bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetics of adsorption of methylene blue and rhodamine 6G on acrylic acid‐based superabsorbents
Authors: Shukla Neelesh Bharti , Madras Giridhar
Published: April 2012

Superabsorbent polymers (SAPs) of acrylic acid, sodium acrylate, and acrylamide (AM), crosslinked with ethylene glycol dimethacrylate, were synthesized by inverse suspension polymerization. The equilibrium swelling capacities of the SAPs were determined and these decreased with increasing AM content. The adsorption of the two cationic dyes, methylene blue and rhodamine 6G, on the dry as well as equilibrium swollen SAPs was investigated. The amount of the dye adsorbed at equilibrium per unit weight of the SAPs and the rate constants of adsorption were determined. The amount of the dye adsorbed at equilibrium by the SAPs decreased with increasing mol % of AM in the SAPs. The amount of the dye adsorbed at equilibrium was almost equal for the dry and equilibrium swollen SAPs. However, the equilibrium swollen SAPs adsorbed dyes at a higher rate than the dry SAPs. The higher rate of adsorption was attributed to the availability of all the anionic groups present in the fully elongated conformation of the SAPs in the equilibrium swollen state. The effect of initial dye concentration on the adsorption was also investigated and the adsorption was described by Langmuir adsorption isotherms. © 2012 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Effect of zeolite 5A on compatibility and properties of linear low‐density polyethylene/thermoplastic starch blend
Authors: Thipmanee Ranumas , Sane Amporn
Published: April 2012

Polymer composites consisting of linear low‐density polyethylene (LLDPE), thermoplastic starch (TPS), and zeolite 5A (Z), with a constant PE to TPS weight ratio of 70 : 30 and zeolite 5A contents of 1–5 wt % were prepared in the forms of pellets and films by using a co‐rotating intermeshing twin‐screw extruder and a blown film extrusion line, respectively. The objective of this work was to investigate the effect of zeolite 5A on compatibility between PE and TPS, as well as morphological, thermal, and tensile properties of PE/TPS/Z composites. The presence of zeolite 5A increased the miscibility and tensile properties of the PE/TPS blend. Tensile properties of the blend considerably improved after compounding with zeolite 5A, as the tensile strength, modulus, and elongation at break increased significantly (P ≤ 0.05) by up to ∼ 60, 30, and 70%, respectively. Increasing the zeolite 5A content from 1–5 wt % significantly increased (P ≤ 0.05) the tensile strength, modulus, and elongation at break of PE/TPS/Z composites from ∼ 12 to 16 MPa, 133 to 154 MPa, and 305 to 390%, respectively. However, the addition of zeolite 5A slightly decreased the thermal stability of the PE/TPS blend by ∼ 5–15°C. © 2012 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Clinical Outcomes of Percutaneous Interventions in Saphenous Vein Grafts Using Drug‐Eluting Stents Compared to Bare‐Metal Stents: A Comprehensive Meta‐Analysisof All Randomized Clinical Trials
Authors: Alam Mahboob , Bandeali Salman J. , Virani Salim S. , Jneid Hani M. , Shahzad Saima A. , Ramanathan Kodangudi B. , Kar Biswajit , Kleiman Neal S. , Lakkis Nasser
Published: April 2012

Background:

Clinical outcomes of percutaneous coronary intervention (PCI) in patients with saphenous vein grafts (SVGs) remain poor despite the use of drug‐eluting stents (DES). There is a disparity in clinical outcomes in SVG PCI based on various registries, and randomized clinical data remain scant. We conducted a meta‐analysis of all existing randomized controlled trials (RCTS) comparing bare‐metal stents (BMS) and DES in SVGPCIs.

Hypothesis:

PCI in patients with SVG disease using DES may reduce need for repeat revascularization without an excess mortality when compared to BMS.

Methods:

An aggregate data meta‐analysis of clinical outcomes in RCTs comparing PCI with DES vs BMS for SVGs reporting at least 12 months of follow‐up was performed. A literature search between Janurary 1, 2003 and September 30, 2011 identified 4 RCTs (812 patients; DES = 416, BMS = 396). Summary odds ratio (OR) and 95% confidence interval (CI) were calculated using the random‐effects model. The primary endpoint was all‐cause mortality. Secondary outcomes included nonfatal myocardial infarction (MI), repeat revascularization, and major adverse cardiac events (MACE). These outcomes were assessed in a cumulative fashion at 30 days, 18 months, and 36 months.

Results:

There were no intergroup differences in baseline clinical and sociodemographic characteristics. At a median follow‐up of 25 months, patients in the DES and BMS group had similar rates of death (OR: 1.63, 95% CI: 0.45–5.92), MI (OR; 0.83, 95% CI: 0.27‐2.60), and MACE (OR: 0.58, 95% CI: 0.25–1.32). Patients treated with DES had lower rates of repeat revascularization (OR: 0.40, 95% CI: 0.22–0.75).

Conclusions:

In this comprehensive meta‐analysis of all RCTs comparing clinical outcomes of PCI using DES vs BMS in patients with SVG disease, use of DES was associated with a reduction in rate of repeat revascularization and no difference in rates of all‐cause death and MI. Clin. Cardiol. 2012 DOI: 10.1002/clc.21984

Dr. Virani is supported by a Department of Veterans Affairs Health Services Research and Development Service (HSR&D) Career Development Award (CDA‐09‐028), and has research support from Merck and National Football League Charities (all grants to the institution and not individual). The views expressed in this article are those of the authors and do not necessarily represent the views of the Department of Veterans Affairs. The authors have no other funding, financial relationships, or conflicts of interest to disclose.
Preliminary results of 125I interstitial brachytherapy for locally recurrent parotid gland cancer in previously irradiated patients
Authors: Zheng Lei , Zhang Jianguo , Zhang Jie , Song Tieli , Huang Mingwei , Yu Guangyan
Published: April 2012

Background

The purpose of this study was to analyze the treatment of recurrent parotid gland cancers with radioactive iodine (125I) seed implantation.

Methods

Fifteen patients with recurrent previously irradiated parotid gland cancers were treated with postoperative 125I seed implantation between April 2004 and June 2009. Local control, survival rates, and side effects were retrospectively reviewed.

Results

The 3‐year and 5‐year local control rates were 67% and 53.6%, and the overall survival rates were 76.2% and 66.7%, respectively. Four patients with House–Brackman (H–B) grade IV cancer recovered to grade II during follow‐up. Four patients (26.7%) developed grade IV skin ulceration. Two patients (13.3%) developed moderate fibrosis of the subcutaneous tissues, and 2 patients (13.3%) had hearing loss for 1 year after brachytherapy.

Conclusion

This study showed excellent local control and a good survival rate in patients who received 125I brachytherapy. These findings should be interpreted cautiously due to the small number of patients and the relatively short follow‐up. © 2012 Wiley Periodicals, Inc. Head Neck, 2012
Detection of the primary lesion in patients with cervical metastases from unknown primary tumors with narrow band imaging endoscopy: Preliminary report
Authors: Ryu In Sun , Choi Seung‐Ho , Kim Do Hun , Han Myung Woul , Roh Jong‐Lyel , Kim Sang Yoon , Nam Soon Yuhl
Published: April 2012

Background

We investigated whether the addition of narrow band imaging (NBI) to standard diagnostic workups could enhance the detection of primary lesions in patients with carcinoma of unknown primary (CUP).

Methods

Thirty patients with CUP underwent NBI endoscopy and fluorodeoxyglucose–positron emission tomography/CT (FDG‐PET/CT) after thorough conventional diagnostic workups between 2009 and 2011. Sites suspected of harboring primary tumors, as determined by NBI and/or FDG‐PET/CT, were biopsied for histologic confirmation.

Results

Occult primary tumors were identified in 33.3% (10/30), including 13.3% (4/30) by NBI and 20.0% (6/30) by FDG‐PET/CT. All of diagnosed lesions by NBI were confirmed histologically as squamous cell carcinomas with T1 classification and identified at 2 supraglottis, 1 hypopharynx, and 1 esophagus, respectively.

Conclusions

NBI endoscopy may be a useful method for detecting primary tumors, especially for small and superficial squamous cell carcinomas of the upper aerodigestive tract, after conventional workup in patients with CUP. © 2012 Wiley Periodicals, Inc. Head Neck, 2013
Laryngeal tumor volume as a predictor for thyroid cartilage penetration
Authors: Kats Svetlana S. , Muller Susan , Aiken Ashley , Hudgins Patricia A. , Wadsworth J. Trad , Shin Dong M. , Khuri Fadlo , Beitler Jonathan J.
Published: April 2012

Background

Review of laryngectomy specimens demonstrated that preoperative CT scanning is suboptimal in predicting both thyroid cartilage penetration and extralaryngeal spread. We investigated the association between the CT‐based gross tumor volume (GTV) with pathologic evidence of thyroid cartilage penetration among patients undergoing laryngectomy for squamous cell carcinoma (SCC) of the larynx.

Methods

Ninety‐four patients were identified who underwent total laryngectomy for SCC of the larynx. GTV, as defined by preoperative diagnostic CT scan, was contoured and analyzed using treatment‐planning software.

Results

Among the 49 nonirradiated patients, the mean GTVs of patients with (n = 15) and without (n = 34) thyroid cartilage penetration was 60.1 and 28.0 cm3 (p = .004). When the nonirradiated patients were divided into 3 GTV groups (≤25 cm3, 25–50 cm3, >50 cm3), the rates of thyroid cartilage penetration were 23%, 17%, and 78%, respectively (p = .003).

Conclusions

Laryngeal tumor volume is associated with pathologic evidence of thyroid cartilage penetration in nonirradiated patients. © 2012 Wiley Periodicals, Inc. Head Neck, 2013
Status dystonicus: Predictors of outcome and progression patterns of underlying disease
Authors: Fasano Alfonso , Ricciardi Lucia , Bentivoglio Anna Rita , Canavese Carlotta , Zorzi Giovanna , Petrovic Igor , Kresojevic Nikola , Kostić Vladimir S. , Svetel Marina , Kovacs Norbert , Balas Istvan , Roubertie Agathe , Mishra Devendra , Mariotti Paolo , Temudo Teresa , Nardocci Nardo
Published: April 2012

Background:

Status dystonicus (SD) is a rare, life‐threatening disorder characterized by acute worsening of generalized dystonia.

Methods:

This study was conducted to characterize the pathogenesis, clinical course, and prognosis of SD. We reviewed the records of six centers and analyzed them together with all the cases previously reported in the literature.

Results:

Eighty‐nine episodes occurring in 68 patients were studied. The majority of patients were males (64.7%), were <15 years of age (58.8%), and had secondary dystonia as the underlying condition (37.8%). The episodes were mainly characterized by tonic muscle spasms (68.5%), with phasic forms more common in secondary forms and among females. Almost all cases needed a multistaged approach, with surgery being the most successful strategy. Neurological conditions preceding the episode worsened in 16.2% of cases (ending in death in 10.3%).

Conclusions:

The course and outcome of SD is highly variable; male gender and prevalent tonic phenotype predict a poor outcome © 2012 Movement Disorder Society
Antidot effects on the open‐shell characters and second hyperpolarizabilities of rectangular graphene nanoflakes
Authors: Yoneda Kyohei , Minamide Shu , Yamada Taishi , Ito Soichi , Minami Takuya , Kishi Ryohei , Shigeta Yasuteru , Nakano Masayoshi
Published: April 2012

Using the long‐range corrected spin‐unrestricted density functional theory method, the impact of antidot structure on the open‐shell character and the second hyperpolarizability (γ) of graphene nanoflakes (GNFs) has been investigated for rectangular GNFs with and without antidot structure, referred to as antidot and perfect GNFs, respectively. It is found that the two GNFs exhibit different multiradical characters; the antidot GNF shows intermediate open‐shell character in contrast to the perfect GNF presenting nearly pure tetraradical character. This antidot structure dependence of open‐shell character can be explained in terms of their natural orbital distributions. Such difference in open‐shell characters affects their γ values; the γ of the antidot GNF is about 1.7 times larger than that of the perfect GNF, the feature of which is in agreement with our previous results on the diradical character dependence of γ. © 2012 Wiley Periodicals, Inc.
Hydrogen bonds between pyrazine and RCOOH (R = H, CH3, and C6H5): A theoretical study
Authors: Nascimento Renata X. D. , Belarmino Márcia K. D. L. , Lima Nathália B. D.
Published: April 2012

Theoretical calculations using Møller–Plesset perturbation theory (MP2) levels of calculation with a 6‐31++G(d,p) basis set have been performed to determine stable structures and molecular properties for the 1:1 and 1:2 hydrogen complexes involving pyrazine as proton acceptor and RCOOH (R = H, CH3, and C6H5). Six complexes have been characterized as minima as no imaginary frequency was found. As expected, the HO chemical bonds lengths are increased after complexation. For the strongly bound complex, the doubly complexed pyrazine acts as a bridge between the two end molecules while transferring electrons. The vibrational changes that take place in the RCOOH after complexation with pyrazine follow the usual behavior, and the HO stretching frequency is shifted downward whereas its irradiated intensity is much enhanced. As unexpected result, the vibrational modes of the CH stretching of pyrazine has its frequencies shifted to the blue. © 2012 Wiley Periodicals, Inc.
Comparative modeling and QM/MM studies of cysteine protease mutant of Theobroma cacao
Authors: Andrade Deyse Valverde Gomes de , Góes‐Neto Aristóteles , Junior Moacyr Comar , Taranto Alex Gutterres
Published: April 2012

The culture of cacao in Brazil was highly harmed by Moniliophthora perniciosa, the fungus that causes witches' broom disease of cocoa. This disease decreases significantly the cocoa production. An important strategy for control of the witches' broom is the molecular study of the interaction between cacao–M. perniciosa. However, there is little information about of the mechanism of molecular interaction involved in resistance/vulnerability of cacoa tree. To address this problem, the Genome Project showed genes of cysteine protease involved in the mechanism of resistance/vulnerability. Cysteine protease is expressed during the process of the maturation of the seed and it is present in necrofitics period of the disease. Furthermore, proteases have a wide application in feed products, detergents, and pharmaceutical industries. This work constructed the three‐dimensional structure of the cysteine protease of Theobroma cacao by comparative modeling. Thus, the primary sequence of the cysteine protease of T. cacao was submitted to BLASTp obtaining the protein 1PCI with 36% of structural similarity. The model was refined and validated by AMBER 11.0; and evaluated by PROCHECK and ANOLEA software, respectively. This model consists of 171 amino acids, formed by 2693 atoms linked by 2719 chemical bonds. The 3D structure of this enzyme has seven α‐helix, 23 turns, and two β‐sheets. The region of the conserved active site is represented by residues Cys25 and His159. From this model, a mutant model was then generated by replacing His159/Gly. This also was evaluated showing similar characteristics. Studies of the interaction between the mutant structure with the metal ions such as Zn+2, Cu+1, Cu+2, and Cd+2 were performed by Quantum Mechanical/Molecular Mechanical (QM/MM) approach implemented in Gaussian 09W. As a result, the mutant protein is able to complex with all of them, principally with Cd+2 by −3.04 Kcal/mol. This is potentially toxic element present in the environment. Therefore this study suggests that changes in the sequence of the cysteine protease of T. Cacao can lead to development new products of commercial interest. © 2012 Wiley Periodicals, Inc.
Genetic interactions of yeast NEP1 (EMG1), encoding an essential factor in ribosome biogenesis
Authors: Schilling Valeska , Peifer Christian , Buchhaupt Markus , Lamberth Stefanie , Lioutikov Anatoli , Rietschel Benjamin , Kötter Peter , Entian Karl‐Dieter
Published: April 2012

Nep1 methylates the hypermodified ψ1191 base of 18S rRNA and has an additional essential function during ribosome biogenesis. It is strongly conserved in eukaryotes and a point mutation causes the human Bowen–Conradi syndrome. To identify Δnep1‐specific genetic interactions, viable deletions were screened genome‐wide (SGA). Due to its essential function, we used, for the first time, query strain (Δnep1) with two additive suppressor conditions (mcRPS19B, nop6‐1). Nep1 interacting genes correspond to ribosome biogenesis (RPS18A, RPS18B, RRP8, EFG1, UTP30), to ribosome quality control (UBP3, BRE5, UBP6) and to ribosome functional control (DOM34, no‐go decay). Deletions in ribosome quality and functional control genes were synthetically sick with Δnep1. They cope with malfunctions and the respective deletions strengthen the Δnep1 growth deficiency. Except for Δrps18b, deletions in the identified ribosome biogenesis genes were synthetically lethal with Δnep1. While the synthetic lethalities of Δrrp8 and Δefg1 may result from additive defects, the Δutp30 deletion seems to be in close functional relationship. The Δutp30 deletion itself has no phenotype but it enforced all nep1‐1ts mutant phenotypes. Furthermore, its overexpression partially restored the nep1‐1ts growth deficiency. Our genetic and biochemical data suggest that Utp30 and Nep1 act together during pre‐ribosomal complex formation and, along with Rps18, provide the surface for the Rps19 assembly to the 90S pre‐ribosome. Copyright © 2012 John Wiley & Sons, Ltd.
Single yeast cell vacuolar milieu viscosity assessment by fluorescence polarization microscopy with computer image analysis
Authors: Puchkov Evgeny O.
Published: April 2012

This study was undertaken to evaluate the apparent viscosity within the vacuoles of single Saccharomyces cerevisiae cells by steady‐state fluorescence anisotropy measurements of quinacrine, using wide‐field fluorescence polarization microscopy combined with computer image analysis. Quinacrine was shown to be rather specifically accumulated within the vacuoles of the cells. This accumulation was effectively reversed by ATP depletion of the cells, with no detectable binding of the dye within the vacuoles. Quinacrine fluorescence anisotropy in the sucrose solutions of various viscosities obeyed the Perrin equation. The fluorescence anisotropy of quinacrine was measured in the vacuoles of 39 cells. From cell to cell, this parameter changed in the range 0.032–0.086. Using the Perrin plot as a calibration curve, apparent viscosity values of the vacuolar milieu were calculated for each cell. The population of the cells studied was heterogeneous with regard to vacuolar viscosity, which was in the range 3.5 ± 0.4–14.06 ± 0.64 cP. There was a characteristic distribution of the frequencies of cells with apparent viscosities within certain limits, and cells with viscosity values in the range 5–6 cP were the most frequent. No relationship was found between the sizes of the vacuoles and their apparent viscosities. Copyright © 2012 John Wiley & Sons, Ltd.
Gesundheit und integrierte Stadtentwicklung
Authors: Böhme Christa
Published: April 2012

Einleitung

Die Gesundheit des Menschen wird von verschiedenen Faktoren determiniert. Neben Alter, Geschlecht und genetischen Dispositionen, Lebensstil und Verhaltensweisen sowie sozialen Netzwerken sind dies vor allem die Lebensbedingungen und -verhältnisse der Menschen. Aufgabe der Stadtentwicklung ist es, diese Lebensverhältnisse vor Ort in den Kommunen zu gestalten. Entscheidungen zur Stadtentwicklung haben daher seit jeher die Gesundheit der Menschen in den Städten beeinflusst.
Droplet dispensing in digital microfluidic devices: Assessment of long-term reproducibility
Authors: Elvira Katherine S. , Leatherbarrow Robin , Edel Joshua , deMello Andrew
Published: April 2012

We report an in-depth study of the long-term reproducibility and reliability of droplet dispensing in digital microfluidic devices (DMF). This involved dispensing droplets from a reservoir, measuring the volume of both the droplet and the reservoir droplet and then returning the daughter droplet to the original reservoir. The repetition of this process over the course of several hundred iterations offers, for the first time, a long-term view of droplet dispensing in DMF devices. Results indicate that the ratio between the spacer thickness and the electrode size influences the reliability of droplet dispensing. In addition, when the separation between the plates is large, the volume of the reservoir greatly affects the reproducibility in the volume of the dispensed droplets, creating “reliability regimes.” We conclude that droplet dispensing exhibits superior reliability as inter-plate device spacing is decreased, and the daughter droplet volume is most consistent when the reservoir volume matches that of the reservoir electrode.
Tuning bubbly structures in microchannels
Authors: Vuong Sharon M. , Anna Shelley L.
Published: April 2012

Foams have many useful applications that arise from the structure and size distribution of the bubbles within them. Microfluidics allows for the rapid formation of uniform bubbles, where bubble size and volume fraction are functions of the input gas pressure, liquid flow rate, and device geometry. After formation, the microchannel confines the bubbles and determines the resulting foam structure. Bubbly structures can vary from a single row (“dripping”), to multiple rows (“alternating”), to densely packed bubbles (“bamboo” and dry foams). We show that each configuration arises in a distinct region of the operating space defined by bubble volume and volume fraction. We describe the boundaries between these regions using geometric arguments and show that the boundaries are functions of the channel aspect ratio. We compare these geometric arguments with foam structures observed in experiments using flow-focusing, T-junction, and co-flow designs to generate stable nitrogen bubbles in aqueous surfactant solution and stable droplets in oil containing dissolved surfactant. The outcome of this work is a set of design parameters that can be used to achieve desired foam structures as a function of device geometry and experimental control parameters.
High-pressure cell for neutron reflectometry of supercritical and subcritical fluids at solid interfaces
Authors: Carmichael Justin R. , Rother Gernot , Browning James F. , Ankner John F. , Banuelos Jose L. , Anovitz Lawrence M. , Wesolowski David J. , Cole David R.
Published: April 2012

A new high-pressure cell design for use in neutron reflectometry (NR) for pressures up to 50 MPa and a temperature range of 300–473 K is described. The cell design guides the neutron beam through the working crystal without passing through additional windows or the bulk fluid, which provides for a high neutron transmission, low scattering background, and low beam distortion. The o-ring seal is suitable for a wide range of subcritical and supercritical fluids and ensures high chemical and pressure stability. Wafers with a diameter of 5.08 cm (2 in.) and 5 mm or 10 mm thickness can be used with the cells, depending on the required pressure and momentum transfer range. The fluid volume in the sample cell is very small at about 0.1 ml, which minimizes scattering background and stored energy. The cell design and pressure setup for measurements with supercritical fluids are described. NR data are shown for silicon/silicon oxide and quartz wafers measured against air and subsequently within the high-pressure cell to demonstrate the neutron characteristics of the high-pressure cell. Neutron reflectivity data for supercritical CO2 in contact with quartz and Si/SiO2 wafers are also shown.
Optical breakdown threshold investigation of 1064 nm laser induced air plasmas
Authors: Thiyagarajan Magesh , Thompson Shane
Published: April 2012

We present the theoretical and experimental measurements and analysis of the optical breakdown threshold for dry air by 1064 nm infrared laser radiation and the significance of the multiphoton and collisional cascade ionization process on the breakdown threshold measurements over pressures range from 10 to 2000 Torr. Theoretical estimates of the breakdown threshold laser intensities and electric fields are obtained using two distinct theories namely multiphoton and collisional cascade ionization theories. The theoretical estimates are validated by experimental measurements and analysis of laser induced breakdown processes in dry air at a wavelength of 1064 nm by focusing 450 mJ max, 6 ns, 75 MW max high-power 1064 nm IR laser radiation onto a 20 μm radius spot size that produces laser intensities up to 3 – 6 TW/cm2, sufficient for air ionization over the pressures of interest ranging from 10 to 2000 Torr. Analysis of the measured breakdown threshold laser intensities and electric fields are carried out in relation with classical and quantum theoretical ionization processes, operating pressures. Comparative analysis of the laser air breakdown results at 1064 nm with corresponding results of a shorter laser wavelength (193 nm) [M. Thiyagarajan and J. E. Scharer, IEEE Trans. Plasma Sci. 36, 2512 (2008)] and a longer microwave wavelength (108 nm) [A. D. MacDonald, Microwave Breakdown in Gases (Wiley, New York, 1966)]. A universal scaling analysis of the breakdown threshold measurements provided a direct comparison of breakdown threshold values over a wide range of frequencies ranging from microwave to ultraviolet frequencies. Comparison of 1064 nm laser induced effective field intensities for air breakdown measurements with data calculated based on the collisional cascade and multiphoton breakdown theories is used successfully to determine the scaled collisional microwave portion. The measured breakdown threshold of 1064 nm laser intensities are then scaled to classical microwave breakdown theory after correcting for the multiphoton ionization process for different pressures and good agreement, regarding both pressure dependence and breakdown threshold electric fields, is obtained. The effect of the presence of submicron particles on the 1064 nm breakdown threshold was also investigated. The measurements show that higher breakdown field is required, especially at lower pressures, and in close agreement with classical microwave breakdown theory and measurements in air.
Two-dimensional numerical study of a period-two dielectric-barrier discharge in atmospheric argon
Authors: Zhang Dingzong , Wang Yanhui , Sun Jizhong , Wang Dezhen
Published: April 2012

A two-dimensional fluid simulation is performed on an atmospheric dielectric barrier discharge (DBD) in pure argon to explore the formation mechanism and spatiotemporal evolution of period-two DBD at atmospheric pressure. The results show that the formation of the period-two discharge is directly correlated to the spatial distribution of electron density. It is found that when under certain conditions, a local high electron density region occurs before a new discharge is ignited, and the discharge current varies in magnitude depending on whereabouts of the local high electron density region. When the local high electron density region appears near the momentary anode, it barely affects the discharge current. In contrast, when the high electron density region appears in the vicinity of the cathode, it reduces the discharge current greatly, since it restrains the growth of the electric field. The local high electron density region disappears completely before the two voltage cycles end, and thus the discharge exhibits the appearance of period-two state. The radial current and electron density distributions at different times indicate that different discharge events within one oscillation period of period-two discharge possess different radial behaviors. The causes for these radial behaviors are further analyzed and discussed in this paper.
Optimal dielectric thickness for ferroelectric tunnel junctions with a composite barrier
Authors: Ma Z. J. , Zhang T. J. , Pan R. K. , Duan M. G. , He M.
Published: April 2012

Theoretical investigations on ferroelectric tunnel junctions (FTJs) with a fixed-thickness composite layer (Pt/MgO/BaTiO3/Pt and Pt/SrTiO3/BaTiO3/Pt) were conducted. It showed that there is an optimal dielectric thickness that can bring the largest tunneling electroresistance (TER) ratio provided that the ferroelectricity does not change with the dielectric thickness. The optimal dielectric thickness is insensitive to ferroelectric polarization in ferroelectric layer and increases linearly with the composite barrier thickness. Considering the size effect of ferroelectricity, the optimal dielectric thickness (unit cells) changes little if the polarization increases slowly with the ferroelectric thickness. Such studies may help to fabricate FTJs with larger TER ratio and put them into practical application.
Multireference Fock space coupled cluster method in the effective and intermediate Hamiltonian formulation for the (2,0) sector
Authors: Musiał Monika
Published: April 2012

The effective and intermediate Hamiltonian (IH) multireference coupled cluster (CC) method with singles (S) and doubles (D) within the double electron attached (2,0) sector of the Fock space (FS) is formulated and implemented. The intermediate Hamiltonian realization of the (2,0) FS problem allows to replace the iterative scheme of the FS-CC equations based on the effective Hamiltonian with the diagonalization of the properly constructed matrix. The proposed method, IH-FS-CCSD (2,0), is rigorously size-extensive, easy to code, and numerically very efficient with the results comparable or slightly better than equation-of-motion ones at the CCSDT (T—triples) level. The performance of the method is discussed on the basis of test calculations for potential energy curves of the systems for which double positive ions dissociate into closed shell fragments (e.g., Na2 dimer). The double electron attachment (DEA) scheme can be also useful in determination of the excitation spectra for difficult cases. The example is a carbon atom which has two electrons out of the closed shell structure. The newly implemented method is also analyzed by plotting potential energy curve for twisted ethylene case as a function of a dihedral angle between two methylene groups. Using DEA scheme one obtains a smooth, cusp free curve.
Precession frequency and fast switching dependence on the in-plane and out-of-plane dual spin-torque polarizers
Authors: Zhang Hong , Hou Zhiwei , Zhang Jianwei , Zhang Zongzhi , Liu Yaowen
Published: April 2012

Steady magnetization precession can be excited by a DC spin-polarized current in a spin-valve with combined in-plane (IP) and out-of-plane (OP) dual polarizers. The precession frequency is proportional to the strength of spin-torque generated by the OP polarizer but less sensitive to the IP polarizer, which can be successfully interpreted by an analytic model. A single current pulse with its duration as short as 150 ps is able to drive the magnetization switching. The switching probability is dominated by the value of the free layer angle φc at which the free layer magnetization rotation transforms to a damped small angle precession after stopping the current pulse.
A readout for large arrays of microwave kinetic inductance detectors
Authors: McHugh Sean , Mazin Benjamin A. , Serfass Bruno , Meeker Seth , O’Brien Kieran , Duan Ran , Raffanti Rick , Werthimer Dan
Published: April 2012

Microwave kinetic inductance detectors (MKIDs) are superconducting detectors capable of counting single photons and measuring their energy in the UV, optical, and near-IR. MKIDs feature intrinsic frequency domain multiplexing (FDM) at microwave frequencies, allowing the construction and readout of large arrays. Due to the microwave FDM, MKIDs do not require the complex cryogenic multiplexing electronics used for similar detectors, such as transition edge sensors, but instead transfer this complexity to room temperature electronics where they present a formidable signal processing challenge. In this paper, we describe the first successful effort to build a readout for a photon counting optical/near-IR astronomical instrument, the ARray Camera for Optical to Near-infrared Spectrophotometry. This readout is based on open source hardware developed by the Collaboration for Astronomy Signal Processing and Electronics Research. Designed principally for radio telescope backends, it is flexible enough to be used for a variety of signal processing applications.
Continuous-waveform constant-current isolated physiological stimulator
Authors: Holcomb Mark R. , Devine Jack M. , Harder Rene , Sidorov Veniamin Y.
Published: April 2012

We have developed an isolated continuous-waveform constant-current physiological stimulator that is powered and controlled by universal serial bus (USB) interface. The stimulator is composed of a custom printed circuit board (PCB), 16-MHz MSP430F2618 microcontroller with two integrated 12-bit digital to analog converters (DAC0, DAC1), high-speed H-Bridge, voltage-controlled current source (VCCS), isolated USB communication and power circuitry, two isolated transistor-transistor logic (TTL) inputs, and a serial 16 × 2 character liquid crystal display. The stimulators are designed to produce current stimuli in the range of ±15 mA indefinitely using a 20V source and to be used in ex vivo cardiac experiments, but they are suitable for use in a wide variety of research or student experiments that require precision control of continuous waveforms or synchronization with external events. The device was designed with customization in mind and has features that allow it to be integrated into current and future experimental setups. Dual TTL inputs allow replacement by two or more traditional stimulators in common experimental configurations. The MSP430 software is written in C++ and compiled with IAR Embedded Workbench 5.20.2. A control program written in C++ runs on a Windows personal computer and has a graphical user interface that allows the user to control all aspects of the device.
Communication: Bulkiness versus anisotropy: The optimal shape of polarizable Brownian nanoparticles for alignment in electric fields
Authors: Kwaadgras Bas W. , Dijkstra Marjolein , van Roij René
Published: April 2012

Self-assembly and alignment of anisotropic colloidal particles are important processes that can be influenced by external electric fields. However, dielectric nanoparticles are generally hard to align this way because of their small size and low polarizability. In this work, we employ the coupled dipole method to show that the minimum size parameter for which a particle may be aligned using an external electric field depends on the dimension ratio that defines the exact shape of the particle. We show, for rods, platelets, bowls, and dumbbells, that the optimal dimension ratio (the dimension ratio for which the size parameter that first allows alignment is minimal) depends on a nontrivial competition between particle bulkiness and anisotropy because more bulkiness implies more polarizable substance and thus higher polarizability, while more anisotropy implies a larger (relative) difference in polarizability.
The costimulatory immunogen LPS induces the B-Cell clones that infiltrate transplanted human kidneys
Authors: Grover Rajesh K. , Cheng Julong , Peng Yingjie , Jones Teresa M. , Ruiz Diana I. , Ulevitch Richard J. , Glass John I. , Dennis Edward A. , Salomon Daniel R. , Lerner Richard A.
Published: April 2012

The mechanism of chronic rejection of transplanted human kidneys is unknown. An understanding of this process is important because, chronic rejection ultimately leads to loss of the kidney allograft in most transplants. One feature of chronic rejection is the infiltration of ectopic B-cell clusters that are clonal into the transplanted kidney. We now show that the antibodies produced by these B-cells react strongly with the core carbohydrate region of LPS. Since LPS is a costimulatory immunogen that can react with both the B-cell receptor (BCR) and the Toll-like receptor 4 (TLR4), these results suggest a mechanism for the selective pressure that leads to clonality of these B-cell clusters and opens the possibility that infection and the attendant exposure to LPS plays a role in the chronic rejection of human kidney transplants. If confirmed by clinical studies, these results suggest that treating patients with signs of chronic rejection with antibiotics may improve kidney allograft survival.
Bayesian integration of networks without gold standards
Authors: Weile Jochen , James Katherine , Hallinan Jennifer , Cockell Simon J. , Lord Phillip , Wipat Anil , Wilkinson Darren J.
Published: April 2012

Motivation: Biological experiments give insight into networks of processes inside a cell, but are subject to error and uncertainty. However, due to the overlap between the large number of experiments reported in public databases it is possible to assess the chances of individual observations being correct. In order to do so, existing methods rely on high-quality ‘gold standard’ reference networks, but such reference networks are not always available.

Results: We present a novel algorithm for computing the probability of network interactions that operates without gold standard reference data. We show that our algorithm outperforms existing gold standard-based methods. Finally, we apply the new algorithm to a large collection of genetic interaction and protein–protein interaction experiments.

Availability: The integrated dataset and a reference implementation of the algorithm as a plug-in for the Ondex data integration framework are available for download at http://bio-nexus.ncl.ac.uk/projects/nogold/

Contact:  darren.wilkinson@ncl.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Matrix eQTL: ultra fast eQTL analysis via large matrix operations
Authors: Shabalin Andrey A.
Published: April 2012

Motivation: Expression quantitative trait loci (eQTL) analysis links variations in gene expression levels to genotypes. For modern datasets, eQTL analysis is a computationally intensive task as it involves testing for association of billions of transcript-SNP (single-nucleotide polymorphism) pair. The heavy computational burden makes eQTL analysis less popular and sometimes forces analysts to restrict their attention to just a small subset of transcript-SNP pairs. As more transcripts and SNPs get interrogated over a growing number of samples, the demand for faster tools for eQTL analysis grows stronger.

Results: We have developed a new software for computationally efficient eQTL analysis called Matrix eQTL. In tests on large datasets, it was 2–3 orders of magnitude faster than existing popular tools for QTL/eQTL analysis, while finding the same eQTLs. The fast performance is achieved by special preprocessing and expressing the most computationally intensive part of the algorithm in terms of large matrix operations. Matrix eQTL supports additive linear and ANOVA models with covariates, including models with correlated and heteroskedastic errors. The issue of multiple testing is addressed by calculating false discovery rate; this can be done separately for cis- and trans-eQTLs.

Availability: Matlab and R implementations are available for free at http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL

Contact:  shabalin@email.unc.edu
Rigorous assessment of gene set enrichment tests
Authors: Naeem Haroon , Zimmer Ralf , Tavakkolkhah Pegah , Küffner Robert
Published: April 2012

Motivation: Several statistical tests are available to detect the enrichment of differential expression in gene sets. Such tests were originally proposed for analyzing gene sets associated with biological processes. The objective evaluation of tests on real measurements has not been possible as it is difficult to decide a priori, which processes will be affected in given experiments.

Results: We present a first large study to rigorously assess and compare the performance of gene set enrichment tests on real expression measurements. Gene sets are defined based on the targets of given regulators such as transcription factors (TFs) and microRNAs (miRNAs). In contrast to processes, TFs and miRNAs are amenable to direct perturbations, e.g. regulator over-expression or deletion. We assess the ability of 14 different statistical tests to predict the perturbations from expression measurements in Escherichia coli, Saccharomyces cerevisiae and human. We also analyze how performance depends on the quality and comprehensiveness of the regulator targets via a permutation approach. We find that ANOVA and Wilcoxons test consistently perform better than for instance Kolmogorov–Smirnov and hypergeometric tests. For scenarios where the optimal test is not known, we suggest to combine all evaluated tests into an unweighted consensus, which also performs well in our assessment. Our results provide a guide for the selection of existing tests as well as a basis for the development and assessment of novel tests.

Contact:  robert.kueffner@bio.ifi.lmu.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses
Authors: Jourdren Laurent , Bernard Maria , Dillies Marie-Agnès , Le Crom Stéphane
Published: April 2012

Summary: We developed a modular and scalable framework called Eoulsan, based on the Hadoop implementation of the MapReduce algorithm dedicated to high-throughput sequencing data analysis. Eoulsan allows users to easily set up a cloud computing cluster and automate the analysis of several samples at once using various software solutions available. Our tests with Amazon Web Services demonstrated that the computation cost is linear with the number of instances booked as is the running time with the increasing amounts of data.

Availability and implementation: Eoulsan is implemented in Java, supported on Linux systems and distributed under the LGPL License at: http://transcriptome.ens.fr/eoulsan/

Contact:  eoulsan@biologie.ens.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
PaGeFinder: quantitative identification of spatiotemporal pattern genes
Authors: Pan Jian-Bo , Hu Shi-Chang , Wang Hao , Zou Quan , Ji Zhi-Liang
Published: April 2012

Summary: Pattern Gene Finder (PaGeFinder) is a web-based server for on-line detection of gene expression patterns from serial transcriptomic data generated by high-throughput technologies like microarray or next-generation sequencing. Three particular parameters, the specificity measure, the dispersion measure and the contribution measure, were introduced and implemented in PaGeFinder to help quantitative and interactive identification of pattern genes like housekeeping genes, specific (selective) genes and repressed genes. Besides the on-line computation service, the PaGeFinder also provides downloadable Java programs for local detection of gene expression patterns.

Availability:  http://bioinf.xmu.edu.cn:8080/PaGeFinder/index.jsp

Contact:  appo@xmu.edu.cn; zouquan@xmu.edu.cn
Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions
Authors: Teschendorff Andrew E. , Widschwendter Martin
Published: April 2012

Motivation: The standard paradigm in omic disciplines has been to identify biologically relevant biomarkers using statistics that reflect differences in mean levels of a molecular quantity such as mRNA expression or DNA methylation. Recently, however, it has been proposed that differential epigenetic variability may mark genes that contribute to the risk of complex genetic diseases like cancer and that identification of risk and early detection markers may therefore benefit from statistics based on differential variability.

Results: Using four genome-wide DNA methylation datasets totalling 311 epithelial samples and encompassing all stages of cervical carcinogenesis, we here formally demonstrate that differential variability, as a criterion for selecting DNA methylation features, can identify cancer risk markers more reliably than statistics based on differences in mean methylation. We show that differential variability selects features with heterogeneous outlier methylation profiles and that these play a key role in the early stages of carcinogenesis. Moreover, differentially variable features identified in precursor non-invasive lesions exhibit significantly increased enrichment for developmental genes compared with differentially methylated sites. Conversely, differential variability does not add predictive value in cancer studies profiling invasive tumours or whole-blood tissue. Finally, we incorporate the differential variability feature selection step into a novel adaptive index prediction algorithm called EVORA (epigenetic variable outliers for risk prediction analysis), and demonstrate that EVORA compares favourably to powerful prediction algorithms based on differential methylation statistics.

Conclusions: Statistics based on differential variability improve the detection of cancer risk markers in the context of DNA methylation studies profiling epithelial preinvasive neoplasias. We present a novel algorithm (EVORA) which could be used for prediction and diagnosis of precursor epithelial cancer lesions.

Availability: R-scripts implementing EVORA are available from CRAN (www.r-project.org).

Contact:  a.teschendorff@ucl.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies
Authors: Gritsenko Alexey A. , Nijkamp Jurgen F. , Reinders Marcel J.T. , Ridder Dick de
Published: April 2012

Motivation: The increasing availability of second-generation high-throughput sequencing (HTS) technologies has sparked a growing interest in de novo genome sequencing. This in turn has fueled the need for reliable means of obtaining high-quality draft genomes from short-read sequencing data. The millions of reads usually involved in HTS experiments are first assembled into longer fragments called contigs, which are then scaffolded, i.e. ordered and oriented using additional information, to produce even longer sequences called scaffolds. Most existing scaffolders of HTS genome assemblies are not suited for using information other than paired reads to perform scaffolding. They use this limited information to construct scaffolds, often preferring scaffold length over accuracy, when faced with the tradeoff.

Results: We present GRASS (GeneRic ASsembly Scaffolder)—a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which combines contig order, distance and orientation in a single optimization objective. The resulting optimization problem is solved using an expectation–maximization procedure and an unconstrained binary quadratic programming approximation of the original problem. We compared GRASS with existing HTS scaffolders using Illumina paired reads of three bacterial genomes. Our algorithm constructs a comparable number of scaffolds, but makes fewer errors. This result is further improved when additional data, in the form of related genome sequences, are used.

Availability: GRASS source code is freely available from http://code.google.com/p/tud-scaffolding/.

Contact:  a.gritsenko@tudelft.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.