bluuebunny/crossref_metadata_2025 huggingface dataset:
Platelet-derived growth factor-C (PDGF-C) activation by serine proteases: implications for breast cancer progression
Authors: Hurst Newton J. , Najy Abdo J. , Ustach Carolyn V. , Movilla Lisa , Kim Hyeong-Reh Choi
Published: October 2011

The PDGF (platelet-derived growth factor) family members are potent mitogens for cells of mesenchymal origin and serve as important regulators of cell migration, survival, apoptosis and transformation. Tumour-derived PDGF ligands are thought to function in both autocrine and paracrine manners, activating receptors on tumour and surrounding stromal cells. PDGF-C and -D are secreted as latent dimers, unlike PDGF-A and -B. Cleavage of the CUB domain from the PDGF-C and -D dimers is required for their biological activity. At present, little is known about the proteolytic processing of PDGF-C, the rate-limiting step in the regulation of PDGF-C activity. In the present study we show that the breast carcinoma cell line MCF7, engineered to overexpress PDGF-C, produces proteases capable of cleaving PDGF-C to its active form. Increased PDGF-C expression enhances cell proliferation, anchorage-independent cell growth and tumour cell motility by autocrine signalling. In addition, MCF7-produced PDGF-C induces fibroblast cell migration in a paracrine manner. Interestingly, PDGF-C enhances tumour cell invasion in the presence of fibroblasts, suggesting a role for tumour-derived PDGF-C in tumour–stromal interactions. In the present study, we identify tPA (tissue plasminogen activator) and matriptase as major proteases for processing of PDGF-C in MCF7 cells. In in vitro studies, we also show that uPA (urokinase-type plasminogen activator) is able to process PDGF-C. Furthermore, by site-directed mutagenesis, we identify the cleavage site for these proteases in PDGF-C. Lastly, we provide evidence suggesting a two-step proteolytic processing of PDGF-C involving creation of a hemidimer, followed by GFD-D (growth factor domain dimer) generation.
Virtual Bending of Titanium Reconstructive Plates for Mandibular Defect Bridging: Review of Three Clinical Cases
Authors: Rahimov Chingiz , Farzaliyev Ismayil
Published: October 2011

The reconstruction of acquired mandibular defects due to ablative tumor surgery or traumatic injuries is still challenging. The gold standard in such treatment is application of reconstructive titanium plates, which should be contoured and adapted to the defect as much as possible because of their influence on postoperative functional and esthetic results. Traditionally, plate bending is achieved by trial and error intraoperatively. Use of stereolitography (STL) models potentially could reduce the risk of incorrect contouring as well as operating time. On the other hand, fabrication of STL is time-consuming and costly. However, we found only one experimental study dedicating to virtual plate bending in the literature. The aim of this article was to demonstrate clinical application of a method of virtual bending of reconstructive plate for mandibular defect bridging. No significant complications occurred, and satisfactory functional and esthetic results were achieved in all cases. We found this technique precise and applicable in cases of reconstruction of mandibular defects.
First-principles study of hydrogen permeation in palladium-gold alloys
Authors: Xu Shucheng , Sood Parveen , Liu M. L. , Bongiorno Angelo
Published: October 2011

Density functional theory and lattice model calculations are combined to study the permeability of hydrogen in Pd lightly alloyed with Au. This study shows that small amounts of Au substitutions in Pd leads to, respectively, an increase and decrease of the diffusivity and solubility of hydrogen in the alloy. The competition between these two phenomena depends on temperature and can yield dilute PdAu membranes with a hydrogen permeability higher than pure Pd.
Plasmonic reflection grating back contacts for microcrystalline silicon solar cells
Authors: Paetzold U. W. , Moulin E. , Michaelis D. , Böttler W. , Wächter C. , Hagemann V. , Meier M. , Carius R. , Rau U.
Published: October 2011

We report on the fabrication and optical simulation of a plasmonic light-trapping concept for microcrystalline silicon solar cells, consisting of silver nanostructures arranged in square lattice at the ZnO:Al/Ag back contact of the solar cell. Those solar cells deposited on this plasmonic reflection grating back contact showed an enhanced spectral response in the wavelengths range from 500 nm to 1000 nm, when comparing to flat solar cells. For a particular period, even an enhancement of the short circuit current density in comparison to the conventional random texture light-trapping concept is obtained. Full three-dimensional electromagnetic simulations are used to explain the working principle of the plasmonic light-trapping concept.
Science in Japan gets back on its feet
Authors: Feder Toni
Published: October 2011

Looking ahead, a central question will be whether to continue relying on nuclear power.
Taking the pulse of magnet labs
Authors: Feder Toni
Published: October 2011

As fields get stronger and electronics improve, demand for pulsed magnets is growing; the newest lab is in China.
Weather data gap is forecast as satellite is delayed
Authors: Kramer David
Published: October 2011

A new polar-orbiting satellite is only a temporary fix for a more durable spacecraft that has been starved of funding.
Focus on materials
Authors: Mandelis Andreas
Published: October 2011

The descriptions of the new products listed in this section are based on information supplied to us by the manufacturers. PHYSICS TODAY can assume no responsibility for their accuracy. For more information about a particular product, visit the website at the end of the product description.
Conformational dynamics of helix 8 in the GPCR rhodopsin controls arrestin activation in the desensitization process
Authors: Kirchberg Kristina , Kim Tai-Yang , Möller Martina , Skegro Darko , Dasara Raju Gayathri , Granzin Joachim , Büldt Georg , Schlesinger Ramona , Alexiev Ulrike
Published: October 2011

Arrestins are regulatory molecules for G-protein coupled receptor function. In visual rhodopsin, selective binding of arrestin to the cytoplasmic side of light-activated, phosphorylated rhodopsin (P-Rh*) terminates signaling via the G-protein transducin. While the “phosphate-sensor” of arrestin for the recognition of receptor-attached phosphates is identified, the molecular mechanism of arrestin binding and the involvement of receptor conformations in this process are still largely hypothetic. Here we used fluorescence pump-probe and time-resolved fluorescence depolarization measurements to investigate the kinetics of arrestin conformational changes and the corresponding nanosecond dynamical changes at the receptor surface. We show that at least two sequential conformational changes of arrestin occur upon interaction with P-Rh*, thus providing a kinetic proof for the suggested multistep nature of arrestin binding. At the cytoplasmic surface of P-Rh*, the structural dynamics of the amphipathic helix 8 (H8), connecting transmembrane helix 7 and the phosphorylated C-terminal tail, depends on the arrestin interaction state. We find that a high mobility of H8 is required in the low-affinity (prebinding) but not in the high-affinity binding state. High-affinity arrestin binding is inhibited when a bulky, inflexible group is bound to H8, indicating close interaction. We further show that this close steric interaction of H8 with arrestin is mandatory for the transition from prebinding to high-affinity binding; i.e., for arrestin activation. This finding implies a regulatory role for H8 in activation of visual arrestin, which shows high selectivity to P-Rh* in contrast to the broad receptor specificity displayed by the two nonvisual arrestins.
The discursive construction of the separation wall at Abu Dis
Authors: Hanauer David I.
Published: October 2011

The article analyses the discursive function of graffiti on the separation wall in the contested space of Abu Dis on the boundary between Jerusalem and the Occupied Territories. This study explores the role of graffiti as micro-level, political discourse designed to influence national and international actions concerning the Palestinian-Israeli conflict over national borders, self determination and human rights. The data for this study consisted of photographic documentation of the Abu Dis graffiti. This data was analysed for its linguistic and informational characteristic, its political functions, and discursive construction. The results of the study reveal that the separation wall is constructed in five different ways that directly interact with the Palestinian-Israeli conflict. The graffiti on the wall at Abu Dis is a microcosm of the broader conflict and offers an insight into the different chains of political discourse in action in the discussion of the Palestinian-Israeli conflict.
Naming China
Authors: Chang Hui-Ching , Holt Richard
Published: October 2011

In the article, we analyze how names for China are used by five ROC presidents in National Day speeches over 58 years (1949–2007), including “communist bandits”; “Chinese communists”; “mainland” and “opposite shore/both shores”; “China”; and “People’s Republic of China.” Each name registers unique historicity and each displays associated expressions, reshuffling power structures and allowing negotiation of ideological positioning. Sometimes overlapping, sometimes joining at edges, these names cleave to inconsistent layers of meaning, helping presidents negotiate courses of action in Taiwan’s yet-to-be-resolved political identity.
THE WELFARE STATE'S MAKING OF COSMOPOLITAN EUROPE
Authors: van Gerven Minna , Ossewaarde Marinus
Published: October 2011

This article seeks to analyze the extent of welfare state tendencies towards individualization of social citizenship rights from the perspective of Cosmopolitan Europe (Beck and Grande 2007, Cosmopolitan Europe). Empirical study of legislated reforms to national insurance benefit schemes in three European countries since 1980 suggests that individualization processes transform modern West European societies through the construction of self-sufficiency, the individualization of responsibility, and the personalization of social services. Although European welfare states vary with respect to the extent of individualization of social categories, late modernization processes appear to transform national solidarities into a cosmopolitan solidarity and hence affect all modern institutions of welfare states, including bureaucratic categories, legal rights, and meaning of work.
Selective repression of MEF2 activity by PKA-dependent proteolysis of HDAC4
Authors: Backs Johannes , Worst Barbara C. , Lehmann Lorenz H. , Patrick David M. , Jebessa Zegeye , Kreusser Michael M. , Sun Qiang , Chen Lan , Heft Claudia , Katus Hugo A. , Olson Eric N.
Published: October 2011

Histone deacetylase 4 (HDAC4) regulates numerous gene expression programs through its signal-dependent repression of myocyte enhancer factor 2 (MEF2) and serum response factor (SRF) transcription factors. In cardiomyocytes, calcium/calmodulin-dependent protein kinase II (CaMKII) signaling promotes hypertrophy and pathological remodeling, at least in part by phosphorylating HDAC4, with consequent stimulation of MEF2 activity. In this paper, we describe a novel mechanism whereby protein kinase A (PKA) overcomes CaMKII-mediated activation of MEF2 by regulated proteolysis of HDAC4. PKA induces the generation of an N-terminal HDAC4 cleavage product (HDAC4-NT). HDAC4-NT selectively inhibits activity of MEF2 but not SRF, thereby antagonizing the prohypertrophic actions of CaMKII signaling without affecting cardiomyocyte survival. Thus, HDAC4 functions as a molecular nexus for the antagonistic actions of the CaMKII and PKA pathways. These findings have implications for understanding the molecular basis of cardioprotection and other cellular processes in which CaMKII and PKA exert opposing effects.
CIIA functions as a molecular switch for the Rac1-specific GEF activity of SOS1
Authors: Hwang Hyun Sub , Hwang Sang Gil , Cho Jun-Ho , Chae Ji Soo , Yoon Kyoung Wan , Cho Ssang-Goo , Choi Eui-Ju
Published: October 2011

Son of sevenless 1 (SOS1) is a dual guanine nucleotide exchange factor (GEF) that activates the guanosine triphosphatases Rac1 and Ras, which mediate signaling initiated by peptide growth factors. In this paper, we show that CIIA is a new binding partner of SOS1. CIIA promoted the SOS1–Rac1 interaction and inhibited the SOS1–Ras interaction. Furthermore, CIIA promoted the formation of an SOS1–EPS8 complex and SOS1-mediated Rac1 activation, whereas it inhibited SOS1-mediated activation of Ras. Transforming growth factor β (TGF-β) up-regulated the expression of CIIA and thereby promoted the association between CIIA and SOS1 in A549 human lung adenocarcinoma cells. Depletion of CIIA in these cells by ribonucleic acid interference inhibited the TGF-β–induced interaction between SOS1 and EPS8, activation of Rac1, and cell migration. Together, these results suggest that CIIA mediates the TGF-β–induced activation of SOS1–Rac1 signaling and cell migration in A549 cells. They further show that CIIA functions as a molecular switch for the GEF activity of SOS1, directing this activity toward Rac1.
Some biomedical applications of chitosan-based hybrid nanomaterials
Authors: Tran Dai Lam , Pham Gia Dien , Nguyen Xuan Phuc , Vu Dinh Hoang , Nguyen Ngoc Thinh , Tran Vinh Hoang , Mai Thi Thu Trang , Nguyen Hai Binh , Le Quang Duong , Nguyen Thi Ngoan , Ba Thi Cham
Published: October 2011

Being naturally abundant resources and having many interesting physicochemical and biological properties, chitin/chitosan have been found to be useful in many fields, especially biomedical ones. This paper describes the strategy to design multifunctional, hybrid chitosan-based nanomaterials and test them in some typical biomedical applications.
Spatial and temporal impacts on a career in science
Authors: Wente Susan R.
Published: October 2011

In cell biology, subcellular locale is critical for the action of signaling molecules, for regulation of gene expression, and for proper cell division. In simple terms, everything must be in the right place at the right time. For my research, I have focused on understanding the role the nuclear pore complex (NPC) plays in maintaining this balance. With eukaryotic transcription in the nucleus and translation in the cytoplasm, highly selective import and export events at the NPC connect these spatially separated processes to allow gene expression. In a similar way, spatial and temporal events have repeatedly impacted my scientific career. In different places and times, interactions with mentors, collaborators, colleagues, and trainees have shaped my research and mentoring philosophies: aim high, fuel your passions, collaborate, and take risks to find supportive environments and challenging projects that impact scientific discovery.
Molecular motors: forty years of interdisciplinary research
Authors: Spudich James A.
Published: October 2011

A mere forty years ago it was unclear what motor molecules exist in cells that could be responsible for the variety of nonmuscle cell movements, including the “saltatory cytoplasmic particle movements” apparent by light microscopy. One wondered whether nonmuscle cells might have a myosin-like molecule, well known to investigators of muscle. Now we know that there are more than a hundred different molecular motors in eukaryotic cells that drive numerous biological processes and organize the cell's dynamic city plan. Furthermore, in vitro motility assays, taken to the single-molecule level using techniques of physics, have allowed detailed characterization of the processes by which motor molecules transduce the chemical energy of ATP hydrolysis into mechanical movement. Molecular motor research is now at an exciting threshold of being able to enter into the realm of clinical applications.
An evolving paradigm for the secretory pathway?
Authors: Lippincott-Schwartz Jennifer
Published: October 2011

The paradigm that the secretory pathway consists of a stable endoplasmic reticulum and Golgi apparatus, using discrete transport vesicles to exchange their contents, gained important support from groundbreaking biochemical and genetic studies during the 1980s. However, the subsequent development of new imaging technologies with green fluorescent protein introduced data on dynamic processes not fully accounted for by the paradigm. As a result, we may be seeing an example of how a paradigm is evolving to account for the results of new technologies and their new ways of describing cellular processes.
A different kind of quarterback
Authors: Guyden Jerry Charles
Published: October 2011

I am not big on celebrations, nor do I accept many invitations to receive awards. There is much work to be done, and the reward is in the doing. I learned this lesson early from my parents, Martha and Robert Guyden. However, I am humbled that anyone would even mention my name in association with E. E. Just. I, like he, was born into a segregated America, and somehow we both found biology. I think Just's life story instigates a discussion on diversity in science, as well it should. However, after reading Tyrone Hayes' (2010 E. E. Just Award recipient) essay from last year, “Diversifying the Biological Sciences: Past Efforts and Future Challenges” (Hayes, 2010), I have little to add on the subject. His words gave voice to my thoughts. That being said, I would like to use these pages to describe my journey into the “Cell” and the people who “hoed the row ahead of me.”
In the trenches: lessons for scientists from California's Proposition 71 campaign
Authors: Goldstein Lawrence S. B.
Published: October 2011

I describe a number of valuable lessons I learned from participating in California's Proposition 71 effort about the role that scientists and rigorous scientific advice can play in a public political process. I describe how scientists can provide valuable information and advice and how they can also gain a great deal from the experience that is valuable to a practicing research scientist. Finally, I argue that in the future, building similar broad coalitions to support biomedical and other areas of scientific research will be essential to protect publicly funded science. Thus, a key lesson from the Proposition 71 experience is that engagement of scientists with diverse nonscientific groups can make a big difference and that scientists must actively engage with the public in the future if we are to contribute robustly to the medical and economic health of our communities.
How we discovered fluorescent speckle microscopy
Authors: Salmon E. D. , M. Waterman Clare
Published: October 2011

Fluorescent speckle microscopy (FSM) is a method for measuring the movements and dynamic assembly of macromolecular assemblies such as cytoskeletal filaments (e.g., microtubules and actin) or focal adhesions within large arrays in living cells or in preparations in vitro. The discovery of the method depended on recognizing the importance of unexpected fluorescence images of microtubules obtained by time-lapse recording of vertebrate epithelial cells in culture. In cells that were injected with fluorescent tubulin at ∼10% of the cytosol pool, microtubules typically appeared as smooth threads with a nearly constant fluorescence intensity. One day, when an unusually low concentration of fluorescent tubulin was injected into cells, the images from a sensitive cooled charge-coupled detector camera showed microtubules with an unusual “speckled” appearance—there were fluorescent dots with variable intensity and spacing along the microtubules. A first thought was that the speckles were an artifact. With further thought, we surmised that the speckles could be telling us something about stochastic association of tubulin dimers with the growing end of a microtubule. Numerous experiments confirmed the latter hypothesis. Subsequently the method we call FSM has proven to be very valuable. The speckles turned out not to be a meaningless artifact, but rather a serendipitous find.
STRIKE: evaluation of protein MSAs using a single 3D structure
Authors: Kemena Carsten , Taly Jean-Francois , Kleinjung Jens , Notredame Cedric
Published: October 2011

Motivation: Evaluating alternative multiple protein sequence alignments is an important unsolved problem in Biology. The most accurate way of doing this is to use structural information. Unfortunately, most methods require at least two structures to be embedded in the alignment, a condition rarely met when dealing with standard datasets.

Result: We developed STRIKE, a method that determines the relative accuracy of two alternative alignments of the same sequences using a single structure. We validated our methodology on three commonly used reference datasets (BAliBASE, Homestrad and Prefab). Given two alignments, STRIKE manages to identify the most accurate one in 70% of the cases on average. This figure increases to 79% when considering very challenging datasets like the RV11 category of BAliBASE. This discrimination capacity is significantly higher than that reported for other metrics such as Contact Accepted mutation or Blosum. We show that this increased performance results both from a refined definition of the contacts and from the use of an improved contact substitution score.

Contact:  cedric.notredame@crg.eu

Availability: STRIKE is an open source freeware available from www.tcoffee.org

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Determining the evolutionary history of gene families
Authors: Ames Ryan M. , Money Daniel , Ghatge Vikramsinh P. , Whelan Simon , Lovell Simon C.
Published: October 2011

Motivation: Recent large-scale studies of individuals within a population have demonstrated that there is widespread variation in copy number in many gene families. In addition, there is increasing evidence that the variation in gene copy number can give rise to substantial phenotypic effects. In some cases, these variations have been shown to be adaptive. These observations show that a full understanding of the evolution of biological function requires an understanding of gene gain and gene loss. Accurate, robust evolutionary models of gain and loss events are, therefore, required.

Results: We have developed weighted parsimony and maximum likelihood methods for inferring gain and loss events. To test these methods, we have used Markov models of gain and loss to simulate data with known properties. We examine three models: a simple birth–death model, a single rate model and a birth–death innovation model with parameters estimated from Drosophila genome data. We find that for all simulations maximum likelihood-based methods are very accurate for reconstructing the number of duplication events on the phylogenetic tree, and that maximum likelihood and weighted parsimony have similar accuracy for reconstructing the ancestral state. Our implementations are robust to different model parameters and provide accurate inferences of ancestral states and the number of gain and loss events. For ancestral reconstruction, we recommend weighted parsimony because it has similar accuracy to maximum likelihood, but is much faster. For inferring the number of individual gene loss or gain events, maximum likelihood is noticeably more accurate, albeit at greater computational cost.

Availability:  www.bioinf.manchester.ac.uk/dupliphy

Contact:  simon.lovell@manchester.ac.uk; simon.whelan@manchester.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data
Authors: Gusnanto Arief , Wood Henry M. , Pawitan Yudi , Rabbitts Pamela , Berri Stefano
Published: October 2011

Motivation: Comparison of read depths from next-generation sequencing between cancer and normal cells makes the estimation of copy number alteration (CNA) possible, even at very low coverage. However, estimating CNA from patients' tumour samples poses considerable challenges due to infiltration with normal cells and aneuploid cancer genomes. Here we provide a method that corrects contamination with normal cells and adjusts for genomes of different sizes so that the actual copy number of each region can be estimated.

Results: The procedure consists of several steps. First, we identify the multi-modality of the distribution of smoothed ratios. Then we use the estimates of the mean (modes) to identify underlying ploidy and the contamination level, and finally we perform the correction. The results indicate that the method works properly to estimate genomic regions with gains and losses in a range of simulated data as well as in two datasets from lung cancer patients. It also proves a powerful tool when analysing publicly available data from two cell lines (HCC1143 and COLO829).

Availability: An R package, called CNAnorm, is available at http://www.precancer.leeds.ac.uk/cnanorm or from Bioconductor.

Contact:  a.gusnanto@leeds.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure–function results for the Schellman loop
Authors: Newell Nicholas E.
Published: October 2011

Motivation: The extraction of the set of features most relevant to function from classified biological sequence sets is still a challenging problem. A central issue is the determination of expected counts for higher order features so that artifact features may be screened.

Results: Cascade detection (CD), a new algorithm for the extraction of localized features from sequence sets, is introduced. CD is a natural extension of the proportional modeling techniques used in contingency table analysis into the domain of feature detection. The algorithm is successfully tested on synthetic data and then applied to feature detection problems from two different domains to demonstrate its broad utility. An analysis of HIV-1 protease specificity reveals patterns of strong first-order features that group hydrophobic residues by side chain geometry and exhibit substantial symmetry about the cleavage site. Higher order results suggest that favorable cooperativity is weak by comparison and broadly distributed, but indicate possible synergies between negative charge and hydrophobicity in the substrate. Structure–function results for the Schellman loop, a helix-capping motif in proteins, contain strong first-order features and also show statistically significant cooperativities that provide new insights into the design of the motif. These include a new ‘hydrophobic staple’ and multiple amphipathic and electrostatic pair features. CD should prove useful not only for sequence analysis, but also for the detection of multifactor synergies in cross-classified data from clinical studies or other sources.

Availability: Windows XP/7 application and data files available at: https://sites.google.com/site/cascadedetect/home.

Contact:  nacnewell@comcast.net

Supplementary Information: Supplementary information is available at Bioinformatics online.
MissForest—non-parametric missing value imputation for mixed-type data
Authors: Stekhoven Daniel J. , Bühlmann Peter
Published: October 2011

Motivation: Modern data acquisition based on high-throughput technology is often facing the problem of missing data. Algorithms commonly used in the analysis of such large-scale data often depend on a complete set. Missing value imputation offers a solution to this problem. However, the majority of available imputation methods are restricted to one type of variable only: continuous or categorical. For mixed-type data, the different types are usually handled separately. Therefore, these methods ignore possible relations between variable types. We propose a non-parametric method which can cope with different types of variables simultaneously.

Results: We compare several state of the art methods for the imputation of missing values. We propose and evaluate an iterative imputation method (missForest) based on a random forest. By averaging over many unpruned classification or regression trees, random forest intrinsically constitutes a multiple imputation scheme. Using the built-in out-of-bag error estimates of random forest, we are able to estimate the imputation error without the need of a test set. Evaluation is performed on multiple datasets coming from a diverse selection of biological fields with artificially introduced missing values ranging from 10% to 30%. We show that missForest can successfully handle missing values, particularly in datasets including different types of variables. In our comparative study, missForest outperforms other methods of imputation especially in data settings where complex interactions and non-linear relations are suspected. The out-of-bag imputation error estimates of missForest prove to be adequate in all settings. Additionally, missForest exhibits attractive computational efficiency and can cope with high-dimensional data.

Availability: The ℝ package missForest is freely available from http://stat.ethz.ch/CRAN/.

Contact:  stekhoven@stat.math.ethz.ch; buhlmann@stat.math.ethz.ch
Link between decisions regarding resuscitation and preferences for quality over length of life with heart failure
Authors: Dev Sandesh , Clare Robert M. , Felker G. Michael , Fiuzat Mona , Stevenson Lynne Warner , O'Connor Christopher M.
Published: October 2011

Aims

Survival preferences, ascertained from time‐trade‐off utilities, have not been studied in heart failure patients who designate a ‘do not resuscitate’ (DNR) status. Therefore, the aim of this study was to determine the association of heart failure patients' resuscitation preferences with survival preferences and mortality in the ESCAPE trial.

Methods and results

We analysed the association of resuscitation orders at 1 month with time‐trade‐off utilities and 6‐month mortality. There were 26 and 349 patients with a DNR order and Full Code order, respectively. DNR patients were older, had more coronary artery disease, hypertension, renal impairment, and poorer exercise capacity than Full Code patients. DNR patients also experienced longer hospitalization and higher 6‐month mortality. In multivariate analysis, DNR preference was associated with 10‐fold higher odds of willingness to trade survival time (lower time‐trade‐off utility) in favour of improved quality of life [odds ratio 10.33, 95% confidence interval (CI) 1.65–64.80]. DNR preference was the best predictor of mortality (χ2 26.12, P < 0.0001, hazard ratio 6.88, 95% CI 3.28–14.41), despite adjustment for known predictors including brain natriuretic peptide.

Conclusions

Heart failure patients' requests to forgo resuscitation may signify more than simply ‘what‐if’ directives for emergency care. DNR decisions may reflect preferences for intervention to enhance quality rather than prolong survival, which is particularly important as these patients have high early mortality.
Hyperthyroidism and Graves' Disease
Authors: Grayston Fiona
Published: October 2011

Hyperthyroidism is an important condition: it affects 1–2% of the UK population and has a huge impact on quality of life. Because hyperthyroidism often presents asymptomatically or with non-specific symptoms, the diagnosis can be easily missed. A high index of clinical suspicion is required to ensure an early diagnosis and timely management. The GP plays a vital role in managing primary contact with patients with hyperthyroidism, co-ordinating care and organizing disease monitoring and so must have a sound understanding of this disease.
Guttate Psoriasis
Authors: Carroll Timothy
Published: October 2011

Dermatology is an important aspect of primary care with 15% of consultations relating to skin complaints. This article aims to provide a useful guide to diagnosing and managing guttate psoriasis including how to differentiate it from other acute erythematous rashes. We explore the key elements of history and examination, what management strategies can be used in primary care, including the evidence for the use of antibiotics, and when to refer to secondary care.
Uncertainty in science and its role in climate policy
Authors: Smith Leonard A. , Stern Nicholas
Published: October 2011

Policy-making is usually about risk management. Thus, the handling of uncertainty in science is central to its support of sound policy-making. There is value in scientists engaging in a deep conversation with policy-makers and others, not merely ‘delivering’ results or analyses and then playing no further role. Communicating the policy relevance of different varieties of uncertainty, including imprecision, ambiguity, intractability and indeterminism, is an important part of this conversation. Uncertainty is handled better when scientists engage with policy-makers. Climate policy aims both to alter future risks (particularly via mitigation) and to take account of and respond to relevant remaining risks (via adaptation) in the complex causal chain that begins and ends with individuals. Policy-making profits from learning how to shift the distribution of risks towards less dangerous impacts, even if the probability of events remains uncertain. Immediate value lies not only in communicating how risks may change with time and how those risks may be changed by action, but also in projecting how our understanding of those risks may improve with time (via science) and how our ability to influence them may advance (via technology and policy design). Guidance on the most urgent places to gather information and realistic estimates of when to expect more informative answers is of immediate value, as are plausible estimates of the risk of delaying action. Risk assessment requires grappling with probability and ambiguity (uncertainty in the Knightian sense) and assessing the ethical, logical, philosophical and economic underpinnings of whether a target of ‘50 per cent chance of remaining under +2
°
C' is either ‘right’ or ‘safe’. How do we better stimulate advances in the difficult analytical and philosophical questions while maintaining foundational scientific work advancing our understanding of the phenomena? And provide immediate help with decisions that must be made now?
Brain–immune interactions and the neural basis of disease-avoidant ingestive behaviour
Authors: Pacheco-López Gustavo , Bermúdez-Rattoni Federico
Published: October 2011

Neuro–immune interactions are widely manifested in animal physiology. Since immunity competes for energy with other physiological functions, it is subject to a circadian trade-off between other energy-demanding processes, such as neural activity, locomotion and thermoregulation. When immunity is challenged, this trade-off is tilted to an adaptive energy protecting and reallocation strategy that is identified as ‘sickness behaviour’. We review diverse disease-avoidant behaviours in the context of ingestion, indicating that several adaptive advantages have been acquired by animals (including humans) during phylogenetic evolution and by ontogenetic experiences: (i) preventing waste of energy by reducing appetite and consequently foraging/hunting (illness anorexia), (ii) avoiding unnecessary danger by promoting safe environments (preventing disease encounter by olfactory cues and illness potentiation neophobia), (iii) help fighting against pathogenic threats (hyperthermia/somnolence), and (iv) by associative learning evading specific foods or environments signalling danger (conditioned taste avoidance/aversion) and/or at the same time preparing the body to counteract by anticipatory immune responses (conditioning immunomodulation). The neurobiology behind disease-avoidant ingestive behaviours is reviewed with special emphasis on the body energy balance (intake versus expenditure) and an evolutionary psychology perspective.
Mate preferences and infectious disease: theoretical considerations and evidence in humans
Authors: Tybur Joshua M. , Gangestad Steven W.
Published: October 2011

Mate preferences may operate in part to mitigate the threats posed by infectious disease. In this paper, we outline various ways in which preferring healthy mates can offer direct benefits in terms of pathogen avoidance and indirect benefits in terms of heritable immunity to offspring, as well as the costs that may constrain mate preferences for health. We then pay special attention to empirical work on mate preferences in humans given the depth and breadth of research on human mating. We review this literature and comment on the degree to which human mate preferences may reflect preferences for health.
Desulfonatronobacter acidivorans gen. nov., sp. nov. and Desulfobulbus alkaliphilus sp. nov., haloalkaliphilic heterotrophic sulfate-reducing bacteria from soda lakes
Authors: Sorokin Dimitry Yu. , Tourova Tatjana P. , Panteleeva Anzhela N. , Muyzer Gerard
Published: October 2011

Two types of heterotrophic sulfate-reducing bacteria (SRB) were isolated from anoxic sediments of hypersaline soda lakes in Kulunda Steppe (Altai, Russia). The isolates used propionate as an energy and carbon source. Strain APT2Twas enriched and isolated with thiosulfate as the electron acceptor. Strains APS1Tand ASS1 were isolated with sulfate. Strain APT2Twas a short rod and motile with a single subpolar flagellum, while strains APS1Tand ASS1 were lemon-shaped oval rods and motile with a single polar flagellum and thin flagella-like filaments. Strain APT2Tgrew by complete oxidation of C3–C8fatty acids with thiosulfate or sulfate as the electron acceptor, while strains APS1Tand ASS1 were much less versatile and utilized only propionate and pyruvate as the electron donor and carbon source with sulfate or sulfite as the electron acceptor. Furthermore, strains APS1Tand ASS1 oxidized propionate incompletely to form acetate. All of the isolates were moderately halophilic and obligately alkaliphilic. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolates in the orderDesulfobacteralesof the classDeltaproteobacteria. Strain APT2Tbelonged to the familyDesulfobacteraceaeand clustered with a halophilic SRB,Desulfosalsimonas propionicicaPropAT. Strains APS1Tand ASS1 were closely related to each other and clustered with the genusDesulfobulbusof the familyDesulfobulbaceae. On the basis of phenotypic and phylogenetic analysis, the isolates are proposed to represent two novel taxa,Desulfonatronobacter acidivoransgen. nov., sp. nov. (type strain of the type species APT2T = DSM 24257T = UNIQEM U853T) andDesulfobulbus alkaliphilussp. nov. (type strain APS1T = DSM 24258T = UNIQEM U900T).
Salisediminibacterium halotolerans gen. nov., sp. nov., a halophilic bacterium from soda lake sediment
Authors: Jiang Feng , Cao Shu-Juan , Li Zhao-Hu , Fan Hua , Li Hai-Feng , Liu Wei-Jie , Yuan Hong-Li
Published: October 2011

An orange-pigmented, Gram-reaction-positive, non-spore-forming, halophilic, alkali-tolerant rod, designated strain halo-2T, was isolated from sediment of Xiarinaoer soda lake, in China’s Inner Mongolia Autonomous Region. Strain halo-2T grew in a complex medium with 3–30 % (w/v) NaCl and at pH 5–10. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was MK-7. The predominant cellular fatty acids were anteiso-C15 : 0 (43.6 %), anteiso-C17 : 0 (14.8 %) and iso-C15 : 0 (6.8 %) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content of the novel strain was 48.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain halo-2T was most closely related to

Bacillus agaradhaerens

DSM 8721T (93.9 % sequence similarity). However, strain halo-2T could be clearly differentiated from its closest phylogenetic relatives on the basis of several phenotypic, genotypic and chemotaxonomic characteristics. Strain halo-2T therefore represents a novel species in a new genus for which the name Salisediminibacterium halotolerans gen. nov., sp. nov. is proposed. The type strain of the type species is halo-2T ( = CGMCC 1.7654T = NBRC 104935T).
Gluconacetobacter tumulicola sp. nov. and Gluconacetobacter asukensis sp. nov., isolated from the stone chamber interior of the Kitora Tumulus
Authors: Tazato Nozomi , Nishijima Miyuki , Handa Yutaka , Kigawa Rika , Sano Chie , Sugiyama Junta
Published: October 2011

Six Gram-negative, rod-shaped, non-spore-forming bacterial strains were isolated from small holes on plaster walls of the stone chamber interior of the Kitora Tumulus in Asuka village, Nara Prefecture, Japan. These were investigated by means of a polyphasic approach. All the isolates were strictly aerobic and motile by peritrichous flagella. Phylogenetic trees generated based on 16S rRNA gene sequences identified two novel lineages (comprising five isolates and one isolate, respectively) within the genus

Gluconacetobacter

. The isolates were characterized by having Q-10 as the major ubiquinone system and C18 : 1ω7c (58.7–63.1 % of the total) as the predominant fatty acid. DNA–DNA hybridization experiments endorsed the species rank for the two lineages, for which the names Gluconacetobacter
tumulicola sp. nov. (type strain K5929-2-1bT = JCM 17774T = NCIMB 14760T) and Gluconacetobacter asukensis sp. nov. (type strain K8617-1-1bT = JCM 17772T = NCIMB 14759T) are proposed.
Amphibacillus cookii sp. nov., a facultatively aerobic, spore-forming, moderately halophilic, alkalithermotolerant bacterium
Authors: Pugin Benoît , Blamey Jenny M. , Baxter Bonnie K. , Wiegel Juergen
Published: October 2011

Novel strains of facultatively aerobic, moderately alkaliphilic and facultatively halophilic bacteria were isolated from a sediment sample taken from the Southern Arm of Great Salt Lake, Utah. Cells of strain JW/BP-GSL-QDT(and related strains JW/BP-GSL-RA and JW/BP-GSL-WB) were rod-shaped, spore-forming, motile bacteria with variable Gram-staining. Strain JW/BP-GSL-QDTgrew under aerobic conditions between 14.5 and 47 °C (optimum 39 °C), in the pH37 °Crange 6.5–10.3 (optimum pH37 °C8.0), and between 0.1 and 4.5 M Na+(optimum 0.9 M Na+). No growth was observed in the absence of supplemented Na+. Strain JW/BP-GSL-QDTutilizedl-arabinose,d-fructose,d-galactose,d-glucose, inulin, lactose, maltose, mannitol,d-mannose, pyruvate,d-ribose,d-sorbitol, starch, trehalose, xylitol andd-xylose under both aerobic and anaerobic conditions, and used ethanol and methanol only under aerobic conditions. Strains JW/BP-GSL-WB and JW/BP-GSL-RA had the same profiles except that methanol was not used aerobically. During growth on glucose, the major organic compounds formed under aerobic conditions were acetate and lactate, and under anaerobic conditions, the fermentation products were formate, acetate, lactate and ethanol. Oxidase and catalase activities were not detected and cytochrome was absent. No respiratory quinones were detected. The main cellular fatty acids were iso-C15 : 0(39.1 %) and anteiso-C15 : 0(36.3 %). Predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. Additionally, a small amount of an unknown glycolipid was detected. The DNA G+C content of strain JW/BP-GSL-QDTwas 35.4 mol% (determined by HPLC). For strain JW/BP-GSL-QDTthe highest degree of 16S rRNA gene sequence similarity was found withAmphibacillus jilinensis(98.6 %),Amphibacillus sediminis(96.7 %) andAmphibacillus tropicus(95.6 %). The level of DNA–DNA relatedness between strain JW/BP-GSL-QDTandA. jilinensisY1Twas 58 %. On the basis of physiological, chemotaxonomic and phylogenetic data, strain JW/BP-GSL-QDTrepresents a novel species of the genusAmphibacillus, for which the nameAmphibacillus cookiisp. nov. is proposed. The type strain is JW/BP-GSL-QDT( = ATCC BAA-2118T = DSM 23721T).
Candidimonas bauzanensis sp. nov., isolated from soil, and emended description of the genus Candidimonas Vaz-Moreira et al. 2011
Authors: Zhang De-Chao , Busse Hans-Jürgen , Wieser Cornelia , Liu Hong-Can , Zhou Yu-Guang , Schinner Franz , Margesin Rosa
Published: October 2011

A Gram-negative, facultatively anaerobic, psychrophilic, motile rod, designated BZ59T, was isolated from hydrocarbon-contaminated soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ59T belonged to the genus

Candidimonas

and had highest 16S rRNA gene sequence similarity with

Candidimonas nitroreducens

SC-089T (97.7 %) and

Candidimonas humi

SC-092T (97.6 %). The ubiquinone was Q-8 and the major fatty acids were C16 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipid profile contained the major compounds phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and diphosphatidylglycerol. The major polyamines were putrescine and spermidine; a minor amount of 2-hydroxyputrescine was present. The DNA G+C content of strain BZ59T was 61.6 mol%. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain BZ59T represents a novel species of the genus

Candidimonas

, for which the name Candidimonas bauzanensis sp. nov. is proposed. The type strain is BZ59T ( = DSM 22805T = LMG 26046T = CGMCC 1.10190T). The description of the genus

Candidimonas

is emended.
Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment
Authors: Shivaji S. , Reddy P. Vishnu Vardhan , Rao S. S. S. Nageshwara , Begum Zareena , Manasa Poorna , Srinivas T. N. R.
Published: October 2011

A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain M12-11BT, was isolated from a marine sediment sample collected at a depth of 200 m from Kongsfjorden, Svalbard. The colony colour was orangish red due to the presence of carotenoids. Fatty acids were dominated by branched and unsaturated fatty acids (90.8 %), with a high abundance of iso-C15 : 0 (14.9 %), anteiso-C15 : 0 (11.4 %), iso-C15 : 1 G (13.1 %), C15 : 1ω6c (5.4 %), C17 : 1ω6c (6.7 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 9.3 %) and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c; 5.9 %). Strain M12-11BT contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Based on 16S rRNA gene sequence similarities, the type strains of

Cyclobacterium amurskyense

,

Cyclobacterium marinum

and

Cyclobacterium lianum

were most closely related to M12-11BT with sequence similarities of 98.2, 96.8 and 93.3 %, respectively. Other members of the family

Cyclobacteriaceae

had sequence similarities of <92.0 %. However, DNA–DNA hybridization with

Cyclobacterium amurskyense

KCTC 12363T and

Cyclobacterium marinum

DSM 745T showed relatedness values of only 24.5 and 32.5 % with respect to strain M12-11BT. Based on the results of DNA–DNA hybridization experiments and phenotypic and chemotaxonomic data, it appears that strain M12-11BT represents a novel species of the genus

Cyclobacterium

, for which the name Cyclobacterium qasimii sp. nov. is proposed; the type strain is M12-11BT ( = KCTC 23011T = NBRC 106168T) and it has a DNA G+C content of 40.5 mol%.