bluuebunny/crossref_metadata_2025 huggingface dataset:
EPR/Spin‐trapping study of free radical intermediates in the photolysis of trifluoromethyl ketones with initiators
Authors: Rosa Esmeralda , Guerrero Angel , Bosch Mª Pilar , Julià Luis
Published: January 2010

Photolysis of trifluoromethyl ketones (TFMKs) 1a–1e versus the non‐fluorinated ketones 2a–2b in the presence of radical initiators by electron paramagnetic resonance spectroscopy has been studied for the first time. The transient radicals generated after irradiation of the ketones were identified by trapping with 2‐methyl‐2‐nitrosopropane (MNP) and 2,4,6‐tri‐tert‐butylnitrosobenzene (TTBNB) as spin traps. TTBNB is a powerful, particularly useful spin trap in these kinds of processes producing anilino and nitroxyl spin adducts due to the ambivalent reactivity on the N and O atoms. In the presence of t‐butylperoxide, short‐chain TFMKs, such as 1,1,1‐trifluoroacetone (1d) and hexafluoroacetone (1e), give rise to detection of the elusive trifluoromethyl radical. In contrast, long‐chain TFMKs did not provide clues to prove formation of the trifluoromethyl radical but instead to radicals derived by abstraction of one α‐methylene proton to the carbonyl. Although TFMKs are quite stable to photodegradation in the absence of initiator, methyl ketone 2b and phenyl ketone 3 produce radicals resulting from abstraction of a γ‐hydrogen to the carbonyl group. Copyright © 2010 John Wiley & Sons, Ltd.
jTraqX: A free, platform independent tool for isobaric tag quantitation at the protein level
Authors: Muth Thilo , Keller Daniela , Puetz Stephanie Michaela , Martens Lennart , Sickmann Albert , Boehm Andreas M.
Published: January 2010

Many proteomic studies focus on quantitative aspects, using different stable isotope labeling techniques that require specialized software to analyze the generated data. Here we present jTraqX, an easy‐to‐use tool for processing and visualizing protein quantification data. jTraqX is platform independent and is compatible with all available 4‐plex isobaric tags. jTraqX can be freely downloaded at http://sourceforge.net/projects/protms.
MS‐driven protease substrate degradomics
Authors: Impens Francis , Colaert Niklaas , Helsens Kenny , Plasman Kim , Van Damme Petra , Vandekerckhove Joël , Gevaert Kris
Published: January 2010

Proteolytic processing has recently received increased attention in the field of signal propagation and cellular differentiation. Because of its irreversible nature, protein cleavage has been associated with committed steps in cell function. One aspect of protease biology that boomed the past few years is the detailed characterization of protease substrates by both shotgun as well as targeted MS‐driven proteomics techniques. The most promising techniques are discussed in this review and we further elaborate on the bioinformatics challenges that accompany mainly qualitative, MS‐driven protease substrate degradome studies.
Defining topological features of membrane proteins by nanoelectrospray ionisation mass spectrometry
Authors: Jones Lynsey N. , Baldwin Stephen A. , Henderson Peter J. F. , Ashcroft Alison E.
Published: January 2010

The D‐galactose‐H+symport protein, GalP, ofEscherichia coliis the bacterial homologue of the human glucose transport protein, GLUT1. Here we demonstrate that mass spectrometry can be used to map modification by covalently bound reagents, and also to detect structural changes in the GalP protein that occur upon substrate binding. The small thiol‐group‐specific reagentN‐ethylmaleimide (NEM) was used to modify the cysteine residues in GalP(His)6both alone and in the presence of D‐glucose, a known substrate. Employing a mixture of proteolysis and thermal degradation methods, the three cysteine residues were found to undergo sequential reactions with NEM, with Cys374 being modified first, followed by Cys389 and finally Cys19, thus indicating their different accessibilities within the three‐dimensional structure of the protein. Prior binding of the substrate D‐glucose to the protein protected Cys19 and Cys374 against NEM modification, but not Cys389. Cys374 had been expected to be shielded by D‐glucose binding while Cys389 had been expected to be unaffected, consistent with their proposed respective locations in the vicinity of, and distant from, the sugar binding site. However, the inaccessibility of Cys19 was unexpected and suggests a structural change in the protein promoted by D‐glucose binding which changes the proximity of Cys19 with respect to the D‐glucose‐binding site. Copyright © 2010 John Wiley & Sons, Ltd.
Glycogen storage disease type IV: novel mutations and molecular characterization of a heterogeneous disorder
Authors: Li Sing‐Chung , Chen Chiao‐Ming , Goldstein Jennifer L. , Wu Jer‐Yuarn , Lemyre Emmanuelle , Burrow Thomas Andrew , Kang Peter B. , Chen Yuan‐Tsong , Bali Deeksha S.
Published: January 2010

Glycogen storage disease type IV (GSD IV; Andersen disease) is caused by a deficiency of glycogen branching enzyme (GBE), leading to excessive deposition of structurally abnormal, amylopectin‐like glycogen in affected tissues. The accumulated glycogen lacks multiple branch points and thus has longer outer branches and poor solubility, causing irreversible tissue and organ damage. Although classic GSD IV presents with early onset of hepatosplenomegaly with progressive liver cirrhosis, GSD IV exhibits extensive clinical heterogeneity with respect to age at onset and variability in pattern and extent of organ and tissue involvement. With the advent of cloning and determination of the genomic structure of the human GBE gene (GBE1), molecular analysis and characterization of underlying disease‐causing mutations is now possible. A variety of disease‐causing mutations have been identified in the GBE1 gene in GSD IV patients, many of whom presented with diverse clinical phenotypes. Detailed biochemical and genetic analyses of three unrelated patients suspected to have GSD IV are presented here. Two novel missense mutations (p.Met495Thr and p.Pro552Leu) and a novel 1‐bp deletion mutation (c.1999delA) were identified. A variety of mutations in GBE1 have been previously reported, including missense and nonsense mutations, nucleotide deletions and insertions, and donor and acceptor splice‐site mutations. Mutation analysis is useful in confirming the diagnosis of GSD IV—especially when higher residual GBE enzyme activity levels are seen and enzyme analysis is not definitive—and allows for further determination of potential genotype/phenotype correlations in this disease.
Surgical synovectomy of the knee in young haemophiliacs: Long-term results of a monocentric series of 23 patients
Authors: Rampal Virginie , Odent T. , Torchet M. F. , Rothschild C. , Elie C. , Glorion C. , Padovani J. P.
Published: January 2010

Background

In haemophiliacs, synovectomy is indicated for recurrent joint bleedings, despite medical treatment.

Method

We report a series of 23 surgical synovectomies of the knee with a median follow-up of 8.8 years. The median age of patients at surgery was 13.5 years. Clinical and radiological evaluations were made according to the Petrini and the Pettersson scores, at 1 and 5 years after surgery, and at the last follow-up. Wilcoxon and Spearman's tests were used for the statistical analysis.

Result

The Petrini score improved at 1 and 5 years ( P < 0.001). Nine patients have 20 years of follow-up and a stable result. In more than half of the knees, no episode of recurrent bleeding occurred. The effect of surgery on the range of motion (ROM) was moderate and mobilisation under anaesthesia did not improve it significantly. There was a progressive worsening of the radiological score, but no correlation between clinical and radiological score was noticed ( ρ = 0.08, P = 0.77).

Conclusion

Complete synovectomy gives good long-term results in term of bleeding recurrence and overall function.
Point-of-care ultrasound diagnosis of SCFE
Authors: Stone Michael B. , Barrett Chameeka
Published: January 2010

Introduction

A 13-year-old boy presented to the emergency department with left knee pain after a fall. Initial radiographs were unremarkable, but the child returned to the emergency department 6 weeks later with persistent symptoms.

Materials and methods

A bedside sonogram of the left hip performed by the treating emergency physician demonstrated a widened epiphyseal plate and an associated effusion, consisted with a slipped capital femoral epiphysis (SCFE). Repeat radiographs confirmed the diagnosis.

Conclusion

The ultrasound features and test characteristics for the detection of SCFE are reviewed.
Sublingual misoprostol for first trimester termination of pregnancy
Authors: Fekih Myriam , Fathallah Khadija , Regaya Lassad Ben , Bouguizane Sassi , Chaieb Anouar , Bibi Mohamed , Khairi Hedi
Published: January 2010

Objectives

To compare blood loss, efficiency, and acceptability of repeated doses of sublingual misoprostol with the standard Tunisian regimen of mifepristone–misoprostol for first trimester medical abortion.

Methods

A prospective randomized trial of 252 healthy pregnant women requesting medical abortion in the first trimester (up to 56 days). Participants were randomized to receive 200 mg of oral mifepristone followed by 400 µg of oral misoprostol (group 1) or 800 µg of sublingual misoprostol repeated every 4 hours for up to a maximum of 3 doses (group 2). Primary outcome was blood loss assessed by decrease in hematocrit.

Results

Mean decrease in hematocrit at follow‐up was significantly greater in group 1 than in group 2 (3.65% ± 1.18% vs 2.69% ± 1.89%, respectively; P = 0.02). There was no difference in efficiency rates between groups 1 and 2 (94.5% vs 92.1%; P = 0.7). Comparable proportions of women experiencing at least one adverse effect after misoprostol administration were reported in groups 1 and 2 (81.7% vs 79.4%; P = 0.75).

Conclusion

Compared with the most widely used regimen in Tunisia (mifepristone–misoprostol), sublingual misoprostol alone induces less blood loss (although not clinically significant); it is less expensive and offers reduced interval time to expulsion.
Multi-access antenna for an opportunistic radio mobile communication of fourth generation
Authors: El Hajj Walid , Gallée François , Person Christian
Published: January 2010

A new model of two-access reconfigurable antennas for future mobile communication systems is presented in this article. This structure is based on a slot antenna with two separated access ports, isolated and matched at 1 and 2 GHz, respectively. The novelty of this element lies in the fact that first a filtering structure is integrated in the antenna, and then any additional switching or frequency path selecting components that would induce losses and noise degradation is suppressed. Such flexible structures are assumed to be used in a future opportunistic radio, incorporating special features of “spectrum sensing”. The concept of the antenna illustrated by simulation and measurement is presented.
Surface water–groundwater exchange in transitional coastal environments by airborne electromagnetics: The Venice Lagoon example
Authors: Viezzoli A. , Tosi L. , Teatini P. , Silvestri S.
Published: January 2010

A comprehensive investigation of the mixing between salt/fresh surficial water and groundwater in transitional environments is an issue of paramount importance considering the ecological, cultural, and socio‐economic relevance of coastal zones. Acquiring information, which can improve the process understanding, is often logistically challenging, and generally expensive and slow in these areas. Here we investigate the capability of airborne electromagnetics (AEM) at the margin of the Venice Lagoon, Italy. The quasi‐3D interpretation of the AEM outcome by the spatially constrained inversion (SCI) methodology allows us to accurately distinguish several hydrogeological features down to a depth of about 200 m. For example, the extent of the saltwater intrusion in coastal aquifers and the transition between the upper salt saturated and the underlying fresher sediments below the lagoon bottom are detected. The research highlights the AEM capability to improve the hydrogeological characterization of subsurface processes in worldwide lagoons, wetlands, deltas.
Coatings and clusters of carboxylic acids in carbon‐containing atmospheric particles from spectromicroscopy and their implications for cloud‐nucleating and optical properties
Authors: Takahama S. , Liu S. , Russell L. M.
Published: January 2010

Particle shape and distribution of chemical compounds within individual particles are implied in the parameterizations used in air quality and climate models for radiative transfer, volatility, and mass transfer. In this study we employ Scanning Transmission X‐Ray Microscopy with Near‐Edge X‐Ray Absorption Fine Structure Spectroscopy with image analysis and pattern recognition techniques to characterize the chemical structure of 636 particles collected on six field campaigns in the western hemisphere between 2004 and 2008. Many of the particles were chemically heterogeneous. A few observed types include black carbon particles covered by aqueous‐phase components (n = 90), dust particles with organic clumps (106), organic particles enriched in carboxylic acid at the surface (54), and inorganic cores encapsulated by organic shells (10). The 90 particles in the first category collectively contained 95 regions showing a strong black‐carbon spectral signature associated with the aqueous‐phase components, of which 78 were between 0.1 and 1 μm. Organic mass fraction of the organic dust particles varied significantly (mean and standard deviation of 0.3 ± 0.2), and over half of these dust particles were found to be nearly spherical. Thickness of acid‐enriched coatings and carbon on inorganic cores were less than 0.6 μm in most cases, but accounted for <0.01 to 0.98 of the particle volume fraction. More than half of the identified organic particles (359) were found to be chemically heterogeneous, and 32 particles were observed as agglomerations or inclusions but did not meet one or more of the criteria of the categories described here. The acidic coatings on black carbon are calculated to have a significant impact on the critical supersaturation of these particles. The measured distribution of aspect ratios of dust and other particles in our samples ranged nonuniformly between 1.0 and 4.6 with a mean of 1.4, which can affect assessment of extinction‐to‐backscatter ratios over the case where spherical geometry is assumed.
On the use of spatial regularization strategies to improve calibration of distributed watershed models
Authors: Pokhrel Prafulla , Gupta Hoshin V.
Published: January 2010

Hydrologic models require the specification of unknown model parameters via calibration to historical input‐output data. For spatially distributed models, the large number of unknowns makes the calibration problem poorly conditioned. Spatial regularization can help to stabilize the problem by facilitating inclusion of additional information. While a common regularization approach is to apply a scalar multiplier to the prior estimate of each parameter field, this can cause problems by simultaneously changing both the mean and the variance of the distribution. This paper explores a multiple‐criteria regularization approach that facilitates adjustment of the mean, variance, and shape of the parameter distribution, using prior information to constrain the problem while providing sufficient degrees of freedom to enable model performance improvements. We also test simple squashing functions to help in maintaining conceptually reasonable parameter values throughout the spatial domain. We apply the method to three basins in the context of the Distributed Model Intercomparison Project (DMIP2), obtaining considerable performance improvements at the basin outlet. However, the prior parameter estimates are found to give much better performance at the interior points (treated as ungauged), suggesting that the spatial information has not been properly exploited. The results also suggest that basin outlet hydrographs may not be particularly sensitive to spatial parameter variability and that an overall basin mean value may be sufficient for flow forecasting at the outlet, although not at the interior points. We discuss weaknesses in our study approach and suggest diagnostically more powerful strategies to be pursued.
Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons
Authors: Kamke Janine , Taylor Michael W , Schmitt Susanne
Published: January 2010

The phylogenetic diversity of microorganisms in marine sponges is becoming increasingly well described, yet relatively little is known about the activities of these symbionts. Given the seemingly favourable environment provided to microbes by their sponge hosts, as indicated by the extraordinarily high abundance of sponge symbionts, we hypothesized that the majority of sponge-associated bacteria are active in situ. To test this hypothesis we compared, for the first time in sponges, 16S rRNA gene- vs 16S rRNA-derived bacterial community profiles to gain insights into symbiont composition and activity, respectively. Clone libraries revealed a highly diverse bacterial community in Ancorina alata, and a much lower diversity in Polymastia sp., which were identified by electron microscopy as a high- and a low-microbial abundance sponge, respectively. Substantial overlap between DNA and RNA libraries was evident at both phylum and phylotype levels, indicating in situ activity for a large fraction of sponge-associated bacteria. This active fraction included uncultivated, sponge-specific lineages within, for example, Actinobacteria, Chloroflexi and Gemmatimonadetes. This study shows the potential of RNA vs DNA comparisons based on the 16S rRNA gene to provide insights into the activity of sponge-associated microorganisms.
Superior Appetite Hormone Profile After Equivalent Weight Loss by Gastric Bypass Compared to Gastric Banding
Authors: Bose Mousumi , Machineni Sriram , Oliván Blanca , Teixeira Julio , McGinty James J. , Bawa Baani , Koshy Ninan , Colarusso Antonia , Laferrère Blandine
Published: January 2010

The goal of this study was to understand the mechanisms of greater weight loss by gastric bypass (GBP) compared to gastric banding (GB) surgery. Obese weight‐ and age‐matched subjects were studied before (T0), after a 12 kg weight loss (T1) by GBP (n = 11) or GB (n = 9), and at 1 year after surgery (T2). peptide YY3–36 (PYY3–36), ghrelin, glucagon‐like peptide‐1 (GLP‐1), leptin, and amylin were measured after an oral glucose challenge. At T1, glucose‐stimulated GLP‐1 and PYY levels increased significantly after GBP but not GB. Ghrelin levels did not change significantly after either surgery. In spite of equivalent weight loss, leptin and amylin decreased after GBP, but not after GB. At T2, weight loss was greater after GBP than GB (P = 0.003). GLP‐1, PYY, and amylin levels did not significantly change from T1 to T2; leptin levels continued to decrease after GBP, but not after GB at T2. Surprisingly, ghrelin area under the curve (AUC) increased 1 year after GBP (P = 0.03). These data show that, at equivalent weight loss, favorable GLP‐1 and PYY changes occur after GBP, but not GB, and could explain the difference in weight loss at 1 year. Mechanisms other than weight loss may explain changes of leptin and amylin after GBP.
Prepregnancy Obesity and Risk of Stillbirth in Viable Twin Gestations
Authors: Salihu Hamisu M. , Alio Amina P. , Belogolovkin Victoria , Aliyu Muktar H. , Wilson Ronee E. , Reddy Uma M. , Bruder Karen , Whiteman Valerie E.
Published: January 2010

We sought to estimate the impact of prepregnancy obesity on demise of one or both fetuses in twin gestations. We performed a retrospective cohort study using the Missouri maternally linked cohort files (years 1989–2005). Prepregnancy obesity was defined as a BMI ≥30. Outcomes of interest were stillbirth (intrauterine fetal death at ≥20 weeks' gestation) and demise of one (partial loss) or both (complete loss) fetuses, regardless of the cause. We used Cox Proportional Hazards with correction for intracluster correlation to obtain risk estimates. The overall stillbirth rate for twin gestations was 15.5/1,000 (18.4/1,000 vs. 14.5/1,000 in obese and normal weight mothers, respectively; P = 0.02). The rate for complete fetal loss was higher in obese mothers (8.3/1,000 vs. 5.6/1,000; P = 0.01) but was comparable for partial fetal loss (19.1/1,000 for obese vs. 16.3/1,000 for normal weight mothers; P = 0.1). Adjusted estimates confirmed these findings (adjusted hazards ratio (AHR) and 95% confidence interval (CI) = 1.31 (1.02–1.68) for stillbirth; AHR = 1.59; CI = 1.01–2.51) for complete loss; and AHR = 1.21; CI = 0.91–1.62) for partial loss. Subanalysis conducted on stillbirth showed that the risk associated with obesity was only elevated for same‐sex (AHR = 1.54; CI = 1.15–2.04) but not opposite‐sex twins (0.99; CI = 0.56–1.75). Our findings may find utility in counseling of obese women with twin gestations.
Long‐term Successful Weight Loss Improves Vascular Endothelial Function in Severely Obese Individuals
Authors: Bigornia Sherman J. , Mott Melanie M. , Hess Donald T. , Apovian Caroline M. , McDonnell Marie E. , Duess Mai‐Ann , Kluge Matthew A. , Fiscale Antonino J. , Vita Joseph A. , Gokce Noyan
Published: January 2010

Obesity is associated with increased cardiovascular risk. Although short‐term weight loss improves vascular endothelial function, longer term outcomes have not been widely investigated. We examined brachial artery endothelium‐dependent vasodilation and metabolic parameters in 29 severely obese subjects who lost ≥10% body weight (age 45 ± 13 years; BMI 48 ± 9 kg/m2) at baseline and after 12 months of dietary and/or surgical intervention. We compared these parameters to 14 obese individuals (age 49 ± 11 years; BMI 39 ± 7 kg/m2) who failed to lose weight. For the entire group, mean brachial artery flow‐mediated dilation (FMD) was impaired at 6.7 ± 4.1%. Following sustained weight loss, FMD increased significantly from 6.8 ± 4.2 to 10.0 ± 4.7%, but remained blunted in patients without weight decline from 6.5 ± 4.0 to 5.7 ± 4.1%, P = 0.013 by ANOVA. Endothelium‐independent, nitroglycerin‐mediated dilation (NMD) was unaltered. BMI fell by 13 ± 7 kg/m2 following successful weight intervention and was associated with reduced total and low‐density lipoprotein cholesterol, glucose, hemoglobin A1c, and high‐sensitivity C‐reactive protein (CRP). Vascular improvement correlated most strongly with glucose levels (r = −0.51, P = 0.002) and was independent of weight change. In this cohort of severely obese subjects, sustained weight loss at 1 year improved vascular function and metabolic parameters. The findings suggest that reversal of endothelial dysfunction and restoration of arterial homeostasis could potentially reduce cardiovascular risk. The results also demonstrate that metabolic changes in association with weight loss are stronger determinants of vascular phenotype than degree of weight reduction.
Development of an Arterio‐venous Difference Method to Study the Metabolic Physiology of the Femoral Adipose Tissue Depot
Authors: McQuaid Siobhán E. , Manolopoulos Konstantinos N. , Dennis A. Louise , Cheeseman Jane , Karpe Fredrik , Frayn Keith N.
Published: January 2010

Gluteofemoral adipose tissue (AT) has interesting positive associations with metabolic health, yet little is known of its metabolic physiology. Here, we describe a technique for cannulation of a vein draining the femoral fat depot. Using ultrasound guidance, a cannula was introduced into a superficial branch of the great saphenous vein. We also obtained arterialized blood and, for comparison, blood representing drainage from forearm muscle and from subcutaneous abdominal AT. We measured appropriate biomarkers of skeletal muscle (creatinine) and AT (nonesterified fatty acids (NEFAs), glycerol, leptin) drainage. Blood obtained in this way from the saphenous vein did not show creatinine release (creatinine concentration 100.5 ± 0.4%, mean ± s.e.m., of that in arterialized blood), whereas creatinine concentrations in blood draining forearm muscle averaged 121 ± 1% of those in arterialized blood. Fatty acid release from the tissue drained was suppressed after feeding and increased during β‐adrenergic stimulation. We also demonstrated leptin secretion. These findings suggest that blood so obtained is representative of AT drainage with little apparent contribution of skeletal muscle. We believe this technique will facilitate physiological studies of a lower‐body fat depot in humans.
Synthesis of sulfur-containing poly(thioester)s with high refractive indices and high Abbe numbers
Authors: You Nam-Ho , Higashihara Tomoya , Yasuo Suzuki , Ando Shinji , Ueda Mitsuru
Published: January 2010

New poly(thioester)s (PTE)s containing sulfide, alicyclic units in the polymer chains with high refractive indices (1.6149–1.6217) and high Abbe numbers (30.0–32.9) have been developed.
High-pressure crystal structures and superconductivity of Stannane (SnH
4
)
Authors: Gao Guoying , Oganov Artem R. , Li Peifang , Li Zhenwei , Wang Hui , Cui Tian , Ma Yanming , Bergara Aitor , Lyakhov Andriy O. , Iitaka Toshiaki , Zou Guangtian
Published: January 2010

There is great interest in the exploration of hydrogen-rich compounds upon strong compression where they can become superconductors. Stannane (SnH
4
) has been proposed to be a potential high-temperature superconductor under pressure, but its high-pressure crystal structures, fundamental for the understanding of superconductivity, remain unsolved. Using an ab initio evolutionary algorithm for crystal structure prediction, we propose the existence of two unique high-pressure metallic phases having space groups
Ama
2 and
P
6
3
/
mmc
, which both contain hexagonal layers of Sn atoms and semimolecular (perhydride) H
2
units. Enthalpy calculations reveal that the
Ama
2 and
P
6
3
/
mmc
structures are stable at 96–180 GPa and above 180 GPa, respectively, while below 96 GPa SnH
4
is unstable with respect to elemental decomposition. The application of the Allen-Dynes modified McMillan equation reveals high superconducting temperatures of 15–22 K for the
Ama
2 phase at 120 GPa and 52–62 K for the
P
6
3
/
mmc
phase at 200 GPa.
Metabolic remodeling of the human red blood cell membrane
Authors: Park YongKeun , Best Catherine A. , Auth Thorsten , Gov Nir S. , Safran Samuel A. , Popescu Gabriel , Suresh Subra , Feld Michael S.
Published: January 2010

The remarkable deformability of the human red blood cell (RBC) results from the coupled dynamic response of the phospholipid bilayer and the spectrin molecular network. Here we present quantitative connections between spectrin morphology and membrane fluctuations of human RBCs by using dynamic full-field laser interferometry techniques. We present conclusive evidence that the presence of adenosine 5′-triphosphate (ATP) facilitates non-equilibrium dynamic fluctuations in the RBC membrane that are highly correlated with the biconcave shape of RBCs. Spatial analysis of the fluctuations reveals that these non-equilibrium membrane vibrations are enhanced at the scale of spectrin mesh size. Our results indicate that the dynamic remodeling of the coupled membranes powered by ATP results in non-equilibrium membrane fluctuations manifesting from both metabolic and thermal energies and also maintains the biconcave shape of RBCs.
Percolative theories of strongly disordered ceramic high-temperature superconductors
Authors: Phillips J. C.
Published: January 2010

Optimally doped ceramic superconductors (cuprates, pnictides, etc.) exhibit transition temperaturesTcmuch larger than strongly coupled metallic superconductors like Pb (Tc = 7.2 K,Eg/kTc = 4.5) and exhibit many universal features that appear to contradict the Bardeen, Cooper, and Schrieffer theory of superconductivity based on attractive electron-phonon pairing interactions. These complex materials are strongly disordered and contain several competing nanophases that cannot be described effectively by parameterized Hamiltonian models, yet their phase diagrams also exhibit many universal features in both the normal and superconductive states. Here we review the rapidly growing body of experimental results that suggest that these anomalously universal features are the result of marginal stabilities of the ceramic electronic and lattice structures. These dual marginal stabilities favor both electronic percolation of a dopant network and rigidity percolation of the deformed lattice network. This “double percolation” model has previously explained many features of the normal-state transport properties of these materials and is the only theory that has successfully predicted strict lowest upper bounds forTcin the cuprate and pnictide families. Here it is extended to include Coulomb correlations and percolative band narrowing, as well as an angular energy gap equation, which rationalizes angularly averaged gap/Tcratios, and shows that these are similar to those of conventional strongly coupled superconductors.
Glycolipid Trafficking inDrosophilaUndergoes Pathway Switching in Response to Aberrant Cholesterol Levels
Authors: Hortsch Ralf , Lee Esther , Erathodiyil Nandanan , Hebbar Sarita , Steinert Steffen , Lee Jun Yu , Chua Doreen See Kin , Kraut Rachel
Published: January 2010

In lipid storage diseases, the intracellular trafficking of sphingolipids is altered by conditions of aberrant cholesterol accumulation. Drosophila has been used recently to model lipid storage diseases, but the effects of sterol accumulation on sphingolipid trafficking are not known in the fly, and the trafficking of sphingolipids in general has not been studied in this model organism. Here, we examined the uptake and intracellular distribution of a fluorescent glycolipid analog, BODIPY-lactosyl-ceramide, in Drosophila neurons. The uptake mechanism and intracellular trafficking route of this simple glycolipid are largely conserved. Our principle finding is that cholesterol steers trafficking of the glycolipid between Golgi, lysosome, and recycling compartments. Our analyses support the idea that cholesterol storage in Drosophila triggers a switch in glycolipid trafficking from the biosynthetic to the degradative endolysosomal pathway, whereas cholesterol depletion eliminates recycling of the glycolipid. Unexpectedly, we observe a novel phenomenon we term “hijacking,” whereby lactosyl-ceramide diverts the trafficking pathway of an endocytic cargo, dextran, completely away from its lysosomal target. This work establishes that glycolipid trafficking in Drosophila undergoes changes similar to those seen in mammalian cells under conditions of cholesterol storage and therefore validates Drosophila as a suitable model organism in which to study lipid storage diseases.
Structural Mutants of the Spindle Pole Body Cause Distinct Alteration of Cytoplasmic Microtubules and Nuclear Dynamics in Multinucleated Hyphae
Authors: Lang Claudia , Grava Sandrine , Finlayson Mark , Trimble Rhonda , Philippsen Peter , Jaspersen Sue L.
Published: January 2010

In the multinucleate fungus Ashbya gossypii, cytoplasmic microtubules (cMTs) emerge from the spindle pole body outer plaque (OP) in perpendicular and tangential directions. To elucidate the role of cMTs in forward/backward movements (oscillations) and bypassing of nuclei, we constructed mutants potentially affecting cMT nucleation or stability. Hyphae lacking the OP components AgSpc72, AgNud1, AgCnm67, or the microtubule-stabilizing factor AgStu2 grew like wild- type but showed substantial alterations in the number, length, and/or nucleation sites of cMTs. These mutants differently influenced nuclear oscillation and bypassing. In Agspc72Δ, only long cMTs were observed, which emanate tangentially from reduced OPs; nuclei mainly moved with the cytoplasmic stream but some performed rapid bypassing. Agnud1Δ and Agcnm67Δ lack OPs; short and long cMTs emerged from the spindle pole body bridge/half-bridge structures, explaining nuclear oscillation and bypassing in these mutants. In Agstu2Δ only very short cMTs emanated from structurally intact OPs; all nuclei moved with the cytoplasmic stream. Therefore, long tangential cMTs promote nuclear bypassing and short cMTs are important for nuclear oscillation. Our electron microscopy ultrastructural analysis also indicated that assembly of the OP occurs in a stepwise manner, starting with AgCnm67, followed by AgNud1 and lastly AgSpc72.
Essential Role of the p110β Subunit of Phosphoinositide 3-OH Kinase in Male Fertility
Authors: Ciraolo Elisa , Morello Fulvio , Hobbs Robin M. , Wolf Frieder , Marone Romina , Iezzi Manuela , Lu Xiaoyun , Mengozzi Giulio , Altruda Fiorella , Sorba Giovanni , Guan Kaomei , Pandolfi Pier Paolo , Wymann Matthias P. , Hirsch Emilio
Published: January 2010

Phosphoinositide 3-kinases (PI3K) are key molecular players in male fertility. However, the specific roles of different p110 PI3K catalytic subunits within the spermatogenic lineage have not been characterized so far. Herein, we report that male mice expressing a catalytically inactive p110β develop testicular hypotrophy and impaired spermatogenesis, leading to a phenotype of oligo-azoospermia and defective fertility. The examination of testes from p110β-defective tubules demonstrates a widespread loss in spermatogenic cells, due to defective proliferation and survival of pre- and postmeiotic cells. In particular, p110β is crucially needed in c-Kit–mediated spermatogonial expansion, as c-Kit–positive cells are lost in the adult testis and activation of Akt by SCF is blocked by a p110β inhibitor. These data establish that activation of the p110β PI3K isoform by c-Kit is required during spermatogenesis, thus opening the way to new treatments for c-Kit positive testicular cancers.
Disambiguating the species of biomedical named entities using natural language parsers
Authors: Wang Xinglong , Tsujii Jun'ichi , Ananiadou Sophia
Published: January 2010

Motivation: Text mining technologies have been shown to reduce the laborious work involved in organizing the vast amount of information hidden in the literature. One challenge in text mining is linking ambiguous word forms to unambiguous biological concepts. This article reports on a comprehensive study on resolving the ambiguity in mentions of biomedical named entities with respect to model organisms and presents an array of approaches, with focus on methods utilizing natural language parsers.

Results: We build a corpus for organism disambiguation where every occurrence of protein/gene entity is manually tagged with a species ID, and evaluate a number of methods on it. Promising results are obtained by training a machine learning model on syntactic parse trees, which is then used to decide whether an entity belongs to the model organism denoted by a neighbouring species-indicating word (e.g. yeast). The parser-based approaches are also compared with a supervised classification method and results indicate that the former are a more favorable choice when domain portability is of concern. The best overall performance is obtained by combining the strengths of syntactic features and supervised classification.

Availability: The corpus and demo are available at http://www.nactem.ac.uk/deca_details/start.cgi, and the software is freely available as U-Compare components (Kano et al., 2009): NaCTeM Species Word Detector and NaCTeM Species Disambiguator. U-Compare is available at http://-compare.org/

Contact:  xinglong.wang@manchester.ac.uk
The good(ish), the bad, and the ugly: a tripartite classification of ecosystem trends
Authors: Bundy Alida , Shannon Lynne J. , Rochet Marie-Joëlle , Neira Sergio , Shin Yunne-Jai , Hill Louize , Aydin Kerim
Published: January 2010

Bundy, A., Shannon, L. J., Rochet, M-J., Neira, S., Shin, Y-J., Hill, L., and Aydin, K. 2010. The good(ish), the bad, and the ugly: a tripartite classification of ecosystem trends. – ICES Journal of Marine Science, 67: 745–768. Marine ecosystems have been exploited for a long time, growing increasingly vulnerable to collapse and irreversible change. How do we know when an ecosystem may be in danger? A measure of the status of individual stocks is only a partial gauge of its status, and does not include changes at the broader ecosystem level, to non-commercial species or to its structure or functioning. Six ecosystem indicators measuring trends over time were collated for 19 ecosystems, corresponding to four ecological attributes: resource potential, ecosystem structure and functioning, conservation of functional biodiversity, and ecosystem stability and resistance to perturbations. We explored the use of a decision-tree approach, a definition of initial ecosystem state (impacted or non-impacted), and the trends in the ecosystem indicators to classify the ecosystems into improving, stationary, and deteriorating. Ecosystem experts classified all ecosystems as impacted at the time of their initial state. Of these, 15 were diagnosed as “ugly”, because they had deteriorated from an already impacted state. Several also exhibited specific combinations of trends indicating “fishing down the foodweb”, reduction in size structure, reduction in diversity and stability, and changed productivity. The classification provides an initial evaluation for scientists, resource managers, stakeholders, and the general public of the concerning status of ecosystems globally.
Systemic Colonization of Potato Plants by a Soilborne, Green Fluorescent Protein-Tagged Strain of Dickeya sp. Biovar 3
Authors: Czajkowski Robert , de Boer Waldo J. , Velvis Henk , van der Wolf Jan M.
Published: January 2010

Colonization of potato plants by soilborne, green fluorescent protein (GFP)-tagged Dickeya sp. IPO2254 was investigated by selective plating, epifluorescence stereo microscopy (ESM), and confocal laser scanning microscopy (CLSM). Replicated experiments were carried out in a greenhouse using plants with an intact root system and plants from which ca. 30% of the lateral roots was removed. One day after soil inoculation, adherence of the pathogen on the roots and the internal colonization of the plants were detected using ESM and CLSM of plant parts embedded in an agar medium. Fifteen days post-soil inoculation, Dickeya sp. was found on average inside 42% of the roots, 13% of the stems, and 13% of the stolons in plants with undamaged roots. At the same time-point, in plants with damaged roots, Dickeya sp. was found inside 50% of the roots, 25% of the stems, and 25% of the stolons. Thirty days postinoculation, some plants showed true blackleg symptoms. In roots, Dickeya sp. was detected in parenchyma cells of the cortex, both inter- and intracellularly. In stems, bacteria were found in xylem vessels and in protoxylem cells. Microscopical observations were confirmed by dilution spread-plating the plant extracts onto agar medium directly after harvest. The implications of infection from soilborne inoculum are discussed.
Moonlight avoidance in gerbils reveals a sophisticated interplay among time allocation, vigilance and state-dependent foraging
Authors: Kotler Burt P. , Brown Joel , Mukherjee Shomen , Berger-Tal Oded , Bouskila Amos
Published: January 2010

Foraging animals have several tools for managing the risk of predation, and the foraging games between them and their predators. Among these, time allocation is foremost, followed by vigilance and apprehension. Together, their use influences a forager's time allocation and giving-up density (GUD) in depletable resource patches. We examined Allenby's gerbils (
Gerbilus andersoni allenbyi
) exploiting seed resource patches in a large vivarium under varying moon phases in the presence of a red fox (
Vulpes vulpes
). We measured time allocated to foraging patches electronically and GUDs from seeds left behind in resource patches. From these, we estimated handling times, attack rates and quitting harvest rates (QHRs). Gerbils displayed greater vigilance (lower attack rates) at brighter moon phases (full < wane < wax < new). Similarly, they displayed higher GUDs at brighter moon phases (wax > full > new > wane). Finally, gerbils displayed higher QHRs at new and waxing moon phases. Differences across moon phases not only reflect changing time allocation and vigilance, but changes in the state of the foragers and their marginal value of energy. Early in the lunar cycle, gerbils rely on vigilance and sacrifice state to avoid risk; later they defend state at the cost of increased time allocation; finally their state can recover as safe opportunities expand. In the predator–prey foraging game, foxes may contribute to these patterns of behaviours by modulating their own activity in response to the opportunities presented in each moon phase.
The direct effects of increasing CO
2
and temperature on non-calcifying organisms: increasing the potential for phase shifts in kelp forests
Authors: Connell Sean D. , Russell Bayden D.
Published: January 2010

Predictions about the ecological consequences of oceanic uptake of CO
2
have been preoccupied with the effects of ocean acidification on calcifying organisms, particularly those critical to the formation of habitats (e.g. coral reefs) or their maintenance (e.g. grazing echinoderms). This focus overlooks the direct effects of CO
2
on non-calcareous taxa, particularly those that play critical roles in ecosystem shifts. We used two experiments to investigate whether increased CO
2
could exacerbate kelp loss by facilitating non-calcareous algae that, we hypothesized, (i) inhibit the recovery of kelp forests on an urbanized coast, and (ii) form more extensive covers and greater biomass under moderate future CO
2
and associated temperature increases. Our experimental removal of turfs from a phase-shifted system (i.e. kelp- to turf-dominated) revealed that the number of kelp recruits increased, thereby indicating that turfs can inhibit kelp recruitment. Future CO
2
and temperature interacted synergistically to have a positive effect on the abundance of algal turfs, whereby they had twice the biomass and occupied over four times more available space than under current conditions. We suggest that the current preoccupation with the negative effects of ocean acidification on marine calcifiers overlooks potentially profound effects of increasing CO
2
and temperature on non-calcifying organisms.
Learning your own strength: winner and loser effects should change with age and experience
Authors: Fawcett Tim W. , Johnstone Rufus A.
Published: January 2010

Winner and loser effects, in which the outcome of an aggressive encounter influences the tendency to escalate future conflicts, have been documented in many taxa, but we have limited understanding of why they have evolved. One possibility is that individuals use previous victories and defeats to assess their fighting ability relative to others. We explored this idea by modelling a population of strong and weak individuals that do not know their own strength, but keep track of how many fights they have won. Under these conditions, adaptive behaviour generates clear winner and loser effects: individuals who win fights should escalate subsequent conflicts, whereas those who lose should retreat from aggressive opponents. But these effects depend strongly on age and experience. Young, naive individuals should show highly aggressive behaviour and pronounced loser effects. For these inexperienced individuals, fighting is especially profitable because it yields valuable information about their strength. Aggression should then decline as an individual ages and gains experience, with those who lose fights becoming more submissive. Older individuals, who have a better idea of their own strength, should be more strongly influenced by victories than losses. In conclusion, we predict that both aggressiveness and the relative magnitude of winner and loser effects should change with age, owing to changes in how individuals perceive their own strength.
Chloroplastic Phosphoadenosine Phosphosulfate Metabolism Regulates Basal Levels of the Prohormone Jasmonic Acid in Arabidopsis Leaves
Authors: Rodríguez Víctor M. , Chételat Aurore , Majcherczyk Paul , Farmer Edward E.
Published: January 2010

Levels of the enzymes that produce wound response mediators have to be controlled tightly in unwounded tissues. The Arabidopsis (Arabidopsis thaliana) fatty acid oxygenation up-regulated8 (fou8) mutant catalyzes high rates of α -linolenic acid oxygenation and has higher than wild-type levels of the α -linolenic acid-derived wound response mediator jasmonic acid (JA) in undamaged leaves. fou8 produces a null allele in the gene SAL1 (also known as FIERY1 or FRY1). Overexpression of the wild-type gene product had the opposite effect of the null allele, suggesting a regulatory role of SAL1 acting in JA synthesis. The biochemical phenotypes in fou8 were complemented when the yeast (Saccharomyces cerevisiae) sulfur metabolism 3′(2′), 5′-bisphosphate nucleotidase MET22 was targeted to chloroplasts in fou8. The data are consistent with a role of SAL1 in the chloroplast-localized dephosphorylation of 3′-phospho-5′-adenosine phosphosulfate to 5′-adenosine phosphosulfate or in a closely related reaction (e.g. 3′,5′-bisphosphate dephosphorylation). Furthermore, the fou8 phenotype was genetically suppressed in a triple mutant (fou8 apk1 apk2) affecting chloroplastic 3′-phospho-5′-adenosine phosphosulfate synthesis. These results show that a nucleotide component of the sulfur futile cycle regulates early steps of JA production and basal JA levels.
Molecular immunology lessons from therapeutic T‐cell receptor gene transfer
Authors: Thomas Sharyn , Stauss Hans J. , Morris Emma C.
Published: January 2010

The T‐cell receptor (TCR) is critical for T‐cell lineage selection, antigen specificity, effector function and survival. Recently, TCR gene transfer has been developed as a reliable method to generate ex vivo large numbers of T cells of a given antigen‐specificity and functional avidity. Such approaches have major applications for the adoptive cellular therapy of viral infectious diseases, virus‐associated malignancies and cancer. TCR gene transfer utilizes retroviral or lentiviral constructs containing the gene sequences of the TCR‐α and TCR‐β chains, which have been cloned from a clonal T‐cell population of the desired antigen specificity. The TCR‐encoding vector is then used to infect (transduce) primary T cells in vitro. To generate a transduced T cell with the desired functional specificity, the introduced TCR‐α and TCR‐β chains must form a heterodimer and associate with the CD3 complex in order to be stably expressed at the T‐cell surface. In order to optimize the function of TCR‐transduced T cells, researchers in the field of TCR gene transfer have exploited many aspects of basic research in T‐cell immunology relating to TCR structure, TCR–CD3 assembly, cell‐surface TCR expression, TCR‐peptide/major histocompatibility complex (MHC) affinity and TCR signalling. However, improving the introduction of exogenous TCRs into naturally occurring T cells has provided further insights into basic T‐cell immunology. The aim of this review was to discuss the molecular immunology lessons learnt through therapeutic TCR transfer.
TEM investigation of ductile iron alloyed with vanadium
Authors: DYMEK S. , BLICHARSKI M. , MORGIEL J. , FRAŚ E.
Published: January 2010

This article presents results of the processing and microstructure evolution of ductile cast iron, modified by an addition of vanadium. The ductile iron was austenitized closed to the solidus (1095°C) for 100 h, cooled down to 640°C and held on at this temperature for 16 h. The heat treatment led to the dissolution of primary vanadium‐rich carbides and their subsequent re‐precipitation in a more dispersed form. The result of mechanical tests indicated that addition of vanadium and an appropriate heat treatment makes age hardening of ductile iron feasible. The precipitation processes as well as the effect of Si content on the alloy microstructure were examined by scanning and transmission electron microscopy. It was shown that adjacent to uniformly spread out vanadium‐rich carbides with an average size of 50 nm, a dispersoid composed of extremely small ∼1 nm precipitates was also revealed.