bluuebunny/crossref_metadata_2025 huggingface dataset:
The Accuracy of Emergency Medical Dispatcher-Assisted Layperson-Caller Pulse Check Using the Medical Priority Dispatch System Protocol
Authors: Scott Greg , Clawson Jeff , Rector Mark , Massengale Dave , Thompson Mike , Patterson Brett , Olola Christopher H.O.
Published: July 2012

Introduction

Knowing the pulse rate of a patient in a medical emergency can help to determine patient acuity and the level of medical care required. Little evidence exists regarding the ability of a 911 layperson-caller to accurately determine a conscious patient's pulse rate.

Hypothesis

The hypothesis of this study was that, when instructed by a trained emergency medical dispatcher (EMD) using the scripted Medical Priority Dispatch System (MPDS) protocol Pulse Check Diagnostic Tool (PCDxT), a layperson-caller can detect a carotid pulse and accurately determine the pulse rate in a conscious person.

Methods

This non-randomized and non-controlled prospective study was conducted at three different public locations in the state of Utah (USA). A healthy, mock patient's pulse rate was obtained using an electrocardiogram (ECG) monitor. Layperson-callers, in turn, initiated a simulated 911 phone call to an EMD call-taker who provided instructions for determining the pulse rate of the patient. Layperson accuracy was assessed using correlations between the layperson-caller's finding and the ECG reading.

Results

Two hundred sixty-eight layperson-callers participated; 248 (92.5%) found the pulse of the mock patient. There was a high correlation between pulse rates obtained using the ECG monitor and those found by the layperson-callers, overall (94.6%, P < .001), and by site, gender, and age.

Conclusions

Layperson-callers, when provided with expert, scripted instructions by a trained 911 dispatcher over the phone, can accurately determine the pulse rate of a conscious and healthy person. Improvements to the 911 instructions may further increase layperson accuracy.

Scott G, Clawson J, Rector M, Massengale D, Thompson M, Patterson B, Olola CHO. The accuracy of emergency medical dispatcher-assisted layperson-caller pulse check using the Medical Priority Dispatch System protocol. Prehosp Disaster Med. 2012;27(3):1-8.
Cognitive Behavioural Therapy for Unusual Experiences in Children: A Case Series
Authors: Maddox Lucy , Jolley Suzanne , Laurens Kristin R. , Hirsch Colette , Hodgins Sheilagh , Browning Sophie , Bravery Louisa , Bracegirdle Karen , Smith Patrick , Kuipers Elizabeth
Published: July 2012

Background: Over half of children in the general population report unusual or “psychotic-like” experiences (PLEs). The development of a later at-risk mental state is associated with persistent, distressing, PLEs, which are appraised negatively and hard to cope with. We have designed a novel, manualized, cognitive behavioural intervention for children aged 9 to 14 years, which aims to reduce emotional problems, improve coping and resilience, and help children manage PLEs, before an identifiable psychosis risk develops. We report on the feasibility, acceptability and clinical impact of the intervention. Method: Four children who reported PLEs and emotional problems in a community survey completed the intervention, and gave detailed feedback. Clinical outcomes were assessed before, during, and after therapy. Results: Emotional problems, PLE frequency, and PLE impact all decreased during the intervention. Child and therapist satisfaction with the treatment was high. Conclusions: It is feasible, acceptable and helpful to offer psychological interventions to children who report emotional distress and PLEs, prior to the emergence of clear risk factors. Our intervention has the potential to increase resilience to the development of future mental health problems. A larger, randomized controlled evaluation is underway.
Comparing Physical Exercise in Groups to Group Cognitive Behaviour Therapy for the Treatment of Panic Disorder in a Randomized Controlled Trial
Authors: Hovland Anders , Nordhus Inger Hilde , Sjøbø Trond , Gjestad Bente A. , Birknes Birthe , Martinsen Egil W. , Torsheim Torbjørn , Pallesen Ståle
Published: July 2012

Background: Previous studies have suggested that physical exercise can reduce symptoms for subjects suffering from panic disorder (PD). The efficacy of this intervention has so far not been compared to an established psychotherapy, such as cognitive behaviour therapy (CBT). Assessment of controlled long-term effects and the clinical significance of the treatment are also lacking. Aim: To compare physical exercise to CBT as treatment for PD, and assess controlled long-term and clinically significant effects. Method: PD-patients were randomized to either three weekly sessions of physical exercise (n = 17), or one weekly session of CBT (n = 19). Both treatments ran for 12 weeks, were manualized and administered in groups. Patients were assessed twice before the start of treatment, at post-treatment and at 6 and 12 months thereafter. Primary outcome-measures consisted of the Mobility Inventory (MI), the Agoraphobia Cognitions Questionnaire (ACQ) and the Body Sensations Questionnaire (BSQ). Results: A two-way repeated measures MANOVA of these measures demonstrated a significant effect of time, F(16, 544) = 7.28, p < .01, as well as a significant interaction effect, F(16, 544) = 1.71, p < .05, in favour of CBT. This finding was supported by the assessment of clinically significant changes of avoidant behaviour and of treatment-seeking one year later. Conclusion: Group CBT is more effective than group physical exercise as treatment of panic disorder, both immediately following treatment and at follow-up assessments.
Food fortification improves the intake of all fortified nutrients, but fails to meet the estimated dietary requirements for vitamins A and B6, riboflavin and zinc, in lactating South African women
Authors: Papathakis Peggy C , Pearson Kerry E
Published: July 2012

Objective

To investigate the impact of fortification by comparing food records and selected biochemical indicators of nutritional status pre- and post-fortification.

Design

Mean intake from 24 h recalls (n 142) was compared with the Estimated Average Requirement (EAR) to determine the proportion with inadequate intake. In a subsample (n 34), diet and serum retinol, folate, ferritin and Zn were compared pre- and post-fortification for fortified nutrients vitamin A, thiamin, riboflavin, niacin, folic acid, Fe and Zn.

Setting

South Africa.

Subjects

Breast-feeding women (ninety-four HIV-infected, forty eight HIV-uninfected) measured at ∼6, 14, 24 weeks, and 9 and 12 months postpartum.

Results

Pre-fortification, >80 % of women did not meet the EAR for vitamins A, C, D, thiamin, riboflavin, niacin, B6, B12 and folate and minerals Zn, iodine and Ca. Dietary intake post-fortification increased for all fortified nutrients. In post-fortification food records, >70 % did not meet the EAR for Zn and vitamins A, riboflavin and B6. Serum folate and Zn increased significantly post-fortification (P < 0·001 for both), with no change in ferritin and a reduction in retinol. Post-fortification marginal/deficient folate status was reduced (73·5 % pre v. 3·0 % post; P < 0·001), as was Zn deficiency (26·5 % pre v. 5·9 % post; P < 0·05). Pre- and post-fortification, >93 % were retinol replete. There was no change in Fe deficiency (16·7 % pre v. 19·4 % post; P = 0·728).

Conclusions

Micronutrient intake improved with fortification, but >70 % of lactating women did not meet the EAR for Zn, vitamins A, riboflavin and B6. Although 100 % exceeded the EAR for Fe after fortification, Fe status did not improve.
The intestinal microbiome of the pig
Authors: Isaacson Richard , Kim Hyeun Bum
Published: July 2012

The intestinal microbiome has been the subject of study for many decades because of its importance in the health and well being of animals. The bacterial components of the intestinal microbiome have closely evolved as animals have and in so doing contribute to the overall development and metabolic needs of the animal. The microbiome of the pig has been the subject of many investigations using culture-dependent methods and more recently using culture-independent techniques. A review of the literature is consistent with many of the ecologic principles put forth by Rene Dubos. Animals develop an intestinal microbiome over time and space. During the growth and development of the pig, the microbiome changes in composition in a process known as the microbial succession. There are clear and distinct differences in the composition of the pig intestinal microbiome moving from the proximal end of the intestinal tract to the distal end. The majority (>90%) of the bacteria in the pig intestinal microbiome are from two Phyla: Firmicutes and Bacteroidetes. However, the ileum has a high percentage of bacteria in the phylum Proteobacterium (up to 40%). Perturbations to the microbiome occur in response to many factors including stresses, treatment with antibiotics, and diet.
Introduction to the series of papers on animal microbiomes
Authors: MacInnes Janet I. , Isaacson Richard E.
Published: July 2012

There is nothing new except that which is forgotten … Marie Antoinette

Arguably, the first microbiome study, conducted by Antonie van Leewenhoek with his primitive microscopes, was reported in 1673. For much of the next 300 years, microbiologists worked hard to isolate and study organisms in pure culture. It has only been in the past 30 years that interest has arisen in the study of more complex microbial systems, requiring more powerful methodologies and new approaches.
High throughput sequencing methods for microbiome profiling: application to food animal systems
Authors: Highlander Sarah K.
Published: July 2012

Analysis of microbial communities using high throughput sequencing methods began in the mid 2000s permitting the production of 1000s to 10,000s of sequence reads per sample and megabases of data per sequence run. This then unprecedented depth of sequencing allowed, for the first time, the discovery of the ‘rare biosphere’ in environmental samples. The technology was quickly applied to studies in several human subjects. Perhaps these early studies served as a reminder that though the microbes that inhabit mammals are known to outnumber host cells by an order of magnitude or more, most of these are unknown members of our second genome, or microbiome (as coined by Joshua Lederberg), because of our inability to culture them. High throughput methods for microbial 16S ribosomal RNA gene and whole genome shotgun (WGS) sequencing have now begun to reveal the composition and identity of archaeal, bacterial and viral communities at many sites, in and on the human body. Surveys of the microbiota of food production animals have been published in the past few years and future studies should benefit from protocols and tools developed from large-scale human microbiome studies. Nevertheless, production animal-related resources, such as improved host genome assemblies and increased numbers and diversity of host-specific microbial reference genome sequences, will be needed to permit meaningful and robust analysis of 16S rDNA and WGS sequence data.
The rule of synchrotron radiation in the prebiotic evolution
Authors: Naves de Brito A. , da Silva A. Miranda , Mocellin A.
Published: July 2012

Synchrotron radiation-based spectroscopic techniques are discussed. Their relevance to obtain information regarding the prebiotic evolution problem is pointed out. We present photoelectron–photoion coincidence (PEPICO) spectra of adenine and glycine obtained using 12 and 21 eV photons. The fragmentation pattern belonging to these molecules was found to present striking differences, which are discussed. Adenine partial ion yield in the energy region 12–21 eV is also presented. The neutral fragments were found to have very simple assignment. The importance of hydrogen cyanide (HCN) as a building block of these molecules is confirmed. A special instrumentation allowing precise comparisons between photon-induced desorption and energetic ion bombardment desorption is described. As an example, we show, for the first time, the frozen CO2ice mass spectra bombarded by photons and energetic ions, under the same experimental conditions. The comparison shows that prebiotic evolution may only be properly understood if more than one particle, as energy source, is considered.
Magnetic feature tracking, what determines the speed?
Authors: Guerrero Gustavo , Rheinhardt Matthias , Dikpati Mausumi
Published: July 2012

Recent observations revealed that small magnetic elements abundant at the solar surface move poleward with a velocity which seems to be lower than the plasma velocity U. Guerrero et al. (2011) explained this discrepancy as a consequence of diffusive spreading of the magnetic elements due to a positive radial gradient of |Uθ|. As the gradient's sign (inferred by local helioseismology) is still unclear, cases with a negative gradient are studied in this paper. Under this condition, the velocity of the magnetic tracers turns out to be larger than the plasma velocity, in disagreement with the observations. Alternative mechanisms for explaining them independently are proposed. For the turbulent magnetic pumping it is shown that it has to be unrealistically strong to reconcile the model with the observations.
The role of streamers in the deflection of coronal mass ejections
Authors: Zuccarello F. P. , Bemporad A. , Jacobs C. , Mierla M. , Poedts S. , Zuccarello F.
Published: July 2012

On 2009 September 21, a filament eruption and the associated Coronal Mass Ejection (CME) was observed by the STEREO spacecraft. The CME originated from the southern hemisphere and showed a deflection of about 15° towards the heliospheric current sheet (HCS) during its propagation in the COR1 field-of-view (FOV). The aim of this paper is to provide a physical explanation for the strong deflection of the CME. We first use the STEREO observations in order to reconstruct the three dimensional (3D) trajectory of the CME. Starting from a magnetic configuration that closely resembles the potential field extrapolation for that date, we performed numerical magneto-hydrodynamics (MHD) simulations. By applying localized shearing motions, a CME is initiated in the simulation, showing a similar non-radial evolution, structure, and velocity as the observed event. The CME gets deflected towards the current sheet of the larger northern helmet streamer, due to an imbalance in the magnetic pressure and tension forces and finally it gets into the streamer and propagates along the heliospheric current sheet.
Coronal ejections from convective spherical shell dynamos
Authors: Warnecke J. , Käpylä P. J. , Mantere M. J. , Brandenburg A.
Published: July 2012

We present a three-dimensional model of rotating convection combined with a simplified model of a corona in spherical coordinates. The motions in the convection zone generate a large-scale magnetic field which is sporadically ejected into the outer layers above. Our model corona is approximately isothermal, but it includes density stratification due to gravity.
Dynamic evolution of interplanetary shock waves driven by CMEs
Authors: Corona-Romero P. , Gonzalez-Esparza J. A.
Published: July 2012

We present a study about the propagation of interplanetary shock waves driven by super magnetosonic coronal mass ejections (CMEs). The discussion focuses on a model which describes the dynamic relationship between the CME and its driven shock and the way to approximate the trajectory of shocks based on those relationships, from near the Sun to 1 AU. We apply the model to the analysis of a case study in which our calculations show quantitative and qualitative agreements with different kinds of data. We discuss the importance of solar wind and CME initial conditions on the shock wave evolution.
Probing the heliosphere with the directional anisotropy of galactic cosmic-ray intensity
Authors: Munakata Kazuoki
Published: July 2012

Because of the large detector volume that can be deployed, ground-based detectors remain state-of-the-art instrumentation for measuring high-energy galactic cosmic-rays (GCRs). This paper demonstrates how useful information can be derived from observations of the directional anisotropy of the high-energy GCR intensity, introducing the most recent results obtained from the ground-based observations. The anisotropy observed with the global muon detector network (GMDN) provides us with a unique information of the spatial gradient of the GCR density which reflects the large-scale magnetic structure in the heliosphere. The solar cycle variation of the gradient gives an important information on the GCR transport in the heliosphere, while the short-term variation of the gradient enables us to deduce the large-scale geometry of the magnetic flux rope and the interplanetary coronal mass ejection (ICME). Real-time monitoring of the precursory anisotropy which has often been observed at the Earth preceding the arrival of the ICME accompanied by a strong shock may provide us with useful tools for forecasting the space weather with a long lead time. The solar cycle variation of the Sun's shadow observed in the TeV GCR intensity is also useful for probing the large-scale magnetic structure of the solar corona.
Search for solar energetic particle signals in the Mexico City neutron monitor database
Authors: Vargas-Cárdenas B. , Valdés-Galicia J. F.
Published: July 2012

We performed a search for ground level solar cosmic ray enhancements on the full five minute database of the Mexico City neutron monitor using wavelet filters and two different statistical tests. We present a detailed analysis of the time series of November 2, 1992, where we found a previously unreported increment matching the onset time of the impulsive phase of the Ground Level Enhancement No. 54, thus providing evidence of an effective detection of high energy solar cosmic rays. This technique may help to find still undiscovered GLE signals in the Worldwide Neutron Monitor Database, to refine GLE spectra and, probably, to find a relationship between the latter and the solar cycle.
A porcupine Sun? Implications for the solar wind and Earth
Authors: Gibson Sarah E. , Zhao Liang
Published: July 2012

The recent minimum was unusually long, and it was not just the case of the “usual story” slowed down. The coronal magnetic field never became completely dipolar as in recent Space Age minima, but rather gradually evolved into an (essentially axisymmetric) global configuration possessing mixed open and closed magnetic structures at many latitudes. In the process, the impact of the solar wind at the Earth went from resembling that from a sequence of rotating “fire-hoses” to what might be expected from a weak, omnidirectional “lawn-sprinkler”. The previous (1996) solar minimum was a more classic dipolar configuration, and was characterized by slow wind of hot origin localized to the heliospheric current sheet, and fast wind of cold origin emitted from polar holes, but filling most of the heliosphere. In contrast, the more recent minimum solar wind possessed a broad range of speeds and source temperatures (although cooler overall than the prior minimum). We discuss possible connections between these observations and the near-radial expansion and small spatial scales characteristic of the recent minimum's porcupine-like magnetic field.
Investigating stellar surface rotation using observations of starspots
Authors: Korhonen Heidi
Published: July 2012

Rapid rotation enhances the dynamo operating in stars, and thus also introduces significantly stronger magnetic activity than is seen in slower rotators. Many young cool stars still have the rapid, primordial rotation rates induced by the interstellar molecular cloud from which they were formed. Also older stars in close binary systems are often rapid rotators. These types of stars can show strong magnetic activity and large starspots. In the case of large starspots which cause observable changes in the brightness of the star, and even in the shapes of the spectral line profiles, one can get information on the rotation of the star. At times even information on the spot rotation at different stellar latitudes can be obtained, similarly to the solar surface differential rotation measurements using magnetic features as tracers. Here, I will review investigations of stellar rotation based on starspots. I will discuss what we can obtain from ground-based photometry and how that improves with the uninterrupted, high precision, observations from space. The emphasis will be on how starspots, and even stellar surface differential rotation, can be studied using high resolution spectra.
Stellar activity cycles in a model for magnetic flux generation and transport
Authors: Işik Emre
Published: July 2012

We present results from a model for magnetic flux generation and transport in cool stars and a qualitative comparison of models with observations. The method combines an αΩ-type dynamo at the base of the convection zone, buoyant rise of magnetic flux tubes, and a surface flux transport model. Based on a reference model for the Sun, numerical simulations were carried out for model convection zones of G- and K-type main sequence and subgiant stars. We investigate magnetic cycle properties for stars with different rotation periods, convection zone depths, and dynamo strengths. For a Sun-like star with Prot=9 d, we find that a cyclic dynamo can underly an apparently non-cyclic, ‘flat’ surface activity, as observed in some stars. For a subgiant K1 star with Prot=2.8 d the long-term activity variations resemble the multi-periodic cycles observed in V711 Tau, owing to high-latitude flux emergence, weak transport effects and stochastic processes of flux emergence.
Is meridional circulation important in modelling irregularities of the solar cycle?
Authors: Karak Bidya Binay , Choudhuri Arnab Rai
Published: July 2012

We explore the importance of meridional circulation variations in modelling the irregularities of the solar cycle by using the flux transport dynamo model. We show that a fluctuating meridional circulation can reproduce some features of the solar cycle like the Waldmeier effect and the grand minimum. However, we get all these results only if the value of the turbulent diffusivity in the convection zone is reasonably high.
TTVs study in southern stars
Authors: Petrucci Romina , Jofré Emiliano , Schwartz Martín , Buccino Andrea , Mauas Pablo
Published: July 2012

In this contribution we present 4 complete planetary transits observed with the 40-cm telescope “Horacio Ghielmetti” located in San Juan(Argentina). These objects correspond to a continuous photometric monitoring program of Southern planet host-stars that we are carrying out since mid-2011. The goal of this project is to detect additional planetary mass objects around stars with known transiting-planets through Transit Timing Variations (TTVs). For all 4 transits the depth and duration are in good agreement with the values published in the discovery papers.
Common Psychiatric Disorders and Caffeine Use, Tolerance, and Withdrawal: An Examination of Shared Genetic and Environmental Effects
Authors: Bergin Jocilyn E. , Kendler Kenneth S.
Published: July 2012

Background:Previous studies examined caffeine use and caffeine dependence and risk for the symptoms, or diagnosis, of psychiatric disorders. The current study aimed to determine if generalized anxiety disorder (GAD), panic disorder, phobias, major depressive disorder (MDD), anorexia nervosa (AN), or bulimia nervosa (BN) shared common genetic or environmental factors with caffeine use, caffeine tolerance, or caffeine withdrawal.Method:Using 2,270 women from the Virginia Adult Twin Study of Psychiatric and Substance Use Disorders, bivariate Cholesky decomposition models were used to determine if any of the psychiatric disorders shared genetic or environmental factors with caffeine use phenotypes.Results:GAD, phobias, and MDD shared genetic factors with caffeine use, with genetic correlations estimated to be 0.48, 0.25, and 0.38, respectively. Removal of the shared genetic and environmental parameter for phobias and caffeine use resulted in a significantly worse fitting model. MDD shared unique environmental factors (environmental correlation = 0.23) with caffeine tolerance; the genetic correlation between AN and caffeine tolerance and BN and caffeine tolerance were 0.64 and 0.49, respectively. Removal of the genetic and environmental correlation parameters resulted in significantly worse fitting models for GAD, phobias, MDD, AN, and BN, which suggested that there was significant shared liability between each of these phenotypes and caffeine tolerance. GAD had modest genetic correlations with caffeine tolerance, 0.24, and caffeine withdrawal, 0.35.Conclusions:There was suggestive evidence of shared genetic and environmental liability between psychiatric disorders and caffeine phenotypes. This might inform us about the etiology of the comorbidity between these phenotypes.
Validity of Lamellar Body Count as a Fetal Lung Maturity Assessment in Twin Pregnancy
Authors: Tsuda Hiroyuki , Kotani Tomomi , Sumigama Seiji , Kawabata Ichiro , Takahashi Yuichiro , Iwagaki Shigenori , Kigoshi Kaori , Kikkawa Fumitaka
Published: July 2012

Fetal lung maturity assessment in twin pregnancy has been discussed, but is still controversial. The purpose of this study is to predict the occurrence of respiratory distress syndrome (RDS) using lamellar body count (LBC) and analyze the validity of LBC for fetal lung maturity assessment in twin pregnancy. Three-hundred two amniotic fluid samples were obtained at cesarean section from 29 to 38 weeks of gestation. Samples were analyzed immediately with no centrifugation and the number of lamellar bodies was counted using a platelet channel on the Sysmex SF-3000. There were 18 neonates (6.0%) suffering from RDS. An LBC cut-off value of 2.95 × 104/μL resulted in 91.5% sensitivity and 83.3% specificity for predicting RDS. This cut-off value for predicting RDS was the same as that in singleton pregnancy. Moreover, the median LBC value in RDS cases was significantly lower than in non-RDS cases (1.50 ± 1.1 × 104/μL vs. 10.6 ± 7.5 × 104/μL; p < .001). This is the first report on the validity of LBC in twin pregnancy and also the largest study on fetal lung maturity assessment in twin pregnancy. An LBC value of >2.95 × 104/μL means reassuring findings for RDS even in twin pregnancy. We believe the data in this study provide valuable, new information for the management of twin pregnancies.
Causes of Delivery and Outcomes of Very Preterm Twins Stratified to Zygosity
Authors: Spiegler Juliane , Härtel Christoph , Schulz Lena , von Wurmb-Schwark Nicole , Hoehn Thomas , Kribs Angela , Küster Helmut , Siegel Jens , Wieg Christian , Weichert Jan , Herting Egbert , Göpel Wolfgang ,   the German Neonatal Network (GNN)
Published: July 2012

The increasing rates of preterm birth among twins implicate that solid data on associated risks and outcomes are required. Assessment of zygosity is often based on clinical criteria (evaluation of placenta; same gender, birth weight discordance as surrogate criteria for monochorionic/monozygotic twins). The aim of this study was to compare clinical versus genetic assessment of zygosity and to compare causes of preterm delivery as well as outcome data of very-low-birth-weight (VLBW; birth weight <1,500 g) twins stratified to zygosity. In a multicenter study, we selected n = 176 sets of same gender twins and determined zygosity genetically. In a subgroup of 123 sets of twins, the attending physicians at the study centers were asked to document the parameter ‘zygosity’ (monozygotic/dizygotic) on the basis of their clinical judgment. Concordance between genetic and clinical assessment was 62.7% for monozygotic twins and 88.9% for dizygotic twins, respectively. Outcome parameters (death, BPD, ROP, NEC, IVH) were comparable in both groups. Genetically dizygotic twins were significantly more often born due to intrauterine infection (33% vs. 20% in monozygotic twins, p < .01) and antenatal antibiotics were more frequently given to mothers of dizygotic twins (62% vs. 47% in monozygotic twins, p < .01). Obstetric complications such as twin-twin-transfusion-syndrome were only seen in monozygotic twins as expected. The unexpected increase of antenatal antibiotic treatment and birth due to intrauterine infection in dizygotic twins should be confirmed in additional VLBW twin-cohorts.
The effects of CO2‐brine rheology on leakage processes in geologic carbon sequestration
Authors: Wang Shibo , Clarens Andres F.
Published: July 2012

Leakage from geologic carbon sequestration (GCS) sites is inherently challenging to study because CO2, driven by buoyant forces, travels over long distances, undergoing phase changes and encountering numerous connate brine and formation chemistries as it rises to the surface. This work explores the effect that CO2has on the rheological properties of brine solutions over a range of GCS‐relevant temperature, pressure, ionic strength, and shear conditions. Under the fluid‐liquid equilibrium conditions that prevail in the deep subsurface, viscosity of CO2‐brine mixtures was found to be a function of temperature and pressure alone. Once leakage conditions ensue, discrete CO2bubbles form in brine, resulting in the vapor‐liquid equilibrium (VLE), and these mixtures exhibit complex linear viscoelastic, time dependent, and thixotropic behavior. The presence of CO2(g) bubbles on the flow of the bulk fluid could have important impacts on impeding (via shear drag force) leakage depending on the geometrical, geochemical and geophysical characteristics of a storage site. Under VLE conditions, the effective viscosity of CO2‐brine mixtures was found to be up to five times higher than brine alone but the microstructure was easily destroyed, and not readily regained, under high shear conditions. At higher temperatures and higher ionic strength, the effect is less pronounced. These results were considered in the context of flow through porous media, and the effect on buoyancy‐driven flow is significant. Understanding this effect is important for developing an accurate constitutive relationship for leaking CO2, which will lead to better capacity to select and monitor GCS sites.
Bacterial diversity in relation to secondary production and succession on surfaces of the kelp Laminaria hyperborea
Authors: Bengtsson Mia M , Sjøtun Kjersti , Lanzén Anders , Øvreås Lise
Published: July 2012

Kelp forests worldwide are known as hotspots for macroscopic biodiversity and primary production, yet very little is known about the biodiversity and roles of microorganisms in these ecosystems. Secondary production by heterotrophic bacteria associated to kelp is important in the food web as a link between kelp primary production and kelp forest consumers. The aim of this study was to investigate the relationship between bacterial diversity and two important processes in this ecosystem; bacterial secondary production and primary succession on kelp surfaces. To address this, kelp, Laminaria hyperborea, from southwestern Norway was sampled at different geographical locations and during an annual cycle. Pyrosequencing (454-sequencing) of amplicons of the 16S rRNA gene of bacteria was used to study bacterial diversity. Incorporation of tritiated thymidine was used as a measure of bacterial production. Our data show that bacterial diversity (richness and evenness) increases with the age of the kelp surface, which corresponds to the primary succession of its bacterial communities. Higher evenness of bacterial operational taxonomical units (OTUs) is linked to higher bacterial production. Owing to the dominance of a few abundant OTUs, kelp surface biofilm communities may be characterized as low-diversity habitats. This is the first detailed study of kelp-associated bacterial communities using high-throughput sequencing and it extends current knowledge on microbial community assembly and dynamics on living surfaces.
BasyLiCA: a tool for automatic processing of a Bacterial Live Cell Array
Authors: Aïchaoui Leslie , Jules Matthieu , Le Chat Ludovic , Aymerich Stéphane , Fromion Vincent , Goelzer Anne
Published: July 2012

Summary: Live Cell Array (LCA) technology allows the acquisition of high-resolution time-course profiles of bacterial gene expression by the systematic assessment of fluorescence in living cells carrying either transcriptional or translational fluorescent protein fusion. However, the direct estimation of promoter activities by time-dependent derivation of the fluorescence datasets generates high levels of noise. Here, we present BasyLiCA, a user-friendly open-source interface and database dedicated to the automatic storage and standardized treatment of LCA data. Data quality reports are generated automatically. Growth rates and promoter activities are calculated by tunable discrete Kalman filters that can be set to incorporate data from biological replicates, significantly reducing the impact of noise measurement in activity estimations.

Availability: The BasyLiCA software and the related documentation are available at http://genome.jouy.inra.fr/basylica.

Contact:  anne.goelzer@jouy.inra.fr

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Voronto: mapper for expression data to ontologies
Authors: Santamaría Rodrigo , Pierre Philippe
Published: July 2012

Motivation: Several techniques analyze gene expression data from the point of view of biological ontologies. These methods focus on statistical and numerical analyses, but there is an additional need for fast, global and interactive visualizations of gene expression data in the context of biological ontologies.

Results: Voronto addresses these needs with an easy to use integration of custom gene expression data with custom or public ontologies. In order to do that, it implements Voronoi diagrams where ontologies are mapped with gene expression, providing a quick hierarchy browsing and integration with ontology's resources.

Availability: The tool is available at http://vis.usal.es/voronto. Source code available at https:/github.com/rodrigoSantamaria/Voronto.

Contact:  rodri@usal.es

Supplementary information: Supplementary data are available at Bioinformatics online.
Vertical migrations of saithe (Pollachius virens) in Icelandic waters as observed with data storage tags
Authors: Armannsson Hlynur , Jónsson Sigurður Þór
Published: July 2012

Armannsson, H., and Jónsson, S. Þ. 2012. Vertical migrations of saithe (Pollachius virens) in Icelandic waters as observed with data storage tags. – ICES Journal of Marine Science, 69: . Knowledge of fish behaviour is important for general understanding of fish life history and responses to environmental and biological conditions. Vertical migrations can affect bottom trawl indices of the fish through their availability to the trawl and acoustic indices through changes in target strength. Here we present results based on data sets of hourly recordings of depth from 51 saithe. The data were analysed with respect to diel and seasonal differences in saithe vertical movement. Duration and extent of vertical movements were analysed with 1 min resolution, and the daily vertical range (DVR) was analysed with respect to potential use of the free vertical range (FVR). Our results show diel and seasonal differences in hourly depth changes of saithe, indicating reduced activity during night-time and in winter. Individual saithe are capable of rapid depth changes in <1 min, often of the same order as the maximum observed in movements of longer duration. The DVR often exceeded the FVR, and in some instances exceeded critical limits, indicating that saithe may at times only maintain neutral buoyancy near the upper limit of their daily vertical range.
Leaf morphology shift linked to climate change
Authors: Guerin Greg R. , Wen Haixia , Lowe Andrew J.
Published: July 2012

Climate change is driving adaptive shifts within species, but research on plants has been focused on phenology. Leaf morphology has demonstrated links with climate and varies within species along climate gradients. We predicted that, given within-species variation along a climate gradient, a morphological shift should have occurred over time due to climate change. We tested this prediction, taking advantage of latitudinal and altitudinal variations within the Adelaide Geosyncline region, South Australia, historical herbarium specimens (
n
= 255) and field sampling (
n
= 274). Leaf width in the study taxon,
Dodonaea viscosa
subsp.
angustissima
, was negatively correlated with latitude regionally, and leaf area was negatively correlated with altitude locally. Analysis of herbarium specimens revealed a 2 mm decrease in leaf width (total range 1–9 mm) over 127 years across the region. The results are consistent with a morphological response to contemporary climate change. We conclude that leaf width is linked to maximum temperature regionally (latitude gradient) and leaf area to minimum temperature locally (altitude gradient). These data indicate a morphological shift consistent with a direct response to climate change and could inform provenance selection for restoration with further investigation of the genetic basis and adaptive significance of observed variation.
Testing microstructural adaptation in the earliest dental tools
Authors: Jones David , Evans Alistair R. , Rayfield Emily J. , Siu Karen K. W. , Donoghue Philip C. J.
Published: July 2012

Conodont elements are the earliest vertebrate dental structures. The dental tools on elements responsible for food fracture—cusps and denticles—are usually composed of lamellar crown tissue (a putative enamel homologue) and the enigmatic tissue known as ‘white matter’. White matter is unique to conodonts and has been hypothesized to be a functional adaptation for the use of elements as teeth. We test this quantitatively using finite-element analysis. Our results indicate that white matter allowed cusps and denticles to withstand greater tensile stresses than do cusps comprised solely of lamellar crown tissue. Microstructural variation is demonstrably associated with dietary and loading differences in teeth, so secondary loss of white matter through conodont phylogeny may reflect changes in diet and element occlusal kinematics. The presence, development and distribution of white matter could thus provide constraints on function in the first vertebrate dental structures.
Human maternal behaviour is associated with arginine vasopressin receptor 1A gene
Authors: Avinun Reut , Ebstein Richard P. , Knafo Ariel
Published: July 2012

Parenting is one of the main influences on children's early development, and yet its underlying genetic mechanisms have only recently begun to be explored, with many studies neglecting to control for possible child effects. This study focuses on maternal behaviour and on an allele at the RS3 promoter region of the arginine vasopressin receptor 1A (
AVPR1A
) gene, previously associated with autism and with higher amygdala activation in a face-matching task. Mothers were observed during a free-play session with each of their 3.5-year-old twins. Multilevel regression analyses revealed that mothers who are carriers of the
AVPR1A
RS3 allele tend to show less structuring and support throughout the interaction independent of the child's sex and RS3 genotype. This finding advances our understanding of the genetic influences on human maternal behaviour.
Specialization of tendon mechanical properties results from interfascicular differences
Authors: Thorpe Chavaunne T. , Udeze Chineye P. , Birch Helen L. , Clegg Peter D. , Screen Hazel R. C.
Published: July 2012

Tendons transfer force from muscle to bone. Specific tendons, including the equine superficial digital flexor tendon (SDFT), also store and return energy. For efficient function, energy-storing tendons need to be more extensible than positional tendons such as the common digital extensor tendon (CDET), and when testedin vitrohave a lower modulus and failure stress, but a higher failure strain. It is not known how differences in matrix organization contribute to distinct mechanical properties in functionally different tendons. We investigated the properties of whole tendons, tendon fascicles and the fascicular interface in the high-strain energy-storing SDFT and low-strain positional CDET. Fascicles failed at lower stresses and strains than tendons. The SDFT was more extensible than the CDET, but SDFT fascicles failed at lower strains than CDET fascicles, resulting in large differences between tendon and fascicle failure strain in the SDFT. At physiological loads, the stiffness at the fascicular interface was lower in the SDFT samples, enabling a greater fascicle sliding that could account for differences in tendon and fascicle failure strain. Sliding between fascicles prior to fascicle extension in the SDFT may allow the large extensions required in energy-storing tendons while protecting fascicles from damage.
Edward Tyson's
Phocaena
: a case study in the institutional context of scientific publishing
Authors: Moxham Noah
Published: July 2012

This article argues that the prefatory essay to Edward Tyson's 1680 pamphlet
Phocaena
deliberately sets in opposition English and French institutional models of scientific investigation and publication. Tyson took account of
Mémoires pour Servir à l'Histoire Naturelle des Animaux
, produced by the Académie Royale des Sciences in Paris, which was implicitly contrasted with Tyson's own investigations and his plans to extend them. Tyson used the contrast both to frame the Royal Society in terms of an ideal of open collaboration and as a means of demonstrating his independence of action. I suggest that
Phocaena
may be used to illuminate contemporary anxieties about the merits of ephemeral formats for research in natural philosophy, the desirability and the burden of royal patronage, and the fluidity of the Royal Society's experimental and publishing procedures in the wake of Henry Oldenburg's death. Finally, I examine how superficially similar courses of collaborative investigation could be shaped to very different ends and outcomes by their institutional contexts.
Quantitative single-molecule microscopy reveals that CENP-A
Cnp1
deposition occurs during G2 in fission yeast
Authors: Lando David , Endesfelder Ulrike , Berger Harald , Subramanian Lakxmi , Dunne Paul D. , McColl James , Klenerman David , Carr Antony M. , Sauer Markus , Allshire Robin C. , Heilemann Mike , Laue Ernest D.
Published: July 2012

The inheritance of the histone H3 variant CENP-A in nucleosomes at centromeres following DNA replication is mediated by an epigenetic mechanism. To understand the process of epigenetic inheritance, or propagation of histones and histone variants, as nucleosomes are disassembled and reassembled in living eukaryotic cells, we have explored the feasibility of exploiting photo-activated localization microscopy (PALM). PALM of single molecules in living cells has the potential to reveal new concepts in cell biology, providing insights into stochastic variation in cellular states. However, thus far, its use has been limited to studies in bacteria or to processes occurring near the surface of eukaryotic cells. With PALM, one literally observes and ‘counts’ individual molecules in cells one-by-one and this allows the recording of images with a resolution higher than that determined by the diffraction of light (the so-called super-resolution microscopy). Here, we investigate the use of different fluorophores and develop procedures to count the centromere-specific histone H3 variant CENP-A
Cnp1
with single-molecule sensitivity in fission yeast (
Schizosaccharomyces pombe
). The results obtained are validated by and compared with ChIP-seq analyses. Using this approach, CENP-A
Cnp1
levels at fission yeast (
S. pombe
) centromeres were followed as they change during the cell cycle. Our measurements show that CENP-A
Cnp1
is deposited solely during the G2 phase of the cell cycle.
Variation in
Streptococcus pneumoniae
susceptibility to human antimicrobial peptides may mediate intraspecific competition
Authors: Habets Michelle G. J. L. , Rozen Daniel E. , Brockhurst Michael A.
Published: July 2012

Streptococcus pneumoniae
is a facultative pathogen inhabiting the nasopharynx of humans where it is exposed to a range of antimicrobial peptides (AMPs) of the innate immune response. It is possible therefore that the susceptibility of strains to AMPs plays a role in determining their ability to colonize, and furthermore, that AMPs could mediate competitive interactions between co-colonizing genotypes. However, little is known about patterns of natural variation in AMP susceptibility of
S. pneumoniae
, and it is unclear whether the susceptibilities of an isolate to multiple human AMPs are correlated. We tested this by characterizing the susceptibility of 31
S. pneumoniae
natural isolates to human neutrophil peptide (HNP-1) (α-defensin) and LL-37 (cathelicidin). We observed significant variation in susceptibility between isolates to both AMPs, and in the majority of isolates, susceptibilities to HNP-1 and LL-37 were uncorrelated. Clinical isolates were more susceptible to AMPs than were carriage isolates. The polysaccharide capsule of
S. pneumoniae
is thought to protect cells against AMPs. However, serotype alone could not explain the observed variation in susceptibility suggesting that genetic background plays an equally important role. We tested directly whether AMPs could mediate competition between isolates using competition experiments in the presence and absence of AMPs. These experiments demonstrated that AMPs could indeed reverse the outcome of competition between selected isolates. AMP-mediated competition could therefore contribute to the maintenance of intraspecific genetic diversity in
S. pneumoniae
.
Virtual endocranial cast of earliest EoceneDiacodexis(Artiodactyla, Mammalia) and morphological diversity of early artiodactyl brains
Authors: Orliac M. J. , Gilissen E.
Published: July 2012

The study of brain evolution, particularly that of the neocortex, is of primary interest because it directly relates to how behavioural variations arose both between and within mammalian groups. Artiodactyla is one of the most diverse mammalian clades. However, the first 10 Myr of their brain evolution has remained undocumented so far. Here, we used high-resolution X-ray computed tomography to investigate the endocranial cast ofDiacodexis ilicisof earliest Eocene age. Its virtual reconstruction provides unprecedented access to both metric parameters and fine anatomy of the most complete endocast of the earliest artiodactyl. This picture is assessed in a broad comparative context by reconstructing endocasts of 14 other Early and Middle Eocene representatives of basal artiodactyls, allowing the tracking of the neocortical structure of artiodactyls back to its simplest pattern. We show that the earliest artiodactyls share a simple neocortical pattern, so far never observed in other ungulates, with an almond-shaped gyrus instead of parallel sulci as previously hypothesized. Our results demonstrate that artiodactyls experienced a tardy pulse of encephalization during the Late Neogene, well after the onset of cortical complexity increase. Comparisons with Eocene perissodactyls show that the latter reached a high level of cortical complexity earlier than the artiodactyls.