bluuebunny/crossref_metadata_2025 huggingface dataset:
Mortality and morbidity after high-dose methylprednisolone treatment in patients with acute cervical spinal cord injury: a propensity-matched analysis using a nationwide administrative database
Authors: Chikuda Hirotaka , Yasunaga Hideo , Takeshita Katsushi , Horiguchi Hiromasa , Kawaguchi Hiroshi , Ohe Kazuhiko , Fushimi Kiyohide , Tanaka Sakae
Published: March 2013

Objective

To examine the magnitude of the adverse impact of high-dose methylprednisolone treatment in patients with acute cervical spinal cord injury (SCI).

Methods

We examined the abstracted data from the Japanese Diagnosis Procedure Combination database, and included patients with ICD-10 code S141 who were admitted on an emergency basis between 1 July and 31 December in 2007–2009. The investigation evaluated the patients’ sex, age, comorbidities, Japan Coma Scale, hospital volume and the amount of methylprednisolone administered. One-to-one propensity-score matching between high-dose methylprednisolone group (>5000 mg) and control group was performed to compare the rates of in-hospital death and major complications (sepsis; pneumonia; urinary tract infection; gastrointestinal ulcer/bleeding; and pulmonary embolism).

Results

We identified 3508 cervical SCI patients (2652 men and 856 women; mean age, 60.8±18.7 years) including 824 (23.5%) patients who received high-dose methylprednisolone. A propensity-matched analysis with 824 pairs of patients showed a significant increase in the occurrence of gastrointestinal ulcer/bleeding (68/812 vs 31/812; p<0.001) in the high-dose methylprednisolone group. Overall, the high-dose methylprednisolone group demonstrated a significantly higher risk of complications (144/812 vs 96/812;OR, 1.66; 95% CI 1.23 to 2.24; p=0.001) than the control group. There was no significant difference in in-hospital mortality between the high-dose methylprednisolone group and the control group (p=0.884).

Conclusions

Patients receiving high-dose methylprednisolone had a significantly increased risk of major complications, in particular, gastrointestinal ulcer/bleeding. However, high-dose methylprednisolone treatment was not associated with any increase in mortality.
Predictive factors of severe multilobar pneumonia and shock in patients with influenza
Authors: Garcia Gutierrez Susana , Quintana José Maria , Baricot Maretva , Bilbao Amaia , Capelastegui Alberto , Cilla Eguiluz Carlos Gustavo , Domínguez Angela , Castilla Jesús , Godoy Pere , Delgado-Rodríguez Miguel , Soldevila Núria , Astray Jenaro , Mayoral José María , Martín Vicente , González-Candelas Fernando , Galán Juan Carlos , Tamames Sonia , Castro-Acosta Ady Angélica , Garín Olatz , Pumarola Tomás ,   the CIBERESP Cases and Controls in Pandemic Influenza Working Group, Spain
Published: March 2013

Purpose

To identify risk factors present at admission in adult patients hospitalised due to influenza virus infection during the 2009/10 and 2010/11 seasons—including whether infection was from pandemic or seasonal influenza A infections—that were associated with the likelihood of developing severe pneumonia with multilobar involvement and shock.

Methods

Prospective cohort study. Patients hospitalised due to influenza virus infection were recruited. We collected information on sociodemographic characteristics, pre-existing medical conditions, vaccinations, toxic habits, previous medications, exposure to social environments, and EuroQoL-5D (EQ-5D). Severe pneumonia with multilobar involvement and/or shock (SPAS) was the primary outcome of interest. We constructed two multivariate logistic regression models to explain the likelihood of developing SPAS and to create a clinical prediction rule for developing SPAS that includes clinically relevant variables.

Results

Laboratory-confirmed A(H1N1)pdm09, EQ-5D utility score 7 days before admission, more than one comorbidity, altered mental status, dyspnoea on arrival, days from onset of symptoms, and influenza season were associated with SPAS. In addition, not being vaccinated against seasonal influenza in the previous year, anaemia, altered mental status, fever and dyspnoea on arrival at hospital, difficulties in performing activities of daily living in the previous 7 days, and days from onset of symptoms to arrival at hospital were related to the likelihood of SPAS (area under the curve value of 0.75; Hosmer–Lemeshow p value of 0.84).

Conclusions

These variables should be taken into account by physicians evaluating a patient affected by influenza as additional information to that provided by the usual risk scores.
Who makes uric acid stones and why—observations from a renal stones clinic
Authors: Stansbridge Elizabeth M , Griffin Damian G , Walker Valerie
Published: March 2013

Aims

Excessively acidic urine is the dominant factor in uric acid stone formation. Recent evidence implicating insulin resistance has revived interest in its causation. We reviewed data on uric acid stone formers attending a general stones clinic to find out whether this supports and adds to current concepts.

Methods

A retrospective database study of 1504 stone formers investigated at the Southampton renal stones clinic from 1990 to March 2007. Uric acid stone formers and idiopathic calcium stone formers were compared using non-parametric tests.

Results

Fifty-nine patients (3.9%; 43 men) had uric acid stones. In men the commonest associated conditions were diabetes (20%), gout (20%) and an ileostomy (15%); in women, diabetes (33%), urinary infections (27%) and hyperparathyroidism (20%). Most patients with diabetes (85% of men, 75% of women), however, produced calcium stones. Risk factors did not differ significantly between calcium and uric acid stone formers with diabetes, gout or ileostomies. The median urine pH of men with idiopathic calcium stones was 6.20, idiopathic uric acid stones 5.47, diabetes 5.68, gout 6.05, diabetes and gout 5.20 and ileostomy 5.10. Plasma urate was higher with gout and idiopathic uric acid stones. Urate excretion was increased in gout. Oxalate excretion was lower with idiopathic uric acid stones (new finding). Urine volume decreased and oxalate concentration increased with ileostomy.

Conclusions

Uric acid stones are increased in diabetes, but most patients with diabetes make calcium stones. Different mechanisms may explain low pH with diabetes, gout and idiopathic stones. Low oxalate excretion with idiopathic urate stones needs confirmation.
Lost in translation. Homer in English; the patient's story in medicine
Authors: Marshall Robert J , Bleakley Alan
Published: March 2013

In a series of previous articles, we have considered how we might reconceptualise central themes in medicine and medical education through ‘thinking with Homer’. This has involved using textual approaches, scenes and characters from theIliadandOdysseyfor rethinking what is a ‘communication skill’, and what do we mean by ‘empathy’ in medical practice; in what sense is medical practice formulaic, like a Homeric ‘song’; and what is lyrical about medical practice. Our approach is not to historicise medicine and medical education, but to use thinking with Homer as a medium and metaphor for questioning the habitual and the taken-for-granted in contemporary practice.

In this article, we tackle the complex theme of ‘translation’. We use the lens of translation studies to examine the process of turning the patient's story into medical language. We address the questions: what makes a ‘good’ translation? What are the consequences of mistranslation and poor translation? And, while things are inevitably lost in translation, does this matter?
UNKNOTTING NUMBERS AND TRIPLE POINT CANCELLING NUMBERS OF TORUS-COVERING KNOTS
Authors: NAKAMURA INASA
Published: March 2013

It is known that any surface knot can be transformed to an unknotted surface knot or a surface knot which has a diagram with no triple points by a finite number of 1-handle additions. The minimum number of such 1-handles is called the unknotting number or the triple point cancelling number, respectively. In this paper, we give upper bounds and lower bounds of unknotting numbers and triple point cancelling numbers of torus-covering knots, which are surface knots in the form of coverings over the standard torus T. Upper bounds are given by using m-charts on T presenting torus-covering knots, and lower bounds are given by using quandle colorings and quandle cocycle invariants.
An Analysis of the Bankruptcy Reorganization Procedure in China
Authors: Leng Fei
Published: March 2013

This paper analyzes the reorganization procedure introduced into the Chinese bankruptcy system in 2007. It shows that managers devote more effort during the reorganization than before the bankruptcy when the emergence value of the bankrupt firm is substantial. In addition, in the pre-bankruptcy period, managers were shown to input less effort under the new law than under the old law. Finally, the paper demonstrates that the market interest rate under the new bankruptcy law is not necessarily lower than that under the old law. These results call attention to the potential costs of the reorganization procedure.
SOLIPSISTIC HIDDEN VARIABLES
Authors: NIKOLIĆ HRVOJE
Published: March 2013

We argue that it is logically possible to have a sort of both reality and locality in quantum mechanics. To demonstrate this, we construct a new quantitative model of hidden variables (HV's), dubbed solipsistic HV's, that interpolates between the orthodox no-HV interpretation and nonlocal Bohmian interpretation. In this model, the deterministic point-particle trajectories are associated only with the essential degrees of freedom of the observer, and not with the observed objects. In contrast with Bohmian HV's, nonlocality in solipsistic HV's can be substantially reduced down to microscopic distances inside the observer. Even if such HV's may look philosophically unappealing to many, the mere fact that they are logically possible deserves attention.
RECENT DEVELOPMENT OF SUPERSYMMETRIC GAUGE THEORIES ON LATTICE
Authors: SUGINO FUMIHIKO
Published: March 2013

First, we give a brief review of recent development of lattice formulations for supersymmetric Yang-Mills (SYM) theories with extended supersymmetry, which preserves a part of supersymmetry on lattice. For cases of two dimensions, we can see that lattice models in such formulations lead to the target continuum theories with no fine-tuning. Namely, supersymmetries or some other symmetries not realized on the lattice are automatically restored in the continuum limit.

Next, we consider a mass deformation to [Formula: see text] and present its lattice formulation with keeping two supercharges. It provides a nonperturbative framework to investigate IIA matrix string theory. Moreover, since it has fuzzy sphere solutions around which four-dimensional theory is deconstructed, it will serve a nonperturbative formulation of four-dimensional [Formula: see text] which requires no fine-tuning. The rank of the gauge group is not restricted to large N. It opens a quite interesting possibility to test AdS/CFT correspondence in a stringy regime where string loop effects cannot be neglected. Also, for two-dimensional [Formula: see text], a similar argument is possible to obtain four-dimensional [Formula: see text] on noncommutative space.
COUNTING BPS STATES IN E-STRING THEORY
Authors: SAKAI KAZUHIRO
Published: March 2013

We find a Nekrasov-type expression for the Seiberg–Witten prepotential for the six-dimensional non-critical E8 string theory toroidally compactified down to four dimensions. The prepotential represents the BPS partition function of the E8 strings wound around one of the circles of the toroidal compactification with general winding numbers and momenta. We show that our expression exhibits expected modular properties. In particular, we prove that it obeys the modular anomaly equation known to be satisfied by the prepotential.
DIPOLE COUPLING EFFECT OF HOLOGRAPHIC FERMION IN CHARGED DILATONIC GRAVITY
Authors: WEN WEN-YU , WU SHANG-YU
Published: March 2013

In this note, we study the dipole coupling effect of holographic fermion in a charged dilatonic black hole proposed by Gubser and Rocha.1 It is found that the property of Fermi liquid is rigid under perturbation of dipole coupling, and the Fermi momentum is linearly shifted. A gap is dynamically generated as the coupling becomes large enough and the Fermi surface ceases to exist as the bulk dipole coupling further increases.
NLIE METHOD FOR THE SPECTRAL PROBLEM OF AdS5 × S5
Authors: SUZUKI RYO
Published: March 2013

The excited state spectrum of AdS5 × S5 string can be computed exactly by the mirror TBA equations. We discuss an equivalent, smaller set of equations called hybrid nonlinear integral equations (NLIE). The hybrid NLIE is written by new dynamical degrees of freedom, analogous to spinon variables in condensed matter systems. This derivation is applicable to any integrable systems which obey A1 T-system equipped with certain analyticity conditions. A case study of orbifold Konishi state shows that the new method relieves the problem of criticality in the mirror TBA equations.
SPACETIME STRUCTURE OF THE BLACK HOLE EVAPORATION
Authors: KAWAI HIKARU , MATSUO YOSHINORI , YOKOKURA YUKI
Published: March 2013

We study a self-consistent solution of the semi-classical Einstein equation including the back reaction from the Hawking radiation. Our geometry is constructed by connecting flat space and the outgoing Vaidya metric at the locus of the shock wave. In order to prove that this is the self-consistent solution, we first show that the Weyl anomaly is canceled if we take the effects of the fluctuations of the metric into account. We further demonstrate that the Hawking radiation occurs even if the geometry has no horizon. Then, the energy-momentum tensor is found to be consistent with the semi-classical Einstein equation. Since our geometry has neither horizon nor singularity, all matters inside the black hole finally come back to infinity. Therefore, no information is lost by the black hole evaporation. Furthermore, we take into account the gray-body factor. We construct a stationary solution for a black hole in the heat bath and estimate the entropy. The entropy-area law is reproduced by the volume integration of the entropy density over the inside of the horizon, and the black hole can be treated as an ordinary thermodynamic object.
LINE OPERATOR INDEX ON S1 × S3
Authors: GANG DONGMIN
Published: March 2013

We derive a general formula for an index for [Formula: see text] superconformal field theories. In the computation, 1-loop and monopole bubbling effects are taken into account. Our computation is compatible with S-dualities in the [Formula: see text] theories and the holographic principle which maps Wilson line operators in the [Formula: see text] SYMs to macroscopic objects in AdS5 × S5.
NONCOMMUTATIVE ADHM CONSTRUCTION REVISITED
Authors: HAMANAKA MASASHI , NAKATSU TOSHIO
Published: March 2013

The Atiyah-Drinfeld-Hitchin-Manin (ADHM) construction for noncommutative U(N) instantons is revisited. The origin of the instanton number is elucidated, including the case of the U(1) instantons. The group actions on the instantons are argued.
LONG-DISTANCE PROPERTIES OF BARYONS IN THE SAKAI-SUGIMOTO MODEL
Authors: ISHII TAKAAKI
Published: March 2013

We reconsider the realization of baryons in the Sakai-Sugimoto model. It has previously been shown that, at least with the standard approach to calculations of baryon properties in the theory, one does not reproduce some model-independent predictions for the behavior of baryon electromagnetic form factors connected with long-range pion physics. It is suspected that the pion contributions has been dropped because of the linearization approximations. We study the long-range properties of baryons without relying on the approximations. The baryon solution we obtain gives the correct result for the model-independent ratio of the form factors.
LOCALIZATION AND KNOTS
Authors: TANAKA AKINORI
Published: March 2013

We study the 1/2 BPS condition of Wilson loop on squashed three-sphere, and find that the solution becomes torus knot or unknot. We also calculate the expectation value of 1/2 BPS Wilson loops by using localization technique with the gauge group U(2) and Wilson loop as fundamental representation. And it completely matches with known results.
NUMERICAL STUDIES OF THE ABJM THEORY FOR ARBITRARY N AT ARBITRARY COUPLING CONSTANT
Authors: HONDA MASAZUMI , HANADA MASANORI , HONMA YOSHINORI , NISHIMURA JUN , SHIBA SHOTARO , YOSHIDA YUTAKA
Published: March 2013

We show that the ABJM theory, which is an [Formula: see text] superconformal U (N) × U (N) Chern-Simons matter theory, can be studied for arbitrary N at arbitrary coupling constant by applying a simple Monte Carlo method to the matrix model derived by using the localization method. Here we calculate the free energy, and show that some results obtained by the Fermi gas approach can be clearly understood from the constant map contribution obtained by the genus expansion.
Nanobiodevices for Biomolecule Analysis and Imaging
Authors: Yasui Takao , Kaji Noritada , Baba Yoshinobu
Published: March 2013

Nanobiodevices have been developed to analyze biomolecules and cells for biomedical applications. In this review, we discuss several nanobiodevices used for disease-diagnostic devices, molecular imaging devices, regenerative medicine, and drug-delivery systems and describe the numerous advantages of nanobiodevices, especially in biological, medical, and clinical applications. This review also outlines the fabrication technologies for nanostructures and nanomaterials, including top-down nanofabrication and bottom-up molecular self-assembly approaches. We describe nanopillar arrays and nanowall arrays for the ultrafast separation of DNA or protein molecules and nanoball materials for the fast separation of a wide range of DNA molecules, and we present examples of applications of functionalized carbon nanotubes to obtain information about subcellular localization on the basis of mobility differences between free fluorophores and fluorophore-labeled carbon nanotubes. Finally, we discuss applications of newly synthesized quantum dots to the screening of small interfering RNA, highly sensitive detection of disease-related proteins, and development of cancer therapeutics and diagnostics.
Evolving Views of Pectin Biosynthesis
Authors: Atmodjo Melani A. , Hao Zhangying , Mohnen Debra
Published: March 2013

Recent progress in the identification and characterization of pectin biosynthetic proteins and the discovery of pectin domain–containing proteoglycans are changing our view of how pectin, the most complex family of plant cell wall polysaccharides, is synthesized. The functional confirmation of four types of pectin biosynthetic glycosyltransferases, the identification of multiple putative pectin glycosyl- and methyltransferases, and the characteristics of the GAUT1:GAUT7 homogalacturonan biosynthetic complex with its novel mechanism for retaining catalytic subunits in the Golgi apparatus and its 12 putative interacting proteins are beginning to provide a framework for the pectin biosynthetic process. We propose two partially overlapping hypothetical and testable models for pectin synthesis: the consecutive glycosyltransferase model and the domain synthesis model.
Network Analysis of the MVA and MEP Pathways for Isoprenoid Synthesis
Authors: Vranová Eva , Coman Diana , Gruissem Wilhelm
Published: March 2013

Isoprenoid biosynthesis is essential for all living organisms, and isoprenoids are also of industrial and agricultural interest. All isoprenoids are derived from prenyl diphosphate (prenyl-PP) precursors. Unlike isoprenoid biosynthesis in other living organisms, prenyl-PP, as the precursor of all isoprenoids in plants, is synthesized by two independent pathways: the mevalonate (MVA) pathway in the cytoplasm and the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway in plastids. This review focuses on progress in our understanding of how the precursors for isoprenoid biosynthesis are synthesized in the two subcellular compartments, how the underlying pathway gene networks are organized and regulated, and how network perturbations impact each pathway and plant development. Because of the wealth of data on isoprenoid biosynthesis, we emphasize research in Arabidopsis thaliana and compare the synthesis of isoprenoid precursor molecules in this model plant with their synthesis in other prokaryotic and eukaryotic organisms.
Photosystem II Assembly: From Cyanobacteria to Plants
Authors: Nickelsen Jörg , Rengstl Birgit
Published: March 2013

Photosystem II (PSII) is an integral-membrane, multisubunit complex that initiates electron flow in oxygenic photosynthesis. The biogenesis of this complex machine involves the concerted assembly of at least 20 different polypeptides as well as the incorporation of a variety of inorganic and organic cofactors. Many factors have recently been identified that constitute an integrative network mediating the stepwise assembly of PSII components. One recurring theme is the subcellular organization of the assembly process in specialized membranes that form distinct biogenesis centers. Here, we review our current knowledge of the molecular components and events involved in PSII assembly and their high degree of evolutionary conservation.
ROS-Mediated Lipid Peroxidation and RES-Activated Signaling
Authors: Farmer Edward E. , Mueller Martin J.
Published: March 2013

Nonenzymatic lipid oxidation is usually viewed as deleterious. But if this is the case, then why does it occur so frequently in cells? Here we review the mechanisms of membrane peroxidation and examine the genesis of reactive electrophile species (RES). Recent evidence suggests that during stress, both lipid peroxidation and RES generation can benefit cells. New results from genetic approaches support a model in which entire membranes can act as supramolecular sinks for singlet oxygen, the predominant reactive oxygen species (ROS) in plastids. RES reprogram gene expression through a class II TGA transcription factor module as well as other, unknown signaling pathways. We propose a framework to explain how RES signaling promotes cell “REScue” by stimulating the expression of genes encoding detoxification functions, cell cycle regulators, and chaperones. The majority of the known biological activities of oxygenated lipids (oxylipins) in plants are mediated either by jasmonate perception or through RES signaling networks.
The Number, Speed, and Impact of Plastid Endosymbioses in Eukaryotic Evolution
Authors: Keeling Patrick J.
Published: March 2013

Plastids (chloroplasts) have long been recognized to have originated by endosymbiosis of a cyanobacterium, but their subsequent evolutionary history has proved complex because they have also moved between eukaryotes during additional rounds of secondary and tertiary endosymbioses. Much of this history has been revealed by genomic analyses, but some debates remain unresolved, in particular those relating to secondary red plastids of the chromalveolates, especially cryptomonads. Here, I examine several fundamental questions and assumptions about endosymbiosis and plastid evolution, including the number of endosymbiotic events needed to explain plastid diversity, whether the genetic contribution of the endosymbionts to the host genome goes far beyond plastid-targeted genes, and whether organelle origins are best viewed as a singular transition involving one symbiont or as a gradual transition involving a long line of transient food/symbionts. I also discuss a possible link between transporters and the evolution of protein targeting in organelle integration.
Growth Mechanisms in Tip-Growing Plant Cells
Authors: Rounds Caleb M. , Bezanilla Magdalena
Published: March 2013

Tip growth is employed throughout the plant kingdom. Our understanding of tip growth has benefited from modern tools in molecular genetics, which have enabled the functional characterization of proteins mediating tip growth. Here we first discuss the evolutionary role of tip growth in land plants and then describe the prominent model tip-growth systems, elaborating on some advantages and disadvantages of each. Next we review the organization of tip-growing cells, the role of the cytoskeleton, and recent developments concerning the physiological basis of tip growth. Finally, we review advances in the understanding of the extracellular signals that are known to guide tip-growing cells.
Transport and Metabolism in Legume-Rhizobia Symbioses
Authors: Udvardi Michael , Poole Philip S.
Published: March 2013

Symbiotic nitrogen fixation by rhizobia in legume root nodules injects approximately 40 million tonnes of nitrogen into agricultural systems each year. In exchange for reduced nitrogen from the bacteria, the plant provides rhizobia with reduced carbon and all the essential nutrients required for bacterial metabolism. Symbiotic nitrogen fixation requires exquisite integration of plant and bacterial metabolism. Central to this integration are transporters of both the plant and the rhizobia, which transfer elements and compounds across various plant membranes and the two bacterial membranes. Here we review current knowledge of legume and rhizobial transport and metabolism as they relate to symbiotic nitrogen fixation. Although all legume-rhizobia symbioses have many metabolic features in common, there are also interesting differences between them, which show that evolution has solved metabolic problems in different ways to achieve effective symbiosis in different systems.
Systemic Amyloidoses
Authors: Blancas-Mejía Luis M. , Ramirez-Alvarado Marina
Published: March 2013

The amyloidoses are a group of protein misfolding diseases in which the precursor protein undergoes a conformational change that triggers the formation of amyloid fibrils in different tissues and organs, causing cell death and organ failure. Amyloidoses can be either localized or systemic. In localized amyloidosis, amyloid deposits form at the site of precursor protein synthesis, whereas in systemic amyloidosis, amyloid deposition occurs distant from the site of precursor protein secretion. We review the type of proteins and cells involved and what is known about the complex pathophysiology of these diseases. We focus on light chain amyloidosis to illustrate how biochemical and biophysical studies have led to a deeper understanding of the pathogenesis of this devastating disease. We also review current cellular, tissue, and animal models and discuss the challenges and opportunities for future studies of the systemic amyloidoses.
The Underappreciated Role of Allostery in the Cellular Network
Authors: Nussinov Ruth , Tsai Chung-Jung , Ma Buyong
Published: March 2013

Allosteric propagation results in communication between distinct sites in the protein structure; it also encodes specific effects on cellular pathways, and in this way it shapes cellular response. One example of long-range effects is binding of morphogens to cell surface receptors, which initiates a cascade of protein interactions that leads to genome activation and specific cellular action. Allosteric propagation results from combinations of multiple factors, takes place through dynamic shifts of conformational ensembles, and affects the equilibria of macromolecular interactions. Here, we (a) emphasize the well-known yet still underappreciated role of allostery in conveying explicit signals across large multimolecular assemblies and distances to specify cellular action; (b) stress the need for quantitation of the allosteric effects; and finally, (c) propose that each specific combination of allosteric effectors along the pathway spells a distinct function. The challenges are colossal; the inspiring reward will be predicting function, misfunction, and outcomes of drug regimes.
Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects
Authors: Li Zhixiu , Yang Yuedong , Zhan Jian , Dai Liang , Zhou Yaoqi
Published: March 2013

In the past decade, a concerted effort to successfully capture specific tertiary packing interactions produced specific three-dimensional structures for many de novo designed proteins that are validated by nuclear magnetic resonance and/or X-ray crystallographic techniques. However, the success rate of computational design remains low. In this review, we provide an overview of experimentally validated, de novo designed proteins and compare four available programs, RosettaDesign, EGAD, Liang-Grishin, and RosettaDesign-SR, by assessing designed sequences computationally. Computational assessment includes the recovery of native sequences, the calculation of sizes of hydrophobic patches and total solvent-accessible surface area, and the prediction of structural properties such as intrinsic disorder, secondary structures, and three-dimensional structures. This computational assessment, together with a recent community-wide experiment in assessing scoring functions for interface design, suggests that the next-generation protein-design scoring function will come from the right balance of complementary interaction terms. Such balance may be found when more negative experimental data become available as part of a training set.
The Yin-Yang of Rigidity Sensing: How Forces and Mechanical Properties Regulate the Cellular Response to Materials
Authors: Schoen Ingmar , Pruitt Beth L. , Vogel Viola
Published: March 2013

According to the Chinese yin-yang concept, seemingly opposing forces give rise and respond to each other. Opposing forces, whether passive or active, are also at work when cells adhere to a substrate or extracellular matrix, sense environmental properties, and finally respond to them. In this review, we describe molecular elements inside and outside of the cell that establish labile physical connections, and how forces regulate their interplay, namely formation, reinforcement, breakage, and reconfiguration of these elements. What a cell locally feels thus depends not only on the displacement of materials, but also on the stability of molecular interactions, on the conversion of mechanical forces to biochemical signals by stretching proteins into structural intermediates (mechano-chemical signal conversion), and on the micro- and nanoscopic features of the extracellular material. Current methodologies for quantifying forces in the cellular context at different length scales are also critically assessed.
Water Vapor–Mediated Volatilization of High-Temperature Materials
Authors: Meschter Peter J. , Opila Elizabeth J. , Jacobson Nathan S.
Published: March 2013

Volatilization in water vapor–containing atmospheres is an important and often unexpected mechanism of degradation of high-temperature materials during processing and in service. Thermodynamic properties data sets for key (oxy)hydroxide vapor product species that are responsible for material transport and damage are often uncertain or unavailable. Estimation, quantum chemistry calculation, and measurement methods for thermodynamic properties of these species are reviewed, and data judged to be reliable are tabulated and referenced. Applications of water vapor–mediated volatilization include component and coating recession in turbine engines, oxidation/volatilization of ferritic steels in steam boilers, chromium poisoning in solid-oxide fuel cells, vanadium transport in hot corrosion and degradation of hydrocracking catalysts, Na loss from Na β″-Al2O3tubes, and environmental release of radioactive isotopes in a nuclear reactor accident or waste incineration. The significance of water vapor–mediated volatilization in these applications is described.
Media Bias by the Numbers: Challenges and Opportunities in the Empirical Study of Partisan News
Authors: Groeling Tim
Published: March 2013

Partisan bias in the news is a perennial matter of concern and debate for scholars, journalists, politicians, and citizens. Although there are abundant opinions about the magnitude, direction, and even existence of media bias, producing a scholarly consensus on the issue has proven difficult for several reasons. In particular, scholars studying media bias empirically must overcome problems of subjectivity, strategic behavior by the actors involved in the process, and especially the absence of suitable baselines against which to assess bias. This article reviews some approaches to studying media bias and explores several promising strategies and tools scholars have developed to help overcome these obstacles. I conclude with suggestions for future research in the area.
Nebivolol prevents desensitization of β-adrenoceptor signaling and induction of cardiac hypertrophy in response to isoprenaline beyond β1-adrenoceptor blockage
Authors: Ozakca Isil , Arioglu-Inan Ebru , Esfahani Hrag , Altan V. Melih , Balligand Jean-Luc , Kayki-Mutlu Gizem , Ozcelikay A. Tanju
Published: March 2013

The importance of chronic stimulation of β-adrenoceptors in the development of cardiac dysfunction is the rationale for the use of β-blockers in the treatment of heart failure. Nebivolol is a third-generation β-blocker, which has further properties including stimulation of endothelial nitric oxide synthase and/or β3-adrenoceptors. The aim of this study was to investigate whether nebivolol has additional effects on β-adrenoceptor-mediated functional responses along with morphologic and molecular determinants of cardiac hypertrophy compared with those of metoprolol, a selective β1-adrenoceptor blocker. Rats infused by isoprenaline (100 μg·kg−1·day−1, 14 days) were randomized into three groups according to the treatment with metoprolol (30 mg·kg−1·day−1), nebivolol (10 mg·kg−1·day−1), or placebo for 13 days starting on day 1 after implantation of minipump. Both metoprolol and nebivolol caused a similar reduction on heart rate. Nebivolol mediated a significant improvement on cardiac mass, coronary flow, mRNA expression levels of sarcoplasmic reticulum Ca2+ ATPase (SERCA2a) and atrial natriuretic peptide and phospholamban (PLN)/SERCA2a and phospho-PLN/PLN ratio compared with metoprolol and placebo. Nebivolol prevented the detrimental effects of isoprenaline infusion on isoprenaline (68% of control at 30 μM), BRL37344 (63% of control at 0.1 μM), and forskolin (64% of control at 1 μM) responses compared with metoprolol (isoprenaline, 34% of control; BRL37344, no response; forskolin, 26% of control) and placebo (isoprenaline, 33% of control; BRL37344, 28% of control; forskolin, 12% of control). Both β-blockers improved the changes in mRNA expressions of β1- and β3-adrenoceptors. Our results suggest that nebivolol partially protects the responsiveness of β-adrenoceptor signaling and the development of cardiac hypertrophy independent of its β1-adrenoceptor blocking effect.
Assessment of cardiac proteome dynamics with heavy water: slower protein synthesis rates in interfibrillar than subsarcolemmal mitochondria
Authors: Kasumov Takhar , Dabkowski Erinne R. , Shekar Kadambari Chandra , Li Ling , Ribeiro Rogerio F. , Walsh Kenneth , Previs Stephen F. , Sadygov Rovshan G. , Willard Belinda , Stanley William C.
Published: March 2013

Traditional proteomics provides static assessment of protein content, but not synthetic rates. Recently, proteome dynamics with heavy water (2H2O) was introduced, where2H labels amino acids that are incorporated into proteins, and the synthesis rate of individual proteins is calculated using mass isotopomer distribution analysis. We refine this approach with a novel algorithm and rigorous selection criteria that improve the accuracy and precision of the calculation of synthesis rates and use it to measure protein kinetics in spatially distinct cardiac mitochondrial subpopulations. Subsarcolemmal mitochondria (SSM) and interfibrillar mitochondria (IFM) were isolated from adult rats, which were given2H2O in the drinking water for up to 60 days. Plasma2H2O and myocardial2H-enrichment of amino acids were stable throughout the experimental protocol. Multiple tryptic peptides were identified from 28 proteins in both SSM and IFM and showed a time-dependent increase in heavy mass isotopomers that was consistent within a given protein. Mitochondrial protein synthesis was relatively slow (average half-life of 30 days, 2.4% per day). Although the synthesis rates for individual proteins were correlated between IFM and SSM ( R2= 0.84; P < 0.0001), values in IFM were 15% less than SSM ( P < 0.001). In conclusion, administration of2H2O results in stable enrichment of the cardiac precursor amino acid pool, with the use of refined analytical and computational methods coupled with cell fractionation one can measure synthesis rates for cardiac proteins in subcellular compartments in vivo, and protein synthesis is slower in mitochondria located among the myofibrils than in the subsarcolemmal region.
The IGF-I/IGF-R1 pathway regulates postnatal lung growth and is a nonspecific regulator of alveologenesis in the neonatal rat
Authors: Li Jun , Masood Azhar , Yi Man , Lau Mandy , Belcastro Rosetta , Ivanovska Julijana , Jankov Robert P. , Tanswell A. Keith
Published: March 2013

IGF-I, IGF-II, and the IGF-I receptor are widely distributed throughout the neonatal rat lung on days 4, 7, 10, and 14 of life, with a similar abundance at each of these time points. Injection of 20 μg/g of a truncated soluble IGF-I receptor on days 2 and 5 of life, to decoy ligand away from the endogenous IGF-I receptor, reduced lung weight and lung-to-body weight ratio, reduced lung tissue fraction, and impaired alveolar formation, as assessed by secondary crest formation and mean linear intercepts on day 7 of life. Lung procollagen I content and elastin fiber density were also reduced. Injection of 100 μg/day of neutralizing anti-IGF-I, to prevent IGF-I from binding to the IGF-I receptor, on days 3, 4, and 5 of life reduced tissue fraction and elastin fiber density and impaired alveolar formation on day 6 of life. Both interventions reduced total lung cell and secondary crest cell DNA synthesis and small vessel counts per unit area, but these effects were lost after normalization to the reduced tissue fraction. These findings are consistent with a role for IGF-I binding to the IGF-I receptor in postnatal lung growth and on alveologenesis through a nonspecific positive effect on DNA synthesis. Injection of 100 μg/day of neutralizing anti-IGF-II, to prevent IGF-II from binding to the IGF-I receptor, on days 3, 4, and 5 of life had no effect on total lung cell DNA synthesis per unit area on day 6 of life, and a role for IGF-II in postnatal alveologenesis was not further pursued.
Risk of Pancreatic Cancer in Breast Cancer Families from the Breast Cancer Family Registry
Authors: Mocci Evelina , Milne Roger L. , Méndez-Villamil Elena Yuste , Hopper John L. , John Esther M. , Andrulis Irene L. , Chung Wendy K. , Daly Mary , Buys Saundra S. , Malats Nuria , Goldgar David E.
Published: March 2013

Background: Increased risk of pancreatic cancer has been reported in breast cancer families carrying BRCA1and BRCA2 mutations; however, pancreatic cancer risk in mutation-negative (BRCAX) families has not been explored to date. The aim of this study was to estimate pancreatic cancer risk in high-risk breast cancer families according to the BRCA mutation status.

Methods: A retrospective cohort analysis was applied to estimate standardized incidence ratios (SIR) for pancreatic cancer. A total of 5,799 families with ≥1 breast cancer case tested for mutations in BRCA1 and/or BRCA2 were eligible. Families were divided into four classes: BRCA1, BRCA2, BRCAX with ≥2 breast cancer diagnosed before age 50 (class 3), and the remaining BRCAX families (class 4).

Results: BRCA1 mutation carriers were at increased risk of pancreatic cancer [SIR = 4.11; 95% confidence interval (CI), 2.94–5.76] as were BRCA2 mutation carriers (SIR = 5.79; 95% CI, 4.28–7.84). BRCAX family members were also at increased pancreatic cancer risk, which did not appear to vary by number of members with early-onset breast cancer (SIR = 1.31; 95% CI, 1.06–1.63 for class 3 and SIR = 1.30; 95% CI, 1.13–1.49 for class 4).

Conclusions: Germline mutations in BRCA1 and BRCA2 are associated with an increased risk of pancreatic cancer. Members of BRCAX families are also at increased risk of pancreatic cancer, pointing to the existence of other genetic factors that increase the risk of both pancreatic cancer and breast cancer.

Impact: This study clarifies the relationship between familial breast cancer and pancreatic cancer. Given its high mortality, pancreatic cancer should be included in risk assessment in familial breast cancer counseling. Cancer Epidemiol Biomarkers Prev; 22(5); 803–11. ©2013 AACR.
Physical Activity and Fatigue in Breast Cancer Survivors: A Panel Model Examining the Role of Self-efficacy and Depression
Authors: Phillips Siobhan M. , McAuley Edward
Published: March 2013

Background: Physical activity is associated with reductions in fatigue in breast cancer survivors. However, mechanisms underlying this relationship are not well-understood. The purpose of this study was to longitudinally test a model examining the role of self-efficacy and depression as potential mediators of the relationship between physical activity and fatigue in a sample of breast cancer survivors using both self-report and objective measures of physical activity.

Methods: All participants (N = 1,527) completed self-report measures of physical activity, self-efficacy, depression, and fatigue at baseline and 6 months. A subsample was randomly selected to wear an accelerometer at both time points. It was hypothesized that physical activity indirectly influences fatigue via self-efficacy and depression. Relationships among model constructs were examined over the 6-month period using panel analysis within a covariance modeling framework.

Results: The hypothesized model provided a good model-data fit (χ2 = 599.66, df = 105, P ≤ 0.001; CFI = 0.96; SRMR = 0.02) in the full sample when controlling for covariates. At baseline, physical activity indirectly influenced fatigue via self-efficacy and depression. These relationships were also supported across time. In addition, the majority of the hypothesized relationships were supported in the subsample with accelerometer data (χ2 = 387.48, df = 147, P ≤ 0.001, CFI = 0.94, SRMR = 0.04).

Conclusions: This study provides evidence to suggest the relationship between physical activity and fatigue in breast cancer survivors may be mediated by more proximal, modifiable outcomes of physical activity participation.

Impact: Recommendations are made relative to future applications and research concerning these relationships. Cancer Epidemiol Biomarkers Prev; 22(5); 773–81. ©2013 AACR.
Introduction Special Section on Contemporary Art and Religion
Authors: Lerner Loren
Published: March 2013

Abstract

This introduction explores the connections between the worlds of art and religion over the past fifty years. Focusing on the discursive coherence of contemporary art and religion, Lerner examines the attempts to bring some order to a theme that has cyclically and persistently arisen in recent art making. In this overview of critical and curatorial interpretations, crucial areas of inquiry are: the religious and secular paradigms addressed within contemporary art practices; the relationships between works of art and institutional questions; the confrontations of new artistic modes; and the survival of religious symbolic structures.
A Post-Metaphysical Turn: Contingency and Givenness in the Early Work of Dan Flavin (1959–1964)
Authors: Louria-Hayon Adi
Published: March 2013

Abstract

Dan Flavin’s fluorescent light installations have long served art historians by marking the turn from the late modernist illusionist space of painting to the new immanence of specific objects. In the narration of this genealogy, the crux of minimalism, as Hal Foster calls it, rests on a nominal approach that proclaims metaphysical relations as an obstacle and calls out to evade any notion of meaning. By contrast, this essay asserts the primacy of metaphysics in Flavin’s [en]lighted work. By tracing the artist’s scholastic education, his contemporary theo-political stance, and his rejection of objecthood, I argue that Flavin was continuously preoccupied with Catholic theology and that his work is imbued with Christian iconography. Thinking alongside the fourteenth-century philosopher William of Ockham and the twentieth-century post-Husserlian phenomenology of Jean-Luc Marion, the evolution of Flavin’s light constructions proves relevant to the quandary of metaphysics and the role of theology in radical immanence. To bracket his metaphysics is to ignore the full implications of his art.
León Ferrari’s Hell
Authors: Porterfield Todd
Published: March 2013

Abstract

The myth of modernism holds that the process of desacralization was its most emblematic and pervasive effect. However, far from being forgotten in the work of Argentinian conceptualist León Ferrari, religion has had an essential place in it for five decades. This essay sets out to trace the theme of hell in Ferrari’s work, which the artist has linked to oppression and violence in Latin America, Viet Nam, and Iraq, in order to demonstrate the persistence and centrality of religion in Ferrari’s art and in the Argentine milieu, thereby disavowing the illusion that we have been living in a sustained period of secularism that is only now being supplanted by a global return to religion.
“Christianity and Mountainanity”: The Restoration Movement’s Influence on John Muir
Authors: Pierce John
Published: March 2013

Abstract

The theological underpinnings of John Muir’s work and thought have, justifiably, received a fair amount of scholarly attention. Most of the early scholarship, however, focused on correlations between Muir’s beliefs and pantheism, and ignored the more immediate influence exerted on Muir by his upbringing in the Disciples of Christ. More recent scholars, such as Donald Worster, Dennis Williams, and Stephen Holmes, have attested to the significance of Muir’s Disciples of Christ background but have so far failed to explicate its influence. Yet we know from Muir’s letters that he remained engaged with Disciples’ people and issues throughout his life. Despite occasional dissatisfaction expressed toward his childhood faith, he could never entirely escape it, and a consideration of Muir’s thought in relation to the dominant themes of Disciples theology reveals a close relationship between the two. In numerous ways, the tenets of the Disciples of Christ belief system guide Muir’s thought and mission: his anthropological views, his beliefs on sin and salvation, his approach to politics, and his eschatological mission to encourage harmony among all created beings, are shaped by Disciples of Christ theology.
Gustavo Gutiérrez Meets Giuseppe Verdi: The Beauty of Liberation and the Liberation of Beauty
Authors: Nickoloff James B.
Published: March 2013

Abstract

Some have criticized the theology of liberation, especially its Latin American form, for emphasizing ethical concerns while ignoring the aesthetic dimension of Christian faith. At the same time, many see the fine arts—and particularly opera—as unrelated and even opposed to the struggle for justice today. This essay considers the case of liberation theologian Gustavo Gutiérrez and his debt to fellow Peruvian and novelist José María Arguedas. It then examines the ethical import of one of Giuseppe Verdi’s most famous creations, the enslaved princess Aida. Both Gutiérrez and Verdi may be said to belong to what Arguedas called the “fraternity of the broken-hearted” whose members glimpse a new world coming into being in the very beauty of liberated humanity.