bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clean Sweep: Informed Trading through Intermarket Sweep Orders
Authors: Chakravarty Sugato , Jain Pankaj , Upson James , Wood Robert 
Published: January 2012

AbstractAn intermarket sweep order (ISO) is a limit order that automatically executes in a designated market center even if another market center is publishing a better quotation. An investor submitting an ISO must satisfy order protection rules by concurrently submitting orders to the markets with better prices. We find that ISOs represent 46% of trades and 41% of volume in our sample. ISO trades have a significantly larger information share despite their small trade size relative to non-ISO trades. Post trade return analysis suggests that informed institutions are the main users of ISO trades.
A Transmission Electron Microscopy Study of the Effect of Interfaces on Bubble Formation in He-Implanted Cu-Nb Multilayers
Authors: Bhattacharyya D. , Demkowicz M.J. , Wang Y.-Q. , Baumer R.E. , Nastasi M. , Misra A. 
Published: January 2012

AbstractMagnetron sputtered thin films of Cu, Nb, and Cu-Nb multilayers with 2.5 and 5 nm nominal layer thickness were deposited on Si and implanted with 4He+ and 3He+ ions. Secondary ion mass spectroscopy and nuclear reaction analysis, respectively, were used to measure the 4He+ and 3He+ concentration profile with depth inside the films. Cross-sectional transmission electron microscopy was used to characterize the helium bubbles. Analysis of the contrast from helium bubbles in defocused transmission electron microscope images showed a minimum bubble diameter of 1.25 nm. While pure Cu and Nb films showed bubble contrast over the entire range of helium implantation, the multilayers exhibited bubbles only above a critical He concentration that increased almost linearly with decreasing layer thickness. The work shows that large amounts of helium can be trapped at incoherent interfaces in the form of stable, nanometer-size bubbles.
Phase Contrast Synchrotron Microtomography: Improving Noninvasive Investigations of Fossil Embryos In Ovo
Authors: Fernandez Vincent , Buffetaut Eric , Maire Eric , Adrien Jérôme , Suteethorn Varavudh , Tafforeau Paul 
Published: January 2012

AbstractFossil embryos are paramount for our understanding of the development of extinct species. However, although thousands of fossil amniote eggs are known, very few embryos in ovo have been described. First reports of fossil embryos were based on broken eggs, where the embryonic remains were already exposed, because destructive methods on complete eggs were avoided. Investigations of complete eggs therefore required nondestructive approaches, such as X-ray microtomography (μCT). However, due to the general low density contrast between fossilized bones and infilling matrix, only a few specimens have been reported using these techniques. Using propagation phase contrast X-ray synchrotron microtomography (PPC-SR-μCT), we report here the discovery of three well-preserved embryos in Early Cretaceous eggs from Thailand. By scanning these eggs using different imaging techniques, we show that vastly different interpretations can be made regarding the preservation state and/or the developmental stage of these embryos. PPC-SR-μCT also revealed differential contrast between bone categories, presumably reflecting the ossification pattern of these embryos. Applying such an approach to large-scale studies of fossil eggs could lead to more discoveries and detailed studies of fossil embryos, providing important developmental and phylogenetic information on extinct and extant amniotes.
Examination of a Polycrystalline Thin-Film Model to Explore the Relation between Probe Size and Structural Correlation Length in Fluctuation Electron Microscopy
Authors: Treacy M.M.J. , Gibson J.M. 
Published: January 2012

AbstractWe examine simulated electron microdiffraction patterns from models of thin polycrystalline silicon. The models are made by a Voronoi tessellation of random points in a box. The Voronoi domains are randomly selected to contain either a randomly-oriented cubic crystalline grain or a region of continuous random network material. The microdiffraction simulations from coherent probes of different widths are computed at the ideal kinematical limit, ignoring inelastic and multiple scattering. By examining the normalized intensity variance that is obtained in fluctuation electron microscopy experiments, we confirm that intensity fluctuations increase monotonically with the percentage of crystalline grains in the material. However, anomalously high variance is observed for models that have 100% crystalline grains with no imperfections. We confirm that the reduced normalized variance,V(k,R) − 1, that is associated with four-body correlations at scattering vectork, varies inversely with specimen thickness. Further, for probe sizesRlarger than the mean grain size, we confirm that the reduced normalized variance obeys the predicted form given by Gibson et al. [Ultramicroscopy,83, 169–178 (2000)] for the kinematical coherent scattering limit.
Improving Accuracy and Precision of Strain Analysis by Energy-Filtered Nanobeam Electron Diffraction
Authors: Hähnel Angelika , Reiche Manfred , Moutanabbir Oussama , Blumtritt Horst , Geisler Holm , Höntschel Jan , Engelmann Hans-Jürgen 
Published: January 2012

AbstractThis article deals with uncertainty in the analysis of strain in silicon nanoscale structures and devices using nanobeam electron diffraction (NBED). Specimen and instrument related errors and instabilities and their effects on NBED analysis are addressed using a nanopatterned ultrathin strained silicon layer directly on oxide as a model system. We demonstrate that zero-loss filtering significantly improves the NBED precision by decreasing the diffuse background in the diffraction patterns. To minimize the systematic deviations the acquired data were verified through a reliability test and then calibrated. Furthermore, the effect of strain relaxation by specimen preparation using a FIB is estimated by comparing profiles, which were acquired by analyzing slices of strained structures in a 220-nm-thick region of the sample (invasive preparation) and the entire strained nanostructures, which are embedded in a thicker region of the same sample (noninvasive preparation). Together with the random deviation, the corresponding systematic shift results in a total deviation of ∼1 × 10−3for NBED analyses, which is employed to estimate the measurement uncertainty in the thinner sample region. In contrast, the strain in the thick sample region is not affected by the preparation; the systematic shift reduces to a minimum, which improves the total deviation by ∼50%.
The Glomerular Basement Membrane as a Model System to Study the Bioactivity of Heparan Sulfate Glycosaminoglycans
Authors: McCarthy Kevin J. , Wassenhove-McCarthy Deborah J. 
Published: January 2012

AbstractThe glomerular basement membrane and its associated cells are critical elements in the renal ultrafiltration process. Traditionally the anionic charge associated with several carbohydrate moieties in the glomerular basement membrane are thought to form a charge selective barrier that restricts the transmembrane flux of anionic proteins across the glomerular basement membrane into the urinary space. The charge selective function, along with the size selective component of the basement membrane, serves to limit the efflux of plasma proteins from the capillary lumen. Heparan sulfate glycosaminoglycans are anionically charged carbohydrate structures attached to proteoglycan core proteins and have a role in establishing the charge selective function of the glomerular basement membrane. Although there are a large number of studies in the literature that support this concept, the results of several recent studies using molecular genetic approaches to minimize the anionic charge of the glomerular basement membrane would suggest that the role of heparan sulfate glycosaminoglycans in the glomerular capillary wall are still not yet entirely resolved, suggesting that this research area still requires new and novel exploration.
Quantitative Mineralogical Properties (Morphology-Chemistry-Structure) of Pharmaceutical Grade Kaolinites and Recommendations to Regulatory Agencies
Authors: Dogan Meral , Dogan A. Umran , Aburub Aktham , Botha Alta , Wurster Dale Eric 
Published: January 2012

AbstractThe physical and chemical characteristics of kaolinite (kaolin) may be variable, and minor amounts of other clay minerals, nonclay minerals, and other impurities may affect the properties of kaolinites. Thus specific technical properties of pharmaceutical grade kaolinites become very important because these clays are used in medical applications, e.g., as pharmaceutical excipients, and will be consumed by humans. Seven pharmaceutical grade kaolinite specimens were used in this study: K1004, KA105, 2242-01, K2-500, Acros, Acros-mono, and KX0007-1. In addition, two kaolinites from the Clay Minerals Society Source Clays, KGa-1b and KGa-2, were used for comparison purposes. The Acros-mono and 2242-01 kaolinites contained minor amounts of illite, which was demonstrated both compositionally and structurally by using inductively coupled plasma spectroscopy and powder X-ray diffraction. The KX0007-1 kaolinite powder was found to be heavily contaminated with quartz, cristobalite, and alunite. Crystal structure computations also showed excess Si in its tetrahedral site, and the mineral no longer has the typical kaolinite crystal structure. These widely-used industrial standards should be quantitatively characterized morphologically, compositionally, and structurally. Results of the mineralogical characteristics should be clearly labeled on the pharmaceutical grade kaolinites and reported to the relevant regulatory agencies.
SED-ML: Nested Simulation Proposal
Authors: Bergmann Frank 
Published: January 2012

AbstractThis document describes a second version of the proposal for nested simulation experiments for SED-ML (http://sed-ml.org). The proposal has been updated to include the feedback received in the meantime and has been enhanced by examples. A full implementation is available with libSedML (http://libsedml.sf.net) and the SED-ML Web Tools (http://sysbioapps.dyndns.org/SED-ML_Web_Tools/)
Efficient coupling of ATP hydrolysis to translocation by RecQ helicase
Authors: Rad Behzad , Kowalczykowski Stephen C. 
Published: January 2012

Helicases are ubiquitous enzymes that unwind double-stranded DNA (dsDNA) to reveal single-stranded DNA (ssDNA) during essential processes such as replication, transcription, or repair. TheEscherichia coliRecQ protein is a 3′ to 5′ helicase, which functions in the processes of homologous recombination and replication fork restart. Here, we analyzed the relationship between ATP hydrolysis by RecQ and its translocation on ssDNA. We monitored a single round of RecQ translocation on ssDNA by measuring the rates of inorganic phosphate release during translocation, and the dissociation of RecQ from ssDNA. We find that RecQ translocates with a rate of 16( ± 4) nucleotides/s and moves on average only 36( ± 2) nucleotides before dissociating. Fitting to an n-step kinetic model suggests that the helicase displays a nonuniform translocation mechanism in which it moves approximately five nucleotides rapidly before undergoing a rate-limiting kinetic slow step. Unexpectedly, RecQ requires a length of 34( ± 3) nucleotides to bind and translocate on ssDNA. This large site size suggests that several monomers are required to bind DNA prior to translocation. Energetically, the RecQ helicase couples the hydrolysis of one ATP molecule to the translocation of more than one nucleotide (1.6 ± 0.3). Thus, our data show that RecQ translocates on ssDNA by efficiently coupling the hydrolysis of one ATP molecule into structural alterations that result in movement of approximately two nucleotides, presumably by an inchworm mechanism. These attributes are consistent with the function of RecQ in recombination and replication.
Budesonide Use in Pediatric Crohn Disease
Authors: Otley Anthony , LeLeiko Neal , Langton Christine , Lerer Trudy , Mack David , Evans Jonathan , Pfefferkorn Marian , Carvalho Ryan , Rosh Joel , Griffiths Anne , Oliva‐Hemker Maria , Kay Marsha , Bousvaros Athos , Stephens Michael , Samson Charles , Grossman Andrew , Keljo David , Markowitz James , Hyams Jeffrey ,   Pediatric IBD Collaborative Research Group
Published: January 2012

ABSTRACTBackground and Aim:Budesonide (BUD) is being used in pediatric Crohn disease (CD) because it is believed to have the potential to reduce corticosteroid‐related toxicity; however, few data are available describing its use. The aim of the present study was to describe BUD use in an inception cohort of pediatric patients with CD.Methods:Data were derived from the prospective Pediatric IBD Collaborative Research Group Registry established in 2002 in North America. Use of BUD in children with CD was examined.Results:BUD was used in 119 of 932 (13%) of children with newly diagnosed CD, with 56 of 119 (47%) starting BUD ≤30 days of diagnosis (26/56 with ileum and/or ascending colon [IAC] disease). BUD was used as monotherapy (9%), in combination with 5‐aminosalicylates (77%), or in combination with immunomodulators (43%). Forty‐three percent (24/56) went on to receive conventional corticosteroid at some point following their first BUD course. For the 63 of 119 (53%) who started BUD beyond the diagnosis period, 51 of 63 (81%) also received prednisone, with BUD used as a means of weaning from prednisone in 17 of 63 (27%). Patients with IAC disease who received BUD ≤30 days of diagnosis were just as likely to have received conventional corticosteroids by 1 year as were those who did not receive BUD ≤30 days of diagnosis. Two‐thirds (77/119) of patients received BUD for ≤6 months.Conclusions:BUD is being used among pediatric patients newly diagnosed as having CD, although the majority does not have disease limited to the IAC. BUD monotherapy was rare, and further data are required to better define the role of BUD in the treatment of pediatric CD.
The TGB1 Movement Protein ofPotato virus XReorganizes Actin and Endomembranes into the X-Body, a Viral Replication Factory
Authors: Tilsner Jens , Linnik Olga , Wright Kathryn M. , Bell Karen , Roberts Alison G. , Lacomme Christophe , Santa Cruz Simon , Oparka Karl J. 
Published: January 2012

AbstractPotato virus X (PVX) requires three virally encoded proteins, the triple gene block (TGB), for movement between cells. TGB1 is a multifunctional protein that suppresses host gene silencing and moves from cell to cell through plasmodesmata, while TGB2 and TGB3 are membrane-spanning proteins associated with endoplasmic reticulum-derived granular vesicles. Here, we show that TGB1 organizes the PVX “X-body,” a virally induced inclusion structure, by remodeling host actin and endomembranes (endoplasmic reticulum and Golgi). Within the X-body, TGB1 forms helically arranged aggregates surrounded by a reservoir of the recruited host endomembranes. The TGB2/3 proteins reside in granular vesicles within this reservoir, in the same region as nonencapsidated viral RNA, while encapsidated virions accumulate at the outer (cytoplasmic) face of the X-body, which comprises a highly organized virus “factory.” TGB1 is both necessary and sufficient to remodel host actin and endomembranes and to recruit TGB2/3 to the X-body, thus emerging as the central orchestrator of the X-body. Our results indicate that the actin/endomembrane-reorganizing properties of TGB1 function to compartmentalize the viral gene products of PVX infection.
Rhizobial and Fungal Symbioses Show Different Requirements for Calmodulin Binding to Calcium Calmodulin–Dependent Protein Kinase in Lotus japonicus
Authors: Shimoda Yoshikazu , Han Lu , Yamazaki Toshimasa , Suzuki Rintaro , Hayashi Makoto , Imaizumi-Anraku Haruko 
Published: January 2012

Abstract
Ca2+/calmodulin (CaM)–dependent protein kinase (CCaMK) is a key regulator of root nodule and arbuscular mycorrhizal symbioses and is believed to be a decoder for Ca2+ signals induced by microbial symbionts. However, it is unclear how CCaMK is activated by these microbes. Here, we investigated in vivo activation of CCaMK in symbiotic signaling, focusing mainly on the significance of and epistatic relationships among functional domains of CCaMK. Loss-of-function mutations in EF-hand motifs revealed the critical importance of the third EF hand for CCaMK activation to promote infection of endosymbionts. However, a gain-of-function mutation (T265D) in the kinase domain compensated for these loss-of-function mutations in the EF hands. Mutation of the CaM binding domain abolished CaM binding and suppressed CCaMKT265D activity in rhizobial infection, but not in mycorrhization, indicating that the requirement for CaM binding to CCaMK differs between root nodule and arbuscular mycorrhizal symbioses. Homology modeling and mutagenesis studies showed that the hydrogen bond network including Thr265 has an important role in the regulation of CCaMK. Based on these genetic, biochemical, and structural studies, we propose an activation mechanism of CCaMK in which root nodule and arbuscular mycorrhizal symbioses are distinguished by differential regulation of CCaMK by CaM binding.
Leaf-Induced Gibberellin Signaling Is Essential for Internode Elongation, Cambial Activity, and Fiber Differentiation in Tobacco Stems
Authors: Dayan Jonathan , Voronin Nickolay , Gong Fan , Sun Tai-ping , Hedden Peter , Fromm Hillel , Aloni Roni 
Published: January 2012

AbstractThe gibberellins (GAs) are a group of endogenous compounds that promote the growth of most plant organs, including stem internodes. We show that in tobacco (Nicotiana tabacum) the presence of leaves is essential for the accumulation of bioactive GAs and their immediate precursors in the stem and consequently for normal stem elongation, cambial proliferation, and xylem fiber differentiation. These processes do not occur in the absence of maturing leaves but can be restored by application of C19-GAs, identifying the presence of leaves as a requirement for GA signaling in stems and revealing the fundamental role of GAs in secondary growth regulation. The use of reporter genes for GA activity and GA-directed DELLA protein degradation in Arabidopsis thaliana confirms the presence of a mobile signal from leaves to the stem that induces GA signaling.
Cognitive and subjective effects of mephedrone and factors influencing use of a ‘new legal high’
Authors: Freeman Tom P. , Morgan Celia J. A. , Vaughn‐Jones James , Hussain Nahida , Karimi Kash , Curran H. Valerie 
Published: January 2012

ABSTRACTAims  Use of the stimulant drug mephedrone increased dramatically in 2009, and it is still available in the United Kingdom after being controlled in April 2010. This study aimed to assess mephedrone's acute cognitive and subjective effects.Design  A mixed within‐ and between‐subjects design compared 20 mephedrone users, first while intoxicated (T1) and secondly drug free (T2); and 20 controls twice when drug free (T1 and T2).Settings  Participants' own homes.Participants  Healthy adults recruited from the community.Measurements  Subjective effects, episodic and working memory, phonological and semantic fluency, psychomotor speed and executive control at were assessed at T1 and T2. Trait schizotypy, depression, changes in mephedrone use since the ban and attitudes influencing use of a hypothetical new legal high were indexed at T2 only.Findings  Compared with controls, mephedrone users had generally impaired prose recall (P = 0.037) and higher scores in schizotypy (P < 0.001) and depression (P = 0.01). Mephedrone acutely primed a marked ‘wanting’ for the drug (P < 0.001), induced stimulant‐like effects, impaired working memory (P < 0.001) and enhanced psychomotor speed (P = 0.024). Impulsivity in mephedrone users correlated with the number of hours in an average (nearly 8 hour) mephedrone session (r = 0.6). Users would be drawn to use a new legal high if it were pure, had no long/short term harms, and was positively rated by friends or on the internet.Conclusions  Mephedrone impairs working memory acutely, induces stimulant‐like effects in users and is associated with binge use. Factors that influence users' attitudes to new drugs might help to predict future trends in use of the many new psychoactive substances emerging on the internet.
C‐reactive protein, an indicator for maintained response or remission to infliximab in patients with Crohn's disease: a post‐hoc analysis from ACCENT I
Authors: Reinisch W. , Wang Y. , Oddens B. J. , Link R. 
Published: January 2012

SummaryBackgroundSecondary loss of response to anti‐TNF‐α therapy is observed in Crohn's disease patients.AimSerum C‐reactive protein (CRP) levels at baseline and after infliximab induction therapy at week 14 were assessed as predictors for maintained response or remission through 54 weeks of treatment in patients with Crohn's disease who responded to induction therapy.MethodsACCENT I was a multicenter, randomised, placebo‐controlled study. Patients who received infliximab induction (weeks 0, 2 and 6) and maintenance (5 or 10 mg/kg every 8 weeks beginning at week 14) therapy were considered. Patients in clinical response or remission to induction therapy at week 14 (n = 212 or n = 138 respectively) were analysed. Associations between CRP levels (cut‐off points 0.5–3.0 mg/dL), baseline disease variables and maintained clinical response or remission during maintenance therapy were assessed.ResultsA significant association was observed between baseline CRP levels and maintained remission. Forty‐five percent of patients with baseline CRP ≥ 0.7 mg/dL vs. 22.0% with CRP < 0.7 mg/dL maintained remission (P = 0.012). CRP normalisation during infliximab treatment (decrease from 0.5 mg/dL at baseline to < 0.5 mg/dL at week 14) resulted in higher probability of maintained response (P < 0.001) or remission (P = 0.052). At week 14 low CRP levels were associated with maintained response (56.6% of patients with CRP < 0.5 mg/dL vs. 37.2% with higher CRP, P = 0.005). No optimal predictive CRP cut‐off point was observed.ConclusionsHigh baseline CRP levels increased the likelihood of maintained remission. Normalised CRP levels at week 14 increased the likelihood of maintained response or remission during 1 year of infliximab maintenance therapy (Clinical trial: NCT00207662).
Circumstantial evidence of gibel carp, Carassius gibelio, reproductive competition exerted on native fish species in a mesotrophic reservoir
Authors: TARKAN A. S. , GAYGUSUZ Ö. , Gürsoy GAYGUSUZ Ç. , SAÇ G. , COPP G. H. 
Published: January 2012

Abstract  Gibel carp, Carassius gibelio (Bloch), impacts on native fish species have been reported but little studied despite a long history of introductions in Europe. This species is able to reproduce gynogenetically, which involves the use of sperm from males of other species to activate egg development, so reproductive competition is a likely but virtually unstudied impact of gibel carp on native fishes. This study evaluates the impact of introduced C. gibelio on the population biology of native fishes over a 6‐year period in a mesotrophic drinking water reservoir in north‐western Turkey. A dramatic decrease in the relative density (i.e. catch per unit effort) of native species correlated significantly with an increase in C. gibelio relative density. Growth characteristics (back‐calculated ages, growth index and relative condition) and length at maturity did not differ significantly among years in C. gibelio and native fishes. Relative density, duration of spawning, reproductive effort and gonado‐somatic index of C. gibelio increased with some water quality variables [total phosphorus (TP); chlorophyll‐a (Chl‐a)] and coincided with decreasing trends for natives. However, TP and Chl‐a were not correlated with growth features in C. gibelio or natives fishes. The results suggest that the decline in the reservoir’s native cyprinid populations is likely due to a combination of degrading environmental conditions and a disparity in reproductive effort, with introduced C. gibelio invasion facilitated by gynogenetic reproduction and an observed interference with native fishes during spawning.