bluuebunny/crossref_metadata_2025 huggingface dataset:
Domain wall motion on magnetic nanotubes
Authors: Landeros P. , Núñez Álvaro S.
Published: August 2010

In this paper the dynamical regimes of the motion of domain walls in magnetic nanotubes are studied theoretically. We compare results obtained with a simplified model of the magnetic energy with a detailed one that includes an exact treatment of the dipolar field. We demonstrate that the proper inclusion of dipolar effects changes qualitatively the mobility of a vortex domain wall driven by an applied magnetic field. We report that magnetic nanotubes display the characteristic phenomenology of domain wall motion: at low fields we find a steady motion with almost constant mobility (velocity/field) up to a critical field, where steady motion breaks out and a precessional motion appears. It is also found that the initial chirality of a vortex domain wall determines the dynamic regime of the motion near the Walker critical field.
Atomic-scale redistribution of dopants in polycrystalline silicon layers
Authors: Duguay S. , Colin A. , Mathiot D. , Morin P , Blavette D.
Published: August 2010

80 nm thick polycrystalline silicon (poly-Si) layers implanted with As, P, and C were subjected to spike heating (1000 °C, 1.5 s) or laser anneal (1300 °C, 0.25 ms) and analyzed by atom probe tomography. A strong interfacial segregation of dopants to the grain boundaries (GBs) was revealed in the spike annealed samples. The heterogeneous precipitation of C to the GBs was observed, as well as the clustering of C in the interior of the grains. Theses clusters are also rich in As and P. Their shapes (loop, rod) strongly suggest that these clusters are the result of dopant segregation to extended defects. Nanometer size oxygen clusters were also observed. They originate from the recoil of oxygen atoms during the implantation process through the oxide layer. Laser annealed samples showed a lower segregation excess of dopants to GBs. Consequently, the dopant concentration inside grains was found larger compared to the spike annealed sample. The lower segregation rate at GB is explained by the larger temperature in the laser annealing.
Electronic property and bonding configuration at the TiN(111)/VN(111) interface
Authors: Yin Deqiang , Peng Xianghe , Qin Yi , Wang Zhongchang
Published: August 2010

Multilayered TiN(111)/VN(111) coatings find many technological applications where the behaviors of their inside interfaces are known or suspected to influence functionalities in such an engineering surface system. Here, we demonstrate, by first-principles calculations on energetics and electronic structures of a total of 36 candidate interfaces, that the preferred geometries (i.e., that having the largest adhesion energy) are those that retain the interface structures as in either of the nitride bulks both atomically and electronically. Using several analytic methods, we have thoroughly characterized electronic states and determined that the interfacial bondings are mainly ionic, yet maintain a small amount of covalent character. The theoretical calculations presented provide insight into the complex electronic properties of the functional TiN/VN interface that could be difficult to obtain by experiment alone but which are practically important for further understanding and improvement of such a multilayered coating at the atomic scale.
Large inverse magnetic entropy changes and magnetoresistance in the vicinity of a field-induced martensitic transformation in Ni50−xCoxMn32−yFeyGa18
Authors: Pathak Arjun K. , Dubenko Igor , Karaca Haluk E. , Stadler Shane , Ali Naushad
Published: August 2010

Significantly large inverse magnetic entropy changes (ΔSM) and magnetoresistance (MR) were observed at the inverse martensitic phase transitions of the Ga-based magnetic shape memory Heusler alloys: Ni50−xCoxMn32−yFeyGa18. The crystal structures of alloys were tetragonal at 300 K and the phase transition temperatures and magnetic properties were found to be correlated with the degree of tetragonal distortion. The maximum peak values of the ΔSM and MR at H=5 T were determined as ≈(+)31 J Kg−1 K−1 and ≈−21%, respectively, for x=8 and y=2. The relatively small hysteretic loss and large refrigeration capacity observed in this system make these compounds promising materials for applications.
Every state on interval effect algebra is integral
Authors: Dvurečenskij Anatolij
Published: August 2010

We show that every state on an interval effect algebra is an integral through some regular Borel probability measure defined on the Borel σ-algebra of a compact Hausdorff simplex. This is true for every effect algebra satisfying Riesz decomposition property or for every many valued (MV)-algebra. In addition, we show that each state on an effect subalgebra of an interval effect algebra E can be extended to a state on E. Our method represents also every state on the set of effect operators of a Hilbert space as an integral.
Self-similar bending in a flow: The axisymmetric case
Authors: Alben Silas
Published: August 2010

We study how sheets roll up into conical configurations when exposed to fluid flows using simulations and analysis. The simulations couple the bending of thin sheets to axisymmetric flows with vortex shedding. We find quasisteady flows with vortex ring wakes in which the radii of the rings scale with the radii of the cone bases. The cone angles scale with the dimensionless flow speed raised to the power −1/3. The drag coefficients for the cones scale with flow speed to the power −1. We find good agreement with the previously published experimental results. The scalings we have found result from a self-similar behavior of the flow at the outer edges of the cones, with length scales set by the radii of the vortex rings in the wakes.
High-speed tracking control of piezoelectric actuators using an ellipse-based hysteresis model
Authors: Gu GuoYing , Zhu LiMin
Published: August 2010

In this paper, an ellipse-based mathematic model is developed to characterize the rate-dependent hysteresis in piezoelectric actuators. Based on the proposed model, an expanded input space is constructed to describe the multivalued hysteresis function H[u](t) by a multiple input single output (MISO) mapping Γ:R2→R. Subsequently, the inverse MISO mapping Γ−1(H[u](t),H[u̇](t);u(t)) is proposed for real-time hysteresis compensation. In controller design, a hybrid control strategy combining a model-based feedforward controller and a proportional integral differential (PID) feedback loop is used for high-accuracy and high-speed tracking control of piezoelectric actuators. The real-time feedforward controller is developed to cancel the rate-dependent hysteresis based on the inverse hysteresis model, while the PID controller is used to compensate for the creep, modeling errors, and parameter uncertainties. Finally, experiments with and without hysteresis compensation are conducted and the experimental results are compared. The experimental results show that the hysteresis compensation in the feedforward path can reduce the hysteresis-caused error by up to 88% and the tracking performance of the hybrid controller is greatly improved in high-speed tracking control applications, e.g., the root-mean-square tracking error is reduced to only 0.34% of the displacement range under the input frequency of 100 Hz.
Switching of a single propagating plasmon by two quantum dots system
Authors: Kim Nam-Chol , Li Jian-Bo , Yang Zhong-Jian , Hao Zhong-Hua , Wang Qu-Quan
Published: August 2010

We investigated the scattering property of a single plasmon interacting with two quantum dots coupled to one-dimensional surface plasmonic waveguide. We demonstrated that the transmission of a single plasmon could be switched on or off by adjusting spectral detuning and controlling spatial separation of the two quantum dots. These transport properties of the nanosystem could find the applications in plasmonic nanodevices and quantum information processing.
Giant Renner–Teller vibronic coupling in the BF2 radical: An ab initio study of the X̃ A21 and Ã Π2 electronic states
Authors: Tarroni Riccardo , Clouthier Dennis J.
Published: August 2010

The potential energy surfaces (PESs) of the ground X̃ A21 and the first excited Ã Π2 (1 B21,2 A21) electronic states of the BF2 radical have been studied ab initio, using a large basis set and CCSD(T) and EOM-CCSD techniques. The calculated PESs were used to variationally calculate the energy levels up to ≈36 000 cm−1 above the ground state. The Renner–Teller splitting parameter (ε=0.928) found for the Ã Π2 state of this radical is very large which results in an unusual excited state energy level structure.
Modified transmission-line method for contact resistance extraction in organic field-effect transistors
Authors: Xu Yong , Gwoziecki R. , Chartier I. , Coppard R. , Balestra F. , Ghibaudo G.
Published: August 2010

A modified transmission-line method (TLM) for organic transistors contact resistance extraction is proposed. It is shown that the issues of conventional TLM reside in the channel resistance scattering due to parameter variations. These difficulties are overcome in the modified TLM, in which the linear regression slope is directly controlled by the contact resistance rather than by the channel resistance as in conventional TLM. Much smaller transistor-to-transistor dispersion of contact resistance results in a more stable and more reliable extraction method. Moreover, an error study by simulation has been carried out, confirming the greater accuracy of the modified TLM.
Photoswitching of azobenzene multilayers on a layered semiconductor
Authors: Iwicki J. , Ludwig E. , Kalläne M. , Buck J. , Köhler F. , Herges R. , Kipp L. , Rossnagel K.
Published: August 2010

In situ photoelectron spectroscopy is used to study the adsorption and photoisomerization of azobenzene multilayers on the layered semiconductor HfS2 at liquid nitrogen temperatures. The measured valence band spectra indicate weak molecule–substrate coupling and provide evidence for reversible switching of azobenzene multilayers by light with different wavelengths. The photoswitching manifests itself in spectral shifts due to changes in the electrical surface conductance and in modifications of the electronic structure consistent with the results of outer valence Green’s function calculations. The photoemission results appear to establish azobenzene as an optoelectrical molecular switch.
Low-threshold conical microcavity dye lasers
Authors: Grossmann Tobias , Schleede Simone , Hauser Mario , Christiansen Mads Brøkner , Vannahme Christoph , Eschenbaum Carsten , Klinkhammer Sönke , Beck Torsten , Fuchs Jochen , Nienhaus G. Ulrich , Lemmer Uli , Kristensen Anders , Mappes Timo , Kalt Heinz
Published: August 2010

We report on lasing in rhodamine 6G-doped, conical polymeric microcavities with high quality factors fabricated on a silicon substrate. Threshold pump energies as low as 3 nJ are achieved by free-space excitation in the quasistationary pumping regime with lasing wavelengths around 600 nm. Finite element simulations confirm that lasing occurs in whispering gallery modes which corresponds well to the measured multimode laser-emission. The effect of dye concentration on lasing threshold and lasing wavelength is investigated and can be explained using a standard dye laser model.
Serotonin stimulation of cAMP-dependent plasticity in
Aplysia
sensory neurons is mediated by calmodulin-sensitive adenylyl cyclase
Authors: Lin Allison H. , Cohen Jonathan E. , Wan Qin , Niu Katelyn , Shrestha Pragya , Bernstein Steven L. , Abrams Thomas W.
Published: August 2010

Calmodulin (CaM)-sensitive adenylyl cyclase (AC) in sensory neurons (SNs) in
Aplysia
has been proposed as a molecular coincidence detector during conditioning. We identified four putative ACs in
Aplysia
CNS. CaM binds to a sequence in the C1b region of AC-
Apl
A that resembles the CaM-binding sequence in the C1b region of AC1 in mammals. Recombinant AC-
Apl
A was stimulated by Ca
2+
/CaM. AC-
Apl
C is most similar to the Ca
2+
-inhibited AC5 and AC6 in mammals. Recombinant AC-
Apl
C was directly inhibited by Ca
2+
, independent of CaM. AC-
Apl
A and AC-
Apl
C are expressed in SNs, whereas AC-
Apl
B and AC-
Apl
D are not. Knockdown of AC-
Apl
A demonstrated that serotonin stimulation of cAMP-dependent plasticity in SNs is predominantly mediated by this CaM-sensitive AC. We propose that the coexpression of a Ca
2+
-inhibited AC in SNs, together with a Ca
2+
/CaM-stimulated AC, would enhance the associative requirement for coincident Ca
2+
influx and serotonin for effective stimulation of cAMP levels and initiation of plasticity mediated by AC-
Apl
A.
Comprehensive microRNA expression profiling of the hematopoietic hierarchy
Authors: Petriv O. I. , Kuchenbauer F. , Delaney A. D. , Lecault V. , White A. , Kent D. , Marmolejo L. , Heuser M. , Berg T. , Copley M. , Ruschmann J. , Sekulovic S. , Benz C. , Kuroda E. , Ho V. , Antignano F. , Halim T. , Giambra V. , Krystal G. , Takei C. J. F. , Weng A. P. , Piret J. , Eaves C. , Marra M. A. , Humphries R. K. , Hansen C. L.
Published: August 2010

The hematopoietic system produces a large number of highly specialized cell types that are derived through a hierarchical differentiation process from a common stem cell population. miRNAs are critical players in orchestrating this differentiation. Here, we report the development and application of a high-throughput microfluidic real-time quantitative PCR (RT-qPCR) approach for generating global miRNA profiles for 27 phenotypically distinct cell populations isolated from normal adult mouse hematopoietic tissues. A total of 80,000 RT-qPCR assays were used to map the landscape of miRNA expression across the hematopoietic hierarchy, including rare progenitor and stem cell populations. We show that miRNA profiles allow for the direct inference of cell lineage relations and functional similarity. Our analysis reveals a close relatedness of the miRNA expression patterns in multipotent progenitors and stem cells, followed by a major reprogramming upon restriction of differentiation potential to a single lineage. The analysis of miRNA expression in single hematopoietic cells further demonstrates that miRNA expression is very tightly regulated within highly purified populations, underscoring the potential of single-cell miRNA profiling for assessing compartment heterogeneity.
Slipknotting upon native-like loop formation in a trefoil knot protein
Authors: Noel Jeffrey K. , Sułkowska Joanna I. , Onuchic José N.
Published: August 2010

Protein knots and slipknots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Recent experimental results show that knotting, starting from a fully extended polypeptide, has not yet been observed. Understanding the nucleation process of folding knots is thus a natural challenge for both experimental and theoretical investigation. In this study, we employ energy landscape theory and molecular dynamics to elucidate the entire folding mechanism. The full free energy landscape of a knotted protein is mapped using an all-atom structure-based protein model. Results show that, due to the topological constraint, the protein folds through a three-state mechanism that contains (
i
) a precise nucleation site that creates a correctly twisted native loop (first barrier) and (
ii
) a rate-limiting free energy barrier that is traversed by two parallel knot-forming routes. The main route corresponds to a slipknot conformation, a collapsed configuration where the
C
-terminal helix adopts a hairpin-like configuration while threading, and the minor route to an entropically limited plug motion, where the extended terminus is threaded as through a needle. Knot formation is a late transition state process and results show that random (nonspecific) knots are a very rare and unstable set of configurations both at and below folding temperature. Our study shows that a native-biased landscape is sufficient to fold complex topologies and presents a folding mechanism generalizable to all known knotted protein topologies: knotting via threading a native-like loop in a preordered intermediate.
The Earliest ᶜAlid Genealogy for the Safavids: New Evidence for the Pre-dynastic Claim to Sayyid Status
Authors: Morimoto Kazuo
Published: August 2010

Studies on the pre-dynastic claim of the Safavids to sayyid status suffer from a dearth of primary source materials. Scholars have advanced various conjectures, but it is not yet clear when the Safavids began to promote this claim or indeed when the so-called “official” Musavid genealogy was developed. This study presents a genealogical chart drawn in the third quarter of the fifteenth century (most probably in the 1460s) in Iraq (most likely in Najaf), which records the “official” genealogy in an unequivocal manner. This chart is a valuable document in that it testifies to the circulation of the “official” genealogy some three to four decades before the establishment of the Safavid dynasty. A survey of the studies to date on the question of the pre-dynastic claim is also offered in order to clarify the significance of the chart.
ZFP36L1 Negatively Regulates Erythroid Differentiation of CD34+ Hematopoietic Stem Cells by Interfering with the Stat5b Pathway
Authors: Vignudelli Tatiana , Selmi Tommaso , Martello Andrea , Parenti Sandra , Grande Alexis , Gemelli Claudia , Zanocco-Marani Tommaso , Ferrari Sergio
Published: August 2010

ZFP36L1 is a member of a family of CCCH tandem zinc finger proteins (TTP family) able to bind to AU-rich elements in the 3′-untranslated region of mRNAs, thereby triggering their degradation. The present study suggests that such mechanism is used during hematopoiesis to regulate differentiation by posttranscriptionally modulating the expression of specific target genes. In particular, it demonstrates that ZFP36L1 negatively regulates erythroid differentiation by directly binding the 3′ untranslated region of Stat5b encoding mRNA. Stat5b down-regulation obtained by ZFP36L1 overexpression results, in human hematopoietic progenitors, in a drastic decrease of erythroid colonies formation. These observations have been confirmed by silencing experiments targeting Stat5b and by treating hematopoietic stem/progenitor cells with drugs able to induce ZFP36L1 expression. Moreover, this study shows that different members of ZFP36L1 family act redundantly, because cooverexpression of ZFP36L1 and family member ZFP36 determines a cumulative effect on Stat5b down-regulation. This work describes a mechanism underlying ZFP36L1 capability to regulate hematopoietic differentiation and suggests a new target for the therapy of hematopoietic diseases involving Stat5b/JAK2 pathway, such as chronic myeloproliferative disorders.
Cdk Phosphorylation of a Nucleoporin Controls Localization of Active Genes through the Cell Cycle
Authors: Garvey Brickner Donna , Brickner Jason H.
Published: August 2010

Many inducible genes in yeast are targeted to the nuclear pore complex when active. We find that the peripheral localization of the INO1 and GAL1 genes is regulated through the cell cycle. Active INO1 and GAL1 localized at the nuclear periphery during G1, became nucleoplasmic during S-phase, and then returned to the nuclear periphery during G2/M. Loss of peripheral targeting followed the initiation of DNA replication and was lost in cells lacking a cyclin-dependent kinase (Cdk) inhibitor. Furthermore, the Cdk1 kinase and two Cdk phosphorylation sites in the nucleoporin Nup1 were required for peripheral targeting of INO1 and GAL1. Introduction of aspartic acid residues in place of either of these two sites in Nup1 bypassed the requirement for Cdk1 and resulted in targeting of INO1 and GAL1 to the nuclear periphery during S-phase. Thus, phosphorylation of a nuclear pore component by cyclin dependent kinase controls the localization of active genes to the nuclear periphery through the cell cycle.
Keeping the Vimentin Network under Control: Cell–Matrix Adhesion–associated Plectin 1f Affects Cell Shape and Polarity of Fibroblasts
Authors: Burgstaller Gerald , Gregor Martin , Winter Lilli , Wiche Gerhard
Published: August 2010

Focal adhesions (FAs) located at the ends of actin/myosin-containing contractile stress fibers form tight connections between fibroblasts and their underlying extracellular matrix. We show here that mature FAs and their derivative fibronectin fibril-aligned fibrillar adhesions (FbAs) serve as docking sites for vimentin intermediate filaments (IFs) in a plectin isoform 1f (P1f)-dependent manner. Time-lapse video microscopy revealed that FA-associated P1f captures mobile vimentin filament precursors, which then serve as seeds for de novo IF network formation via end-to-end fusion with other mobile precursors. As a consequence of IF association, the turnover of FAs is reduced. P1f-mediated IF network formation at FbAs creates a resilient cage-like core structure that encases and positions the nucleus while being stably connected to the exterior of the cell. We show that the formation of this structure affects cell shape with consequences for cell polarization.
V-ATPase-Mediated Granular Acidification Is Regulated by the V-ATPase Accessory Subunit Ac45 in POMC-Producing Cells
Authors: Jansen Eric J. R. , Hafmans Theo G. M. , Martens Gerard J. M.
Published: August 2010

The vacuolar (H+)-ATPase (V-ATPase) is an important proton pump, and multiple critical cell-biological processes depend on the proton gradient provided by the pump. Yet, the mechanism underlying the control of the V-ATPase is still elusive but has been hypothesized to involve an accessory subunit of the pump. Here we studied as a candidate V-ATPase regulator the neuroendocrine V-ATPase accessory subunit Ac45. We transgenically manipulated the expression levels of the Ac45 protein specifically in Xenopus intermediate pituitary melanotrope cells and analyzed in detail the functioning of the transgenic cells. We found in the transgenic melanotrope cells the following: i) significantly increased granular acidification; ii) reduced sensitivity for a V-ATPase-specific inhibitor; iii) enhanced early processing of proopiomelanocortin (POMC) by prohormone convertase PC1; iv) reduced, neutral pH–dependent cleavage of the PC2 chaperone 7B2; v) reduced 7B2-proPC2 dissociation and consequently reduced proPC2 maturation; vi) decreased levels of mature PC2 and consequently reduced late POMC processing. Together, our results show that the V-ATPase accessory subunit Ac45 represents the first regulator of the proton pump and controls V-ATPase-mediated granular acidification that is necessary for efficient prohormone processing.
Coordination of Substrate Binding and ATP Hydrolysis in Vps4-Mediated ESCRT-III Disassembly
Authors: Davies Brian A. , Azmi Ishara F. , Payne Johanna , Shestakova Anna , Horazdovsky Bruce F. , Babst Markus , Katzmann David J.
Published: August 2010

ESCRT-III undergoes dynamic assembly and disassembly to facilitate membrane exvagination processes including multivesicular body (MVB) formation, enveloped virus budding, and membrane abscission during cytokinesis. The AAA-ATPase Vps4 is required for ESCRT-III disassembly, however the coordination of Vps4 ATP hydrolysis with ESCRT-III binding and disassembly is not understood. Vps4 ATP hydrolysis has been proposed to execute ESCRT-III disassembly as either a stable oligomer or an unstable oligomer whose dissociation drives ESCRT-III disassembly. An in vitro ESCRT-III disassembly assay was developed to analyze Vps4 function during this process. The studies presented here support a model in which Vps4 acts as a stable oligomer during ATP hydrolysis and ESCRT-III disassembly. Moreover, Vps4 oligomer binding to ESCRT-III induces coordination of ATP hydrolysis at the level of individual Vps4 subunits. These results suggest that Vps4 functions as a stable oligomer that acts upon individual ESCRT-III subunits to facilitate ESCRT-III disassembly.
BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets
Authors: Dorff Kevin C. , Chambwe Nyasha , Srdanovic Marko , Campagne Fabien
Published: August 2010

Summary: High-throughput data can be used in conjunction with clinical information to develop predictive models. Automating the process of developing, evaluating and testing such predictive models on different datasets would minimize operator errors and facilitate the comparison of different modeling approaches on the same dataset. Complete automation would also yield unambiguous documentation of the process followed to develop each model. We present the BDVal suite of programs that fully automate the construction of predictive classification models from high-throughput data and generate detailed reports about the model construction process. We have used BDVal to construct models from microarray and proteomics data, as well as from DNA-methylation datasets. The programs are designed for scalability and support the construction of thousands of alternative models from a given dataset and prediction task.

Availability and Implementation: The BDVal programs are implemented in Java, provided under the GNU General Public License and freely available at http://bdval.campagnelab.org

Contact:  fac2003@med.cornell.edu
Labeling the Good: Alternative Visions and Organic Branding in Sweden in the Late Twentieth Century
Authors: Broberg Oskar
Published: August 2010

The past decade's rapid expansion of a global market for organic food has set powerful economic and political forces in motion. The most important dividing line is whether organic food production should be an alternative to or a niche within a capitalist mode of production. To explore this conflict the article analyzes the formation of a market for eco-labeled milk in Sweden. The analysis draws on three aspects: the strategy of agri-business, the role of eco-labeling, and the importance of inter-organizational dynamics. Based on archival studies, daily press, and interviews, three processes are emphasized: the formative years of the alternative movement in the 1970s, the founding of an independent eco-label (KRAV) in the 1980s, and a discursive shift from alternative visions to organic branding in the early 1990s following the entry of agri-business.
A Single‐center Experience With Methotrexate After Thiopurine Therapy in Pediatric Crohn Disease
Authors: Boyle Brendan , Mackner Laura , Ross Christina , Moses Jonathan , Kumar Soma , Crandall Wallace
Published: August 2010

Background and Aim:

Thiopurines are a common, effective means of maintaining remission in pediatric Crohn disease (CD). Methotrexate (MTX) may be considered for those intolerant of or unresponsive to thiopurines. The purpose of this study was to examine the effectiveness of MTX as maintenance therapy in patients previously treated with thiopurines.

Patients and Methods:

All of the patients at Nationwide Children's Hospital from 1998 to 2007 with an International Classification of Diseases code indicative of CD were identified. Patients with a diagnosis of CD, a history of prior thiopurine use, no current infliximab therapy, and at least 6 months of follow‐up after MTX initiation were included. The primary outcome was defined as steroid‐/infliximab‐free remission determined by the physician global assessment at 6 and 12 months. Secondary outcomes included subsequent treatment with infliximab and/or corticosteroids, rate of discontinuation of MTX, and adverse events (AEs).

Results:

Twenty‐seven patients (17 boys, 63%) with a mean age at diagnosis of 12.3 ± 0.7 years and mean disease duration of 1.49 ± 0.3 years were identified. Indications for MTX included nonresponse to thiopurines, AE, and poor adherence to thiopurines. At 6 and 12 months, 13 of 27 patients (48.1%) and 9 of 27 patients (33.3%), respectively, were in steroid‐/infliximab‐free remission. A total of 10 patients (37.0%) required infliximab therapy during the 12‐month period and 5 patients discontinued MTX. Nausea was the most commonly reported AE. Transient transaminase elevation occurred in 4 patients and transient leukopenia in 2 patients.

Conclusions:

MTX can be effective as maintenance therapy for patients with pediatric CD previously intolerant of or unresponsive to thiopurines; however, greater than one third of this cohort required escalation to antitumor necrosis factor therapy within 12 months following MTX initiation. MTX was well tolerated.
Butyrate and Type 1 Diabetes Mellitus: Can We Fix the Intestinal Leak?
Authors: Li Nan , Hatch Marguerite , Wasserfall Clive H , Douglas‐Escobar Martha , Atkinson Mark A , Schatz Desmond A , Neu Josef
Published: August 2010

Objectives:

An intestinal permeability defect precedes type 1 diabetes mellitus and may be a permissive factor in its pathogenesis. Butyrate strengthens the intestinal tight junctions. We hypothesized that enteral administration of sodium butyrate (NaB) in preweaned rats would result in differences in the development of diabetes associated with decreased inflammation and pancreatic β‐cell destruction.

Materials and Methods:

Using biobreeding diabetes‐prone rat pups, oral NaB or saline was administered twice per day via micropipette from postnatal days 10 to 23. Rat pups were randomly assigned to 1 of 4 groups for the first experiment (control group, n = 7) and 3 different doses of butyrate groups (n = 8 for each group) and 2 groups for the second and third experiments (control n = 23; NaB at 400 mg · kg−1 · day−1, n = 20). Animals were studied into adulthood (up to day 140) for development of diabetes.

Results:

The results showed that the survival rates were 28% versus 20% (butyrate vs control). No significant differences in survival were seen; however, there was a trend of delaying of onset of diabetes in the butyrate group. There were no differences of pancreatic histology score of islet inflammation between the 2 groups. Cytokine‐induced neutrophil chemoattractant‐1 was lower in the butyrate group at a dose of 400 mg · kg−1 · day−1 in the distal small intestine (P = 0.008) and in the liver (P = 0.01). There were no significant differences in the tracer flux measurements across the distal ileum and colon between the 2 animal groups.

Conclusions:

Oral NaB given during the preweaning period did not significantly decrease the subsequent development of death from diabetes in biobreeding diabetes‐prone rats.
Does Laparoscopy Lower the Threshold for the Surgical Treatment of Gastroesophageal Reflux Disease in Children?
Authors: Driessen Caroline , Verhoeven BH , Ten WE Tjon A , Van Heurn LWE
Published: August 2010

Objective:

To assess whether laparoscopic surgery lowers the threshold for surgical intervention, we examined whether the introduction of the laparoscopic technique at our institution in 1997 has resulted in an increase in antireflux surgery in children at our clinic.

Patients and Methods:

The number of annual fundoplications between 1997 and 2008 at a single institution was assessed in children younger than 18 years. The number of fundoplications was compared with the number of pyloromyotomies and appendicectomies per year in the same period of time to prove or exclude a general increase in the referral of children.

Results:

Since 1997, the proportion of laparoscopic fundoplications increased from 60% in 1997 to 100% in 2008. During this period, 109 laparoscopic fundoplications were performed: 31 in the period from 1997 to 2002 and 78 from 2003 to 2008. Regression analysis shows a significant increase in the number of performed fundoplications (slope: 1.03 ± 0.28, P = 0.0043), whereas both the number of pyloromyotomies and appendicectomies remained stable (slopes: −0.14 ± 0.40, P = 0.73, and −0.75 ± 0.47, P = 0.14, respectively).

Conclusions:

Since the introduction of minimally invasive surgery at our tertiary referral center in 1997, the number of patients referred for an antireflux operation has increased. This cannot be explained by an increase of referrals from outside the region or a change in the indication for surgery. We conclude that laparoscopy lowers the threshold for the surgical treatment of gastroesophageal reflux disease in children.
Seasonal Variation of Enteropathogens in Infants and Preschoolers With Acute Diarrhea in Western Mexico
Authors: Larrosa‐Haro Alfredo , Macias‐Rosales Rocío , Sánchez‐Ramírez Carmen A , Cortés‐López M Carmen , Aguilar‐Benavides Sergio
Published: August 2010

The present study estimates the prevalence of some enteropathogens in infants and preschoolers with acute diarrhea. From 2006 to 2007, 5459 consecutive stool samples were evaluated. Cryptosporidium parvum was the parasite identified with the higher frequency (5.1%), followed by Giardia lamblia (1.2%). Campylobacter jejuni was isolated in 858 cases (15.7%) and was the most frequent enteropathogen overall. The rates of C parvum, Shigella, and Salmonella were higher in the summer. Rotavirus had the expected winter peak and it was the third enteropathogen because of its frequency. Overall frequency of stool‐reducing substances was 15.6% and was associated with a rotavirus‐positive test.
Interaction of Saccharomyces boulardii With Intestinal Brush Border Membranes: Key to Probiotic Effects?
Authors: Buts Jean‐Paul , De Keyser Nadine
Published: August 2010

The probiotic Saccharomyces boulardii exerts beneficial effects in humans, which include trophic effects, anti‐inflammatory effects, antisecretory effects, inhibition of toxins, immunostimulatory effects, and resistance to bacterial overgrowth. This short communication discusses the interactions of the probiotic with brush border membrane (BBM) constituents because most of these effects are BBM mediated. The use of bacterial and yeast probiotics has increased dramatically in more and more clinical states, but their exact mechanisms of action remain largely unknown. The present communication focuses on the interactions of a confirmed yeast probiotic (S boulardii) on the constituents of BBMs.
Orangutan pantomime: elaborating the message
Authors: Russon Anne , Andrews Kristin
Published: August 2010

We present an exploratory study of forest-living orangutan pantomiming, i.e. gesturing in which they act out their meaning, focusing on its occurrence, communicative functions, and complexities. Studies show that captive great apes may elaborate messages if communication fails, and isolated reports suggest that great apes occasionally pantomime. We predicted forest-living orangutans would pantomime spontaneously to communicate, especially to elaborate after communication failures. Mining existing databases on free-ranging rehabilitant orangutans' behaviour identified 18 salient pantomimes. These pantomimes most often functioned as elaborations of failed requests, but also as deceptions and declaratives. Complexities identified include multimodality, re-enactments of past events and several features of language (productivity, compositionality, systematicity). These findings confirm that free-ranging rehabilitant orangutans pantomime and use pantomime to elaborate on their messages. Further, they use pantomime for multiple functions and create complex pantomimes that can express propositionally structured content. Thus, orangutan pantomime serves as a medium for communication, not a particular function. Mining cases of complex great ape communication originally reported in functional terms may then yield more evidence of pantomime.
Hibernation does not affect memory retention in bats
Authors: Ruczynski Ireneusz , Siemers Björn M.
Published: August 2010

Long-term memory can be critically important for animals in a variety of contexts, and yet the extreme reduction in body temperature in hibernating animals alters neurochemistry and may therefore impair brain function. Behavioural studies on memory impairment associated with hibernation have been almost exclusively conducted on ground squirrels (Rodentia) and provide conflicting results, including clear evidence for memory loss. Here, we for the first time tested memory retention after hibernation for a vertebrate outside rodents—bats (Chiroptera). In the light of the high mobility, ecology and long life of bats, we hypothesized that maintenance of consolidated memory through hibernation is under strong natural selection. We trained bats to find food in one out of three maze arms. After training, the pre-hibernation performance of all individuals was at 100 per cent correct decisions. After this pre-test, one group of bats was kept, with two interruptions, at 7°C for two months, while the other group was kept under conditions that prevented them from going into hibernation. The hibernated bats performed at the same high level as before hibernation and as the non-hibernated controls. Our data suggest that bats benefit from an as yet unknown neuroprotective mechanism to prevent memory loss in the cold brain.
Genomics in the ecological arena
Authors: Orsini Luisa , Decaestecker Ellen , De Meester Luc , Pfrender Michael E. , Colbourne John K.
Published: August 2010

This meeting report presents the cutting-edge research that is developing around the waterflea
Daphnia
, an emerging model system in environmental genomics.
Daphnia
has been a model species in ecology, toxicology and evolution for many years and is supported by a large community of ecologists, evolutionary biologists and ecotoxicologists. Thanks to new advances in genomics and transciptomics and to the sustained efforts of the
Daphnia
Genomics Consortium (DGC),
Daphnia
is also rapidly developing as a model system in environmental genomics. Advances in this emerging field were presented at the DGC 2010, held for the first time in a European University. During the meeting, a plethora of elegant studies were presented on the mechanisms of responses to environmental challenges using recently developed genomic tools. The DGC 2010 is a concrete example of the new trends in ecology and evolution. The times are mature for the application of innovative genomic and transcriptomic tools for studies of environmental genomics in non-model organisms.
A linguist’s comment on ‘Pictish symbols revealed as a written language through application of Shannon entropy’
Authors: Fournet Arnaud
Published: August 2010

The original paper proposed a method to investigate the linguistic features embedded in undeciphered symbols. The authors concluded that ‘it is likely that the [Pictish] symbols are actually words’. This comment points to linguistic issues which have a bearing on the conclusion but have not been addressed thoroughly enough. The transformation of Pictish carvings into linear symbols and the features of archaic writing systems are likely to introduce biases, which stand unassessed. The proposed method could be tested against other items. The line between writing and drawing is not as clear-cut as categorized in the original paper. On the whole, the conclusion reached by the authors remains pending.
On the convergence of second-order spectra and multiplicity
Authors: Boulton Lyonell , Strauss Michael
Published: August 2010

The notion of second-order relative spectrum of a self-adjoint operator acting on a Hilbert space has been studied recently in connection with the phenomenon of spectral pollution in the Galerkin method. In this paper we examine how the second-order spectrum encodes precise information about the multiplicity of the isolated eigenvalues of the underlying operator. Our theoretical findings are supported by various numerical experiments on the computation of guaranteed eigenvalue inclusions via finite element bases.
Irrational decision-making in an amoeboid organism: transitivity and context-dependent preferences
Authors: Latty Tanya , Beekman Madeleine
Published: August 2010

Most models of animal foraging and consumer choice assume that individuals make choices based on the absolute value of items and are therefore ‘economically rational’. However, frequent violations of rationality by animals, including humans, suggest that animals use comparative valuation rules. Are comparative valuation strategies a consequence of the way brains process information, or are they an intrinsic feature of biological decision-making? Here, we examine the principles of rationality in an organism with radically different information-processing mechanisms: the brainless, unicellular, slime mouldPhysarum polycephalum. We offeredP. polycephalumamoebas a choice between food options that varied in food quality and light exposure (P. polycephalumis photophobic). The use of an absolute valuation rule will lead to two properties: transitivity and independence of irrelevant alternatives (IIA). Transitivity is satisfied if preferences have a consistent, linear ordering, while IIA states that a decision maker's preference for an item should not change if the choice set is expanded. A violation of either of these principles suggests the use of comparative rather than absolute valuation rules.Physarum polycephalumsatisfied transitivity by having linear preference rankings. However,P. polycephalum's preference for a focal alternative increased when a third, inferior quality option was added to the choice set, thus violating IIA and suggesting the use of a comparative valuation process. The discovery of comparative valuation rules in a unicellular organism suggests that comparative valuation rules are ubiquitous, if not universal, among biological decision makers.
The structure of the genomicBacillus subtilisdUTPase: novel features in the Phe-lid
Authors: García-Nafría Javier , Burchell Lynn , Takezawa Mine , Rzechorzek Neil J. , Fogg Mark J. , Wilson Keith S.
Published: August 2010

dUTPases are a ubiquitous family of enzymes that are essential for all organisms and catalyse the breakdown of 2-deoxyuridine triphosphate (dUTP). InBacillus subtilisthere are two homotrimeric dUTPases: a genomic and a prophage form. Here, the structures of the genomic dUTPase and of its complex with the substrate analogue dUpNHpp and calcium are described, both at 1.85 Å resolution. The overall fold resembles that of previously solved trimeric dUTPases. The C-terminus, which contains one of the conserved sequence motifs, is disordered in both structures. The crystal of the complex contains six independent protomers which accommodate six dUpNHpp molecules, with three triphosphates in thetransconformation and the other three in the activegaucheconformation. The structure of the complex confirms the role of several key residues that are involved in ligand binding and the position of the catalytic water. Asp82, which has previously been proposed to act as a general base, points away from the active site. In the complex Ser64 reorients in order to hydrogen bond the phosphate chain of the substrate. A novel feature has been identified: the position in the sequence of the `Phe-lid', which packs against the uracil moiety, is adjacent to motif III, whereas in all other dUTPase structures the lid is in a conserved position in motif V of the flexible C-terminal arm. This requires a reconsideration of some aspects of the accepted mechanism.
Percentile-based spread: a more accurate way to compare crystallographic models
Authors: Pozharski Edwin
Published: August 2010

The comparison of biomacromolecular crystal structures is traditionally based on the root-mean-square distance between corresponding atoms. This measure is sensitive to the presence of outliers, which inflate it disproportionately to their fraction. An alternative measure, the percentile-based spread (p.b.s.), is proposed and is shown to represent the average variation in atomic positions more adequately. It is discussed in the context of isomorphous crystal structures, conformational changes and model ensembles generated by repetitive automated rebuilding.
Is too `creative' language acceptable in crystallography?
Authors: Wlodawer Alexander , Lubkowski Jacek , Minor Wladek , Jaskolski Mariusz
Published: August 2010

While figures of speech are often useful and even educational, flashy titles combined with hyperbole and imprecise language can mislead or deceive non-specialist readers and should therefore be avoided. The possibility of such confusion exists when poorly defined terms like `structure quality' or `super-resolution' are used to describe a protein structure.
Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides
Authors: Haffke Matthias , Menzel Anja , Carius Yvonne , Jahn Dieter , Heinz Dirk W.
Published: August 2010

The human ATP-binding cassette (ABC) transporter ABCB6 is involved in haem-precursor transport across the mitochondrial membrane. The crystal structure of its nucleotide-binding domain (NBD) has been determined in the apo form and in complexes with ADP, with ADP and Mg2+ and with ATP at high resolution. The overall structure is L-shaped and consists of two lobes, consistent with other reported NBD structures. Nucleotide binding is mediated by the highly conserved Tyr599 and the Walker A motif, and induces notable structural changes. Structural comparison with other structurally characterized NBDs and full-length ABC transporters gives the first insight into the possible catalytic mechanism of ABCB6 and the role of the N-terminal helix α1 in full-length ABCB6.
Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase fromBacillus anthracis
Authors: Morgunova Ekaterina , Illarionov Boris , Saller Sabine , Popov Aleksander , Sambaiah Thota , Bacher Adelbert , Cushman Mark , Fischer Markus , Ladenstein Rudolf
Published: August 2010

The crystal structure of lumazine synthase fromBacillus anthraciswas solved by molecular replacement and refined toRcryst= 23.7% (Rfree= 28.4%) at a resolution of 3.5 Å. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active againstB. anthracis.
Inclusion of weak high-resolution X-ray data for improvement of a group II intron structure
Authors: Wang Jimin
Published: August 2010

It is common to report the resolution of a macromolecular structure with the highest resolution shell having an averaged I/σ(I) ≥ 2. Data beyond the resolution thus defined are weak and often poorly measured. The exclusion of these weak data may improve the apparent statistics and also leads to claims of lower resolutions that give some leniency in the acceptable quality of refined models. However, the inclusion of these data can provide additional strong constraints on atomic models during structure refinement and thus help to correct errors in the original models, as has recently been demonstrated for a protein structure. Here, an improved group II intron structure is reported arising from the inclusion of these data, which helped to define more accurate solvent models for density modification during experimental phasing steps. With the improved resolution and accuracy of the experimental phases, extensive revisions were made to the original models such that the correct tertiary interactions of the group II intron that are essential for understanding the chemistry of this ribozyme could be described.