bluuebunny/crossref_metadata_2025 huggingface dataset:
Titanium‐containing magnetic mesoporous silica spheres: Effective enrichment of peptides and simultaneous separation of nonphosphopeptides and phosphopeptides
Authors: Li Xiao‐Shui , Su Xin , Zhu Gang‐tian , Zhao Yong , Yuan Bi‐Feng , Guo Lin , Feng Yu‐Qi
Published: June 2012

Protein phosphorylation is a common posttranslational modification, and involved in many cellular processes. Like endogenous peptides, endogenous phosphopeptides contain many biomarkers of preclinical screening and disease diagnosis. In this work, titanium‐containing magnetic mesoporous silica spheres were synthesized and applied for effective enrichment of peptides from both tryptic digests of standard proteins and human serum. Besides, the enriched peptides can be further separated into nonphosphopeptides and phosphopeptides by a simple elution. First, titanium‐containing magnetic mesoporous silica spheres were synthesized by a sol–gel method and found to have high surface area, narrow pore size distribution, and useful magnetic responsivity. Then, as the prepared material was used for selective capturing of phosphopeptides, it demonstrated to have higher selectivity than commercial titanium dioxide. Moreover, via combination of size‐exclusion mechanism, hydrophobic interaction, and affinity chromatography, titanium‐containing magnetic mesoporous silica spheres were successfully applied to simultaneously extract and separate nonphosphopeptides and phosphopeptides from standard protein digestion and human serum.
Non‐water‐suppressed proton MR spectroscopy improves spectral quality in the human spinal cord
Authors: Hock Andreas , MacMillan Erin L. , Fuchs Alexander , Kreis Roland , Boesiger Peter , Kollias Spyros S. , Henning Anke
Published: June 2012

Magnetic resonance spectroscopy enables insight into the chemical composition of spinal cord tissue. However, spinal cord magnetic resonance spectroscopy has rarely been applied in clinical work due to technical challenges, including strong susceptibility changes in the region and the small cord diameter, which distort the lineshape and limit the attainable signal to noise ratio. Hence, extensive signal averaging is required, which increases the likelihood of static magnetic field changes caused by subject motion (respiration, swallowing), cord motion, and scanner‐induced frequency drift. To avoid incoherent signal averaging, it would be ideal to perform frequency alignment of individual free induction decays before averaging. Unfortunately, this is not possible due to the low signal to noise ratio of the metabolite peaks. In this article, frequency alignment of individual free induction decays is demonstrated to improve spectral quality by using the high signal to noise ratio water peak from non‐water‐suppressed proton magnetic resonance spectroscopy via the metabolite cycling technique. Electrocardiography (ECG)‐triggered point resolved spectroscopy (PRESS) localization was used for data acquisition with metabolite cycling or water suppression for comparison. A significant improvement in the signal to noise ratio and decrease of the Cramér Rao lower bounds of all metabolites is attained by using metabolite cycling together with frequency alignment, as compared to water‐suppressed spectra, in 13 healthy volunteers. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Natural intracellular peptides can modulate the interactions of mouse brain proteins and thimet oligopeptidase with 14‐3‐3ε and calmodulin
Authors: Russo Lilian C. , Asega Amanda F. , Castro Leandro M. , Negraes Priscilla D. , Cruz Lilian , Gozzo Fabio C. , Ulrich Henning , Camargo Antonio C. M. , Rioli Vanessa , Ferro Emer S.
Published: June 2012

Protein interactions are crucial for most cellular process. Thus, rationally designed peptides that act as competitive assembly inhibitors of protein interactions by mimicking specific, determined structural elements have been extensively used in clinical and basic research. Recently, mammalian cells have been shown to contain a large number of intracellular peptides of unknown function. Here, we investigate the role of several of these natural intracellular peptides as putative modulators of protein interactions that are related to Ca2+‐calmodulin (CaM) and 14‐3‐3ε, which are proteins that are related to the spatial organization of signal transduction within cells. At concentrations of 1–50 μM, most of the peptides that are investigated in this study modulate the interactions of CaM and 14‐3‐3ε with proteins from the mouse brain cytoplasm or recombinant thimet oligopeptidase (EP24.15) in vitro, as measured by surface plasmon resonance. One of these peptides (VFDVELL; VFD‐7) increases the cytosolic Ca2+ concentration in a dose‐dependent manner but only if introduced into HEK293 cells, which suggests a wide biological function of this peptide. Therefore, it is exciting to suggest that natural intracellular peptides are novel modulators of protein interactions and have biological functions within cells.
A styryl tipno‐based nitroxide as efficient mediator for the synthesis of multiblock polystyrenes and well‐grafted polymers
Authors: Souchal Pauline , Roels Thomas , Hémery Patrick , Marx Lucien
Published: June 2012

The chloromagnesium exchange of 4‐chlorostyrene provides an easy access to a new versatile polymerizable 2,2,5‐trimethyl‐4‐phenyl‐3‐azahexane‐3‐nitroxide (TIPNO)‐based nitroxide. Indeed, first, its alkoxyamine based on the α‐methyl benzyl radical fragment efficiently mediates the polymerization of styrene (respectively n‐butyl acrylate) to yield branched polystyrene [respectively poly(n‐butyl acrylate)] with alkoxyamine function as branch point and well‐defined branches. Second, the self‐condensing of this polymerizable nitroxide by manganese coupling affords a mixture of oligomeric linear polyalkoxyamines. Polymerization of styrene mediated with these polyalkoxyamines gives multiblock polystyrenes with alkoxyamine group as linker between polystyrene blocks and exhibits the following features: the synthesis of the polystyrene blocks is controlled as their average molecular weight Mn(block) increases linearly with conversion and their average dispersity Mw/Mn(block) decreases with it. At a given temperature, the molecular weight and the dispersity of the polyalkoxyamines weakly impact Mn(block) and Mw/Mn(block). In contrast, the molecular weight of the multiblock polystyrene increases linearly with conversion until reaching a constant value. The number of block is independent of the molecular weight of the polyalkoxyamines. These unusual results can be explained by the fact that during polymerization, mediating TIPNO‐based polymeric nitroxides with different lengths are generated and are exchanged. Finally the dispersity of the multiblock polystyrene is quite broad and lies between 1.7 and 2.8. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Attenuation of treatment effect due to measurement variability in assessment of progression‐free survival
Authors: Hong S. , Schmitt N. , Stone A. , Denne J.
Published: June 2012

For normally distributed data analyzed with linear models, it is well known that measurement error on an independent variable leads to attenuation of the effect of the independent variable on the dependent variable. However, for time‐to‐event variables such as progression‐free survival (PFS), the effect of the measurement variability in the underlying measurements defining the event is less well understood. We conducted a simulation study to evaluate the impact of measurement variability in tumor assessment on the treatment effect hazard ratio for PFS and on the median PFS time, for different tumor assessment frequencies. Our results show that scan measurement variability can cause attenuation of the treatment effect (i.e. the hazard ratio is closer to one) and that the extent of attenuation may be increased with more frequent scan assessments. This attenuation leads to inflation of the type II error. Therefore, scan measurement variability should be minimized as far as possible in order to reveal a treatment effect that is closest to the truth. In disease settings where the measurement variability is shown to be large, consideration may be given to inflating the sample size of the study to maintain statistical power. Copyright © 2012 John Wiley & Sons, Ltd.
Referencing of markerless CT data sets with cone beam subvolume including registration markers to ease computer‐assisted surgery ‐ A clinical and technical research
Authors: Essig Harald , Rana Majeed , Kokemueller Horst , Zizelmann Christoph , von See Constantin , Ruecker Martin , Tavassol Frank , Gellrich Nils‐Claudius
Published: June 2012

Background

As a prerequisite in navigation‐assisted surgery, a three‐dimensional image data set with registration marker is necessary. Often patients are presented, not being aware of facing a computer‐assisted surgical intervention (CAS), with an already performed computed tomography (CT) data set without marker. The aim of this study was to evaluate the accuracy of a new method which allows performing CAS by enhancing the initial markerless data set with a marked subvolume gained by cone beam (CBCT) scan.

Methods

Therefore four registration markers are inserted and afterwards the patient is strongly limited to the field of interest scanned by CBCT scan (marked data set). Superimposed with the initial data set, a data set with reference markers and with full information is obtained.

Registration procedure was performed with group A (25 patients, superimposed marked CBCT scan) and group B (25 patients, initially marked CT scan) using BrainLab® navigation by two observers and overall system accuracy was measured using the registration landmarks and additional intraoperative landmarks (tooth cusps).

Results

Adequate image quality assumed, no significant difference between group A and B was detected. Enhancing an initially performed data set with registration marker by using a marked subvolume could improve the workflow for navigation‐assisted surgery due to the availability of cone beam scan technology, provide excellent resolution with reduced metal artifacts nearby dental restorations, and reduce radiation dose for the patient.

Conclusion

Regarding the advantages of the new method which allows performing CAS by enhancing the initial markerless data set with a marked subvolume gained by cone beam (CBCT) scan, this technique will play a major part in navigation‐assisted surgery and will address widespread general methodological solutions that are of great interest in multidisciplinary treatment. Copyright © 2013 John Wiley & Sons, Ltd.
Constraint-based correctness proofs for logic program transformations
Authors: Pettorossi Alberto , Proietti Maurizio , Senni Valerio
Published: June 2012

Many approaches proposed in the literature for proving the correctness of unfold/fold transformations of logic programs make use of measures associated with program clauses. When from a program
P
1
we derive a program
P
2
by applying a sequence of transformations, suitable conditions on the measures of the clauses in
P
2
guarantee that the transformation of
P
1
into
P
2
is correct, that is,
P
1
and
P
2
have the same least Herbrand model. In the approaches proposed so far, clause measures are fixed in advance, independently of the transformations to be proved correct. In this paper we propose a method for the automatic generation of clause measures which, instead, takes into account the particular program transformation at hand. During the application of a sequence of transformations we construct a system of linear equalities and inequalities over nonnegative integers whose unknowns are the clause measures to be found, and the correctness of the transformation is guaranteed by the satisfiability of that system. Through some examples we show that our method is more powerful and practical than other methods proposed in the literature. In particular, we are able to establish in a fully automatic way the correctness of program transformations which, by using other methods, are proved correct at the expense of fixing in advance sophisticated clause measures.
Using refinement calculus techniques to prove linearizability
Authors: Jonsson Bengt
Published: June 2012

Stepwise refinement is a method for systematically transforming a high-level program into an efficiently executable one. A sequence of successively refined programs can also serve as a correctness proof, which makes different mechanisms in the program explicit. We present rules for refinement of multi-threaded shared-variable concurrent programs. We apply our rules to the problem of verifying linearizability of concurrent objects, that are accessed by an unbounded number of concurrent threads. Linearizability is an established correctness criterion for concurrent objects, which states that the effect of each method execution can be considered to occur atomically at some point in time between its invocation and response. We show how linearizability can be expressed in terms of our refinement relation, and present rules for establishing this refinement relation between programs by a sequence of local transformations of method bodies. Contributions include strengthenings of previous techniques for atomicity refinement, as well as an absorption rule, which is particularly suitable for reasoning about concurrent algorithms that implement atomic operations. We illustrate the application of the refinement rules by proving linearizability of Treiber’s concurrent stack algorithm and Michael and Scott’s concurrent queue algorithm.
The Relationship Between Cumulative Risk and Promotive Factors and Violent Behavior Among Urban Adolescents
Authors: Stoddard Sarah A. , Whiteside Lauren , Zimmerman Marc A. , Cunningham Rebecca M. , Chermack Stephen T. , Walton Maureen A.
Published: June 2012

Resiliency theory posits that some youth exposed to risk factors do not develop negative behaviors due to the influence of promotive factors. This study examines the effects of cumulative risk and promotive factors on adolescent violent behavior and tests two models of resilience—the compensatory model and the protective model—in a sample of adolescent patients (14–18 years old; n = 726) presenting to an urban emergency department who report violent behavior. Cumulative measures of risk and promotive factors consist of individual characteristics and peer, family, and community influences. Hierarchical multiple regression was used to test the two models of resilience (using cumulative measures of risk and promotive factors) for violent behavior within a sample of youth reporting violent behavior. Higher cumulative risk was associated with higher levels of violent behavior. Higher levels of promotive factors were associated with lower levels of violent behavior and moderated the association between risk and violent behaviors. Our results support the risk‐protective model of resiliency and suggest that promotive factors can help reduce the burden of cumulative risk for youth violence.
The Impact of HIV Testing on Subjective Expectations and Risky Behavior in Malawi
Authors: Delavande Adeline , Kohler Hans-Peter
Published: June 2012

We investigate the causal impact of learning HIV status on HIV/AIDS-related expectations and sexual behavior in the medium run. Our analyses document several unexpected results about the effect of learning one’s own, or one’s spouse’s, HIV status. For example, receiving an HIV-negative test result implies higher subjective expectations about being HIV-positive after two years, and individuals tend to have larger prediction errors about their HIV status after learning their HIV status. If individuals in HIV-negative couples also learn the status of their spouse, these effects disappear. In terms of behavioral outcomes, our analyses document that HIV-positive individuals who learned their status reported having fewer partners and using condoms more often than those who did not learn their status. Among married respondents in HIV-negative couples, learning only one’s own status increases risky behavior, while learning both statuses decreases risky behavior. In addition, individuals in sero-discordant couples who learned both statuses are more likely to report some condom use. Overall, our analyses suggest that ensuring that each spouse learns the HIV status of the other, either through couple’s testing or through spousal communication, may be beneficial in high-prevalence environments.
Inheritance of male flower production in Cryptomeria japonica (sugi) estimated from analysis of a diallel mating test
Authors: Tsubomura Miyoko , Fukatsu Eitaro , Nakada Ryogo , Fukuda Yoko
Published: June 2012

Context

Clonal variation of flower production has been investigated thoroughly in coniferous tree species because of the importance of flowering in seed production from seed orchards. However, the inheritance of flower production by progeny test has not been previously studied well, so the heritability of male flower production of Cryptomeria japonica, the most important species for forestry and the main cause of pollinosis in Japan, was estimated to provide fundamental data for pollen control in seed orchards and plantation forests.

Methods

Male flower production in C. japonica was investigated for three years using 20 full-sib families created by a diallel mating design with six parents using gibberellin treatment to promote flowering.

Results

The narrow-sense individual tree heritability of male flower production in each year was estimated as ranging from 0.777 ± 0.339 to 1.050 ± 0.346 by sib analyses. The contribution of general combining ability to the total variance varied from 24.1 to 35.6 %. The highest contribution of specific combining ability was 1.42 %. By selecting the top 50 % of parental clones for reduced male flower production, the genetic gain in lowering male flower productivity was predicted as 46.1–53.0 %.

Conclusion

Our results suggest that male flower production in C. japonica is under strong genetic control and that control of male flowering by breeding is possible with a well-designed program.
Flat chains of finite size in metric spaces
Authors: Ambrosio Luigi , Ghiraldin Francesco
Published: June 2012

In this paper we investigate the notion of flat current in the metric spaces setting, and in particular we provide a definition of size of a flat current with possibly infinite mass. Exploiting the special nature of the 0-dimensional slices and the theory of metric-space valued
BV
functions we prove that a
k
-current with finite size
T
sits on a countably

\mathscr{H}^{k}

-rectifiable set, denoted by

\mathrm{set}(T)

. Moreover we relate the size measure of
T
to the geometry of the tangent space

\mathrm{Tan}^{(k)}(\mathrm{set}(T),x)

.
The cation‐dependent G‐proteins: In a class of their own
Authors: Ash Miriam-Rose , Maher Megan J. , Mitchell Guss J. , Jormakka Mika
Published: June 2012

G‐proteins are some of the most important and abundant enzymes, yet their intrinsic nucleotide hydrolysis reaction is notoriously slow and must be accelerated in vivo. Recent experiments on dynamin and GTPases involved in ribosome assembly have demonstrated that their hydrolysis activities are stimulated by potassium ions. This article presents the hypothesis that cation‐mediated activation of G‐proteins is more common than currently realised, and that such GTPases represent a structurally and functionally unique class of G‐proteins. Based on sequence analysis we provide a list of predicted cation‐dependent GTPases, which encompasses almost all members of the TEES, Obg‐HflX, YqeH‐like and dynamin superfamilies. The results from this analysis effectively re‐define the conditions under which many of these G‐proteins should be studied in vitro.
Improved protocol for measurement of plasma β‐amyloid in longitudinal evaluation of Alzheimer's Disease Neuroimaging Initiative study patients
Authors: Figurski Michal J. , Waligórska Teresa , Toledo Jon , Vanderstichele Hugo , Korecka Magdalena , Lee Virginia M.Y. , Trojanowski John Q. , Shaw Leslie M.
Published: June 2012

Background

The interassay variability and inconsistency of plasma β‐amyloid (Aβ) measurements among centers are major factors precluding the interpretation of results and a substantial obstacle in the meta‐analysis across studies of this biomarker. The goal of this investigation was to address these problems by improving the performance of the bioanalytical method.

Methods

We used the Luminex immunoassay platform with a multiplex microsphere‐based reagent kit from Innogenetics. A robotic pipetting system was used to perform crucial steps of the procedure. The performance of this method was evaluated using two kit control samples and two quality control plasma samples from volunteer donors, and by retesting previously assayed patient samples in each run. This setup was applied to process 2454 patient plasma samples from the Alzheimer's Disease Neuroimaging Initiative study biofluid repository. We have additionally evaluated the correlations between our results and cerebrospinal fluid (CSF) biomarker data using mixed‐effects modeling.

Results

The average precision values of the kit controls were 8.3% for Aβ1‐40 and 4.0% for Aβ1‐42, whereas the values for the plasma quality controls were 6.4% for Aβ1‐40 and 4.8% for Aβ1‐42. From the test–retest evaluation, the average precision was 7.2% for Aβ1‐40 and 4.5% for Aβ1‐42. The range of final plasma results for Alzheimer's Disease Neuroimaging Initiative patients was 13 to 372 pg/mL (median: 164 pg/mL) for Aβ1‐40 and 3.5 to 103 pg/mL (median: 39.3 pg/mL) for Aβ1‐42. We found that sample collection parameters (blood volume and time to freeze) have a small, but significant, influence on the result. No significant difference was found between plasma Aβ levels for patients with Alzheimer's disease and healthy control subjects. We have determined multiple significant correlations of plasma Aβ1‐42 levels with CSF biomarkers. The relatively strongest, although modest, correlation was found between plasma Aβ1‐42 levels and CSF p‐tau181/Aβ1‐42 ratio in patients with mild cognitive impairment. Plasma Aβ1‐40 correlations with CSF biomarkers were weaker and diminished completely when we used longitudinal data. No significant correlations were found for the plasma Aβ1‐42/Aβ1‐40 ratio.

Conclusions

The precision of our robotized method represents a substantial improvement over results reported in the literature. Multiple significant correlations between plasma and CSF biomarkers were found. Although these correlations are not strong enough to support the use of plasma Aβ measurement as a diagnostic screening test, plasma Aβ1‐42 levels are well suited for use as a pharmacodynamic marker.
Editorial
Authors: FELLEISEN MATTHIAS
Published: June 2012

With this issue of the Journal of Functional Programming, we transition to a new leadership. Xavier Leroy, who has faithfully served as co-Editor in Chief since 2007, is stepping down. After a short apprenticeship over the past year, Benjamin Pierce is taking his place.
The double auroral oval in the dusk‐midnight sector: Formation, mapping and dynamics
Authors: Ohtani S. , Korth H. , Wing S. , Talaat E. R. , Frey H. U. , Gjerloev J. W.
Published: June 2012

The present study observationally examines the double auroral oval structure in the evening‐premidnight sector. The results are summarized as follows; (1) The poleward auroral branch can be attributed to accelerated auroral precipitation, occasionally accompanied by Alfvénic precipitation, and it is collocated with the upward R1 current; (2) The equatorward auroral branch, which is embedded in the downward R2 current, very often if not always consists of the diffuse precipitation of energetic electrons and extends mostly poleward of the b2i boundary collocated with energetic ion precipitation; (3) The associated ionospheric convection is consistent with the two‐cell pattern, and the poleward branch is located at the zonal flow shear. It is inferred that the equatorward branch is mapped to the geosynchronous region and outside, whereas the poleward branch is mapped farther down the tail to the source region of the R1 system. It is suggested that the intense ring current and injection of energetic electrons are necessary for the equatorward branch to be distinct, but the substorm expansion phase is not favorable for the formation of the emission gap. This explains why the double oval often takes place during magnetospheric storms and during the recovery phase of intense substorms. The equatorial magnetic field is expected to be strong in the mid‐tail region, which might be related to the auroral gap region. It is also found that the poleward branch occasionally intensifies in an extended MLT sector in a few minutes, which may be explained in terms of the sudden enhancement of the return (sunward) convection flow.
Propagation of whistler mode waves through the ionosphere
Authors: Streltsov A. V. , Woodroffe J. R. , Huba J. D.
Published: June 2012

We present results from numerical studies of whistler mode wave propagation in the Earth's ionosphere when artificially created plasma ducts are present. Using realistic density profiles from the SAMI2 ionospheric code, we solve the two‐dimensional electron magnetohydrodynamics equations to study the trans‐ionospheric propagation of artificially generated whistler waves at HAARP latitudes (L = 4.9). Both ducted and non‐ducted propagation is considered, but only ducted whistlers are able to propagate without a significant reduction in wave amplitude. The conditions necessary for the trapping of waves in both high‐ and low‐density ducts are discussed with particular attention paid to the practical accessibility of these parameter regimes.
High interglacial diatom paleoproductivity in the westernmost Indo‐Pacific Warm Pool during the past 130,000 years
Authors: Romero Oscar E. , Mohtadi Mahyar , Helmke Peer , Hebbeln Dierk
Published: June 2012

A wealth of sedimentary records aimed at reconstructing late Quaternary changes in productivity and temperature have been devoted to understanding linkages between the Indo‐Pacific Warm Pool (IPWP) and other distant oceanic areas. Most of these reconstructions are based, however, on biogeochemical and sedimentological proxies, with comparatively less attention devoted to microfossils. A high‐resolution (<1 ka) study of diatom concentrations and the community at site GeoB10038‐4, recovered off southern Sumatra (ca. 6°S, 103°E), closely tracks the variations of diatom concentrations in the westernmost IPWP during the last glacial‐interglacial cycle. The diatom record provides evidence that diatom paleoproductivity was highest during interglacials, primarily due to the input of lithogenics and nutrients following the rise in sea level after full glacials. In addition, the co‐variation of total diatom concentration and Northern Hemisphere forcing for Marine Isotope Stage 5 suggests a direct response of diatom productivity and upwelling intensity to boreal summer insolation. Temporal shifts of the diverse diatom community at site GeoB10038‐4 correspond well with the present‐day seasonal monsoon pattern and the strengthening and weakening phases of upwelling along the southern coast of Sumatra. Resting spores ofChaetoceros, typical of nutrient‐rich waters, were dominant during periods of highest diatom paleoproductivity and responded to the strengthening of the SE monsoon, while diatoms of oligotrophic to mesotrophic waters characterized intermonsoon periods. The close correspondence between the dominance of upwelling diatoms and the boreal summer insolation resembles the present‐day dynamics of diatom production. The observed interglacial highs and glacial lows of diatom productivity at site GeoB10038‐4 is a unique pattern in the late Quaternary tropics.
Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates
Authors: Bowen Jennifer L , Morrison Hilary G , Hobbie John E , Sogin Mitchell L
Published: June 2012

Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because variability of rare taxa among environmental replicates may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences between samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and within-site variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. We demonstrate that the salt marsh sediments we sampled contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish site-specific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.
The arthropod, but not the vertebrate host or its environment, dictates bacterial community composition of fleas and ticks
Authors: Hawlena Hadas , Rynkiewicz Evelyn , Toh Evelyn , Alfred Andrew , Durden Lance A , Hastriter Michael W , Nelson David E , Rong Ruichen , Munro Daniel , Dong Qunfeng , Fuqua Clay , Clay Keith
Published: June 2012

Bacterial community composition in blood-sucking arthropods can shift dramatically across time and space. We used 16S rRNA gene amplification and pyrosequencing to investigate the relative impact of vertebrate host-related, arthropod-related and environmental factors on bacterial community composition in fleas and ticks collected from rodents in southern Indiana (USA). Bacterial community composition was largely affected by arthropod identity, but not by the rodent host or environmental conditions. Specifically, the arthropod group (fleas vs ticks) determined the community composition of bacteria, where bacterial communities of ticks were less diverse and more dependent on arthropod traits—especially tick species and life stage—than bacterial communities of fleas. Our data suggest that both arthropod life histories and the presence of arthropod-specific endosymbionts may mask the effects of the vertebrate host and its environment.
USP18 establishes the transcriptional and anti-proliferative interferon α/β differential
Authors: Francois-Newton Véronique , Livingstone Mark , Payelle-Brogard Béatrice , Uzé Gilles , Pellegrini Sandra
Published: June 2012

Type I IFNs (interferons) are pathogen-induced immunoregulatory cytokines that exert anti-viral and anti-proliferative activities through binding to a common cell-surface receptor. Among the 17 human IFN subtypes, IFNβ binds the IFNAR (IFNα receptor) 1/IFNAR2 receptor chains with particularly high affinity and is especially potent in select bioactivities (e.g. anti-proliferative and pro-apoptotic) when compared with IFNα2. However, no molecular basis has been ascribed to this differential action, since the two ligands are equipotent in immediate early signalling events. In the present study we report that IFNβ induces Stat (signal transducer and activator of transcription) phosphorylation and transcriptional activation of ISGs (interferon-stimulated genes), including two genes with pro-apoptotic functions, for a considerably longer time frame than does IFNα2. We show that the diversification of α2/β responses progressively builds up at the receptor level as a result of accumulating USP18 (ubiquitin specific protease 18), itself an ISG, which exerts its negative feedback action by taking advantage of the weakness of IFNα2 binding to the receptor. This represents a novel type of signalling regulation that diversifies the biological potential of IFNs α and β.
Influence of film structure and light on charge trapping and dissipation dynamics in spun-cast organic thin-film transistors measured by scanning Kelvin probe microscopy
Authors: Teague L. C. , Loth M. A. , Anthony J. E.
Published: June 2012

Herein, time-dependent scanning Kelvin probe microscopy of solution processed organic thin film transistors (OTFTs) reveals a correlation between film microstructure and OTFT device performance with the location of trapped charge within the device channel. The accumulation of the observed trapped charge is concurrent with the decrease in ISD during operation (VG = −40 V, VSD = −10 V). We discuss the charge trapping and dissipation dynamics as they relate to the film structure and show that application of light quickly dissipates the observed trapped charge.
Decomposition driven interface evolution for layers of binary mixtures. III. Two-dimensional steady films with flat and modulated surfaces
Authors: Bribesh Fathi A. M. , Fraštia Ľubor , Thiele Uwe
Published: June 2012

We study two-dimensional steady concentration and film thickness profiles for isothermal free surface films of a binary liquid mixture on a solid substrate employing model-H that couples the diffusive transport of the components of the mixture (convective Cahn-Hilliard equation) and the transport of momentum (Navier-Stokes-Korteweg equations). The analysis is based on minimising the underlying free energy equivalent to solving the static limit of model-H. Additionally, the linear stability (in time) of relevant layered films is analyzed. This allows for a comparison of the position of certain branching points in the bifurcation diagrams of steady solutions with the value predicted as onset of a linear instability. Results are presented for the cases of (i) a flat film without energetic bias at the free surface, (ii) a flat film with energetic bias, (iii) a height-modulated film without energetic bias, and (iv) a height-modulated film with energetic bias. In all cases we discuss symmetries of the various steady solutions allowing us to order them and to infer properties of solution branches and relations between them.
Solubility of NaCl in water by molecular simulation revisited
Authors: Aragones J. L. , Sanz E. , Vega C.
Published: June 2012

In this paper, the solubility of NaCl in water is evaluated by using computer simulations for three different force fields. The condition of chemical equilibrium (i.e., equal chemical potential of the salt in the solid and in the solution) is obtained at room temperature and pressure to determine the solubility of the salt. We used the same methodology that was described in our previous work [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)]10.1063/1.2397683 although several modifications were introduced to improve the accuracy of the calculations. It is found that the predictions of the solubility are quite sensitive to the details of the force field used. Certain force fields underestimate the experimental solubility of NaCl in water by a factor of four, whereas the predictions of other force fields are within 20% of the experimental value. Direct coexistence molecular dynamic simulations were also performed to determine the solubility of the salt. Reasonable agreement was found between the solubility obtained from free energy calculations and that obtained from direct coexistence simulations. This work shows that the evaluation of the solubility of salts in water can now be performed in computer simulations. The solubility depends on the ion-ion, ion-water, and water-water interactions. For this reason, the prediction of the solubility can be quite useful in future work to develop force fields for ions in water.
On the accurate direct computation of the isothermal compressibility for normal quantum simple fluids: Application to quantum hard spheres
Authors: Sesé Luis M.
Published: June 2012

A systematic study of the direct computation of the isothermal compressibility of normal quantum fluids is presented by analyzing the solving of the Ornstein-Zernike integral (OZ2) equation for the pair correlations between the path-integral necklace centroids. A number of issues related to the accuracy that can be achieved via this sort of procedure have been addressed, paying particular attention to the finite-N effects and to the definition of significant error bars for the estimates of isothermal compressibilities. Extensive path-integral Monte Carlo computations for the quantum hard-sphere fluid (QHS) have been performed in the (N, V, T) ensemble under temperature and density conditions for which dispersion effects dominate the quantum behavior. These computations have served to obtain the centroid correlations, which have been processed further via the numerical solving of the OZ2 equation. To do so, Baxter-Dixon-Hutchinson's variational procedure, complemented with Baumketner-Hiwatari's grand-canonical corrections, has been used. The virial equation of state has also been obtained and several comparisons between different versions of the QHS equation of state have been made. The results show the reliability of the procedure based on isothermal compressibilities discussed herein, which can then be regarded as a useful and quick means of obtaining the equation of state for fluids under quantum conditions involving strong repulsive interactions.
Note: Improving spatial resolution of optical frequency-domain reflectometry against frequency tuning nonlinearity using non-uniform fast Fourier transform
Authors: Ding Zhenyang , Liu Tiegen , Meng Zhuo , Liu Kun , Chen Qinnan , Du Yang , Li Dingjie , Yao X. Steve
Published: June 2012

We propose using non-uniform FFT to minimize the degrading effect of frequency tuning nonlinearity of a tunable laser source (TLS) in an optical frequency-domain reflectometry (OFDR) system. We use an auxiliary interferometer to obtain the required instantaneous optical frequency of the TLS and successfully demonstrate 100 times enhancement in spatial resolution of OFDR with only a 20% increase in computation time. The corresponding measurement reflectivity sensitivity is better than −80 dB, sufficient to detect bending induced index changes in an optical fiber.
Thickness dependent absorption and polaron photogeneration in poly-(2-metoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylene-vinylene)
Authors: Petrović J. P. , Matavulj P. S. , Pinto L. R. , Thapa A. , Živanović S. R.
Published: June 2012

A comprehensive photocurrent spectra analysis of the ITO/PEDOT:PSS/MEH-PPV/Al devices with three different poly-(2-metoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylene-vinylene) or MEH-PPV thin-film thicknesses is used to investigate charge carrier photogeneration in this polymer. The photocurrent is calculated based on the hole polaron drift-diffusion model including Poole-Frenkel (P-F) transport. Two mechanisms (monomolecular and Langevin-type bimolecular) for hole polaron recombination are considered separately. The MEH-PPV absorption coefficient spectra dependence on the thin film thickness is experimentally determined and included in our model. By comparing the simulated photocurrent spectra to measured data in the wide range of bias voltages and for devices with different MEH-PPV film thicknesses the polaron photogeneration quantum efficiency (θp) as a function of the electric field is extracted. The θp curves obtained for different devices are perfectly fitted by the P-F expression. It is shown that polaron photogeneration process in the thin MEH-PPV films is affected by the film thickness. A unique polaron photogeneration model which accounts for the field and thickness dependences is achieved when one of the P-F parameters is left to be thickness dependent.
Free energy landscape of protein-like chains with discontinuous potentials
Authors: Movahed Hanif Bayat , van Zon Ramses , Schofield Jeremy
Published: June 2012

In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond interactions, electrostatic repulsion, and covalent bond vibrations are modeled by discontinuous step, shoulder, and square-well potentials, respectively. The protein-like chains exhibit a secondary alpha helix structure in their folded states at low temperatures, and allow a natural definition of a configuration by considering which beads are bonded. Free energies and entropies of configurations are computed using the parallel tempering method in combination with hybrid Monte Carlo sampling of the canonical ensemble of the discontinuous potential system. The probability of observing the most common configuration is used to analyze the nature of the free energy landscape, and it is found that the model with the least number of possible bonds exhibits a funnel-like free energy landscape at low enough temperature for chains with fewer than 30 beads. For longer proteins, the free landscape consists of several minima, where the configuration with the lowest free energy changes significantly by lowering the temperature and the probability of observing the most common configuration never approaches one due to the degeneracy of the lowest accessible potential energy.
Reduced leakage currents and possible charge carriers tuning in Mg-doped Ga0.6Fe1.4O3 thin films
Authors: Lefevre C. , Shin R. H. , Lee J. H. , Oh S. H. , Roulland F. , Thomasson A. , Autissier E. , Meny C. , Jo W. , Viart N.
Published: June 2012

Ga0.6Fe1.4O3 is predicted to be magnetoelectric with non zero magnetization at room temperature. However, in thin films, electric properties are overshadowed by strong leakage currents. In this Letter, we show that Mg doping in Ga0.6Fe1.4O3 thin films grown by pulsed laser deposition allows decreasing the leakage current density by four orders of magnitude and might simultaneously allow tuning the carriers’ nature. These results suggest the possibility to develop a new class of material exhibiting room temperature magnetization, tunable transport properties, and magnetoelectric properties.
Biotemplated hierarchical surfaces and the role of dual length scales on the repellency of impacting droplets
Authors: McCarthy Matthew , Gerasopoulos Konstantinos , Enright Ryan , Culver James N. , Ghodssi Reza , Wang Evelyn N.
Published: June 2012

We fabricated biomimetic hierarchical superhydrophobic surfaces using the Tobacco mosaic virus and investigated the role of each length scale during droplet impact by decomposing the micro and nanoscale components. We found that 10 μl water droplets rebounded at impact velocities greater than 4.3 m/s on the hierarchical surfaces, outperforming the nanostructured surfaces, which underwent an observable wetting transition at an impact velocity of 2.7 m/s. This finding demonstrates that each length scale plays a distinct, but complementary, role in maximizing water repellency during droplet impact and, thus, provides insight into the evolutionary development of highly water-repellant hierarchical plant leaves.
The microwave and millimeter spectrum of ZnCCH ($\tilde {X}$X̃2Σ+): A new zinc-containing free radical
Authors: Min J. , Halfen D. T. , Sun M. , Harris B. , Ziurys L. M.
Published: June 2012

The pure rotational spectrum of the ZnCCH ($\tilde X$X̃2Σ+) radical has been measured using Fourier transform microwave (FTMW) and millimeter direct-absorption methods in the frequency range of 7–260 GHz. This work is the first study of ZnCCH by any type of spectroscopic technique. In the FTMW system, the radical was synthesized in a mixture of zinc vapor and 0.05% acetylene in argon, using a discharge assisted laser ablation source. In the millimeter-wave spectrometer, the molecule was created from the reaction of zinc vapor, produced in a Broida-type oven, with pure acetylene in a dc discharge. Thirteen rotational transitions were recorded for the main species, 64ZnCCH, and between 4 and 10 for the 66ZnCCH, 68ZnCCH, 64ZnCCD, and 64Zn13C13CH isotopologues. The fine structure doublets were observed in all the data, and in the FTMW spectra, hydrogen, deuterium, and carbon-13 hyperfine splittings were resolved. The data have been analyzed with a 2Σ Hamiltonian, and rotational, spin-rotation, and H, D, and 13C hyperfine parameters have been established for this radical. From the rotational constants, an rm(1) structure was determined with rZn-C = 1.9083 Å, rC-C = 1.2313 Å, and rC-H = 1.0508 Å. The geometry suggests that ZnCCH is primarily a covalent species with the zinc atom singly bonded to the C≡C—H moiety. This result is consistent with the hyperfine parameters, which suggest that the unpaired electron is localized on the zinc nucleus. The spin-rotation constant indicates that an excited 2Π state may exist ∼19 000 cm−1 in energy above the ground state.
Origins of concentration dependence of waiting times for single-molecule fluorescence binding
Authors: Yang Jin , Pearson John E.
Published: June 2012

Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence intensity changes. In many cases, rate constants inferred from fluorescence time series exhibit nonintuitive dependence on ligand concentration. Here, we examine several possible mechanistic and technical origins that may induce ligand dependence of rate constants. Using aggregated Markov models, we show under the condition of detailed balance that non-fluorescent bindings and missed events due to transient interactions, instead of conformation fluctuations, may underly the dependence of waiting times and thus apparent rate constants on ligand concentrations. In general, waiting times are rational functions of ligand concentration. The shape of concentration dependence is qualitatively affected by the number of binding sites in the single molecule and is quantitatively tuned by model parameters. We also show that ligand dependence can be caused by non-equilibrium conditions which result in violations of detailed balance and require an energy source. As to a different but significant mechanism, we examine the effect of ambient buffers that can substantially reduce the effective concentration of ligands that interact with the single molecules. To demonstrate the effects by these mechanisms, we applied our results to analyze the concentration dependence in a single-molecule experiment EGFR binding to fluorophore-labeled adaptor protein Grb2 by Morimatsu et al. [Proc. Natl. Acad. Sci. U.S.A. 104, 18013 (2007)]10.1073/pnas.0701330104.
Ferromagnetic resonance and magnetooptic study of submicron epitaxial Fe(001) stripes
Authors: Paz E. , Cebollada F. , Palomares F. J. , González J. M. , Martins J. S. , Santos N. M. , Sobolev N. A.
Published: June 2012

We present a combined magnetooptic and ferromagnetic resonance study of a series of arrays of single-crystalline Fe stripes fabricated by electron beam lithography on epitaxial Au(001)/Fe(001)/MgO(001) films grown by pulsed laser deposition. The analysis of the films revealed a clear four-fold magnetocrystalline anisotropy, with no significant presence of other anisotropy sources. The use of a large series of arrays, with stripe widths between 140 and 1000 nm and separation between them of either 200 nm or 500 nm, allowed studying their magnetization processes and resonance modes as well as the effects of the dipolar interactions on both. The magnetization processes of the stripes were interpreted in terms of a macrospin approximation, with a good agreement between experiments and calculations and negligible influence of the dipolar interactions. The ferromagnetic resonance spectra evidenced two types of resonances linked to bulk oscillation modes, essentially insensitive to the dipolar interactions, and a third one associated with edge-localized oscillations, whose resonance field is strongly dependent on the dipolar interactions. The ability to produce a high quality, controlled series of stripes provided a good opportunity to achieve an agreement between the experiments and calculations, carried out by taking into account just the Fe intrinsic properties and the morphology of the arrays, thus evidencing the relatively small role of other extrinsic factors.