bluuebunny/crossref_metadata_2025 huggingface dataset:
Benchmarking the Self‐Assembly of Surfactin Biosurfactant at the Liquid–Air Interface to those of Synthetic Surfactants
Authors: Onaizi Sagheer A. , Nasser M. S. , Al‐Lagtah Nasir M. A.
Published: February 2016

The adsorption of surfactin, a lipopeptide biosurfactant, at the liquid–air interface has been investigated in this work. The maximum adsorption density and the nature and the extent of lateral interaction between the adsorbed surfactin molecules at the interface were estimated from surface tension data using the Frumkin model. The quantitative information obtained using the Frumkin model was also compared to those obtained using the Gibbs equation and the Langmuir–Szyszkowski model. Error analysis showed a better agreement between the experimental and the calculated values using the Frumkin model relative to the other two models. The adsorption of surfactin at the liquid–air interface was also compared to those of synthetic anionic, sodium dodecylbenzenesulphonate (SDBS), and nonionic, octaethylene glycol monotetradecyl ether (C14E8), surfactants. It has been estimated that the area occupied by a surfactin molecule at the interface is about 3‐ and 2.5‐fold higher than those occupied by SDBS and C14E8 molecules, respectively. The interaction between the adsorbed molecules of the anionic biosurfactant (surfactin) was estimated to be attractive, unlike the mild repulsive interaction between the adsorbed SDBS molecules.
Ventricular Septal Defect with Overriding Great Artery, Differential Diagnosis, Case Presentation, and Review of Literature
Authors: Choudhary Sandeep Bajaj , Choudhary Rajeev
Published: February 2016

Embryologically, conotruncal abnormalities result from abnormal development of the conotruncal septum expressing variably as double outlet right ventricle, tetralogy of Fallot, absent pulmonary valve syndrome, complete transposition, corrected transposition, and pulmonary atresia with ventricular septal defect (PA-VSD). It is not very uncommon to see a VSD with one single large artery overriding the defect, along with nonvisualization of the right ventricular outflow tract and ventricular origin of the Pulmonary artery. In situations with above findings and a near normal four chamber heart view the differential diagnosis include common arterial trunk (CAT), and pulmonary atresia with VSD and rare disorders like aortic atresia. CAT is characterized by a single great artery supplying the coronary, cranial and pulmonary circulation. Similar findings in PA-VSD may create confusion in prenatal diagnosis of these two conditions, more so in CAT type II/III. The diagnosis of CAT type I is comparatively easy as the pulmonary artery arises immediately beyond the origin of the trunk. This article discusses a case, the approach to and differential diagnosis of a single great artery overriding a VSD with a near normal four chamber view. The role of cardiac screening during the early morphology scan and the role of 4D imaging with color and power Doppler angiography are also highlighted for the correct diagnosis and description of spatial relationships of the vessels and chambers. Correct prenatal diagnosis of these conditions is important for patient counseling and prognostication.
Viscoelastic flows in a rough channel: A multiscale analysis
Authors: Chupin Laurent , Martin Sébastien
Published: February 2016

We investigate the influence of the rough boundaries on viscoelastic flows, described by the diffusive Oldroyd model. The fluid domain has a rough wall modeled by roughness patterns of size

\varepsilon \ll 1

. We present and rigorously justify an asymptotic expansion with respect to
ε
, at any order, based upon the definition of elementary problems: Oldroyd-type problems at the global scale defined on a smoothened domain and boundary-layer corrector problems. The resulting analysis guarantees optimality with respect to the truncation error and leads to a numerical algorithm which allows us to build the approximation of the solution at any required precision.
Physical health comorbidities in women with personality disorder: Data from the Geelong Osteoporosis Study
Authors: Quirk SE , Stuart AL , Brennan-Olsen SL , Pasco JA , Berk M , Chanen AM , Koivumaa-Honkanen H , Kotowicz MA , Lukkala PS , Williams LJ
Published: February 2016

Background

Associations between common psychiatric disorders, psychotic disorders and physical health comorbidities are frequently investigated. The complex relationship between personality disorders (PDs) and physical health is less understood, and findings to date are varied. This study aims to investigate associations between PDs with a number of prevalent physical health conditions.

Methods

This study examined data collected from women (n = 765; ≥ 25 years) participating in a population-based study located in south-eastern Australia. Lifetime history of psychiatric disorders was assessed using the semi-structured clinical interviews (SCID-I/NP and SCID-II). The presence of physical health conditions (lifetime) were identified via a combination of self-report, medical records, medication use and clinical data. Socioeconomic status, and information regarding medication use, lifestyle behaviors, and sociodemographic information was collected via questionnaires. Logistic regression models were used to investigate associations.

Results

After adjustment for sociodemographic variables (age, socioeconomic status) and health-related factors (body mass index, physical activity, smoking, psychotropic medication use), PDs were consistently associated with a range of physical health conditions. Novel associations were observed between Cluster A PDs and gastro-oesophageal reflux disease (GORD); Cluster B PDs with syncope and seizures, as well as arthritis; and Cluster C PDs with GORD and recurrent headaches.

Conclusions

PDs were associated with physical comorbidity. The current data contribute to a growing evidence base demonstrating associations between PDs and a number of physical health conditions independent of psychiatric comorbidity, sociodemographic and lifestyle factors. Longitudinal studies are now required to investigate causal pathways, as are studies determining pathological mechanisms.
The relevance of professionals’ attachment style, expectations and job attitudes for therapeutic relationships with young people who experience psychosis
Authors: Berry C. , Greenwood K.
Published: February 2016

Background

Therapeutic relationships are a central component of community treatment for psychosis and thought to influence clinical and social outcomes, yet there is limited research regarding the potential influence of professional characteristics on positive therapeutic relationships in community care. It was hypothesised that professionals’ relating style and attitudes toward their work might be important, and thus this exploratory study modelled associations between these characteristics and therapeutic relationships developed in community psychosis treatment.

Methods

Dyads of professionals and young patients with psychosis rated their therapeutic relationships with each other. Professionals also completed measures of attachment style, therapeutic optimism, outcome expectancy, and job attitudes regarding working with psychosis.

Results

Professionals’ anxious attachment predicted less positive professional therapeutic relationship ratings. In exploratory directed path analysis, data also supported indirect effects, whereby anxious professional attachment predicts less positive therapeutic relationships through reduced professional therapeutic optimism and less positive job attitudes.

Conclusions

Professional anxious attachment style is directly associated with the therapeutic relationship in psychosis, and indirectly associated through therapeutic optimism and job attitudes. Thus, intervening in professional characteristics could offer an opportunity to limit the impact of insecure attachment on therapeutic relationships in psychosis.
Non-pharmacological interventions for reducing aggression and violence in serious mental illness: A systematic review and narrative synthesis
Authors: Rampling J , Furtado V , Winsper C , Marwaha S , Lucca G , Livanou M , Singh SP
Published: February 2016

Background

For people with mental illness that are violent, a range of interventions have been adopted with the aim of reducing violence outcomes. Many of these interventions have been borrowed from other (offender) populations and their evidence base in a Serious Mental Illness (SMI) population is uncertain.

Aims

To aggregate the evidence base for non-pharmacological interventions in reducing violence amongst adults with SMI and PD (Personality Disorder), and to assess the efficacy of these interventions. We chose to focus on distinct interventions rather than on holistic service models where any element responsible for therapeutic change would be difficult to isolate.

Methods

We performed a systematic review and narrative synthesis of non-pharmacological interventions intended to reduce violence in a SMI population and in patients with a primary diagnosis of PD. Five online databases were searched alongside a manual search of seven relevant journals, and expert opinion was sourced. Eligibility of all returned articles was independently assessed by two authors, and quality of studies was appraised via the Cochrane Collaboration Tool for Assessing Risk of Bias.

Results

We included 23 studies of diverse psychological and practical interventions, with a range of experimental and quasi-experimental study designs that included 7 Randomised Controlled Trials (RCTs). The majority were studies of Mentally Disordered Offenders. The stronger evidence existed for patients with a SMI diagnosis receiving Cognitive Behavioural Therapy or modified Reasoning & Rehabilitation (R&R). For patients with a primary diagnosis of PD, a modified version of R&R appeared tolerable and Enhanced Thinking Skills showed some promise in improving attitudes over the short-term, but studies of Dialectical Behaviour Therapy in this population were compromised by high risk of experimental bias. Little evidence could be found for non-pharmacological, non-psychological interventions.

Conclusions

The evidence for non-pharmacological interventions for reducing violence in this population is not conclusive. Long-term outcomes are lacking and good quality RCTs are required to develop a stronger evidence base.
Ocean Waves Vibrating the Ross Ice Shelf
Authors: Strelich Lily
Published: February 2016

Scientists use seismic stations to study ice shelf vibrations generated by ocean waves to better understand their impact on the integrity of the Ross Ice Shelf.
Court Delay on U.S. Climate Plan Won't Stop Clean Energy Efforts
Authors: Showstack Randy
Published: February 2016

While many states wait for judicial clarity, analysts predict that the move toward clean energy and emissions reductions will continue.
A transcriptional repressive role for epithelial-specific ETS factor ELF3 on oestrogen receptor alpha in breast cancer cells
Authors: Gajulapalli Vijaya Narasihma Reddy , Samanthapudi Venkata Subramanyam Kumar , Pulaganti Madhusudana , Khumukcham Saratchandra Singh , Malisetty Vijaya Lakhsmi , Guruprasad Lalitha , Chitta Suresh Kumar , Manavathi Bramanandam
Published: February 2016

Oestrogen receptor-α (ERα) is a ligand-dependent transcription factor that primarily mediates oestrogen (E2)-dependent gene transcription required for mammary gland development. Coregulators critically regulate ERα transcription functions by directly interacting with it. In the present study, we report that ELF3, an epithelial-specific ETS transcription factor, acts as a transcriptional repressor of ERα. Co-immunoprecipitation (Co-IP) analysis demonstrated that ELF3 strongly binds to ERα in the absence of E2, but ELF3 dissociation occurs upon E2 treatment in a dose- and time-dependent manner suggesting that E2 negatively influences such interaction. Domain mapping studies further revealed that the ETS (E-twenty six) domain of ELF3 interacts with the DNA binding domain of ERα. Accordingly, ELF3 inhibited ERα’s DNA binding activity by preventing receptor dimerization, partly explaining the mechanism by which ELF3 represses ERα transcriptional activity. Ectopic expression of ELF3 decreases ERα transcriptional activity as demonstrated by oestrogen response elements (ERE)-luciferase reporter assay or by endogenous ERα target genes. Conversely ELF3 knockdown increases ERα transcriptional activity. Consistent with these results, ELF3 ectopic expression decreases E2-dependent MCF7 cell proliferation whereas ELF3 knockdown increases it. We also found that E2 induces ELF3 expression in MCF7 cells suggesting a negative feedback regulation of ERα signalling in breast cancer cells. A small peptide sequence of ELF3 derived through functional interaction between ERα and ELF3 could inhibit DNA binding activity of ERα and breast cancer cell growth. These findings demonstrate that ELF3 is a novel transcriptional repressor of ERα in breast cancer cells. Peptide interaction studies further represent a novel therapeutic option in breast cancer therapy.
Sticky swinging arm dynamics: studies of an acyl carrier protein domain from the mycolactone polyketide synthase
Authors: Vance Steven , Tkachenko Olga , Thomas Ben , Bassuni Mona , Hong Hui , Nietlispach Daniel , Broadhurst William
Published: February 2016

Type I modular polyketide synthases (PKSs) produce polyketide natural products by passing a growing acyl substrate chain between a series of enzyme domains housed within a gigantic multifunctional polypeptide assembly. Throughout each round of chain extension and modification reactions, the substrate stays covalently linked to an acyl carrier protein (ACP) domain. In the present study we report on the solution structure and dynamics of an ACP domain excised from MLSA2, module 9 of the PKS system that constructs the macrolactone ring of the toxin mycolactone, cause of the tropical disease Buruli ulcer. After modification of apo ACP with 4′-phosphopantetheine (Ppant) to create the holo form, 15N nuclear spin relaxation and paramagnetic relaxation enhancement (PRE) experiments suggest that the prosthetic group swings freely. The minimal chemical shift perturbations displayed by Ppant-attached C3 and C4 acyl chains imply that these substrate-mimics remain exposed to solvent at the end of a flexible Ppant arm. By contrast, hexanoyl and octanoyl chains yield much larger chemical shift perturbations, indicating that they interact with the surface of the domain. The solution structure of octanoyl-ACP shows the Ppant arm bending to allow the acyl chain to nestle into a nonpolar pocket, whereas the prosthetic group itself remains largely solvent exposed. Although the highly reduced octanoyl group is not a natural substrate for the ACP from MLSA2, similar presentation modes would permit partner enzyme domains to recognize an acyl group while it is bound to the surface of its carrier protein, allowing simultaneous interactions with both the substrate and the ACP.
The leucine-rich repeat protein PRELP binds fibroblast cell-surface proteoglycans and enhances focal adhesion formation
Authors: Bengtsson Eva , Lindblom Karin , Tillgren Viveka , Aspberg Anders
Published: February 2016

PRELP (proline/arginine-rich end leucine-rich repeat protein) is a member of the leucine-rich repeat (LRR) family of extracellular matrix proteins in connective tissue. In contrast with other members of the family, the N-terminal domain of PRELP has a high content of proline and positively charged amino acids. This domain has previously been shown to bind chondrocytes and to inhibit osteoclast differentiation. In the present study, we show that PRELP mediates cell adhesion by binding to cell-surface glycosaminoglycans (GAGs). Thus, rat skin fibroblasts (RSFs) bound to full-length PRELP and to the N-terminal part of PRELP alone, but not to truncated PRELP lacking the positively charged N-terminal region. Cell attachment to PRELP was inhibited by addition of soluble heparin or heparan sulfate (HS), by blocking sulfation of the fibroblasts or by treating the cells with a combination of chondroitinase and heparinase. Using affinity chromatography, we identified syndecan-1, syndecan-4 and glypican-1 as cell-surface proteoglycans (PGs) binding to the N-terminal part of PRELP. Finally, we show that the N-terminal domain of PRELP in combination with the integrin-binding domain of fibronectin, but neither of the fragments alone, induced fibroblast focal adhesion formation. These findings provide support for a role of the N-terminal region of PRELP as an important regulator of cell adhesion and behaviour, which may be of importance in pathological conditions.
A dynamic regularized gradient model of the subgrid-scale stress tensor for large-eddy simulation
Authors: Vollant A. , Balarac G. , Corre C.
Published: February 2016

Large-eddy simulation (LES) solves only the large scales part of turbulent flows by using a scales separation based on a filtering operation. The solution of the filtered Navier-Stokes equations requires then to model the subgrid-scale (SGS) stress tensor to take into account the effect of scales smaller than the filter size. In this work, a new model is proposed for the SGS stress model. The model formulation is based on a regularization procedure of the gradient model to correct its unstable behavior. The model is developed based on a priori tests to improve the accuracy of the modeling for both structural and functional performances, i.e., the model ability to locally approximate the SGS unknown term and to reproduce enough global SGS dissipation, respectively. LES is then performed for a posteriori validation. This work is an extension to the SGS stress tensor of the regularization procedure proposed by Balarac et al. [“A dynamic regularized gradient model of the subgrid-scale scalar flux for large eddy simulations,” Phys. Fluids 25(7), 075107 (2013)] to model the SGS scalar flux. A set of dynamic regularized gradient (DRG) models is thus made available for both the momentum and the scalar equations. The second objective of this work is to compare this new set of DRG models with direct numerical simulations (DNS), filtered DNS in the case of classic flows simulated with a pseudo-spectral solver and with the standard set of models based on the dynamic Smagorinsky model. Various flow configurations are considered: decaying homogeneous isotropic turbulence, turbulent plane jet, and turbulent channel flows. These tests demonstrate the stable behavior provided by the regularization procedure, along with substantial improvement for velocity and scalar statistics predictions.
Thermal conductivity of molten salt mixtures: Theoretical model supported by equilibrium molecular dynamics simulations
Authors: Gheribi Aïmen E. , Chartrand Patrice
Published: February 2016

A theoretical model for the description of thermal conductivity of molten salt mixtures as a function of composition and temperature is presented. The model is derived by considering the classical kinetic theory and requires, for its parametrization, only information on thermal conductivity of pure compounds. In this sense, the model is predictive. For most molten salt mixtures, no experimental data on thermal conductivity are available in the literature. This is a hindrance for many industrial applications (in particular for thermal energy storage technologies) as well as an obvious barrier for the validation of the theoretical model. To alleviate this lack of data, a series of equilibrium molecular dynamics (EMD) simulations has been performed on several molten chloride systems in order to determine their thermal conductivity in the entire range of composition at two different temperatures: 1200 K and 1300 K. The EMD simulations are first principles type, as the potentials used to describe the interactions have been parametrized on the basis of first principle electronic structure calculations. In addition to the molten chlorides system, the model predictions are also compared to a recent similar EMD study on molten fluorides and with the few reliable experimental data available in the literature. The accuracy of the proposed model is within the reported numerical and/or experimental errors.
Effective low-order models for atmospheric dynamics and time series analysis
Authors: Gluhovsky Alexander , Grady Kevin
Published: February 2016

The paper focuses on two interrelated problems: developing physically sound low-order models (LOMs) for atmospheric dynamics and employing them as novel time-series models to overcome deficiencies in current atmospheric time series analysis. The first problem is warranted since arbitrary truncations in the Galerkin method (commonly used to derive LOMs) may result in LOMs that violate fundamental conservation properties of the original equations, causing unphysical behaviors such as unbounded solutions. In contrast, the LOMs we offer (G-models) are energy conserving, and some retain the Hamiltonian structure of the original equations. This work examines LOMs from recent publications to show that all of them that are physically sound can be converted to G-models, while those that cannot lack energy conservation. Further, motivated by recent progress in statistical properties of dynamical systems, we explore G-models for a new role of atmospheric time series models as their data generating mechanisms are well in line with atmospheric dynamics. Currently used time series models, however, do not specifically utilize the physics of the governing equations and involve strong statistical assumptions rarely met in real data.
Transsexual Attractions and Sexual Reassignment Surgery: Risks and Potential Risks
Authors: Fitzgibbons Richard P.
Published: February 2016

Transsexual issues and sexual reassignment surgery (SRS) are receiving a great deal of attention and support in the media, schools, and government. Given the early age at which youth seek treatment for transsexual attractions (TSA) and gender dysphoria and given the serious risks associated with such treatment, it is essential that family and youth be advised about these risks and alternative treatment options. Physicians and mental-health professionals have a professional responsibility to know and communicate the serious risks, in particular risk of suicide, that are associated with SRS; the spontaneous resolution of TSA in youth; the psychological conflicts that have been identified in such patients and in their parents; the successful treatment of conflicts associated TSA and the regrets of those who have been through SRS. SRS and gender theory are also viewed from the faith perspective of Pope Francis and Pope Emeritus Benedict XVI.

Lay summary

Transsexuals and sex-change operations are receiving a great deal of attention. Young people may seek treatment for transsexual attractions at an early age even though these attractions may go away on their own. Psychological conflicts have been identified in these patients and their parents and may be successfully treated. There are serious risks associated with sex change. They include the risk of depressive illness and suicide. Physicians and mental-health professionals should know these risks and the regrets of those who have been through sex-change operations. These patients and their families also should be informed of other treatment options.
Effect of medium-density direct current on dendrites of directionally solidified Pb–50Sn alloy
Authors: Zhang L. M. , Li N. , Zhang R. , Xing H. , Song K. , Wang J. Y.
Published: February 2016

This paper investigated the effect of coupling of direct current (DC) and pulling rate on dendrites and cooling behaviours of directionally solidified Pb–50Sn alloy. Experimental results indicated that the secondary dendritic arm spacing (SDAS) decreased and temperature gradient increased as increasing current densities. Moreover, temperature rise and SDAS under positive DC were higher than those under negative DC. It was speculated that Joule heating and electromigration were obviously induced by the present DC. The effect of DC on the microstructure and solidification parameters was weakened as the pulling rate increases. The coarsening rate reduced from tf1/3 toward a value of tf0.29 when DC of ±200 A cm–2 were applied. The refinement mechanism of SDAS was discussed.
Co-electrodeposition and characterisation of platinum nanoparticle-multi-walled carbon nanotube nanocomposite films as good electrocatalysts
Authors: Momeni M. M.
Published: February 2016

Platinum nanoparticle-multi-walled carbon nanotube (Pt-MWCNT) nanocomposite films supported on titanium substrate were prepared by the co-electrodeposition method. This nanocomposite catalyst was characterised by scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy and electrochemical methods. The SEM images reveal that nanostructures are distributed at the surface of the titanium plate. Electro-oxidation of methanol was investigated in acidic media on Pt-MWCNTs/Ti electrodes via cyclic voltammetric analysis in the mixed 0.1 M methanol and 0.1 M H2SO4 solutions. The Pt-MWCNTs/Ti catalyst has good electro-catalytic activity for methanol oxidation. This novel Pt-MWCNTs/Ti catalyst can be used repeatedly and exhibits stable electro-catalytic activity for the methanol oxidation.
Fabrication of thick multilayered steel structure using A516 Grade 70 by multipass friction stir welding
Authors: Lim Y. C. , Sanderson S. , Mahoney M. , Wang Y. , Chen J. , David S. A. , Feng Z.
Published: February 2016

In the present work, a thick-sectioned multilayered steel structure was fabricated by multipass friction stir welding on A516 Grade 70 steel. Tensile strength of the multilayered samples was comparable to that of the base metal. Failure was located in the base metal when a defect-free sample was tested. Charpy impact toughness was higher in the stir zone and heat affected zone than in the base metal. Higher microhardness values were found in the stir zone and heat affected zone than the base metal due to grain refinement and modification of the microstructures. Consequently, improved mechanical properties compared to the base metal were found in the weld zones of friction stir welded A516 Grade 70 steel.
Phylogeography of a widespread species: pre-glacial vicariance, refugia,
occasional blocking straits and long-distance migrations
Authors: Santiso Xabier , Lopez Lúa , Retuerto Rubén , Barreiro Rodolfo
Published: February 2016

Phylogeographic studies give us the opportunity to reconstruct the historical migrations of species and link them with climatic and geographic variation. They are, therefore, a key tool to understanding the relationships among biology, geology and history. One of the most interesting biogeographical areas of the world is the Mediterranean region. However, in this area, the description of concordant phylogeographic patterns is quite scarce, which limits the understanding of evolutionary patterns related to climate. Species with one-dimensional distribution ranges, such as the strawberry tree ( Arbutus unedo ), are particularly useful to unravel these patterns. Here, we describe its phylogeographic structure and check for concordance with patterns seen in other Mediterranean plants: longitudinal/latitudinal clines of diversity, evidence for glacial refugia and the role of sea straits in dispersal. We also identify the most likely source for the disjunct Irish population. With this aim, we sequenced four chloroplast non-coding fragments of A. unedo from 23 populations covering its whole distribution. We determined the genetic diversity, population structure, haplotype genealogy and time to the most recent common ancestor. The genealogy revealed two clades that separated during the last 700 ky but before the last glacial maximum. One clade occupies Atlantic Iberia and North Africa, while the other occurs in the Western Mediterranean. The Eastern Mediterranean is inhabited by newer haplotypes derived from both clades, while the Irish population is closely related to Iberian demes. The straits of Sicily and Gibraltar partially restricted the gene flow. We concluded that a vicariance event during the Late Quaternary in the western end of the species' range followed by eastward migration seems a likely explanation for the observed phylogeographic pattern. The role of straits indicates an occasional communication between Europe and North Africa, suggesting that the latter was a novel refugia. The East–West genetic split in Iberia is consistent with the refugia-within-refugia model. Finally, the strawberry tree possibly reached Ireland from Iberia instead of throughout the maritime fringe of France as previously thought.
Trait responses of invasive aquatic macrophyte congeners: colonizing diploid outperforms polyploid
Authors: Grewell Brenda J. , Skaer Thomason Meghan J. , Futrell Caryn J. , Iannucci Maria , Drenovsky Rebecca E.
Published: February 2016

Understanding traits underlying colonization and niche breadth of invasive plants is key to developing sustainable management solutions to curtail invasions at the establishment phase, when efforts are often most effective. The aim of this study was to evaluate how two invasive congeners differing in ploidy respond to high and lowresource availability following establishment from asexual fragments. Because polyploids are expected to have wider niche breadths than diploid ancestors, we predicted that a decaploid species would have superior ability to maximize resource uptake and use, and outperform a diploid congener when colonizing environments with contrasting light and nutrient availability. A mesocosm experiment was designed to test the main and interactive effects of ploidy (diploid and decaploid) and soil nutrient availability (low and high) nested within light environments (shade and sun) of two invasive aquatic plant congeners. Counter to our predictions, the diploid congener outperformed the decaploid in the early stage of growth. Although growth was similar and low in the cytotypes at low nutrient availability, the diploid species had much higher growth rate and biomass accumulation than the polyploid with nutrient enrichment, irrespective of light environment. Our results also revealed extreme differences in time to anthesis between the cytotypes. The rapid growth and earlier flowering of the diploid congener relative to the decaploid congener represent alternate strategies for establishment and success.
PhamDB: a web-based application for building Phamerator databases
Authors: Lamine James G. , DeJong Randall J. , Nelesen Serita M.
Published: February 2016

Summary: PhamDB is a web application which creates databases of bacteriophage genes, grouped by gene similarity. It is backwards compatible with the existing Phamerator desktop software while providing an improved database creation workflow. Key features include a graphical user interface, validation of uploaded GenBank files, and abilities to import phages from existing databases, modify existing databases and queue multiple jobs.

Availability and implementation: Source code and installation instructions for Linux, Windows and Mac OSX are freely available at https://github.com/jglamine/phage. PhamDB is also distributed as a docker image which can be managed via Kitematic. This docker image contains the application and all third party software dependencies as a pre-configured system, and is freely available via the installation instructions provided.

Contact:  snelesen@calvin.edu
An algorithm for designing minimal microbial communities with desired metabolic capacities
Authors: Eng Alexander , Borenstein Elhanan
Published: February 2016

Motivation: Recent efforts to manipulate various microbial communities, such as fecal microbiota transplant and bioreactor systems’ optimization, suggest a promising route for microbial community engineering with numerous medical, environmental and industrial applications. However, such applications are currently restricted in scale and often rely on mimicking or enhancing natural communities, calling for the development of tools for designing synthetic communities with specific, tailored, desired metabolic capacities.

Results: Here, we present a first step toward this goal, introducing a novel algorithm for identifying minimal sets of microbial species that collectively provide the enzymatic capacity required to synthesize a set of desired target product metabolites from a predefined set of available substrates. Our method integrates a graph theoretic representation of network flow with the set cover problem in an integer linear programming (ILP) framework to simultaneously identify possible metabolic paths from substrates to products while minimizing the number of species required to catalyze these metabolic reactions. We apply our algorithm to successfully identify minimal communities both in a set of simple toy problems and in more complex, realistic settings, and to investigate metabolic capacities in the gut microbiome. Our framework adds to the growing toolset for supporting informed microbial community engineering and for ultimately realizing the full potential of such engineering efforts.

Availability and implementation: The algorithm source code, compilation, usage instructions and examples are available under a non-commercial research use only license at https://github.com/borenstein-lab/CoMiDA.

Contact:  elbo@uw.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
FRED 2: an immunoinformatics framework for Python
Authors: Schubert Benjamin , Walzer Mathias , Brachvogel Hans-Philipp , Szolek András , Mohr Christopher , Kohlbacher Oliver
Published: February 2016

Summary: Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable in immunological research and usually requires comprehensive pipelines including multiple tools and data sources. Non-standard input and output formats of immunoinformatics tools make the development of such applications difficult. Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications. FRED 2 is implemented in Python and designed to be extendable and flexible to allow rapid prototyping of complex applications.

Availability and implementation: FRED 2 is available at http://fred-2.github.io

Contact:  schubert@informatik.uni-tuebingen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
A single-sided homogeneous Green's function representation for
holographic imaging, inverse scattering, time-reversal acoustics and
interferometric Green's function retrieval
Authors: Wapenaar Kees , Thorbecke Jan , van der Neut Joost
Published: February 2016

Green's theorem plays a fundamental role in a diverse range of wavefield imaging applications, such as holographic imaging, inverse scattering, time-reversal acoustics and interferometric Green's function retrieval. In many of those applications, the homogeneous Green's function (i.e. the Green's function of the wave equation without a singularity on the right-hand side) is represented by a closed boundary integral. In practical applications, sources and/or receivers are usually present only on an open surface, which implies that a significant part of the closed boundary integral is by necessity ignored. Here we derive a homogeneous Green's function representation for the common situation that sources and/or receivers are present on an open surface only. We modify the integrand in such a way that it vanishes on the part of the boundary where no sources and receivers are present. As a consequence, the remaining integral along the open surface is an accurate single-sided representation of the homogeneous Green's function. This single-sided representation accounts for all orders of multiple scattering. The new representation significantly improves the aforementioned wavefield imaging applications, particularly in situations where the first-order scattering approximation breaks down.
Comparison of visual biofeedback system with a guiding waveform and abdomen-chest motion self-control system for respiratory motion management
Authors: Nakajima Yujiro , Kadoya Noriyuki , Kanai Takayuki , Ito Kengo , Sato Kiyokazu , Dobashi Suguru , Yamamoto Takaya , Ishikawa Yojiro , Matsushita Haruo , Takeda Ken , Jingu Keiichi
Published: February 2016

Irregular breathing can influence the outcome of 4D computed tomography imaging and cause artifacts. Visual biofeedback systems associated with a patient-specific guiding waveform are known to reduce respiratory irregularities. In Japan, abdomen and chest motion self-control devices (Abches) (representing simpler visual coaching techniques without a guiding waveform) are used instead; however, no studies have compared these two systems to date. Here, we evaluate the effectiveness of respiratory coaching in reducing respiratory irregularities by comparing two respiratory management systems. We collected data from 11 healthy volunteers. Bar and wave models were used as visual biofeedback systems. Abches consisted of a respiratory indicator indicating the end of each expiration and inspiration motion. Respiratory variations were quantified as root mean squared error (RMSE) of displacement and period of breathing cycles. All coaching techniques improved respiratory variation, compared with free-breathing. Displacement RMSEs were 1.43 ± 0.84, 1.22 ± 1.13, 1.21 ± 0.86 and 0.98 ± 0.47 mm for free-breathing, Abches, bar model and wave model, respectively. Period RMSEs were 0.48 ± 0.42, 0.33 ± 0.31, 0.23 ± 0.18 and 0.17 ± 0.05 s for free-breathing, Abches, bar model and wave model, respectively. The average reduction in displacement and period RMSE compared with the wave model were 27% and 47%, respectively. For variation in both displacement and period, wave model was superior to the other techniques. Our results showed that visual biofeedback combined with a wave model could potentially provide clinical benefits in respiratory management, although all techniques were able to reduce respiratory irregularities.
The (impossible?) formation of acetaldehyde on the grain surfaces: insights from quantum chemical calculations
Authors: Enrique-Romero J. , Rimola A. , Ceccarelli C. , Balucani N.
Published: February 2016

Complex Organic Molecules (COMs) have been detected in the interstellar medium (ISM). However, it is not clear whether their synthesis occurs on the icy surfaces of interstellar grains or via a series of gas-phase reactions. As a test case of the COMs synthesis in the ISM, we present new quantum chemical calculations on the formation of acetaldehyde (CH3CHO) from the coupling of the HCO and CH3 radicals, both in gas phase and on water ice surfaces. The binding energies of HCO and CH3 on the amorphous water ice were also computed (2333 and 734 K, respectively). Results indicate that, in gas phase, the products could be either CH3CHO, CH4 + CO, or CH3OCH, depending on the relative orientation of the two radicals. However, on the amorphous water ice, only the CH4 + CO product is possible due to the geometrical constraints imposed by the water ice surface. Therefore, acetaldehyde cannot be synthesized by the CH3 + HCO coupling on the icy grains. We discuss the implications of these results and other cases, such as ethylene glycol and dimethyl ether, in which similar situations can occur, suggesting that formation of these molecules on the grain surfaces might be unlikely.
Acute Kidney Injury Is Common in Pediatric Severe Malaria and Is Associated With Increased Mortality
Authors: Conroy Andrea L. , Hawkes Michael , Elphinstone Robyn E. , Morgan Catherine , Hermann Laura , Barker Kevin R. , Namasopo Sophie , Opoka Robert O. , John Chandy C. , Liles W. Conrad , Kain Kevin C.
Published: February 2016

Background.  Acute kidney injury (AKI) is a well recognized complication of severe malaria in adults, but the incidence and clinical importance of AKI in pediatric severe malaria (SM) is not well documented.

Methods.  One hundred eighty children aged 1 to 10 years with SM were enrolled between 2011 and 2013 in Uganda. Kidney function was monitored daily for 4 days using serum creatinine (Cr). Acute kidney injury was defined using the Kidney Disease: Improving Global Outcomes (KDIGO) guidelines. Blood urea nitrogen (BUN) and Cr were assessed using i-STAT, and cystatin C (CysC) was measured by enzyme-linked immunosorbent assay.

Results.  Eighty-one (45.5%) children had KDIGO-defined AKI in the study: 42 (51.9%) stage 1, 18 (22.2%) stage 2, and 21 (25.9%) stage 3. Acute kidney injury evolved or developed in 50% of children after admission of hospital. There was an increased risk of AKI in children randomized to inhaled nitric oxide (iNO), with 47 (54.0%) of children in the iNO arm developing AKI compared with 34 (37.4%) in the placebo arm (relative risk, 1.36; 95% confidence interval [CI], 1.03–1.80). Duration of hospitalization increased across stages of AKI (P = .002). Acute kidney injury was associated with neurodisability at discharge in the children receiving placebo (25% in children with AKI vs 1.9% in children with no AKI, P = .002). Mortality increased across stages of AKI (P = .006) in the placebo arm, reaching 37.5% in stage 3 AKI. Acute kidney injury was not associated with neurodisability or mortality at discharge in children receiving iNO (P > .05 for both). Levels of kidney biomarkers were predictive of mortality with areas under the curves (AUCs) of 0.80 (95% CI, .65–.95; P = .006) and 0.72 (95% CI, .57–.87; P < .001), respectively. Admission levels of CysC and BUN were elevated in children who died by 6 months (P < .0001 and P = .009, respectively).

Conclusions.  Acute kidney injury is an underrecognized complication in young children with SM and is associated with increased mortality.
Effects of Modified Hearing Aid Fittings on Loudness and Tone Quality for Different Acoustic Scenes
Authors: Moore Brian C. J. , Baer Thomas , Ives D. Timothy , Marriage Josephine , Salorio-Corbetto Marina
Published: February 2016

Objective:

To compare loudness and tone-quality ratings for sounds processed via a simulated five-channel compression hearing aid fitted using NAL-NL2 or using a modification of the fitting designed to be appropriate for the type of listening situation: speech in quiet, speech in noise, music, and noise alone.

Design:

Ratings of loudness and tone quality were obtained for stimuli presented via a loudspeaker in front of the participant. For normal-hearing participants, levels of 50, 65, and 80 dB SPL were used. For hearing-impaired participants, the stimuli were processed via a simulated hearing aid with five-channel fast-acting compression fitted using NAL-NL2 or using a modified fitting. Input levels to the simulated hearing aid were 50, 65, and 80 dB SPL. All participants listened with one ear plugged. For speech in quiet, the modified fitting was based on the CAM2B method. For speech in noise, the modified fitting used slightly (0 to 2 dB) decreased gains at low frequencies. For music, the modified fitting used increased gains (by 5 to 14 dB) at low frequencies. For noise alone, the modified fitting used decreased gains at all frequencies (by a mean of 1 dB at low frequencies increasing to 8 dB at high frequencies).

Results:

For speech in quiet, ratings of loudness with the NAL-NL2 fitting were slightly lower than the mean ratings for normal-hearing participants for all levels, while ratings with CAM2B were close to normal for the two lower levels, and slightly greater than normal for the highest level. Ratings of tone quality were close to the optimum value (“just right”) for both fittings, except that the CAM2B fitting was rated as very slightly boomy for the 80-dB SPL level. For speech in noise, the ratings of loudness were very close to the normal values and the ratings of tone quality were close to the optimal value for both fittings and for all levels. For music, the ratings of loudness were close to the normal values for NAL-NL2 and slightly above normal for the modified fitting. The tone quality was rated as very slightly tinny for NAL-NL2 and very slightly boomy for the modified fitting. For noise alone, the NAL-NL2 fitting was rated as slightly louder than normal for all levels, while the modified fitting was rated as close to normal. Tone quality was rated as slightly sharper for the NAL-NL2 fitting than for the modified fitting.

Conclusions:

Loudness and tone quality can sometimes be made slightly closer to “normal” by modifying gains for different listening situations. The modification for music required to achieve “normal” tone quality appears to be less than used in this study.
Minimally Invasive versus Conventional Aortic Valve Replacement: A Propensity-Matched Study from the UK National Data
Authors: Attia Rizwan Q. , Hickey Graeme L. , Grant Stuart W. , Bridgewater Ben , Roxburgh James C. , Kumar Pankaj , Ridley Paul , Bhabra Moninder , Millner Russell W. J. , Athanasiou Thanos , Casula Roberto , Chukwuemka Andrew , Pillay Thasee , Young Christopher P.
Published: February 2016

Objective

Minimally invasive aortic valve replacement (MIAVR) has been demonstrated as a safe and effective option but remains underused. We aimed to evaluate outcomes of isolated MIAVR compared with conventional aortic valve replacement (CAVR).

Methods

Data from The National Institute for Cardiovascular Outcomes Research (NICOR) were analyzed at seven volunteer centers (2006–2012). Primary outcomes were in-hospital mortality and midterm survival. Secondary outcomes were postoperative length of stay as well as cumulative bypass and cross-clamp times. Propensity modeling with matched cohort analysis was used.

Results

Of 307 consecutive MIAVR patients, 151 (49%) were performed during the last 2 years of study with a continued increase in numbers. The 307 MIAVR patients were matched on a 1:1 ratio. In the matched CAVR group, there was no statistically significant difference in in-hospital mortality [MIAVR, 4/307,(1.3%); 95% confidence interval (CI), 0.4%-3.4% vs CAVR, 6/307 (2.0%); 95% CI, 0.8%-4.3%; P = 0.752]. One-year survival rates in the MIAVR and CAVR groups were 94.4% and 94.6%, respectively. There was no statistically significant difference in midterm survival (P = 0.677; hazard ratio, 0.90; 95% CI, 0.56–1.46). Median postoperative length of stay was lower in the MIAVR patients by 1 day (P = 0.009). The mean cumulative bypass time (94.8 vs 91.3 minutes; P = 0.333) and cross-clamp time (74.6 vs 68.4 minutes; P = 0.006) were longer in the MIAVR group; however, this was significant only in the cross-clamp time comparison.

Conclusions

Minimally invasive aortic valve replacement is a safe alternative to CAVR with respect to operative and 1-year mortality and is associated with a shorter postoperative stay. Further studies are required in high-risk (logistic EuroSCORE > 10) patients to define the role of MIAVR.
Allergic Reactions With Intravenous Compared With Intramuscular Pegaspargase in Children With High-risk Acute Lymphoblastic Leukemia: A Population-based Study From the Maritimes, Canada
Authors: MacDonald Tamara , Kulkarni Ketan , Bernstein Mark , Fernandez Conrad V.
Published: February 2016

Intravenous (IV) administration of pegaspargase in children with acute lymphoblastic leukemia (ALL) may be associated with an increased risk of allergic reactions, and thus the need for more costly intramuscular (IM) erwinia asparaginase. In 128 patients allergic reactions were documented in 3% and 14% of those who received IM and IV pegaspargase, respectively (P=0.029). These reactions were primarily contributed to by high risk (HR)-ALL patients (P<0.01). The possible decreased efficacy and quality of life and the substantial costs entailed by switching from IV pegaspargase to IM erwinia should prompt reconsideration of the IV administration route for pegaspargase in HR-ALL patients.