bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep draft icebergs from the Barents Ice Sheet during MIS 6 are consistent with erosional evidence from the Lomonosov Ridge, central Arctic
Authors: Green Clare L. , Bigg Grant R. , Green J. A. Mattias
Published: December 2010

Iceberg scour marks on the Lomonosov Ridge in the central Arctic imply that bergs with drafts exceeding 850 m once existed in the Arctic, whereas similar erosion patterns observed on the Yermak Plateau suggest that some of these deep‐keeled icebergs exited the Arctic through the Fram Strait into the Nordic Seas. An intermediate complexity climate model with a dynamic and thermodynamic iceberg model is used to simulate the collapse of the Barents Ice Sheet during MIS 6 with the purpose of investigating if deep‐draft “mega”‐icebergs can reach and ground on the Lomonosov Ridge. A number of simulations with different iceberg sizes show that deep‐draft bergs seeded from near the Franz Victoria Trough could indeed have reached the Ridge, whereas other bergs crossed the Yermak Plateau and exited through the Fram Strait. The draft of the bergs mainly determines the trajectory, with only minor influence from the mass, and length and width of the bergs. This work is consistent with previous speculation that these icebergs originated from the disintegration of the Barents Ice Sheet during Marine Isotope Stage 6 (MIS 6; 140 ka BP), but suggests their origin was more likely to be from the western, rather than eastern, major ice stream of that ice sheet. The long‐term impact on the overturning circulation from melting icebergs is more severe than that from a freshwater pulse of equivalent magnitude, and a correct representation of icebergs in paleoclimate models is therefore of importance.
Open ocean gas transfer velocity derived from long‐term direct measurements of the CO2 flux
Authors: Prytherch John , Yelland Margaret J. , Pascal Robin W. , Moat Bengamin I. , Skjelvan Ingunn , Srokosz Meric A.
Published: December 2010

Air‐sea open ocean CO2 flux measurements have been made using the Eddy Covariance (EC) technique onboard the weathership Polarfront in the North Atlantic between September 2006 and December 2009. Flux measurements were made using an autonomous system ‘AutoFlux’. CO2 mass density was measured with an open‐path infrared gas analyzer. Following quality control procedures, 3938 20‐minute flux measurements were made at mean wind speeds up to 19.6 m/s, significantly higher wind speeds than previously published results. The uncertainty in the determination of gas transfer velocities is large, but the mean relationship to wind speed allows a new parameterisation of the gas transfer velocity to be determined. A cubic dependence of gas transfer on wind speed is found, suggesting a significant influence of bubble‐mediated exchange on gas transfer.
One‐way coupled OpenGGCM/RCM simulation of the 23 March 2007 substorm event
Authors: Hu B. , Toffoletto F. R. , Wolf R. A. , Sazykin S. , Raeder J. , Larson D. , Vapirev A.
Published: December 2010

We present results of a simulation of a substorm on 23 March 2007 using the one‐way coupled Open Geospace General Circulation Model–Rice Convection Model (OpenGGCM/RCM). In the standalone RCM, inputs are typically taken from empirical models or inferred from satellite data; however, in this simulation, the OpenGGCM magnetic field and plasma information are used to supply inputs and boundary conditions for the RCM. The OpenGGCM ionospheric potential is used to drive a RCM run. That simulation is used to investigate the short time scale dynamics that occurred around substorm onset and assumes the OpenGGCM has a realistic representation of the inner magnetospheric magnetic field during this event. In these runs, a channel of low total entropy plasma opened up on the RCM tailward boundary around substorm onset, and plasma bubbles were injected into the inner magnetosphere. These bubbles were produced by nonadiabatic processes in the OpenGGCM such as magnetic reconnection. We compare the RCM energetic particle flux with measurements from two Los Alamos National Laboratory (LANL) satellites. A dispersionless electron injection is reproduced at the LANL‐89 location and a dispersed flux increase at the LANL‐97A location. The results indicate the low‐PV5/3 plasma accompanying magnetic field dipolarization produced earthward plasma motion as the result of these low‐entropy flux tubes interchanging their way into the inner magnetosphere; this process may play an important role in substorm particle injection. A comparison simulation in which the electric field is solved by the RCM is also presented, suggesting the need to use RCM's electric field for more accurate inner magnetosphere modeling.
Direct measurements of the Poynting flux associated with convection electric fields in the magnetosphere
Authors: Nishimura Y. , Kikuchi T. , Shinbori A. , Wygant J. , Tsuji Y. , Hori T. , Ono T. , Fujita S. , Tanaka T.
Published: December 2010

Observations of Poynting fluxes associated with onset of convection electric fields are essential for understanding of electromagnetic energy transport from the solar wind toward the magnetosphere leading to changes in the convection electric field, which is one of the most fundamental parameters in the magnetosphere‐ionosphere coupled system. We present Cluster multispacecraft observations of Poynting fluxes associated with abrupt changes in large‐scale electric fields during sudden commencements and southward turning of the interplanetary magnetic field (IMF). The Cluster spacecraft detected Poynting fluxes dominated by the field‐aligned upward component during the preliminary impulse of sudden commencements and in the initial period after southward turning of the IMF. The upward Poynting flux indicates existence of Alfvén waves transporting electromagnetic energy from the ionosphere toward the magnetosphere leading to magnetospheric convection changes. The waveguide model and global magnetohydrodynamic (MHD) simulation calculating evolution of the Poynting flux following solar wind pressure enhancements also show upward Poynting fluxes propagating from the ionosphere toward the magnetosphere faster than the propagation of compressional waves. We conclude that the ionosphere acts as a channel to transmit electromagnetic energy supplied as field‐aligned currents toward a wide region in the magnetosphere‐ionosphere system instantaneously, leading to changes in magnetospheric convection electric fields.
Thermosphere extension of the Whole Atmosphere Community Climate Model
Authors: Liu H.‐L. , Foster B. T. , Hagan M. E. , McInerney J. M. , Maute A. , Qian L. , Richmond A. D. , Roble R. G. , Solomon S. C. , Garcia R. R. , Kinnison D. , Marsh D. R. , Smith A. K. , Richter J. , Sassi F. , Oberheide J.
Published: December 2010

In atmospheric and space environment studies it is key to understand and to quantify the coupling of atmospheric regions and the solar impacts on the whole atmosphere system. There is thus a need for a numerical model that encompasses the whole atmosphere and can self‐consistently simulate the dynamic, physical, chemical, radiative, and electrodynamic processes that are important for the Sun‐Earth system. This is the goal for developing the National Center for Atmospheric Research (NCAR) Whole Atmosphere Community Climate Model (WACCM). In this work, we report the development and preliminary validation of the thermospheric extension of WACCM (WACCM‐X), which extends from the Earth's surface to the upper thermosphere. The WACCM‐X uses the finite volume dynamical core from the NCAR Community Atmosphere Model and includes an interactive chemistry module resolving most known neutral chemistry and major ion chemistry in the middle and upper atmosphere, and photolysis and photoionization. Upper atmosphere processes, such as nonlocal thermodynamic equilibrium, radiative transfer, auroral processes, ion drag, and molecular diffusion of major and minor species, have been included in the model. We evaluate the model performance by examining the quantities essential for the climate and weather of the upper atmosphere: the mean compositional, thermal, and wind structures from the troposphere to the upper thermosphere and their variability on interannual, seasonal, and daily scales. These quantities are compared with observational and previous model results.
Global distributions of suprathermal electrons observed on THEMIS and potential mechanisms for access into the plasmasphere
Authors: Li W. , Thorne R. M. , Bortnik J. , Nishimura Y. , Angelopoulos V. , Chen L. , McFadden J. P. , Bonnell J. W.
Published: December 2010

Statistical results on the global distribution of suprathermal electron (0.1–10 keV) fluxes are shown both outside and inside the plasmasphere separately, using electron data from THEMIS. Significant electron fluxes are found within the plasmasphere, although they are nevertheless smaller than the populations outside the plasmasphere. Electron fluxes outside of the plasmapause increase with stronger magnetic activity on the nightside and decrease as a function of increasing magnetic local time (MLT). Inside the plasmasphere, electron fluxes increase just inside of the plasmapause, particularly from the midnight to the dawn sector during active times, while electron distributions are less MLT‐dependent during quiet times. Inside the plasmasphere, electron fluxes are larger and more stable at smaller L shells at higher energy (a few to 10 keV), while electron fluxes decrease at smaller L shells at lower energy (less than a few keV). Our new statistical results on the suprathermal electron distribution both inside and outside the plasmasphere provide essential information for the evaluation of wave propagation characteristics. Case analyses have been performed in order to understand potential mechanisms responsible for electron access into the plasmasphere. The first case analysis shows that during a relatively quiet time following a disturbed interval, deeply injected suprathermal electrons remain trapped at low L shells during the refilling of the plasmasphere and eventually form the plasmaspheric population. The second case analysis suggests that a combination of locally enhanced electric field and subsequent energy‐dependent azimuthal magnetic drift may be able to trap the suprathermal electrons inside the plasmasphere during a geomagnetically active period.
Ion Bernstein instability in the terrestrial magnetosphere: Linear dispersion theory
Authors: Gary S. Peter , Liu Kaijun , Winske Dan , Denton Richard E.
Published: December 2010

Linear kinetic dispersion theory for electromagnetic fluctuations in a homogeneous, magnetized, collisionless plasma is used to study the properties of an ion Bernstein mode instability driven by a proton velocity distribution fp(v) such that ∂fp(ν⊥)/∂ν⊥ > 0, where ⊥ denotes directions perpendicular to the background magnetic field Bo. Here fp(v) = f1(ν) − f2(ν), where f1 and f2 are Maxwellian velocity distributions with slightly different densities and temperatures; plasma parameters are taken from magnetospheric observations. Then the growth rate of this instability has relative maxima at ωr ≃ nΩp, where n = 1, 2, 3, … and Ωp is the proton cyclotron frequency; wave vector k at 0 < k∥ ≪ k⊥, where ∥ and ⊥ denote the directions parallel and perpendicular to Bo; and wavelengths of the order of or smaller than the proton gyroradius. The maximum instability growth rate is a monotonically decreasing function of the electron‐to‐proton temperature ratio but has its largest value at an intermediate value of the proton β (∼0.5 for the parameters considered here).
Impact of horizontal resolution on climate model forecasts of tropical precipitation and diabatic heating for the TWP‐ICE period
Authors: Boyle James , Klein Stephen A.
Published: December 2010

In order to study the impact of horizontal resolution on climate model simulations of tropical moist processes, short‐term forecasts using the Community Atmospheric Model (version 4) at several resolutions are performed for a time period encompassing the Tropical Warm Pool‐International Cloud Experiment (TWP‐ICE). TWP‐ICE occurred in the environment of Darwin, Australia in January and February 2006. The experimental period encompasses a number of atmospheric phenomena, such as an MJO passage, mesoscale convective systems, monsoon trough, and active and dry conditions. The CAM is run with four horizontal resolutions: 2°, 1°, 0.5°, and 0.25° latitude‐longitude. Simulated profiles of diabatic heating and moistening at the TWP‐ICE site show that the model parameterizations respond reasonably well for all resolutions to the sequence of varying conditions imposed by the analyses used to initialize the model. The spatial patterns of global model biases in time mean precipitation are largely unchanged over resolutions, and in some regions the 0.25° model significantly overestimates the observed precipitation. However, there are substantive positive aspects of finer resolution. The diurnally forced circulations over the Maritime continent are more realistically captured by the 0.25° simulation, which is able to better resolve the land‐sea breeze. The intensity distribution of rainfall events is also improved at higher resolution through an increased frequency of very intense events and an increased frequency of little or no precipitation. Finally, the ratio of stratiform to convective precipitation systematically increases toward better agreement with observational estimates with increases in resolution.
Low‐latitude boundary layer clouds as seen by CALIPSO
Authors: Medeiros Brian , Nuijens Louise , Antoniazzi Chiara , Stevens Bjorn
Published: December 2010

The distribution of low‐level cloud in the tropical belt is investigated using 6 months of Level 2 retrievals from Cloud‐Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) at 333 m and 1 km horizontal resolutions. Regional patterns of tropical clouds emerge from the data, matching expectations from existing observations. The advantage of the lidar is highlighted by the distribution of cloud‐top height, revealing the preponderance of low‐level clouds over the tropical oceans. Over land, cloud top is more uniformly distributed under the influence of diurnal variation. The integrated cloud‐top distribution suggests tropical, marine low‐cloud amount around 25–30%; a merged CALIPSO‐CloudSat product has a similar cloud‐top distribution and includes a complementary estimate of cloud fraction based on the lidar detections. The low‐cloud distribution is similar to that found in fields of shallow cumulus observed during the Rain in Cumulus Over the Ocean (RICO) field study. The similarity is enhanced by sampling near the RICO site or sampling large‐scale conditions similar to those during RICO. This finding shows how satellite observations can help to generalize findings from detailed field observations.
Wetland inundation dynamics in a model of land surface climate: Evaluation in the Niger inland delta region
Authors: Dadson Simon J. , Ashpole Ian , Harris Phil , Davies Helen N. , Clark Douglas B. , Blyth Eleanor , Taylor Christopher M.
Published: December 2010

Observed river gauging data show significant evaporative losses from the land and water surface in the Niger inland delta. These losses indicate an important potential feedback between the land surface and atmosphere. Moreover, the reduction in river flow downstream of the wetland has clear implications for water management in the region and beyond. Here we have modeled the evaporative losses that occur over the Niger inland delta by adding an overbank flow parameterization to the Joint UK Land‐Environment Simulator (JULES) land surface model. The hydrological component of this model comprises a probability‐distributed model of soil moisture and runoff production coupled with a discrete approximation to the one‐dimensional kinematic wave equation to route river water downslope. We use subgrid‐resolution topographic data to derive a two‐parameter frequency distribution of inundated areas for each grid box which we then employ to represent overbank inundation in the model. The model was driven using data from the ALMIP experiment (ALMIP stands for AMMA Land surface Model Intercomparison Project, wherein AMMA stands for African Monsoon Multidisciplinary Analyses). The model reproduces the salient features of the observed river flow and inundation patterns; these include significant evaporative losses from the inundated region accounting for doubling of the total land‐atmosphere water flux during periods of greatest flooding. Our predictions of inundated area are in good agreement with observed estimates of the extent of inundation obtained using satellite infrared and microwave remote sensing.
Terrestrial water budget of the Eurasian pan‐Arctic from GRACE satellite measurements during 2003–2009
Authors: Landerer Felix W. , Dickey Jean O. , Güntner Andreas
Published: December 2010

We assess the controls of the terrestrial water budget over the Eurasian pan‐Arctic drainage region from 2003 to 2009 by combining observations from the Gravity Recovery and Climate Experiment (GRACE) with reanalysis estimates of net precipitation and observations of river discharge from gauges. Of particular interest are the expansive permafrost regions. Thawing permafrost has been implicated to contribute to the observed discharge increases through the melting of excess ground ice. We show that terrestrial water storage (TWS) over large areas of the Eurasian pan‐Arctic region has increased during 2003–2009. However, significant interannual TWS variability is present and most TWS increases occur over nonpermafrost regions in the Ob and Yenisei basins. Over the central Lena basin, which is mostly underlain by permafrost, TWS steadily increased until 2007 but has slightly declined since. By combining GRACE observations of TWS anomalies with discharge and net precipitation, we show that the terrestrial water budget is at least qualitatively closed over the Eurasian Arctic basins. The observed TWS and discharge increases over the study time period were driven by increased atmospheric moisture fluxes. Therefore, we conclude that melting of excess ground ice in permafrost regions did not act as a source to observed changes in discharge. Nonetheless, the signature of significant TWS increases points to ongoing thickening of the active layer in particular over the discontinuous permafrost regions in the central Lena basin.
Shapes of two‐layer models of rotating planets
Authors: Kong D. , Zhang K. , Schubert G.
Published: December 2010

To first approximation the interiors of many planetary bodies consist of a core and mantle with significantly different densities. The shapes of the surface and interface between the core and the mantle are basic properties reflecting planetary structure and rotation. In addition, interface shape is an important parameter controlling the dynamics of a fluid core. We present a theory for the rotational distortion of a two‐layer model of a planet (two‐layer Maclaurin spheroid) that determines the shapes of both the interface and the outer free surface without treating departure from sphericity as a small perturbation. Since the interface and the outer free surface, in general, have different shapes, two different spheroidal coordinates are required in the mathematical analysis, and the transformation between them is at the heart of the complexity of the theory. Furthermore, two different cases have to be considered. In the first case, the core is sufficiently large, or the rate of rotation is sufficiently small, that the foci of the outer free surface are located within the core. In the second case, the core is sufficiently small, or the rate of rotation is sufficiently fast, that the foci of the free surface are located within the outer layer. In comparison to the classical Maclaurin solution which is explicitly analytical, the relevant multiple integrals for the equilibrium solution of a two‐layer Maclaurin spheroid have to be evaluated numerically. The shape of a two‐layer rotating planet is characterized by three dimensionless parameters that are explored systematically in the present study.
Values of natural and human‐made wetlands: A meta‐analysis
Authors: Ghermandi Andrea , van den Bergh Jeroen C. J. M. , Brander Luke M. , de Groot Henri L. F. , Nunes Paulo A. L. D.
Published: December 2010

The values of goods and services provided by wetland ecosystems are examined through a meta‐analysis of an expanded database of wetland value estimates and with a focus on human‐made wetlands. This study extends and improves upon previous meta‐analyses of the wetland valuation literature in terms of the number of observations, geographical coverage, wetland class and integrity, and the measurement of the effects of scarcity and anthropogenic pressure. We find that water quality improvement, nonconsumptive recreation, and provision of natural habitat and biodiversity are highly valued services. Substitution effects are observed through the negative correlation between values and abundance of other wetlands. Wetland values are found to increase with anthropogenic pressure. An extended metaregression model with cross effects shows that the valuation of specific services varies with the type of wetland producing them. Human‐made wetlands are highly valued for biodiversity enhancement, water quality improvement, and flood control.
What is value–adding? Contradictions in the practice of BPR in a Danish Social Service Administration
Authors: Hagedorn–Rasmussen Peter , Vogelius Peter
Published: December 2010

This article explores the implementation of BPR in the Social Service Administration in a Danish municipality. The technical rationality inherited in BPR marginalises broader conceptions of work–rationality represented by the social workers. This results in a ‘clash’ between rationalities in the Family Group, causing increased strain and lower job satisfaction.
A review of mast cell biology
Authors: Hill  , Martin
Published: December 2010

In recent years, the mast cell has been a focus of intense scientific study, predominantly because of its role as a key effector cell in immediate hypersensitivity reactions. Continuous research over the last 20 years has finally characterized the origin of mast cells, and determined many of the factors involved in mast cell differentiation and proliferation. In addition, different subpopulations of mast cell have been defined with distinct biochemical and functional characteristics. The mechanisms involved in stimulus–secretion coupling, the process by which mast cells release their inflammatory mediators, has received particular attention because these mechanisms may be future targets for anti‐allergic drugs. However, it is now recognized that mast cells play a much wider role than mediating allergic diseases. They are involved in non specific inflammatory reactions, fibrosis, angiogenesis and wound healing, and play an important role in protection of the host against gastrointestinal nematodes and certain bacterial infections. In this review, the advances made in determining the origins, heterogeneity and function of mast cells are described.
The Relative Contribution of Relative Height, Linear Perspective, and Texture Gradients to Pictorial Depth Perception in 7-Month-Old Infants
Authors: Hemker Laura , Kavšek Michael
Published: December 2010

In the current preferential-reaching experiments, 7-month-olds were tested for their ability to respond to a combination of relative height and texture gradients. The infants were presented with a display in which these pictorial depth cues specified that two toys were at different distances. The experimental displays differed from the textured surfaces employed in earlier studies in that linear perspective of the contours of the texture elements was omitted. Experiment A shows that the infants still preferred to reach for the apparently nearer toy under monocular, but not binocular, viewing conditions, indicating that they responded to the pictorial depth cues. In experiment B, relative height and texture provided the infants with conflicting information for depth. Here, relative height outperformed texture information. A statistical comparison between the experiments as well as systematic comparisons with experimental conditions from an earlier study (Hemker et al, 2010 Infancy15 6 – 27) revealed that texture gradients, unlike linear perspective, neither enhanced nor weakened the effect exerted by relative height. In sum, 7-month-old infants are obviously more sensitive to relative height and to the linear perspective of the surface contours than to the texture gradients of compression, perspective, and density.
Children and young people in out-of-home care: are GPs ready and willing to provide comprehensive health assessments for this vulnerable group?
Authors: Webster Susan M. , Temple-Smith Meredith
Published: December 2010

Children living in out-of-home care because of abuse or neglect are among the most vulnerable in Australia. In 2005 the Royal Australasian College of Physicians highlighted the need for increased attention to the health of such children and recommended regular health assessment. This qualitative study explored the views of a purposive sample of 20 GPs about what would influence GP willingness and readiness to undertake comprehensive health assessments for children entering out-of-home care. Ethical concerns, training, professional development needs, medico-legal issues, workforce and financial pressures and communication problems with the child protection sector were among key factors identified. Professional values about continuity of health care for children emerged as a new issue with important policy implications. This is the first in-depth study in Australia of GP perspectives about systematic health assessments for children in child protection and sheds new light on the low GP uptake of such assessments for at-risk population groups.
Less germs, less mucus, less snot: teachers' and health workers' perceptions of the benefits and barriers of ear health programs in lower primary school classes
Authors: Doyle June , Ristevski Eli
Published: December 2010

This study explored health and education professionals’ perceptions of the health benefits and barriers of different ear health programs used in lower primary school classes in two district education areas in the Goldfields South East Health Region, Western Australia. Health and education staff providing services to children in kindergarten to year three primary school classes were sent a questionnaire about ear health programs provided in their school. Sixty-one questionnaires were returned from 43 teachers, 14 community health nurses, three Aboriginal health workers and one teacher’s assistant. Some schools implemented all the ear health programs examined at all year levels while others implemented only one of the programs. Teachers, community health nurses and Aboriginal health workers identified that all ear health programs were beneficial to students. Reported physical health benefits included reduced ear infections, early detection of ear infections and improved hearing. Behavioural benefits included improved concentration, alertness and attention in the classroom. Barriers to implementing the programs were obtaining consent from parents/carers, student transience and attendance, time to implement and conduct the programs and human and physical resources. Evaluation methods used varied from no evaluation for the Breathe Blow Cough and tissue spearing programs to limited data collection for audiometry, otoscopy and ear toilet programs. Respondents perceived that ear health programs were effective in improving health and behavioural outcomes for children. A formal pre-post evaluation to provide objective data to confirm this is needed to inform policy around this important health issue.
Apurinic/apyrimidinic (AP) site recognition by the 5′-dRP/AP lyase in poly(ADP-ribose) polymerase-1 (PARP-1)
Authors: Khodyreva S. N. , Prasad R. , Ilina E. S. , Sukhanova M. V. , Kutuzov M. M. , Liu Y. , Hou E. W. , Wilson S. H. , Lavrik O. I.
Published: December 2010

The capacity of human poly(ADP-ribose) polymerase-1 (PARP-1) to interact with intact apurinic/apyrimidinic (AP) sites in DNA has been demonstrated. In cell extracts, sodium borohydride reduction of the PARP-1/AP site DNA complex resulted in covalent cross-linking of PARP-1 to DNA; the identity of cross-linked PARP-1 was confirmed by mass spectrometry. Using purified human PARP-1, the specificity of PARP-1 binding to AP site-containing DNA was confirmed in competition binding experiments. PARP-1 was only weakly activated to conduct poly(ADP-ribose) synthesis upon binding to AP site-containing DNA, but was strongly activated for poly(ADP-ribose) synthesis upon strand incision by AP endonuclease 1 (APE1). By virtue of its binding to AP sites, PARP-1 could be poised for its role in base excision repair, pending DNA strand incision by APE1 or the 5′-dRP/AP lyase activity in PARP-1.
Molecular recognition between ketosynthase and acyl carrier protein domains of the 6-deoxyerythronolide B synthase
Authors: Kapur Shiven , Chen Alice Y. , Cane David E. , Khosla Chaitan
Published: December 2010

Every polyketide synthase module has an acyl carrier protein (ACP) and a ketosynthase (KS) domain that collaborate to catalyze chain elongation. The same ACP then engages the KS domain of the next module to facilitate chain transfer. Understanding the mechanism for this orderly progress of the growing polyketide chain represents a fundamental challenge in assembly line enzymology. Using both experimental and computational approaches, the molecular basis for KS–ACP interactions in the 6-deoxyerythronolide B synthase has been decoded. Surprisingly, KS–ACP recognition is controlled at different interfaces during chain elongation versus chain transfer. In fact, chain elongation is controlled at a docking site remote from the catalytic center. Not only do our findings reveal a new principle in the modular control of polyketide antibiotic biosynthesis, they also provide a rationale for the mandatory homodimeric structure of polyketide synthases, in contrast to the monomeric nonribosomal peptide synthetases.
Soap-film Möbius strip changes topology with a twist singularity
Authors: Goldstein Raymond E. , Moffatt H. Keith , Pesci Adriana I. , Ricca Renzo L.
Published: December 2010

It is well-known that a soap film spanning a looped wire can have the topology of a Möbius strip and that deformations of the wire can induce a transformation to a two-sided film, but the process by which this transformation is achieved has remained unknown. Experimental studies presented here show that this process consists of a collapse of the film toward the boundary that produces a previously unrecognized finite-time twist singularity that changes the linking number of the film’s Plateau border and the centerline of the wire. We conjecture that it is a general feature of this type of transition that the singularity always occurs at the surface boundary. The change in linking number is shown to be a consequence of a viscous reconnection of the Plateau border at the moment of the singularity. High-speed imaging of the collapse dynamics of the film’s throat, similar to that of the central opening of a catenoid, reveals a crossover between two power laws. Far from the singularity, it is suggested that the collapse is controlled by dissipation within the fluid film surrounding the wire, whereas closer to the transition the power law has the classical form arising from a balance between air inertia and surface tension. Analytical and numerical studies of minimal surfaces and ruled surfaces are used to gain insight into the energetics underlying the transition and the twisted geometry in the neighborhood of the singularity. A number of challenging mathematical questions arising from these observations are posed.
Tunable spectral range slow light interferometer based on the temperature characteristics of semiconductor GaAs
Authors: Zhang Yundong , Cai Yuanxue , Dang Boshi , Wang Jinfang , Wu Hao , Yuan Ping
Published: December 2010

A method based on the temperature dependence of optical property of semiconductor GaAs is provided to improve the spectral performance of a slow light interferometer, and its effect on the sensitivity of the slow light interferometer is also discussed. We theoretically demonstrate that the method ensures that the interferometer has a wide spectral range and high sensitivity simultaneously. This result also provides a viable method that can be extended to the whole spectral region.
MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks
Authors: Gori Fabio , Folino Gianluigi , Jetten Mike S. M. , Marchiori Elena
Published: December 2010

Motivation: Metagenomics is a recent field of biology that studies microbial communities by analyzing their genomic content directly sequenced from the environment. A metagenomic dataset consists of many short DNA or RNA fragments called reads. One interesting problem in metagenomic data analysis is the discovery of the taxonomic composition of a given dataset. A simple method for this task, called the Lowest Common Ancestor (LCA), is employed in state-of-the-art computational tools for metagenomic data analysis of very short reads (about 100 bp). However LCA has two main drawbacks: it possibly assigns many reads to high taxonomic ranks and it discards a high number of reads.

Results: We present MTR, a new method for tackling these drawbacks using clustering at Multiple Taxonomic Ranks. Unlike LCA, which processes the reads one-by-one, MTR exploits information shared by reads. Specifically, MTR consists of two main phases. First, for each taxonomic rank, a collection of potential clusters of reads is generated, and each potential cluster is associated to a taxon at that rank. Next, a small number of clusters is selected at each rank using a combinatorial optimization algorithm. The effectiveness of the resulting method is tested on a large number of simulated and real-life metagenomes. Results of experiments show that MTR improves on LCA by discarding a significantly smaller number of reads and by assigning much more reads at lower taxonomic ranks. Moreover, MTR provides a more faithful taxonomic characterization of the metagenome population distribution.

Availability: Matlab and C++ source codes of the method available at http://cs.ru.nl/˜gori/software/MTR.tar.gz.

Contact:  gori@cs.ru.nl; elenam@cs.ru.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain–peptide interaction from primary sequence
Authors: Shao Xiaojian , Tan Chris S. H. , Voss Courtney , Li Shawn S. C. , Deng Naiyang , Bader Gary D.
Published: December 2010

Motivation: Predicting protein interactions involving peptide recognition domains is essential for understanding the many important biological processes they mediate. It is important to consider the binding strength of these interactions to help us construct more biologically relevant protein interaction networks that consider cellular context and competition between potential binders.

Results: We developed a novel regression framework that considers both positive (quantitative) and negative (qualitative) interaction data available for mouse PDZ domains to quantitatively predict interactions between PDZ domains, a large peptide recognition domain family, and their peptide ligands using primary sequence information. First, we show that it is possible to learn from existing quantitative and negative interaction data to infer the relative binding strength of interactions involving previously unseen PDZ domains and/or peptides given their primary sequence. Performance was measured using cross-validated hold out testing and testing with previously unseen PDZ domain–peptide interactions. Second, we find that incorporating negative data improves quantitative interaction prediction. Third, we show that sequence similarity is an important prediction performance determinant, which suggests that experimentally collecting additional quantitative interaction data for underrepresented PDZ domain subfamilies will improve prediction.

Availability and Implementation: The Matlab code for our SemiSVR predictor and all data used here are available at http://baderlab.org/Data/PDZAffinity.

Contact:  gary.bader@utoronto.ca; dengnaiyang@cau.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
New approach for segmentation and quantification of two-dimensional gel electrophoresis images
Authors: dos Anjos António , Møller Anders L. B. , Ersbøll Bjarne K. , Finnie Christine , Shahbazkia Hamid R.
Published: December 2010

Motivation: Detection of protein spots in two-dimensional gel electrophoresis images (2-DE) is a very complex task and current approaches addressing this problem still suffer from significant shortcomings. When quantifying a spot, most of the current software applications include a lot of background due to poor segmentation. Other software applications use a fixed window for this task, resulting in omission of part of the protein spot, or including background in the quantification. The approach presented here for the segmentation and quantification of 2-DE aims to minimize these problems.

Results: Five sections from different gels are used to test the performance of the presented method concerning the detection of protein spots, and three gel sections are used to test the quantification of sixty protein spots. Comparisons with a state-of-the-art commercial software and an academic state-of-the-art approach are presented. It is shown that the proposed approach for segmentation and quantification of 2-DE images can compete with the available commercial and academic software packages.

Availability: A command-line prototype may be downloaded, for non-commercial use, from http://w3.ualg.pt/~aanjos/prototypes.html.

Contact:  antoniodosanjos@gmail.com

Supplementary information:  Supplementary data are available at Bioinformtaics online.
Point vortex equilibria and optimal packings of circles on a sphere
Authors: Newton Paul K. , Sakajo Takashi
Published: December 2010

We answer the question of whether optimal packings of circles on a sphere are equilibrium solutions to the logarithmic particle interaction problem for values of
N
=3–12 and 24, the only values of
N
for which the optimal packing problem (also known as the Tammes problem) has rigorously known solutions. We also address the cases
N
=13–23 where optimal packing solutions have been computed, but not proven analytically. As in Jamaloodeen & Newton (Jamaloodeen & Newton 2006
Proc. R. Soc. Lond. Ser. A
462
, 3277–3299. (
doi:10.1098/rspa.2006.1731
)), a logarithmic, or point vortex equilibrium is determined by formulating the problem as the one in linear algebra,

, where
A
is a
N
(
N
−1)/2×
N
non-normal configuration matrix obtained by requiring that all interparticle distances remain constant. If
A
has a kernel, the strength vector

is then determined as a right-singular vector associated with the zero singular value, or a vector that lies in the nullspace of
A
where the kernel is multi-dimensional. First we determine if the known optimal packing solution for a given value of
N
has a configuration matrix
A
with a non-empty nullspace. The answer is yes for
N
=3–9, 11–14, 16 and no for
N
=10, 15, 17–24. We then determine a basis set for the nullspace of
A
associated with the optimally packed state, answer the question of whether
N
-equal strength particles,

, form an equilibrium for this configuration, and describe what is special about the icosahedral configuration from this point of view. We also find new equilibria by implementing two versions of a random walk algorithm. First, we cluster sub-groups of particles into patterns during the packing process, and ‘grow’ a packed state using a version of the ‘yin-yang’ algorithm of Longuet-Higgins (Longuet-Higgins 2008
Proc. R. Soc. A
(doi:10.1098/rspa.2008.0219)). We also implement a version of our ‘Brownian ratchet’ algorithm to find new equilibria near the optimally packed state for
N
=10, 15, 17–24.
Bacteraemia and breast abscess: unusual extra-intestinal manifestations of Clostridium difficile infection
Authors: Durojaiye Oyewole , Gaur Soma , Alsaffar Layth
Published: December 2010

Extra-intestinal manifestations of Clostridium difficile infection are uncommon. Most cases are associated with gastrointestinal disease and often occur as a mixed infection with other gut flora. We report a case of breast abscess following monomicrobial C. difficile bacteraemia in a female with background chronic hepatitis C infection and alcoholic liver disease. No evidence of colitis was found. Our case shows that C. difficile is indeed capable of spreading from the gastrointestinal tract.
The in vitro and in vivo anti‐tumor effect of KO‐202125, a sauristolactam derivative, as a novel epidermal growth factor receptor inhibitor in human breast cancer
Authors: Oh Miyun , Lee Jeong‐Yeon , Shin Dong‐Hui , Park Ji‐Hye , Oian Tingting , Kim Hyun‐Jun , Cho Sung‐Dae , Oh Seung‐Hyun , Min Young Ki , Kong Gu
Published: December 2010

Epidermal growth factor receptor (EGFR) is one of the most promising targets for cancer therapy. Here, we show the in vitro and in vivo anticancer effects and associated mechanisms of KO‐202125, one of the synthesized aristolactam analogs, as a novel EGFR inhibitor, in EGFR‐overexpressing cancer cell lines. KO‐202125 showed more effective growth inhibition and apoptosis induction than gefitinib, a representative EGFR inhibitor, in various EGFR‐overexpressing human cancers including estrogen receptor (ER)‐negative MDA‐MB‐231 human breast cancer cells. Epidermal growth factor receptor phosphorylation at Tyr1068 was reduced and, consequently, the association of EGFR with p85 was decreased by KO‐202125 treatment in MDA‐MB‐231 cell lines. This led to inactivation of the PI3K/Akt pathway, and consequently suppression of activation of the Wnt pathway and enhancement of the nuclear import of p27Kip1. KO‐202125 treatment in nude mice injected with MDA‐MB‐231 cells showed inhibition of tumor growth without toxicity. Collectively, our results showed the possibility of KO‐202125 as an effective therapy agent of EGFR‐overexpressing cancer cells through reduced EGFR activity and downregulation of the Akt pathway. (Cancer Sci 2011; 102: 597–604)
Characterization of innate immune signalling receptors in virus‐induced acute asthma
Authors: Wood L. G. , Simpson J. L. , Wark P. A. B. , Powell H. , Gibson P. G.
Published: December 2010

Background
The role of toll‐like receptors (TLRs) and innate immune activation in clinical asthma exacerbations and their relationship to virus infection are unclear.

Objective
This study aimed to characterize TLR expression and innate immune activity during virus infection in acute asthma.

Methods
Subjects with acute asthma, stable asthma and healthy controls were recruited and underwent spirometry and sputum induction with isotonic saline. Selected sputum was dispersed with dithiothreitol and total and differential leucocyte counts were performed. Selected sputum was also used for quantitative real‐time PCR for TLR2, TLR3, TLR4, IL‐10 and IP‐10mRNA expression. Sputum supernatant was used for the measurement of innate immune markers, including IL‐8, matrix metalloproteinase‐9 and neutrophil elastase activity. Viruses were detected using real‐time and gel‐based PCR.

Results
Sputum TLR2 mRNA expression was up‐regulated in both acute and stable asthma compared with healthy controls and decreased 4–6 weeks after acute exacerbation. Sputum TLR2 mRNA expression was elevated in viral, compared with non‐viral, acute asthma. Sputum TLR3 mRNA expression was similar in controls, stable and acute asthma. However, in acute asthma, subjects with virus‐induced acute asthma had significantly higher sputum TLR3 mRNA expression. Induced sputum gene expression for IP‐10 and IL‐10 were increased in viral, compared with non‐viral, acute asthma. In virus‐induced acute asthma, levels of IP‐10 and IL‐10 mRNA expression were correlated with the mRNA expression of TLR2 and TLR3.

Conclusions and Clinical Relevance
Virus‐induced acute asthma leads to specific induction of TLR2, TLR3, IP‐10 and IL‐10, suggesting that signalling via TLRs may play an important role in mediating airway inflammation, via both innate and adaptive pathways, in virus‐induced exacerbations. These mediators may provide potential treatment targets for virus‐induced asthma. They may also be useful in diagnosing the nature of acute asthma exacerbations and monitoring treatment responses, which would be useful in the clinical management of asthma exacerbations.

Cite this as: L. G. Wood, J. L. Simpson, P. A. B. Wark, H. Powell and P. G. Gibson, Clinical & Experimental Allergy, 2011 (41) 640–648.
Role of bone marrow imprints in haematological diagnosis: a detailed study of 3781 cases
Authors: Gong X. , Lu X. , Wu X. , Xu R. , Tang Q. , Xu G. , Wang L. , Zhang X. , Zhao X.
Published: December 2010

X. Gong, X. Lu, X. Wu, R. Xu, Q. Tang, G. Xu, L. Wang, X. Zhang and X. Zhao

Role of bone marrow imprints in haematological diagnosis: a detailed study of 3781 cases

Objectives:  To explore the role of imprints in routine bone marrow (BM) diagnosis.

Methods:  The cellularity and diagnostic accuracy of BM imprints, aspirate smears and trephine biopsy sections from 3781 patients were assessed using routine cytochemical staining. Seventy‐nine cases of lymphoma and 114 cases of plasma cell myeloma (PCM) were selected for correlation analysis of tumour cell infiltration patterns. Another 21 cases of lymphoma were selected to detect t(14;18)(q32;q21) and t(11;14)(q13;q32) by fluorescent in situ hybridization (FISH) on BM imprints, and the G‐banding technique was performed for comparison.

Results:  BM imprints were better than smears for evaluating cellularity. In the BM imprint group, diagnostic accuracy for metastatic carcinoma, myeloproliferative neoplasm, myelodysplastic/myeloproliferative neoplasm and PCM was better than in the smear group, while accuracy for megaloblastic anaemia, acute myeloid leukaemia, refractory cytopenia with unilineage or multilineage dysplasia, refractory anaemia with excess blasts and lymphoplasmacytic lymphoma was higher than in the section group, but not statistically different from the smear group. Good correlation of infiltration patterns of lymphoma and myeloma cells was found between BM imprints and sections (r = 0.90 and 0.78, respectively). Detection of t(11;14)(q13;q32) by FISH on imprints was higher than G‐banding analysis.

Conclusions:  BM imprints show features of both smears and trephine sections. Imprints are superior to smears for evaluation of cellularity, and are also better than sections for analysis of cytological changes. In addition, FISH on BM imprints markedly improves the identification of chromosomal abnormalities.