
Published: May 2012

We study Uranium isotopes and surrounding elements at very large neutron number excess. Relativistic mean field and Skyrme-type approaches with different parameterizations are adopted in the study. Most models show clear indications for isotopes that are stable with respect to neutron emission far beyond N = 184 up to the range of around N = 258.
DYNAMICAL COUPLING OF ROTATION WITH THE PAIRING FIELD IN HEAVY NUCLEI
Authors: NERLO-POMORSKA B. , POMORSKI K. , BARTEL J.
Published: May 2012

The macroscopic–microscopic model with the Lublin–Strasbourg Drop, the Yukawa–folded single-particle potential and a monopole pairing force is used together with the cranking model to describe rotational bands in even–even actinide ( Ra – Cn ) isotopes. The pairing strength is adjusted for every nucleus to reproduce the experimentally known energy of the rotational 2+ state. The average pairing strength obtained in this way is used to predict the rotational states in superheavy No – Cn nuclei. A simple mechanism which takes into account a dynamical coupling of rotation with the pairing field is explained in detail.
AID TO THE POOR IN MIDDLE INCOME COUNTRIES AND THE FUTURE OF THE INTERNATIONAL DEVELOPMENT ASSOCIATION
Authors: KANBUR RAVI
Published: May 2012

We are sleep walking into a situation where over the next decade and a half concessional development assistance will disengage from the bulk of the world's poor. This is happening because countries that are graduating into Middle Income status still have large numbers of poor people. This new situation, where three quarters of the world's poor live in Middle Income Countries, raises fundamental questions about the salience of national level achievements in determining global responsibilities towards the poor in each nation. They also raise basic questions for the operational rules of access to concessional development assistance such as that provided by the International Development Association (IDA). This paper set out the issues, and presents a proposal for a new window of IDA which recognizes that poverty persists and development problems remain despite the welcome graduation of many countries to Middle Income status.
SOLOW'S RETURN: INVENTIONS, IDEAS AND THE QUALITY OF LIFE
Authors: KENNY CHARLES
Published: May 2012

Robert Solow's model of "exogenous" economic growth driven by the global diffusion of technology is out of fashion because it is contradicted by empirical evidence of income divergence. Today, economic growth is considered "endogenous" and institutions are seen as central to the long-term growth process. At the same time, non-income measures of quality of life do see strong patterns of global growth and convergence. This suggests that institutions may be less important to achieve progress in broader quality of life while a larger and important role concerns the factors that drive exogenous change, including the flow of technology and ideas.
FISCAL COMPETITION IN DEVELOPING COUNTRIES: A SURVEY OF THE THEORETICAL AND EMPIRICAL LITERATURE
Authors: MADIÈS THIERRY , DETHIER JEAN-JACQUES
Published: May 2012

Fiscal competition between governments to attract investment can take the form of business tax rebates, productivity-enhancing public infrastructure, tax holidays, accelerated depreciation allowances or loss carry-forward for income tax purposes. This paper surveys the recent theoretical and empirical economic literature and deals with three issues. First, it examines if the theoretical literature on fiscal competition and bidding races contribute to a better understanding of these phenomena in developing countries. Second, it examines whether FDI inflows in developing countries are sensitive to fiscal incentives and if there is empirical evidence of strategic behavior by developing country governments in order to attract FDI. Finally, it reviews the literature's conclusions about fiscal competition among local governments in developing countries.
MEASURING LONG-TERM COMMODITY-LEVEL TRADE COSTS: THE CASE OF ASIA
Authors: HAMANAKA SHINTARO , DOMINGO ROMANA
Published: May 2012

Despite its several inherent weaknesses, Doing Business compiled by the World Bank is still the most widely used assessment of the trade facilitation status among developing country policymakers as well as economists. In this paper, we suggest that the use of trade costs calculated based on trade statistics in conjunction with Doing Business data is helpful in drawing up sector-specific trade facilitation policies. Unlike Doing Business, we can obtain long-term commodity-level trade costs if trade statistics are used.
AN INTRODUCTION TO LOCAL BLACK HOLE HORIZONS IN THE 3+1 APPROACH TO GENERAL RELATIVITY
Authors: JARAMILLO JOSÉ LUIS
Published: May 2012

We present an introduction to dynamical trapping horizons as quasi-local models for black hole horizons, from the perspective of an Initial Value Problem approach to the construction of generic black hole spacetimes. We focus on the geometric and structural properties of these horizons aiming, as a main application, at the numerical evolution and analysis of black hole spacetimes in astrophysical scenarios. In this setting, we discuss their dual role as an a priori ingredient in certain formulations of Einstein equations and as an a posteriori tool for the diagnosis of dynamical black hole spacetimes. Complementary to the first-principles discussion of quasi-local horizon physics, we place an emphasis on the rigidity properties of these hypersurfaces and their role as privileged geometric probes into near-horizon strong-field spacetime dynamics.
ANATOMY OF EINSTEIN'S THEORY: ABELIAN DECOMPOSITION OF GENERAL RELATIVITY
Authors: CHO Y. M.
Published: May 2012

Treating Einstein's theory as a gauge theory of Lorentz group, we decompose the gravitational connection (the gauge potential of Lorentz group) Γμ into the restricted connection of the maximal Abelian subgroup of Lorentz group and the valence connection which transforms covariantly under Lorentz gauge transformation. With this decomposition we show that the Einstein's theory can be decomposed into the restricted part made of the restricted connection which has the full Lorentz gauge invariance and the valence part made of the valence connection which plays the role of gravitational source of the restricted gravity. We show that there are two different Abelian decomposition of Einstein's theory, the light-like (or null) decomposition and the non light-like (or non-null) decomposition. In this decomposition the role of the metric gμν is replaced by a four-index metric tensor gμν which transforms covariantly under the Lorentz group, and the metric-compatibility condition ∇αgμν = 0 of the connection is replaced by the gauge and generally covariant condition [Formula: see text]. The decomposition shows the existence of a restricted theory of gravitation which has the full general invariance but is much simpler and has less physical degrees of freedom than Einstein's theory. Moreover, it tells that the restricted gravity can be written as an Abelian gauge theory, which implies that the graviton can be described by a massless spin-one field.
BRANS-DICKE COSMOLOGY WITH FERMIONS AND CHAMELEON MECHANISM
Authors: LIU DAO-JUN , YANG BIN , JIN XING-HUA
Published: May 2012

We study the cosmological dynamics of Brans-Dicke theory in which there are fermions with a coupling to BD scalar field as well as a self-interaction potential. The conditions that there exists a solution which is stable and represents a late-time accelerated expansion of the universe are found. It is shown that the late-time acceleration depends completely on the self-interaction of the fermion field if our investigation is restricted to the theory with positive BD parameter ω. Provided a negative ω is allowed, there will be another two class of stable solutions describing late-time accelerated expansion of the universe. Besides, we find that chameleon mechanism will be possessed in our theory when a suitable self-interaction of fermion field is considered.
ANISOTROPIC BEHAVIOR OF A POINT CHARGE MOVING IN THE PRESENCE OF THE CONDUCTING PLATE UNDER THE INFLUENCE OF THE STOCHASTIC LORENTZ FORCES
Authors: WU TAI-HUNG
Published: May 2012

The influence of quantized electromagnetic fields on a nonrelativistic charged particle near a conducting plate is investigated by studying the the non-Markovian Langevin equation of the particle. This stochastic approach incorporates not only the stochastic noise manifested from electromagnetic vacuum fluctuations, but also dissipation backreaction on a charge in the form of the retarded Lorentz forces. Since the imposition of the boundary is expected to anisotropically modify the effects of the fields on the evolution of the particle, we consider the motion of a charge undergoing small-amplitude oscillations in the direction either parallel or normal to the plane boundary. Laplace transform technique is applied to find the solutions to these two configurations.
SEVERE CHALLENGES IN GRAVITY THEORIES
Authors: HA YUAN K.
Published: May 2012

Gravity is specifically the attractive force between two masses separated at a distance. Is this force a derived or a fundamental interaction? We believe that all fundamental interactions are quantum in nature but a derived interaction may be classical. Severe challenges have appeared in many quantum theories of gravity. None of these theories has thus far attained its goal in quantizing gravity and some have met remarkable defeat. We are led to ponder whether gravitation is intrinsically classical and that there would exist a deeper and structurally different underlying theory which would give rise to classical gravitation, in the sense that statistical mechanics, quantum or classical, provides the underlying theory of classical thermodynamics.
THE KERR-NEWMAN/CFTS CORRESPONDENCE
Authors: CHEN CHIANG-MEI , SUN JIA-RUI
Published: May 2012

In this article, we review recent studies on multiple dual 2D CFT descriptions of the Kerr-Newman black hole, in terms of the Kerr/CFT and Reissner-Nordström/CFT correspondences. A microscopic hair conjecture is suggested.
ANGULAR EIGENVALUES OF HIGHER-DIMENSIONAL KERR-(A)dS BLACK HOLES WITH TWO ROTATIONS
Authors: CHO H. T. , CORNELL A. S. , DOUKAS JASON , NAYLOR WADE
Published: May 2012

In this paper, following the work of Chen, Lü and Pope, we present the general metric for Kerr-(A)dS black holes with two rotations. The corresponding Klein-Gordon equation is separated explicitly, from which we develop perturbative expansions for the angular eigenvalues in powers of the rotation parameters with D ≥ 6.
HYPERCYLINDRICAL VACUUM SPACETIME SOLUTIONS
Authors: KANG GUNGWON
Published: May 2012

A brief report is given on hypercylindrical vacuum spacetime solutions and their geometrical properties. The five-dimensional Schwarzschild black string solution characterized by the mass density, which is known to reveal the so-called Gregory-Laflamme instability, turns out to be a special case of a wider class of hypercylindrical vacuum spacetime solutions characterized by two parameters, i.e., mass density and tension. Recent work on the solution space even including a momentum flow or a cosmological constant, higher dimensional extensions than five and some stability analysis under small perturbations are briefly summarized.
18-GHz, 4.0-aJ/bit Operation of Ultra-Low-Energy Rapid Single-Flux-Quantum Shift Registers
Authors: Tanaka Masamitsu , Ito Masato , Kitayama Atsushi , Kouketsu Tomohito , Fujimaki Akira
Published: May 2012

We demonstrate rapid single-flux-quantum (RSFQ) circuits with reduced energy consumption by lowering the driving voltages and critical currents of Josephson junctions (JJs). At lowered voltages, the energy statically consumed by bias resistors (which is dominant in RSFQ circuits) is reduced. In addition, we show that when RSFQ circuits are driven by lowered constant voltages, the dynamic energy consumption resulting from the switching of JJs is reduced because of the suppression of the amplitudes of the signal voltage pulses, even though the switching speed becomes slower. Utilization of miniaturized JJs with smaller critical currents also leads to the reduction of static and dynamic energy consumption without decreasing the switching speed. We have designed and tested ultra-low-energy 8-bit shift registers, and verified the correctness of high-speed operations up to 18 GHz. The average energy consumption, including that at the bias resistors, was measured at 4.0 aJ/bit, which represents an energy efficiency two orders of magnitude better than that of standard RSFQ circuits.
Fabrication and Characterization of an FeBNdNb Magnetic Metallic Glass Thin Film
Authors: Phan Tuan Anh , Lee Sangmin , Makino Akihiro , Oguchi Hiroyuki , Okamoto Hiroshi , Kuwano Hiroki
Published: May 2012

We have fabricated an Fe67.46B22.5Nd6.3Nb3.74 magnetic metallic glass thin film on a (100) silicon substrate by electron cyclotron resonance ion beam sputtering. We confirmed the metallic glass state of the thin film by observing its crystallographically amorphous state using X-ray diffractometry and transmission electron microscopy, and we obtained the glass transition temperature using differential scanning calorimetry. We also confirmed the magnetization of the thin film using a physical property measurement system. The thin film showed the largest reported width of the supercooled liquid region (96 K) and the smallest reported value of coercivity (7.5 A/m) among the existing magnetic metallic glass thin films. This study is expected to lead to an increase in the variety of materials available and greater knowledge of the physical properties of magnetic metallic glass thin films and to facilitate research on developing magnetic metallic glass thin films as base materials for magnetic microelectromechanical systems.
Occurrence of inherited supra-subduction zone mantle in the oceanic lithosphere as inferred from mantle xenoliths from Dragon Seamount (southern Tore–Madeira Rise)
Authors: Merle Renaud , Kaczmarek Mary-Alix , Tronche Elodie , Girardeau Jacques
Published: May 2012

Spinel-bearing peridotite and pyroxenite xenoliths dredged from the Dragon Seamount (southern Tore–Madeira Rise, West Iberia and Morocco margin) give an insight into the composition of the underlying lithosphere. These xenoliths are devoid of evidence of strong host lava–peridotite interaction and re-equilibration or late impregnation in the plagioclase facies. The spinels and pyroxenes from the Dragon peridotites have compositions distinct from those of both lherzolites and harzburgites from the Iberia margin and the Mid-Atlantic Ridge. They display a highly depleted composition, in particular, high Cr-number, up to 0.63 in the spinels, consistent with a melting degree between 12 and 19%. Because of the strong chemical similarities between the Tore–Madeira Rise, Newfoundland peridotites, and peridotites from supra-subduction zones, we propose that the Dragon peridotites formed in a similar context. The pyroxenites display a cumulate texture and are probably a high-temperature–high-pressure cumulate formed by fractional crystallization from a melt. The Tore–Madeira Rise peridotites may represent a former mantle wedge in an oceanic arc, later included into the continental lithosphere and finally tectonically disseminated within the lithosphere during the rifting of the Newfoundland–Iberia continental lithosphere. As a consequence, rifting processes may produce heterogeneities in the oceanic lithosphere and influence isotopic compositions of ocean island basalt-type lavas during plume–lithosphere interactions, as inferred for the southern Tore–Madeira Rise.

Supplementary material:

Further information on the analytical results is available at
http://www.geolsoc.org.uk/SUP18512
.
The influence of depositional processes on the porosity of chalk
Authors: Anderskouv Kresten , Surlyk Finn
Published: May 2012

Chalk constitutes challenging low-permeability reservoirs with porosity variations attributable to complex interactions between numerous processes. The influence of depositional processes, and thus the value of depositional models to predict porosity, is subject to continuing debate. In this study, a new approach is applied to investigate the influence of depositional and early post-depositional processes on chalk porosity, based on the 303 m thick Upper Cretaceous chalk succession in the Mona-1 core from the Danish North Sea. The influence of depositional processes on porosity is isolated by a mathematical correction of porosity data. Results confirm that mass-transport deposits are on average more porous than pelagites, whereas turbidites are less porous, given similar composition, burial history, and hydrocarbon migration history. The porosity variation between 12 chalk facies suggests that grain packing of the sediment in the consolidated state caused the facies-dependent porosity variation. Bioturbation caused a relatively tight grain packing compared with deposits that escaped bioturbation. Early plastic shear deformation of tightly packed bioturbated units resulted in dilative behaviour, which increased porosity, whereas more loosely packed units responded contractively, resulting in decreased porosity preservation. A firm understanding of chalk facies and thorough facies analyses are thus considered instrumental in chalk reservoir prediction.
Receptor Signaling Clusters in the Immune Synapse
Authors: Dustin Michael L. , Groves Jay T.
Published: May 2012

Signaling processes between various immune cells involve large-scale spatial reorganization of receptors and signaling molecules within the cell-cell junction. These structures, now collectively referred to as immune synapses, interleave physical and mechanical processes with the cascades of chemical reactions that constitute signal transduction systems. Molecular level clustering, spatial exclusion, and long-range directed transport are all emerging as key regulatory mechanisms. The study of these processes is drawing researchers from physical sciences to join the effort and represents a rapidly growing branch of biophysical chemistry. Recent advances in physical and quantitative analyses of signaling within the immune synapses are reviewed here.
Cooperativity in Cellular Biochemical Processes: Noise-Enhanced Sensitivity, Fluctuating Enzyme, Bistability with Nonlinear Feedback, and Other Mechanisms for Sigmoidal Responses
Authors: Qian Hong
Published: May 2012

Cooperativity in classical biophysics originates from molecular interactions; nonlinear feedbacks in biochemical networks regulate dynamics inside cells. Using stochastic reaction kinetic theory, we discuss cooperative transitions in cellular biochemical processes at both the macromolecular and the cellular levels. We show that fluctuation-enhanced sensitivity (stochastic focusing) shares an essential feature with the transition in a bistable system. The same theory explains zeroth-order ultrasensitivity with temporal cooperativity. Dynamic cooperativity in fluctuating enzyme (i.e., dynamic disorder), stochastic focusing, and the recently proposed stochastic binary decision all have a shared mechanism: They are generalizations of the hyperbolic response of Michaelis-Menten kinetics x/(K+x), with fluctuating K or stochastic x. Sigmoidal dependence on substrate concentration necessarily yields affinity amplification for competing ligands; both sigmoidal response and affinity amplification exhibit a square law. We suggest two important characteristics in a noise: its multimodal distribution structure and its temporal irreversibility. The former gives rise to self-organized complexity, and the latter contains useful, albeit hidden, free energy that can be utilized for biological functions. There could be structures and energy in biochemical fluctuations.
Single-Molecule Mechanoenzymatics
Authors: Puchner Elias M. , Gaub Hermann E.
Published: May 2012

The ability of cellular signaling networks to sense, process, and respond to internal and external stimuli relies on their specific detection and transduction based on molecular recognition. The molecular mechanisms by which force is specifically sensed by mechanoenzymatic processes, translated into biochemical signals, and wired to cellular signaling networks recently became accessible with single-molecule force spectroscopy. By stretching such mechanobiochemical converters along their natural reaction coordinate, complex mechanical activation pathways and subsequent biochemical reactions may be measured in a dynamic and highly precise manner. The discovered mechanisms have in common well-tuned force-induced conformational changes that lead to exposure of active recognition sites. Newly developed strategies allow investigators to test different conformational states for activity and to elucidate mechanical architectures leading to highly specific mechanical activation pathways. Here, we discuss the advances in the new field of single-molecule mechanoenzymatics and highlight complementary examples studied in bulk and in vivo.
Network-Based Models as Tools Hinting at Nonevident Protein Functionality
Authors: Atilgan Canan , Okan Osman Burak , Atilgan Ali Rana
Published: May 2012

Network-based models of proteins are popular tools employed to determine dynamic features related to the folded structure. They encompass all topological and geometric computational approaches idealizing proteins as directly interacting nodes. Topology makes use of neighborhood information of residues, and geometry includes relative placement of neighbors. Coarse-grained approaches efficiently predict alternative conformations because of inherent collectivity in the protein structure. Such collectivity is moderated by topological characteristics that also tune neighborhood structure: That rich residues have richer neighbors secures robustness toward random loss of interactions/nodes due to environmental fluctuations/mutations. Geometry conveys the additional information of force balance to network models, establishing the local shape of the energy landscape. Here, residue and/or bond perturbations are critically evaluated to suggest new experiments, as network-based computational techniques prove useful in capturing domain movements and conformational shifts resulting from environmental alterations. Evolutionarily conserved residues are optimally connected, defining a subnetwork that may be utilized for further coarsening.
Disulfide Bonding in Protein Biophysics
Authors: Fass Deborah
Published: May 2012

It has been known for many decades that cell surface, soluble-secreted, and extracellular matrix proteins are generally rich in disulfide bonds, but only more recently has the functional diversity of disulfide bonding in extracellular proteins been appreciated. In addition to the classic mechanisms by which disulfide bonds enhance protein thermodynamic stability, disulfides in certain configurations contribute particular mechanical properties to proteins that sense and respond to tensile forces. Disulfides may help warp protein folds for the evolution of new functions, or they may fasten aggregation-prone flaps of polypeptide to protein surfaces to prevent fibrilization or oligomerization. Disulfides can also be used to package and secure macromolecular cargo for intercellular transport. A series of case studies illustrating diverse biophysical roles of disulfide bonding are reviewed, with a focus on proteins functioning in the extracellular environment.
Richardson in the Information Age: Geographic Information Systems and Spatial Data in International Studies
Authors: Gleditsch Kristian Skrede , Weidmann Nils B.
Published: May 2012

There is an enduring interest in how geographic features influence political interactions and outcomes, and many key factors highlighted in international relations and cross-national research vary spatially within countries. Starting with the pioneering research of Richardson, we show how geographic information systems (GIS) technology and the increasing availability of spatial data can provide new opportunities to answer old and new questions. We focus on key motivations for using spatial disaggregated data and show how such data can be used in current research, drawing on examples from the study of violent conflict.
Domestic Explanations of International Relations
Authors: Bueno de Mesquita Bruce , Smith Alastair
Published: May 2012

Theories that link domestic politics, domestic institutional structures, and leader incentives to foreign affairs have flowered in the past 25 years or so. By unpacking institutional variation across states and by drawing attention to agency issues between leaders, key backers, and citizens, models and empirical studies of linkage help explain even such fundamental phenomena between states as war and peace. In addition, theories of linkage politics explain phenomena not envisioned under earlier unitary-actor state models. We address how the linkage literature explains war and peace decisions, the democratic peace, nation building, foreign aid, and economic sanctions by tying international politics and foreign policy to domestic political considerations.
Impaired mucin synthesis and bicarbonate secretion in the colon of NHE8 knockout mice
Authors: Xu Hua , Zhang Bo , Li Jing , Wang Chunhui , Chen Huacong , Ghishan Fayez K.
Published: May 2012

Sodium/hydrogen exchanger 8 (NHE8), the newest member of the SLC9 family, is expressed at the apical membrane of the epithelial cells in the intestine and the kidney. Although NHE8 has been shown to be an important player for intestinal sodium absorption early in development, its physiological role in the intestine remains unclear. Here, we successfully created a NHE8 knockout (NHE8−/−) mouse model to study the function of this transporter in the intestinal tract. Embryonic stem cells containing interrupted NHE8 gene were injected into mouse blastocyst to produce NHE8+/−chimeras. NHE8−/−mice showed no lethality during embryonic and fetal development. These mice had normal serum sodium levels and no signs of diarrhea. Apically expressed NHE2 and NHE3 were increased in the small intestine of the NHE8−/−mice in compensation. The number of goblet cells and mucin (MUC)-positive cells in the colon was reduced in NHE8−/−mice along with mucosal pH, MUC2 expression as well as downregulated in adenoma (DRA) expression. Therefore, the role of NHE8 in the intestine involves both sodium absorption and bicarbonate secretion.
Service Virtualization Using a Non-von Neumann Parallel, Distributed, and Scalable Computing Model
Authors: Mikkilineni Rao , Morana Giovanni , Zito Daniele , Di Sano Marco
Published: May 2012

This paper describes a prototype implementing a high degree of transaction resilience in distributed software systems using a non-von Neumann computing model exploiting parallelism in computing nodes. The prototype incorporates fault, configuration, accounting, performance, and security (FCAPS) management using a signaling network overlay and allows the dynamic control of a set of distributed computing elements in a network. Each node is a computing entity endowed with self-management and signaling capabilities to collaborate with similar nodes in a network. The separation of parallel computing and management channels allows the end-to-end transaction management of computing tasks (provided by the autonomous distributed computing elements) to be implemented as network-level FCAPS management. While the new computing model is operating system agnostic, a Linux, Apache, MySQL, PHP/Perl/Python (LAMP) based services architecture is implemented in a prototype to demonstrate end-to-end transaction management with auto-scaling, self-repair, dynamic performance management and distributed transaction security assurance. The implementation is made possible by a non-von Neumann middleware library providing Linux process management through multi-threaded parallel execution of self-management and signaling abstractions. We did not use Hypervisors, Virtual machines, or layers of complex virtualization management systems in implementing this prototype.
The Transcription Factor ZNF217 Is a Prognostic Biomarker and Therapeutic Target during Breast Cancer Progression
Authors: Littlepage Laurie E. , Adler Adam S. , Kouros-Mehr Hosein , Huang Guiqing , Chou Jonathan , Krig Sheryl R. , Griffith Obi L. , Korkola James E. , Qu Kun , Lawson Devon A. , Xue Qing , Sternlicht Mark D. , Dijkgraaf Gerrit J.P. , Yaswen Paul , Rugo Hope S. , Sweeney Colleen A. , Collins Colin C. , Gray Joe W. , Chang Howard Y. , Werb Zena
Published: May 2012

The transcription factor ZNF217 is a candidate oncogene in the amplicon on chromosome 20q13 that occurs in 20% to 30% of primary human breast cancers and that correlates with poor prognosis. We show that Znf217 overexpression drives aberrant differentiation and signaling events, promotes increased self-renewal capacity, mesenchymal marker expression, motility, and metastasis, and represses an adult tissue stem cell gene signature downregulated in cancers. By in silico screening, we identified candidate therapeutics that at low concentrations inhibit growth of cancer cells expressing high ZNF217. We show that the nucleoside analogue triciribine inhibits ZNF217-induced tumor growth and chemotherapy resistance and inhibits signaling events [e.g., phospho-AKT, phospho-mitogen-activated protein kinase (MAPK)] in vivo. Our data suggest that ZNF217 is a biomarker of poor prognosis and a therapeutic target in patients with breast cancer and that triciribine may be part of a personalized treatment strategy in patients overexpressing ZNF217. Because ZNF217 is amplified in numerous cancers, these results have implications for other cancers.

Significance: This study finds that ZNF217 is a poor prognostic indicator and therapeutic target in patients with breast cancer and may be a strong biomarker of triciribine treatment efficacy in patients. Because previous clinical trials for triciribine did not include biomarkers of treatment efficacy, this study provides a rationale for revisiting triciribine in the clinical setting as a therapy for patients with breast cancer who overexpress ZNF217. Cancer Discov; 2(7); 638–51. ©2012 AACR.

This article is highlighted in the In This Issue feature, p. 569.
Ginseng Reverses Established Cardiomyocyte Hypertrophy and Postmyocardial Infarction-Induced Hypertrophy and Heart Failure
Authors: Moey Melissa , Gan Xiaohong T. , Huang Cathy Xiaoling , Rajapurohitam Venkatesh , Martínez-Abundis Eduardo , Lui Edmund M.K. , Karmazyn Morris
Published: May 2012

Background—

A major challenge in the treatment of heart failure is the ability to reverse already-established myocardial remodeling and ventricular dysfunction, with few available pharmacological agents prescribed for the management of heart failure having demonstrated successful reversal of the remodeling and hypertrophic processes. North American ginseng (
Panax quinquefolius
) has previously been shown to effectively prevent cardiomyocyte hypertrophy and heart failure. Here, we determined whether North American ginseng can reverse established cardiomyocyte hypertrophy in cultured myocytes as well as hypertrophy and left ventricular dysfunction in experimental heart failure secondary to coronary artery occlusion.

Methods and Results—

Ginseng was administered in drinking water (0.9 g/L) ad libitum to rats after 4 weeks of sustained coronary artery ligation when heart failure was established or to angiotensin II- (100 nmol/L), endothelin-1- (10 nmol/L), or phenylephrine- (10 µmol/L) induced hypertrophic cultured neonatal ventricular cardiomyocytes. Echocardiographic and catheter-based measurements of hemodynamic parameters 4 weeks after starting ginseng treatment (8 weeks postinfarction) revealed nearly complete reversibility of systolic and diastolic abnormalities. Similarly, ginseng administration to hypertrophic cardiomyocytes resulted in a complete reversal to a normal phenotype after 24 hours as determined by cell surface area and expression of molecular markers. The effects of ginseng both in vivo and in cultured cardiomyocytes were associated with reversal of calcineurin activation and reduced nuclear translocation of the transcription factor NFAT3 (nuclear factor of activated T cells 3) in cultured myocytes. Moreover, the beneficial effect of ginseng was associated with normalization in the gene expression of profibrotic markers, including collagen (I and III) and fibronectin.

Conclusions—

This study demonstrates a marked ability of ginseng to reverse cardiac hypertrophy, myocardial remodeling, and heart failure, which was associated with and likely mediated by reversal of calcineurin activation. Ginseng may offer a potentially effective approach to reverse the myocardial remodeling and heart failure processes, particularly in combination with other treatment modalities.