bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial and temporal ecological diversity amongst eocene primates of france: Evidence from teeth
Authors: Ramdarshan Anusha , Merceron Gildas , Marivaux Laurent
Published: November 2011

Diet is of paramount importance in the life of a primate. It is also highly variable, as potential food sources vary in spatial distribution and availability over time. The fossil record, due to its fragmentary nature, offers few possibilities to assess the dietary range of a given primate across its spatial and temporal distribution. Here we focus on three taxa, Leptadapis magnus (Adapidae, Adapiformes), Necrolemur cf. antiquus (Microchoeridae, Omomyiformes), and Pseudoloris parvulus (Microchoeridae, Omomyiformes). These taxa occur at different localities of the Late Eocene in the south of France ranging from MP16 (Robiac, Lavergne; 39 Ma), MP17a (La Bouffie, Euzet, Fons 4; 38 Ma) to MP17b (Perrière; 37 Ma). Diets of fossil taxa are assessed here by dental microwear analysis using a comparative database of 11 species of living strepsirhines. On the whole, leaves were a preferred food for the large‐bodied Leptadapis (4–5 kg). However, the diet of this taxon varied from a mix of leaves and fruit at La Bouffie, a closed tropical rain forest environment, to a strictly leaf‐eating one in the more open environment of Perrière. Based on body mass (200–350 g) and dental microwear patterns, Necrolemur had a mainly fruit‐based diet, perhaps supplemented by insects. However, the comparison of the different localities reveals the dietary range of this small‐bodied omomyiform which seems to vary between insects and a much softer diet. Pseudoloris had a diet strictly based on insects. Contrary to Leptadapis or Necrolemur, its diet seems to have been confined to insects whatever the locality considered. Am J Phys Anthropol 147:201–216, 2012. © 2011 Wiley Periodicals, Inc.
Descriptive epidemiology of selected heritable birth defects in Texas
Authors: Moffitt Karen B. , Abiri Oseni O. , Scheuerle Angela E. , Langlois Peter H.
Published: November 2011

BACKGROUND Few population‐based studies exist on descriptive epidemiologic characteristics of rare heritable birth defects. The number of birth defect cases in the Texas Birth Defects Registry (one of the largest active birth defects surveillance systems in the world) enabled us to examine six different heritable disorders (aqueductal stenosis, infantile polycystic kidney disease, achondroplasia, thanatophoric dwarfism, chondrodysplasia/dwarfism not otherwise specified (NOS), and osteogenesis imperfecta) for a variety of descriptive demographic variables. METHODS The Texas Birth Defects Registry was used to identify infants or fetuses with heritable birth defects. Crude prevalence rates were calculated and Poisson regression was used to test the association of each demographic variable (e.g., maternal age) with each of the selected genetic birth defects. RESULTS White non‐Hispanics exhibited higher rates of achondroplasia and osteogenesis imperfecta than other race/ethnic groups. Lower maternal education level and to a lesser extent, paternal education level, was associated with higher rates of several disorders. The birth prevalence rate for achondroplasia decreased from 1999 through 2006. CONCLUSION The use of a large birth defects registry provides a sufficient count of cases to perform some basic epidemiologic analysis on selected rare heritable birth defects. Birth Defects Research (Part A) 2011. © 2011 Wiley Periodicals, Inc.
Contrasting weathering and climate regimes in forested and cleared sandstone temples of the Angkor region
Authors: André Marie‐Françoise , Voldoire Olivier , Roussel Erwan , Vautier Franck , Phalip Bruno , Peou Hang
Published: November 2011

Comparative assessment of stone weathering intensities and bioclimatic conditions was conducted at four temples located in cleared and forested sites of the Angkor Park, based on similar protocols. Four thousand sculpted lotus petals carved in the same grey sandstone were categorized by using two customized scales of weathering intensity, and climate monitoring was conducted from December 2008 to November 2009. Whereas 70% of the sandstone lotus petals are almost completely destroyed by mechanical weathering in cleared areas, 74% of petals located in forested environments appear to be totally free of mechanical weathering and are only affected by superficial biochemical weathering. Ambient conditions are also contrasting, with the magnitude of the diurnal surface temperature and relative humidity ranges being three times higher at cleared sites than in wooded areas. As wetting–drying cycles are the driving force of sandstone decay at Angkor, causal links are suggested between weathering and climate regimes. In wooded areas, the microclimate is buffered by the forest and the associated lithobionts, which maintain constant humidity levels, reduce thermal stresses at the stone surface and induce a slow biochemical weathering regime. In cleared areas, direct exposure to sunshine and monsoon rains induces pronounced wetting–drying cycles conducive to swelling–shrinking movements and other potential processes, provoking the rapid mechanical decay of the sandstone. Even if local damage can be caused by tree roots, the forest cover and the associated lithobionts obviously play an overall protective role. Additionally, microtopographical factors related to architectural designs and post‐building events probably explain intra‐site and between site minor differences in the amount of sandstone decay, by influencing key factors such as the water residence time at the stone surface. Last, the contrasting weathering regimes in forested and cleared sites are but a trend, for besides overwhelming mechanical weathering, chemical weathering is also operative at cleared sites, as indicated by salt efflorescences and ferric oxidation. Copyright © 2012 John Wiley & Sons, Ltd.
How natural are Alpine mountain rivers? Evidence from the Italian Alps
Authors: Comiti Francesco
Published: November 2011

Historical, human‐induced channel adjustments in lowland gravel‐bed rivers have been documented in several geographical contexts worldwide. In particular, it is now widely accepted that the vast majority of European rivers are far from any natural, reference state prior to anthropic disturbances, and a ‘complete’ restoration is hardly achievable. However, few investigations have addressed changes that have occurred in mountain rivers of the Alps, and these channels are commonly reckoned quite ‘natural’ by society. This paper intends to describe how human pressure on Italian Alpine basins has been quite relevant for several centuries – in terms of land‐use variations, in‐channel structures, timber transport (splash damming) and riparian vegetation management – such that nowadays ‘reference conditions’ cannot be found even in small mountain creeks. In addition, recent natural climatic variations (e.g. the Little Ice Age) are superimposed on human disturbances, thus defying the definition of any ‘equilibrium’ morphological conditions even under ‘human‐free’ states. A summary of published as well as unpublished works on historical channel adjustments in rivers of the Italian Alps is presented in order to document the impacts deriving from human pressure at different basin scales and for different river morphologies, from steep confined streams to large unconfined rivers. General options for river management and restoration actions aiming to combine geomorphological functionality and flood hazard mitigation are discussed, in the light of the current European legislative context. Copyright © 2011 John Wiley & Sons, Ltd.
Myocardial edema imaging in acute coronary syndromes
Authors: Walls Michael C. , Verhaert David , Min James K. , Raman Subha V.
Published: November 2011

Acute coronary syndromes (ACS) continue to be the most common morbid condition of industrialized nations. The advent of and technical improvements in revascularization and medical therapy have led to a steady decline in mortality rates. However, many patients who suffer unstable angina or myocardial infarction require further testing and risk stratification to guide therapeutic selection and prognosis assignment. Myocardial edema imaging with cardiac magnetic resonance (CMR) affords the ability to define the amount of myocardium at risk, refine estimates of prognosis and provide guidance for therapies with excellent sensitivity compared with standard clinical markers. This review will discuss the rationale for edema imaging, how it is performed using CMR, and potential clinical applications. J. Magn. Reson. Imaging 2011;. © 2011 Wiley Periodicals, Inc.
MR spectroscopy in schizophrenia
Authors: Port John D. , Agarwal Nivedita
Published: November 2011

The purpose of this study is to review the MR spectroscopic literature regarding schizophrenia. However, as there are over 250 primary MRS articles and dozens of MRS review articles on the subject already, this study will take a different approach. First, the clinical features of schizophrenia will be described. The background neuroanatomy and biochemistry relevant to schizophrenia will be reviewed, as many readers of this journal are unlikely to be familiar with these fields. A current model of the abnormal neural circuitry in schizophrenia will be presented, and predictions extrapolated about relevant metabolite changes over time. Finally, the existing MRS literature will be reviewed in the context of our existing anatomical and chemical knowledge, and future MRS research directions will be elaborated. J. Magn. Reson. Imaging 2011;. © 2011 Wiley Periodicals, Inc.
Pressure dependence of phenylperoxy radical formation in the reaction of phenyl radical with molecular oxygen
Authors: Tanaka K. , Ando M. , Sakamoto Y. , Tonokura K.
Published: November 2011

Pressure dependence of the phenylperoxy radical (C6H5O2) formation in the reaction of phenyl radical (C6H5) with molecular oxygen (O2) has been investigated with the cavity ring‐down method by detecting the C6H5O2at 504 nm. The rate constant of the C6H5+ O2reaction was determined to bek= (1.2 ± 0.1) × 10−11cm3molecule−1s−1by the least‐square analysis of several sets of the C6H5O2rise profiles at 30 Torr and at 296 K. This value is almost identical to those previously obtained at 40 Torr (Yu and Lin,J Am Chem Soc1994, 98, 9571–9576) and 760 Torr (Tonokura et al.,J Phys Chem A2002, 106, 5908–5917), indicating that the rate constant has no pressure dependence in the pressure range of 30–760 Torr. The signal intensity ratio of C6H5O2to C6H5was obtained in the pressure range of 5–120 Torr. Varying the third body carrier gas (N2) had a significant effect on the production of the C6H5O2. To validate thekdetermination by C6H5O2rise detection and determine the branching ratio of C6H5O2in the C6H5+ O2reaction system, theoretical calculations were also performed. The rate constant obtained with Rice–Ramsperger–Kassel–Marcus/master equation calculations is in good agreement with that measured in this experiment. The branching ratio forming C6H5O2obtained by the theoretical calculation also exhibited pressure dependence, which is consistent with the experimental results. The branching ratio increases with increasing pressure and reaches approximately 0.85 at 120 Torr. © 2011 Wiley Periodicals, Inc. Int J Chem Kinet 44: 41–50, 2012
A quadratic semidefinite relaxation approach for resource allocation in orthogonal frequency division multiple access
Authors: Adasme Pablo , Lisser Abdel , Soto Ismael
Published: November 2011

This paper proposes two binary quadratically constrained quadratic programs for minimizing power subject to bit rate and subcarrier allocation constraints over wireless orthogonal frequency division multiple access. The first model represents a restricted case in which users are allowed to use only one modulation size in each subcarrier while the second, a more flexible real case in which they can use any size. We propose two semidefinite programming relaxations and compare with the linear programs obtained by applying Fortet linearization method. Numerical results show a total average tightness gain of 42.78 and 97.17% for the first and second quadratic model, respectively. Moreover, we get in average, near optimal lower bounds of 0.5 and 1% for the second model over random and realistic data, respectively. © 2011 Wiley Periodicals, Inc. NETWORKS, 2012
On a stochastic bilevel programming problem
Authors: Kosuch Stefanie , Le Bodic Pierre , Leung Janny , Lisser Abdel
Published: November 2011

In this article, a mixed integer bilevel problem having a probabilistic knapsack constraint in the first level is proposed. The problem formulation is mainly motivated by practical pricing and service provision problems as it can be interpreted as a model for the interaction between a service provider and customers. A discrete probability space is assumed which allows a reformulation of the problem as an equivalent deterministic bilevel problem. The problem is further transformed into a linear bilevel problem, which in turn yields a quadratic optimization problem, namely the global linear complementarity problem. Based on this quadratic problem, a procedure to compute upper bounds on the initial problem by using a Lagrangian relaxation and an iterative linear minmax scheme is proposed. Numerical experiments confirm that the scheme practically converges.© 2011 Wiley Periodicals, Inc. NETWORKS, 2012
Development of innovative voltage control for distribution networks with high photovoltaic penetration
Authors: Bletterie B. , Goršek A. , Fawzy T. , Premm D. , Deprez W. , Truyens F. , Woyte A. , Blazič B. , Uljanič B.
Published: November 2011

The voltage rise caused by photovoltaic (PV) power feed‐in is one of the main network constraints limiting the PV penetration in distribution networks. In this paper, a local voltage control approach for PV inverters based on reactive power management is proposed and investigated into detail. Through a parametric study, various inverter settings are considered and compared for a real medium voltage network with a high PV penetration level and for which a demonstration is planned within the project MetaPV. The purpose of this work is to investigate the suitability of such control concepts to compensate the voltage rise caused by the PV power feed‐in and to provide some guidance on the adjustment of the settings of such control mechanisms. For the assessment of the performance of the control concept with different settings, extensive load flow simulations have been performed for a voltage‐dependent reactive power control (Q(V) characteristics) on the basis of 15‐minute profiles. As a result, voltage time‐series over a period of 1 year are obtained for each case and analysed into details. Apart from the voltage profiles, other features such as network losses and reactive energy import have been quantified because they are also of noticeable importance for network operators. The simulation results show that suitable settings are necessary to maintain the voltage within the prescribed limits. A comparison between the considered cases shows that reactive power control Q(V) with a power factor down to 0.9 is necessary to achieve satisfying results. The use of a dead‐band is recommended for the voltage‐dependent reactive power control in order to limit the losses and reactive energy import. Copyright © 2011 John Wiley & Sons, Ltd.
Nonviral gene delivery using poly‐D/L aspartate‐diethylenetriamine cationic polymers and polyethylene glycol: A two‐step approach
Authors: Mirosevich Janni , Cardoen Gregoire , Burke Brian , Costich Tara , Sill Kevin
Published: November 2011

Cationic polymers have received much attention as promising nonviral vectors for gene transfer. However, development of polymers with low cell toxicities and high transfection efficiencies continue to be a significant problem and a major hurdle to their success. Poly‐D/L aspartate‐diethylenetriamine poly(D/L Asp‐DET) polymers were synthesized and evaluated as nonviral gene delivery agents. Poly(D/L Asp‐DET) polymers display endosome buffering capacity. The polymers condense plasmid DNA above N:P ratios of 1 and form polyplex particles of ∼50–100 nm, with zeta potentials between neutral and +40 mV. Transmission electron microscopy shows the polyplexes to be uniform in size and shape. Polyplexes maintain the structural integrity of DNA following incubation in nucleases and also show high transfection efficiencies with minimal toxicity in both HCT‐116 and PC‐3 cell culture. However, it is found that these poly(D/L Asp‐DET)/DNA polyplexes immediately aggregate in salt and serum conditions, making them unsuitable for use in vivo. Therefore, the polyplexes were further modified by covalent addition of polyethylene glycol (PEG). Introduction of this second step produces PEG‐polyplexes of uniform size (below 100 nm), with neutral zeta potentials that are also stable in both salt and serum conditions. These results suggest poly(D/L Asp‐DET) cationic polymers as potentially safe and efficient nonviral gene delivery agents. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Ligand‐free Cu(0)‐mediated controlled radical polymerization of methyl methacrylate at ambient temperature
Authors: Wang Wenxiang , Zhang Zhengbiao , Wu Yang , Zhu Jian , Cheng Zhenping , Zhou Nianchen , Zhang Wei , Zhu Xiulin
Published: November 2011

For the first time, ligand‐free Cu(0)‐mediated polymerization of methyl methacrylate (MMA) was realized by the selection of ethyl‐2‐bromo‐2‐phenylacetate as initiator at ambient temperature. The polymerization can reach up to 90% conversion within 5 h with dimethyl sulfoxide (DMSO) as solvent, while keeping manners of the controlled radical polymerization. Extensive investigation of this system revealed that for a well‐controlled Cu(0)‐mediated polymerization of MMA, the initiator should be selected with the structure as alkyl 2‐bromo‐2‐phenylacetate, and the solvent should be DMSO or N,N‐dimethylformamide. The selectivity for solvents indicated a typical single‐electron transfer‐living radical polymerization process. Scanning for other monomers indicated that under equal conditions, the polymerizations of other alkyl (meth)acrylates were uncontrollable. Based on these results, plausible reasons were discussed. The ligand‐free Cu(0)‐mediated polymerization showed its superiority with economical components and needless removal of Cu species from the resultant products. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Characterization of phase separation of polystyrene/poly(vinyl methyl ether) blends using fluorescence
Authors: Kriisa Annika , Park Sung S. , Roth Connie B.
Published: November 2011

We have investigated the fluorescence emission spectra of pyrene and anthracene dyes covalently bonded to polystyrene (PS) upon phase separation from poly(vinyl methyl ether) (PVME). The specific chemical structure of the fluorescent labels is found to affect the measured phase separation temperature TS, with fluorophores covalently attached in closer proximity to the PS backbone identifying phase separation a few degrees earlier. The sharp increase in fluorescence intensity upon phase separation that occurs for all fluorophores with little change in spectral shape is consistent with a mechanism of static fluorescence quenching resulting from the specific interaction with a nearby quenching molecular unit. Based on recent work that has identified a weak hydrogen bond occurring between the aromatic hydrogens of PS and the ether oxygen of PVME, we believe a similar weak hydrogen bond is likely occurring between the PVME oxygen and the aromatic dyes providing a local (few nanometer) sensitivity to phase separation. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Stiffness constants prediction of nanocomposites using a periodic 3D‐FEM model
Authors: Cricrì Gabriele , Garofalo Emilia , Naddeo Francesco , Incarnato Loredana
Published: November 2011

Predictive models, which enable the prediction of nanocomposite properties from their morphologies and account for polymer orientation, could greatly assist the exploitation of this new class of materials in more diversified and demanding market fields. This article focuses on the prediction of effective elastic properties (Young's moduli) of polymer nanocomposite films (copolyamide‐6/nanoclay) using 3D analytical (based on the Mori‐Tanaka theory) and 3D finite element (FE) models. The analytical model accounts for the orientation of polymer chains induced by drawing. 3D FE model exploits the representative volume element concept and accounts for the nanocomposite morphology as determined from transmission electron microscopy experiments. Model predictions were compared with experimental results obtained for nanocomposite films produced by means a pilot‐scale film blowing equipment and collected at different draw ratios. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012
Optically induced birefringence and holography in silk
Authors: Cronin‐Golomb Mark , Murphy Amanda R. , Mondia Jessica P. , Kaplan David L. , Omenetto Fiorenzo G.
Published: November 2011

In this study, we demonstrated that thin films of azobenzene‐modified Bombyx mori silk showed optically induced effects similar to those found in other polymers incorporating azobenzene moieties. Optically induced anisotropy in refractive index reached 7 × 10−3 with 18 J cm−2 required to reach 50% of steady state. Holograms were formed with diffraction efficiencies reaching 2.5%. The holograms were accompanied by surface relief gratings and measurements of the mechanical properties of films with surface relief gratings showed that the raised areas were more adhesive than the lower areas. We also demonstrated the fidelity of holographic images. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Does aboveground vegetation composition resemble soil seed bank during succession in specialized vegetation on gypsum soil?
Authors: Martinez‐Duro Esmeralda , Luzuriaga Arantzazu L. , Ferrandis Pablo , Escudero Adrián , Herranz José M.
Published: November 2011

This paper evaluates the aboveground vegetation in relation to the soil seed bank throughout a 60‐year succession process following agricultural abandonment in a semi‐arid Mediterranean gypsum habitat. There is little information regarding the relationship between these two community components in the context of succession on semi‐arid gypsum soils. Aboveground vegetation and the corresponding seed bank of gypsum plant communities were sampled through a chronosequence of 24 abandoned fields. Generalized linear models were used to model seed species richness and density, redundancy analyses to model the effect of time since abandonment and the effect of soil physicochemical parameters on seed bank species composition, and Mantel tests to analyze resemblance between above‐ and belowground species composition. In this last case, the effect of time since abandonment was controlled using a partial Mantel test. Mantel correlograms using time intervals instead of distances were used to describe the resemblance of above‐ to belowground species occurrence in different aged fields. No significant variability in seed species richness, seed density, or species composition due to time since abandonment was found. Differences in seed species composition were mainly due to small spatial scale predictors such as slope and soil calcium content. High correlations between species composition in the soil seed bank and the aboveground vegetation were detected during succession. The lack of a significant trend in aboveground species replacement over time was also reflected in seed bank composition. We concluded that the rapid establishment of strict gypsophyte species relied mainly on the long‐term persistence of these species in the seed bank.
Separation of Lipid Classes by HPLC on a Cyanopropyl Column
Authors: Olsson Petter , Holmbäck Jan , Herslöf Bengt
Published: November 2011

A new method for the separation and identification of lipid classes by normal‐phase HPLC on a cyanopropyl column is described. The use of a simple binary gradient, with toluene as a component, provided a rapid separation of non‐polar as well as phospholipid classes. The inherent small differences in performances between possible non‐polar eluent components of the gradient, such as hexane, heptane, and iso‐octane, had a pronounced impact on retention times for individual phospholipid classes. Separation of molecular species within a lipid class could also be observed.
Density is in the eye of the beholder: visual versus semi-automated assessment of breast density on standard mammograms
Authors: Lobbes M. B. I. , Cleutjens J. P. M. , Lima Passos V. , Frotscher C. , Lahaye M. J. , Keymeulen K. B. M. I. , Beets-Tan R. G. , Wildberger J. , Boetes C.
Published: November 2011

Objectives

Visual inspection is generally used to assess breast density. Our study aim was to compare visual assessment of breast density of experienced and inexperienced readers with semi-automated analysis of breast density.

Methods

Breast density was assessed by an experienced and an inexperienced reader in 200 mammograms and scored according to the quantitative BI-RADS classification. Breast density was also assessed by dedicated software using a semi-automated thresholding technique. Agreement between breast density classification of both readers as well as agreement between their assessment versus the semi-automated analysis as reference standard was expressed as the weighted kappa value.

Results

Using the semi-automated analysis, agreement between breast density measurements of both breasts in both projections was excellent (ICC >0.9, P < 0.0001). Reproducibility of the semi-automated analysis was excellent (ICC >0.8, P < 0.0001). The experienced reader correctly classified the BI-RADS breast density classification in 58.5% of the cases. Classification was overestimated in 35.5% of the cases and underestimated in 6.0% of the cases. Results of the inexperienced reader were less accurate. Agreement between the classification of both readers versus the semi-automated analysis was considered only moderate with weighted kappa values of 0.367 (experienced reader) and 0.232 (inexperienced reader).

Conclusion

Visual assessment of breast density on mammograms is inaccurate and observer-dependent.
Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants
Authors:   China Plant BOL Group, Li De-Zhu , Gao Lian-Ming , Li Hong-Tao , Wang Hong , Ge Xue-Jun , Liu Jian-Quan , Chen Zhi-Duan , Zhou Shi-Liang , Chen Shi-Lin , Yang Jun-Bo , Fu Cheng-Xin , Zeng Chun-Xia , Yan Hai-Fei , Zhu Ying-Jie , Sun Yong-Shuai , Chen Si-Yun , Zhao Lei , Wang Kun , Yang Tuo , Duan Guang-Wen
Published: November 2011

A two-marker combination of plastidrbcLandmatKhas previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastidtrnH–psbAand nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1–92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9–79.1% of species, compared with only 49.7% withrbcL+matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.
Magneto-optical contrast in liquid-state optically detected NMR spectroscopy
Authors: Pagliero Daniela , Meriles Carlos A.
Published: November 2011

We use optical Faraday rotation (OFR) to probe nuclear spins in real time at high-magnetic field in a range of diamagnetic sample fluids. Comparison of OFR-detected NMR spectra reveals a correlation between the relative signal amplitude and the fluid Verdet constant, which we interpret as a manifestation of the variable detuning between the probe beam and the sample optical transitions. The analysis of chemical-shift-resolved, optically detected spectra allows us to set constraints on the relative amplitudes of hyperfine coupling constants, both for protons at chemically distinct sites and other lower-gyromagnetic-ratio nuclei including carbon, fluorine, and phosphorous. By considering a model binary mixture we observe a complex dependence of the optical response on the relative concentration, suggesting that the present approach is sensitive to the solvent-solute dynamics in ways complementary to those known in inductive NMR. Extension of these experiments may find application in solvent suppression protocols, sensitivity-enhanced NMR of metalloproteins in solution, the investigation of solvent-solute interactions, or the characterization of molecular orbitals in diamagnetic systems.
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
Authors: Jones David T. , Buchan Daniel W. A. , Cozzetto Domenico , Pontil Massimiliano
Published: November 2011

Motivation: The accurate prediction of residue–residue contacts, critical for maintaining the native fold of a protein, remains an open problem in the field of structural bioinformatics. Interest in this long-standing problem has increased recently with algorithmic improvements and the rapid growth in the sizes of sequence families. Progress could have major impacts in both structure and function prediction to name but two benefits. Sequence-based contact predictions are usually made by identifying correlated mutations within multiple sequence alignments (MSAs), most commonly through the information-theoretic approach of calculating mutual information between pairs of sites in proteins. These predictions are often inaccurate because the true covariation signal in the MSA is often masked by biases from many ancillary indirect-coupling or phylogenetic effects. Here we present a novel method, PSICOV, which introduces the use of sparse inverse covariance estimation to the problem of protein contact prediction. Our method builds on work which had previously demonstrated corrections for phylogenetic and entropic correlation noise and allows accurate discrimination of direct from indirectly coupled mutation correlations in the MSA.

Results: PSICOV displays a mean precision substantially better than the best performing normalized mutual information approach and Bayesian networks. For 118 out of 150 targets, the L/5 (i.e. top-L/5 predictions for a protein of length L) precision for long-range contacts (sequence separation >23) was ≥0.5, which represents an improvement sufficient to be of significant benefit in protein structure prediction or model quality assessment.

Availability: The PSICOV source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/PSICOV

Contact:  d.jones@cs.ucl.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
An Allosteric Coagonist Model for Propofol Effects on α1β2γ2L γ-Aminobutyric Acid Type A Receptors
Authors: Ruesch Dirk , Neumann Elena , Wulf Hinnerk , Forman Stuart A.
Published: November 2011

Background

Propofol produces its major actions via γ-aminobutyric acid type A (GABA(A)) receptors. At low concentrations, propofol enhances agonist-stimulated GABA(A) receptor activity, and high propofol concentrations directly activate receptors. Etomidate produces similar effects, and there is convincing evidence that a single class of etomidate sites mediate both agonist modulation and direct GABA(A) receptor activation. It is unknown if the propofol binding site(s) on GABA(A) receptors that modulate agonist-induced activity also mediate direct activation.

Methods

GABA(A) α1β2γ2L receptors were heterologously expressed in Xenopus oocytes and activity was quantified using voltage clamp electrophysiology. We tested whether propofol and etomidate display the same linkage between agonist modulation and direct activation of GABA(A) receptors by identifying equiefficacious drug solutions for direct activation. We then determined whether these drug solutions produce equal modulation of GABA-induced receptor activity. We also measured propofol-dependent direct activation and modulation of low GABA responses. Allosteric coagonist models similar to that established for etomidate, but with variable numbers of propofol sites, were fitted to combined data.

Results

Solutions of 19 μM propofol and 10 μM etomidate were found to equally activate GABA(A) receptors. These two drug solutions also produced indistinguishable modulation of GABA-induced receptor activity. Combined electrophysiological data behaved in a manner consistent with allosteric coagonist models with more than one propofol site. The best fit was observed when the model assumed three equivalent propofol sites.

Conclusions

Our results support the hypothesis that propofol, like etomidate, acts at GABA(A) receptor sites mediating both GABA modulation and direct activation.
Musculotendinous Infraspinatus Rupture and Shoulder Weakness
Authors: Lipford Melissa C , Bond Jeffrey R , Steinmann Scott P , Kumar Neeraj
Published: November 2011

We report a patient with bilateral simultaneous onset of weakness of shoulder lateral rotation due to musculotendinous infraspinatus rupture that occurred after shoulder steroid injections. Disruption of the musculotendinous junction of the infraspinatus is a rare recently described entity. Electromyography is normal, and magnetic resonance image findings are characteristic.
Neuromuscular Manifestations of HIV/AIDS
Authors: Harrison Taylor B , Smith Bryan
Published: November 2011

The human immunodeficiency virus (HIV) epidemic, now entering its fourth decade, affects approximately 33 million people living in both developed and resource-limited countries. Neurological complications of the peripheral nervous system are common in HIV-infected patients, and neuromuscular pathology is associated with significant morbidity. Peripheral neuropathy is the most common neuromuscular manifestation observed in HIV/AIDS, and in the antiretroviral era, its prevalence has increased. The purpose of this review was to describe the clinical spectrum of neuromuscular disorders in the setting of HIV infection and to provide an approach to diagnosis and management.
Rituximab and Mycophenolate Combination Therapy in Refractory Dermatomyositis With Multiple Autoimmune Disorders
Authors: Parziale Nicholas , Kovacs Susan C , Thomas Christine B , Srinivasan Jayashri
Published: November 2011

We report a case of dermatomyositis associated with rheumatoid arthritis, Hashimoto thyroiditis, and diabetes mellitus responsive only to combination of rituximab with mycophenolate. A 42-year-old woman presented with proximal muscle weakness, myalgias, fever, night sweats, and shortness of breath. Creatinine kinase was 8155 IU/L, and muscle biopsy was diagnostic of dermatomyositis. She was started on glucocorticoids; her systemic symptoms improved, but her muscle weakness persisted. She was serially treated with intravenous immunoglobulin, azathioprine, and mycophenolate mofetil without improvement in her weakness. She responded dramatically to combination therapy with rituximab and mycophenolate, with improvement in strength and normalization of creatinine kinase. She has been well controlled on rituximab infusion every 6 months and maintenance mycophenolate mofetil.
On the auxetic properties of generic rotating rigid triangles
Authors: Grima Joseph N. , Chetcuti Elaine , Manicaro Elaine , Attard Daphne , Camilleri Matthew , Gatt Ruben , Evans Kenneth E.
Published: November 2011

Materials having a negative Poisson's ratio (auxetic) get fatter rather than thinner when uniaxially stretched. This phenomenon has been often explained through models that describe how particular geometric features in the micro or nanostructure of the material deform when subjected to uniaxial loads. Here, a new model based on scalene rigid triangles rotate relative to each other will be presented and analysed. It is shown that this model can afford a very wide range of Poisson's ratio values, the sign and magnitude of which depends on the shape of the triangles and the angles between them. This new model has the advantage that it is very generic and may be potentially used to describe the properties in various types of materials, including auxetic foams and their relative surface density. Specific applications of this model, such as a blueprint for a system that can exhibit temperature-dependent Poisson's ratios, are also discussed.
CONCORD: a consensus method for protein secondary structure prediction via mixed integer linear optimization
Authors: Wei Y. , Thompson J. , Floudas C. A.
Published: November 2011

Most of the protein structure prediction methods use a multi-step process, which often includes secondary structure prediction, contact prediction, fragment generation, clustering, etc. For many years, secondary structure prediction has been the workhorse for numerous methods aimed at predicting protein structure and function. This paper presents a new mixed integer linear optimization (MILP)-based consensus method: a Consensus scheme based On a mixed integer liNear optimization method for seCOndary stRucture preDiction (CONCORD). Based on seven secondary structure prediction methods, SSpro, DSC, PROF, PROFphd, PSIPRED, Predator and GorIV, the MILP-based consensus method combines the strengths of different methods, maximizes the number of correctly predicted amino acids and achieves a better prediction accuracy. The method is shown to perform well compared with the seven individual methods when tested on the PDBselect25 training protein set using sixfold cross validation. It also performs well compared with another set of 10 online secondary structure prediction servers (including several recent ones) when tested on the CASP9 targets (
http://predictioncenter.org/casp9/
). The average Q3 prediction accuracy is 83.04 per cent for the sixfold cross validation of the PDBselect25 set and 82.3 per cent for the CASP9 targets. We have developed a MILP-based consensus method for protein secondary structure prediction. A web server, CONCORD, is available to the scientific community at
http://helios.princeton.edu/CONCORD
.
Massilia tieshanensis sp. nov., isolated from mining soil
Authors: Du Yan , Yu Xiang , Wang Gejiao
Published: November 2011

A bacterial isolate, designated strain TS3T, was isolated from soil collected from a metal mine in Tieshan District, Daye City, Hubei Province, in central China. Cells of this strain were Gram-negative, motile and rod-shaped. The strain had ubiquinone Q-8 as the predominant respiratory quinone, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c as the major fatty acids. The G+C content was 65.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TS3T was most closely related to

Massilia niastensis

5516S-1T (98.5 %),

Massilia consociata

CCUG 58010T (97.6 %),

Massilia aerilata

5516S-11T (97.4 %) and

Massilia varians

CCUG 35299T (97.2 %). DNA–DNA hybridization revealed low relatedness between strain TS3T and

M. niastensis

KACC 12599T (36.5 %),

M. consociata

CCUG 58010T (27.1 %),

M. aerilata

KACC 12505T (22.7 %) and

M. varians

CCUG 35299T (46.5 %). On the basis of phenotypic and phylogenetic characteristics, strain TS3T belongs to the genus

Massilia

, but is clearly differentiated from other members of the genus. The strain represents a novel species, for which the name Massilia tieshanensis sp. nov. is proposed. The type strain is TS3T ( = CCTCC AB 2010202T  = KACC 14940T).
Reclassification of Lactobacillus kimchii and Lactobacillus bobalius as later subjective synonyms of Lactobacillus paralimentarius
Authors: Pang Huili , Kitahara Maki , Tan Zhongfang , Wang Yanping , Qin Guangyong , Ohkuma Moriya , Cai Yimin
Published: November 2011

Characterization and identification of strain CW 1 ( = JCM 17161) isolated from corn silage were performed. Strain CW 1 was a Gram-positive, catalase-negative and homofermentative rod that produced the dl-form of lactic acid. This strain exhibited more than 99.6 % 16S rRNA gene sequence similarity and greater than 82 % DNA–DNA reassociation with type strains of

Lactobacillus kimchii

,

L. bobalius

and

L. paralimentarius

. To clarify the taxonomic positions of these type strains, phenotypic characterization, 16S rRNA gene sequencing, ribotyping and DNA–DNA relatedness were examined. The three type strains displayed different l-arabinose, lactose, melibiose, melezitose, raffinose and N-acetyl-β-glucosaminidase fermentation patterns. Phylogenetic analysis showed that

L. paralimentarius

is a closer neighbour of

L. kimchii

and

L. bobalius

, sharing 99.5–99.9 % 16S rRNA gene sequence similarity, which was confirmed by the high DNA–DNA relatedness (≥82 %) between

L. paralimentarius

JCM 10415T,

L. bobalius

JCM 16180T and

L. kimchii

JCM 10707T. Therefore, it is proposed that

L. kimchii

and

L. bobalius

should be reclassified as later synonyms of

L. paralimentarius

.
Delftia litopenaei sp. nov., a poly-β-hydroxybutyrate-accumulating bacterium isolated from a freshwater shrimp culture pond
Authors: Chen Wen-Ming , Lin Yang-Shun , Sheu Der-Shyan , Sheu Shih-Yi
Published: November 2011

A Gram-negative, short-rod-shaped, motile, non-spore-forming and poly-β-hydroxybutyrate-accumulating bacterial strain, designated wsw-7T, was isolated from a freshwater shrimp culture pond in Taiwan and was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain wsw-7T were

Delftia lacustris

332T,

Delftia tsuruhatensis

T7T and

Delftia acidovorans

ATCC 15668T, with sequence similarities of 98.5, 98.4 and 97.9 %, respectively. Phylogenetic trees obtained with 16S rRNA gene sequences or the polyhydroxyalkanoate synthase (phaC) gene sequences revealed that strain wsw-7T and these three closest relatives formed an independent phylogenetic clade within the order

Burkholderiales

. Strain wsw-7T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as predominant fatty acids. The major isoprenoid quinone was Q-8 and the DNA G+C content was 67.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminolipid and several uncharacterized phospholipids. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain wsw-7T represents a novel species in the genus

Delftia

, for which the name Delftia litopenaei sp. nov. is proposed; the type strain is wsw-7T ( = BCRC 80212T = LMG 25724T).
Bidirectional plasticity in striatonigral synapses: A switch to balance direct and indirect basal ganglia pathways
Authors: Aceves Jose J. , Rueda-Orozco Pavel E. , Hernandez-Martinez Ricardo , Galarraga Elvira , Bargas Jose
Published: November 2011

There is no hypothesis to explain how direct and indirect basal ganglia (BG) pathways interact to reach a balance during the learning of motor procedures. Both pathways converge in the substantia nigra pars reticulata (SNr) carrying the result of striatal processing. Unfortunately, the mechanisms that regulate synaptic plasticity in striatonigral (direct pathway) synapses are not known. Here, we used electrophysiological techniques to describe dopamine D1-receptor-mediated facilitation in striatonigral synapses in the context of its interaction with glutamatergic inputs, probably coming from the subthalamic nucleus (STN) (indirect pathway) and describe a striatonigral cannabinoid-dependent long-term synaptic depression (LTD). It is shown that striatonigral afferents exhibit D1-receptor-mediated facilitation of synaptic transmission when NMDA receptors are inactive, a phenomenon that changes to cannabinoid-dependent LTD when NMDA receptors are active. This interaction makes SNr neurons become coincidence-detector switching ports: When inactive, NMDA receptors lead to a dopamine-dependent enhancement of direct pathway output, theoretically facilitating movement. When active, NMDA receptors result in LTD of the same synapses, thus decreasing movement. We propose that SNr neurons, working as logical gates, tune the motor system to establish a balance between both BG pathways, enabling the system to choose appropriate synergies for movement learning and postural support.
Exaggerated NMDA mediated LTD in a mouse model of Down syndrome and pharmacological rescuing by memantine
Authors: Scott-McKean Jonah J. , Costa Alberto C.S.
Published: November 2011

The Ts65Dn mouse is the best-studied animal model for Down syndrome. In the experiments described here, NMDA-mediated or mGluR-mediated LTD was induced in the CA1 region of hippocampal slices from Ts65Dn and euploid control mice by bath application of 20 µM NMDA for 3 min and 50 µM DHPG for 5 min, respectively. We found that Ts65Dn mice display exaggerated NMDA-induced, but not mGluR-induced, LTD in the CA1 region of the hippocampus compared with euploid control animals. In addition, this abnormal level of LTD can be pharmacologically rescued by the NMDA receptor antagonist memantine.
The Phosphoglucan Phosphatase Like Sex Four2 Dephosphorylates Starch at the C3-Position in Arabidopsis
Authors: Santelia Diana , Kötting Oliver , Seung David , Schubert Mario , Thalmann Matthias , Bischof Sylvain , Meekins David A. , Lutz Andy , Patron Nicola , Gentry Matthew S. , Allain Frédéric H.-T. , Zeeman Samuel C.
Published: November 2011

Starch contains phosphate covalently bound to the C6-position (70 to 80% of total bound phosphate) and the C3-position (20 to 30%) of the glucosyl residues of the amylopectin fraction. In plants, the transient phosphorylation of starch renders the granule surface more accessible to glucan hydrolyzing enzymes and is required for proper starch degradation. Phosphate also confers desired properties to starch-derived pastes for industrial applications. In Arabidopsis thaliana, the removal of phosphate by the glucan phosphatase Starch Excess4 (SEX4) is essential for starch breakdown. We identified a homolog of SEX4, LSF2 (Like Sex Four2), as a novel enzyme involved in starch metabolism in Arabidopsis chloroplasts. Unlike SEX4, LSF2 does not have a carbohydrate binding module. Nevertheless, it binds to starch and specifically hydrolyzes phosphate from the C3-position. As a consequence, lsf2 mutant starch has elevated levels of C3-bound phosphate. SEX4 can release phosphate from both the C6- and the C3-positions, resulting in partial functional overlap with LSF2. However, compared with sex4 single mutants, the lsf2 sex4 double mutants have a more severe starch-excess phenotype, impaired growth, and a further change in the proportion of C3- and C6-bound phosphate. These findings significantly advance our understanding of the metabolism of phosphate in starch and provide innovative options for tailoring novel starches with improved functionality for industry.