bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constraining planetary interiors with the Love number k2
Authors: Kramm Ulrike , Nettelmann Nadine , Redmer Ronald 
Published: November 2011

AbstractFor the solar sytem giant planets the measurement of the gravitational moments J2 and J4 provided valuable information about the interior structure. However, for extrasolar planets the gravitational moments are not accessible. Nevertheless, an additional constraint for extrasolar planets can be obtained from the tidal Love number k2, which, to first order, is equivalent to J2. k2 quantifies the quadrupolic gravity field deformation at the surface of the planet in response to an external perturbing body and depends solely on the planet's internal density distribution. On the other hand, the inverse deduction of the density distribution of the planet from k2 is non-unique. The Love number k2 is a potentially observable parameter that can be obtained from tidally induced apsidal precession of close-in planets (Ragozzine & Wolf 2009) or from the orbital parameters of specific two-planet systems in apsidal alignment (Mardling 2007). We find that for a given k2, a precise value for the core mass cannot be derived. However, a maximum core mass can be inferred which equals the core mass predicted by homogeneous zero metallicity envelope models. Using the example of the extrasolar transiting planet HAT-P-13b we show to what extend planetary models can be constrained by taking into account the tidal Love number k2.
Exoplanet transit spectro-photometry with SOFIA
Authors: Angerhausen Daniel , Krabbe Alfred , Zinnecker Hans 
Published: November 2011

AbstractWe present the prospects of observing extrasolar planets with the Stratospheric Observatory for Infrared Astronomy (SOFIA). Our analysis shows that optical and near-infrared photometric and spectrophotometric follow-up observations during planetary transits and\break eclipses will be feasible with SOFIA's instrumentation, especially with the HIPO-FLITECAM optical/NIR instruments. SOFIA has unique advantages in comparison to ground- and space-based observatories in this field of research which will be outlined.
Detection of small-size planetary candidates with CoRoT data
Authors: Bonomo Aldo S. , Chabaud Pierre-Yves , Deleuil Magali , Moutou Claire , Bordé Pascal 
Published: November 2011

AbstractWith the discovery of CoRoT-7b, the first transiting super-Earth, the CoRoT space mission has shown the capability to detect short-period rocky planets around solar-like stars. By performing a blind test with real CoRoT light curves, we want to establish the detection threshold of small-size planets in CoRoT data. We investigate the main obstacles to the detection of transiting super-Earths in CoRoT data, notably the presence of short-time scale variability and hot pixels.
A microvariability study of nearby M dwarfs from the Western Italian Alps: Status update
Authors: Damasso Mario , Bernagozzi Andrea , Bertolini Enzo , Calcidese Paolo , Giacobbe Paolo , Lattanzi Mario G. , Perdoncin Matteo , Sozzetti Alessandro , Smart Richard , Toso Giorgio 
Published: November 2011

AbstractSmall ground-based telescopes can effectively be used to look for transiting rocky planets around nearby low-mass M stars, as recently demonstrated for example by the MEarth project. Since December 2009 at the Astronomical Observatory of the Autonomous Region of Aosta Valley (OAVdA) we are monitoring photometrically a sample of red dwarfs with accurate parallax measurements. The primary goal of this ‘pilot study’ is the characterization of the photometric microvariability of each target over a typical period of approximately 2 months. This is the preparatory step to long-term survey with an array of identical small telescopes, with kick-off in early 2011. Here we discuss the present status of the study, describing the stellar sample, and presenting the most interesting results obtained so far, including the aggressive data analysis devoted to the characterization of the variability properties of the sample and the search for transit-like signals.
Stellar noise and planet detection. II. Radial-velocity noise induced by magnetic cycles
Authors: Dumusque Xavier , Lovis Cristophe , Udry Stephane , Santos Nuno C. 
Published: November 2011

AbstractFor the 451 stars of the HARPS high precision program, we study correlations between the radial-velocity (RV) variation and other parameters of the Cross Correlated Function (CCF). After a careful target selection, we found a very good correlation between the slope of the RV-activity index (log(R'HK)) correlation and the Teff for dwarf stars. This correlation allow us to correct RV from magnetic cycles given the activity index and the Teff.
Space interferometry beyond exoplanetology: Can interdisciplinary collaboration contribute to the future of this technique?
Authors: Gabor Pavel 
Published: November 2011

AbstractAlthough a formation-flying space interferometer designed for exoplanet spectroscopy is feasible in principle, the novelty and cost of such an instrument is likely to remain daunting unless the scientific benefits of this technology are demonstrated by intermediary, precursor missions. Such instruments would represent intermediary steps in the real-life testing of the technology, and therefore, by the very reason of being intermediary, they may not have the resolving or collecting power needed for the study of the objects where biomarkers could be hoped to be detected, i.e., exo-Earths in the habitable zone of their stars. This paper examines the potential applications of such intermediary instruments. The direct line of thought focuses on exoplanetology (gas giants, protoplanetary discs, Neptunes, super-Earths, etc.); what we would like to stimulate is an exercise in lateral thinking, looking at what might an intermediary interferometric mission contribute to other fields of astrophysical research (galaxies, supernova precursors, planetary nebulae, molecular clouds, etc.). The paper raises the question of collaboration with astrophysicists studying areas other than exoplanets and its potential gains for the future of space interferometry.
Practical suggestions on detecting exomoons in exoplanet transit light curves
Authors: Szabó Gyula M. , Simon A. E. , Kiss Laszlo L. , Regály Zsolt 
Published: November 2011

AbstractThe number of known transiting exoplanets is rapidly increasing, which has recently inspired significant interest as to whether they can host a detectable moon. Although there has been no such example where the presence of a satellite was proven, several methods have already been investigated for such a detection in the future. All these methods utilize post-processing of the measured light curves, and the presence of the moon is decided by the distribution of a timing parameter. Here we propose a method for the detection of the moon directly in the raw transit light curves. When the moon is in transit, it puts its own fingerprint on the intensity variation. In realistic cases, this distortion is too little to be detected in the individual light curves, and must be amplified. Averaging the folded light curve of several transits helps decrease the scatter, but it is not the best approach because it also reduces the signal. The relative position of the moon varies from transit to transit, the moon's wing will appear in different positions on different sides of the planet's transit. Here we show that a careful analysis of the scatter curve of the folded light curves enhances the chance of detecting the exomoons directly.
The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments
Authors: Bienhold Christina , Boetius Antje , Ramette Alban 
Published: November 2011

Abstract
The availability of nutrients and energy is a main driver of biodiversity for plant and animal communities in terrestrial and marine ecosystems, but we are only beginning to understand whether and how energy–diversity relationships may be extended to complex natural bacterial communities. Here, we analyzed the link between phytodetritus input, diversity and activity of bacterial communities of the Siberian continental margin (37–3427 m water depth). Community structure and functions, such as enzymatic activity, oxygen consumption and carbon remineralization rates, were highly related to each other, and with energy availability. Bacterial richness substantially increased with increasing sediment pigment content, suggesting a positive energy–diversity relationship in oligotrophic regions. Richness leveled off, forming a plateau, when mesotrophic sites were included, suggesting that bacterial communities and other benthic fauna may be structured by similar mechanisms. Dominant bacterial taxa showed strong positive or negative relationships with phytodetritus input and allowed us to identify candidate bioindicator taxa. Contrasting responses of individual taxa to changes in phytodetritus input also suggest varying ecological strategies among bacterial groups along the energy gradient. Our results imply that environmental changes affecting primary productivity and particle export from the surface ocean will not only affect bacterial community structure but also bacterial functions in Arctic deep-sea sediment, and that sediment bacterial communities can record shifts in the whole ocean ecosystem functioning.
The Western English Channel contains a persistent microbial seed bank
Authors: Caporaso J Gregory , Paszkiewicz Konrad , Field Dawn , Knight Rob , Gilbert Jack A 
Published: November 2011

Abstract
Robust seasonal dynamics in microbial community composition have previously been observed in the English Channel L4 marine observatory. These could be explained either by seasonal changes in the taxa present at the L4 site, or by the continuous modulation of abundance of taxa within a persistent microbial community. To test these competing hypotheses, deep sequencing of 16S rRNA from one randomly selected time point to a depth of 10 729 927 reads was compared with an existing taxonomic survey data covering 6 years. When compared against the 6-year survey of 72 shallow sequenced time points, the deep sequenced time point maintained 95.4% of the combined shallow OTUs. Additionally, on average, 99.75%±0.06 (mean±s.d.) of the operational taxonomic units found in each shallow sequenced sample were also found in the single deep sequenced sample. This suggests that the vast majority of taxa identified in this ecosystem are always present, but just in different proportions that are predictable. Thus observed changes in community composition are actually variations in the relative abundance of taxa, not, as was previously believed, demonstrating extinction and recolonization of taxa in the ecosystem through time.
MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services
Authors: Pratt Brian , Howbert J. Jeffry , Tasman Natalie I. , Nilsson Erik J. 
Published: November 2011

Abstract
Summary: MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows.
Availability and implementation: MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL.
Contact: brian.pratt@insilicos.com
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq
Authors: Hu Ming , Zhu Yu , Taylor Jeremy M. G. , Liu Jun S. , Qin Zhaohui S. 
Published: November 2011

Abstract
Motivation: RNA sequencing (RNA-Seq) is a powerful new technology for mapping and quantifying transcriptomes using ultra high-throughput next-generation sequencing technologies. Using deep sequencing, gene expression levels of all transcripts including novel ones can be quantified digitally. Although extremely promising, the massive amounts of data generated by RNA-Seq, substantial biases and uncertainty in short read alignment pose challenges for data analysis. In particular, large base-specific variation and between-base dependence make simple approaches, such as those that use averaging to normalize RNA-Seq data and quantify gene expressions, ineffective.
Results: In this study, we propose a Poisson mixed-effects (POME) model to characterize base-level read coverage within each transcript. The underlying expression level is included as a key parameter in this model. Since the proposed model is capable of incorporating base-specific variation as well as between-base dependence that affect read coverage profile throughout the transcript, it can lead to improved quantification of the true underlying expression level.
Availability and implementation: POME can be freely downloaded at http://www.stat.purdue.edu/~yuzhu/pome.html.
Contact: yuzhu@purdue.edu; zhaohui.qin@emory.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Airway challenges in critical care
Authors: Nolan J. P. , Kelly F. E. 
Published: November 2011

SummaryAirway management in the intensive care unit is more problematic than during anaesthesia. In general, critically ill patients have less physiological reserve and complications are more common, both during the initial airway intervention (which includes risks associated with induction of anaesthesia), and later once the airway has been secured. Despite these known risks, those managing the airway of a critically ill patient, particularly out of hours, may be relatively inexperienced. Solutions to these challenging airway problems include: recognition of those patients with a potential airway problem; implementation of a plan to deal with their airway; immediate availability of a difficult airway trolley; use of capnography for every airway intervention and continuously in all ventilator‐dependent patients; and appropriate training of all intensive care unit staff including use of simulation.
More than meets the eye. Feminist poststructuralism as a lens towards understanding obesity
Authors: Aston Megan , Price Sheri , Kirk Sara Frances Louise , Penney Tarra 
Published: November 2011

aston m., price s., kirk s.f.l. & penney t. (2011) More than meets the eye. Feminist poststructuralism as a lens towards understanding obesity. Journal of Advanced Nursing 68(5), 1187–1194.AbstractAim.  This paper presents a discussion of the application of a feminist poststructuralist‐based theoretical framework as an innovative approach towards understanding and managing the complex health issue of obesity.Background.  Obesity is often viewed as a lifestyle choice for which the individual is blamed. This individualistic, dichotomous and behavioural perspective only allows for a narrow understanding of obesity and may even lead to misperceptions, stereotypes and marginalization of clients experiencing obesity. Feminist poststructuralism can provide a critical lens to understand the social construction of obesity and the broader environmental and cultural contexts of this health issue.Data sources.  The theoretical framework draws from the writings of Foucault, Scott, Butler, Cheek, and Powers, published between 1983 and 2005.Discussion.  The concepts of discourse analysis and power relations are explored and discussed in a clear manner so that nurses can easily apply this framework to their practice as they observe, question, analyse, critique and assess the care experienced by clients who are obese. The concepts of personal and social beliefs, values and stereotypes are also discussed and examples of how to apply them in practice are provided.Implications.  It is imperative that we continue to question our everyday nursing practices as we work to support clients, especially those who feel marginalized. This focus on power relations and reflective practice can give direction to new possibilities for change in obesity management.
The role of Government policy in supporting nurse‐led care in general practice in the United Kingdom, New Zealand and Australia: an adapted realist review
Authors: Hoare Karen J. , Mills Jane , Francis Karen 
Published: November 2011

hoare k.j., mills j. & francis k. (2011) The role of government policy in supporting nurse‐led care in general practice in the United Kingdom, New Zealand and Australia: an adapted realist review. Journal of Advanced Nursing 68(5), 963–980.AbstractAim.  This article is a report on a review that examined the role of Government policy in primary care and its association with nurse‐led care in the United Kingdom, New Zealand and Australia between 1998 and 2009.Background.  The United Kingdom, New Zealand and Australia share a similar model of first point access to the healthcare system via general practitioners. General practice is synonymous with the term primary care.Data sources.  Medline, CINAHL, EMBASE, Scopus, PsychInfo, Google, Department of Health, England (United Kingdom), Ministry of Health, New Zealand, Department of Health and Ageing, Australia. Searches of electronic databases from 1998 to December 2009 and hand searches of identified leads and key journals. Historical papers accessed to describe the genesis of practice nursing and historical Government policy documents prior to 1998, were examined.Review methods.  A modified realist review was used to synthesize research and policy documents relating to government policies pertaining to nurse‐led care. In addition, a systematic review was used to identify literature that described practice nurse‐led care.Results.  Nurse‐led primary care services are well described in the United Kingdom with a total of 45 studies meeting the inclusion criteria for the second review. There are no published studies from New Zealand, and only two from Australia describing nurse‐led primary care.Conclusion.  New Zealand and Australia lag behind the United Kingdom in practice nurse development. Implementation of clinical governance was fundamental to the development of nurse‐led care in the UK.
Patients of parish nurses experience renewed spiritual identity: a grounded theory study
Authors: Van Dover Leslie , Pfeiffer Jane 
Published: November 2011

van dover l. & pfeiffer j. (2011) Patients of parish nurses experience renewed spiritual identity: a grounded theory study. Journal of Advanced Nursing68(6), 1824–1833.AbstractAim.  This article is a report of a study of the process that patients of parish nurses experience when they are provided spiritual care in Christian churches, a context where patients and nurses share a common set of values.Background.  Many studies have explored hospitalized patients’ views and experiences of spiritual care. However, little is known about the spiritual changes that patients experience as they receive care from parish nurses.Methods.  The grounded theory method was used to explore what patients of the parish nurses experienced in spiritual care. Half of the participants were interviewed in 1999–2001 at the time of the parish nurse interviews, and half in 2005. Audiotapes were transcribed verbatim. Constant comparative methods were used to analyse the incidents of receiving spiritual care.Findings.  Theoretical memos described how the ‘main concern’ of the patients to resolve their health challenge resulted in changes to their spiritual identity. Phases in the change process included: facing a health challenge, finding a safe place, releasing burdens, changing perspectives and joining or rejoining the family of faith. The essence the patients experienced was an enhanced understanding of who they were in God/Christ.Conclusion.  The patient’s spiritual challenge is to re‐conceptualize the self (as one who is known and loved by God) in the context of a particular health challenge. Spiritual care helps them find a new equilibrium in faith.
Small CAB‐like proteins prevent formation of singlet oxygen in the damaged photosystem II complex of the cyanobacterium Synechocystis sp. PCC 6803
Authors: SINHA RAKESH KUMAR , KOMENDA JOSEF , KNOPPOVÁ JANA , SEDLÁŘOVÁ MICHAELA , POSPÍŠIL PAVEL 
Published: November 2011

ABSTRACTThe cyanobacterial small CAB‐like proteins (SCPs) are single‐helix membrane proteins mostly associated with the photosystem II (PSII) complex that accumulate under stress conditions. Their function is still ambiguous although they are assumed to regulate chlorophyll (Chl) biosynthesis and/or to protect PSII against oxidative damage. In this study, the effect of SCPs on the PSII‐specific light‐induced damage and generation of singlet oxygen (1O2) was assessed in the strains of the cyanobacterium Synechocystis sp. PCC 6803 lacking PSI (PSI‐less strain) or lacking PSI together with all SCPs (PSI‐less/scpABCDE‐ strain). The light‐induced oxidative modifications of the PSII D1 protein reflected by a mobility shift of the D1 protein and by generation of a D1‐cytochrome b‐559 adduct were more pronounced in the PSI‐less/scpABCDE‐ strain. This increased protein oxidation correlated with a faster formation of 1O2 as detected by the green fluorescence of Singlet Oxygen Sensor Green assessed by a laser confocal scanning microscopy and by electron paramagnetic resonance spin‐trapping technique using 2, 2, 6, 6‐tetramethyl‐4‐piperidone (TEMPD) as a spin trap. In contrast, the formation of hydroxyl radicals was similar in both strains. Our results show that SCPs prevent 1O2 formation during PSII damage, most probably by the binding of free Chl released from the damaged PSII complexes.