bluuebunny/crossref_metadata_2025 huggingface dataset:
Differences and similarities between chronic obstructive pulmonary disease and asthma
Authors: Jeffery P. K.
Published: November 2010

Asthma and chronic obstructive pulmonary disease (COPD) are complex conditions with imprecise definitions, which make definitive morphological comparisons difficult. The airways in asthma are occluded by tenacious plugs of exudate and mucus, and there is fragility of airway surface epithelium, thickening of the reticular layer beneath the epithelial basal lamina (the last two not usually features of COPD), and bronchial vessel congestion and oedema. There is an increased inflammatory infiltrate comprising ‘activated’ lymphocytes and eosinophils with release of granular content in the latter, and enlargement of bronchial smooth muscle, particularly in medium‐sized bronchi. CD4+ve lymphocytes predominate over CD8+ve cells and neutrophils are sparse.

In contrast, three conditions contribute to COPD. In chronic bronchitis there is cough and mucous hypersecretion with enlargement of tracheobronchial submucosal glands and a disproportionate increase of mucous acini. CD8+ve lymphocytes predominate over CD4+ve cells and there are increased numbers of subepithelial macrophages and intra‐epithelial neutrophils. Exacerbations of bronchitis are associated with a tissue eosinophilia, apparent absence of IL‐5 protein but gene expression for IL‐4 and IL‐5 is present. In small or peripheral airways disease, there is inflammation of bronchioli and mucous metaplasia and hyperplasia, with increased intraluminal mucus, increased wall muscle, fibrosis, and airway stenoses (also referred to as chronic obstructive bronchiolitis). Respiratory bronchiolitis involving increased numbers of pigmented macrophages is a critically important early lesion. Increasingly severe peribronchiolitis includes infiltration of T lymphocytes in which the CD8+ subset again predominates. These inflammatory changes may predispose to the development of centrilobular emphysema and reduced FEV1 via the destruction of alveolar attachments. In emphysema there is abnormal, permanent enlargement of airspaces distal to the terminal bronchiolus (i.e. within the acinus) accompanied by destruction of alveolar walls and without obvious fibrosis. The severity of emphysema, rather than type, appears to be the most important determinant of chronic deterioration of airflow, and in this there may be significant loss of elastic recoil and microscopic emphysema prior to the observed macroscopic destruction of the acinus.
Non‐H1‐receptor effects of antihistamines
Authors: Church M. K.
Published: November 2010

Visit any international allergy meeting and you will soon learn that there are a plethora of very potent and effective histamine H1‐receptor antagonists, or antihistamines as they are more often called. Thus, in order to make any particular antihistamine stand out therapeutically or commercially from the others, additional properties, e.g. anti‐inflammatory properties, are often claimed. But are these claims valid and, if so, are the ‘additional properties' clinically relevant? This document will review the evidence behind some of the ‘additional properties' of antihistamines and lay the basis for discussion of their relevance.
H1‐receptor antagonists: effects on leukocytes, myth or reality?
Authors: De Vos C.
Published: November 2010

H1‐receptor antagonists of the first and second generation have been used for many years to relieve symptoms arising from the action of histamine on the H1receptor. However, allergic inflammation is more than histamine release and action. Leukocyte infiltration during late allergic manifestations was demonstrated as being a hallmark of allergic inflammation. Second‐generation H1‐receptor antagonists were studied in models of mast cell degranulationin vitroand of leukocyte infiltrationin vivo. Analysis of the literature showed that a drug which is no more metabolized than cetirizine and fexofenadine allows a better relevance ofin vitromodels. Up to now, cetirizine was the only productin vivoable to reduce eosinphil infiltration in skin, nose, eyes and lungs during experimental allergenic challenges and late allergic inflammatory manifestations. Today, relevance of these properties can be seen in the recently published clinical results showing that cetirizine prevents the development of asthma in specifically sensitized infants with atopic dermatitis.
Clinical assessment of antihistamines in rhinitis
Authors: Scadding G. K.
Published: November 2010

The first line of treatment for allergic rhinitis must be identification and avoidance as far as possible of the relevant allergens. This is rarely completely successful and so pharmaceutical treatment is also needed. Antihistamines are effective in allergic rhinitis, which comprises approximately 80% of rhinitis found in children and 30% in adults. Antihistamines antagonize the effect of histamine at the H1 receptor and their major clinical effects are related to this. They are effective against rhinorrhoea, itch and sneezing but have little effect on nasal obstruction. Clinical trials show between 36% and 80% of patients experiencing good to excellent symptom relief (approximately twice that induced by placebo), in seasonal allergic rhinitis; between 55% and 86% of patients experience moderate to excellent symptom relief in perennial allergic rhinitis. Meta‐analysis reveals that antihistamines are inferior to corticosteroids in allergic rhinitis therapy. Antihistamines are generally well tolerated, although serious cardiac dysrhythmias have occurred with terfenadine and astemizole. Their place in therapy is probably as sole agent in mild, intermittent rhinitis and in combination with topical corticosteroids in more severe disease not controlled by corticosteroids alone.
Clinical practice evaluation of atosiban in preterm labour management in six European countries
Authors: Husslein P , Roura LC , Dudenhausen J , Helmer H , Frydman R , Rizzo N , Schneider D ,   TREASURE study group
Published: November 2010

Objective  To evaluate the efficacy and safety of early administration compared with standard administration of atosiban, when predefined eligibility criteria were met.

Design  A prospective, open‐label, randomised clinical trial. Women were randomised to receive atosiban either immediately (early) or when specified criteria, in terms of duration/frequency of uterine contraction or status of cervical dilation/effacement, were fulfilled (standard).

Setting  Carried out at 105 centres in six European countries.

Population  Pregnant women admitted to hospital in threatened preterm labour between 24 and 34 weeks of gestation, comprising a subgroup of women enrolled in the Tractocile Efficacy Assessment Survey in Europe (TREASURE) clinical experience review.

Main outcome measures  Efficacy was defined as the successful delay of delivery with no alternative tocolytic agent for 48 hours.

Results  More women in the early group remained undelivered at 48 hours with no alternative tocolytic agent compared with those who received atosiban when specified criteria were fulfilled (88.9 versus 76.1%; P = 0.03). Safety was comparable between the groups. There were no statistical differences in maternal, fetal or neonatal adverse events between the early and standard atosiban arms.

Conclusions  The use of atosiban was effective for the delay of preterm labour and presented no safety concerns irrespective of the time it was administered.
Intrapartum ultrasound estimation of total bladder volume
Authors: Gyampoh B. , Crouch N. , O'Brien P. , O'Sullivan C. , Cutner A.
Published: November 2010

Objective  To determine whether real‐time ultrasound measurement of multiple linear dimensions of the bladder could be used to estimate total bladder volumes of women in labour.

Aim  To create a simple reproducible formula using ultrasound techniques to help estimate total bladder volumes of women in labour. This may prevent unnecessary catheterisation and conversely, avoid failure to catheterise when indicated, thereby reducing the complications associated with catheterisation and bladder overdistension.

Design  Prospective, observational study of women in labour.

Setting  Delivery Suite, Obstetric Hospital, University College London Hospitals.

Population  Forty‐nine women in labour recommended for catheterisation by their attending midwives.

Method  A real‐time ultrasound scanner was used to measure bladder diameters in two planes: transverse width and height, and sagittal width and height. A Foley's catheter was inserted and the bladder drained into a graduated bowl under sterile conditions. These values and urine volumes were recorded and a formula for detecting bladder volumes above 300 mL was developed using linear regression methods and the Bland–Altman limits of agreement.

Main outcome measure  Sensitivity and specificity of derived formulae in predicting bladder volume from ultrasound measurements. Correctly predicted volumes greater than 300 mL.

Results  Among the 49 women, 36 were nulliparous and 13 were multiparous. All had full‐term pregnancies with cephalic presentation and were in active labour with cervical dilatations ranging from 3 to 10 cm. There were no previous caesarean sections among the multiparous women. Thirty‐nine women had epidural analgesia. Indications for catheterisation included a palpable bladder per abdomen, or the interval from last urine voided. The catheterised volumes ranged from 30 to 720 mL with a median of 150 mL. The new equation (0.68 ×h×d×w) had a sensitivity of 77% (95% CI 46–95%) and specificity of 86% (95% CI 71–95%) for detecting bladder volumes greater than 300 mL. In order to ensure that about 95% of women in need of catheterisation are detected, the above equation was improved using the Bland–Altman limits of agreement. The sensitivity of this final equation (1.74 ×h×d×w) was 100% (95% CI 75–100%) and the specificity dropped to 36% (95% CI 21–54%).

Conclusion  It is possible to use real‐time ultrasound in estimation of total bladder volumes of women in labour. The implications are that all of those normally selected as being in need of catheterisation could be detected, while about a quarter of those women would avoid unnecessary catheterisation.
Ethics and Equipoise: Rationale for a Placebo‐Controlled Study Design of Platelet Glycoprotein IIb/IIIa Inhibition in Coronary Intervention
Authors: TCHENG JAMES E. , MADAN MINA , O'SHEA J. CONOR , COHEN ERIC A. , BULLER CHRISTOPHER E. , LINCOFF A. MICHAEL , POPMA JEFFREY J. , TEIRSTEIN PAUL S. , KITT MICHAEL M. , LORENZ TODD J. , GREENBERG SALLY , FOST NORMAN , CALIFF ROBERT M.
Published: November 2010

Rarely is it straightforward to specify the design and parameters of a clinical trial investigating an alternative therapy where effective therapies already exist. If existing therapeutic interventions are highly efficacious, safe, inexpensive, and firmly entrenched, an active‐control design becomes the logical first choice. Short of this absolute condition, however, the merits and realities of the scientific, clinical, corporate, and regulatory environments need to be weighed before determining the appropriate approach. A state of clinical equipoise with regard to the use of glycoprotein (GP) IIb/IIIa therapy in percutaneous coronary intervention (PCI) provided the unique opportunity to address the complexities in selecting a placebo‐controlled design for the Enhanced Suppression of the Platelet IIb/IIIa Receptor with Integrilin Trial (ESPRIT). ESPRIT investigators assessed whether a high dose of eptifibatide would improve the outcomes of patients undergoing coronary stenting. By using the example of the ESPRIT trial, we examine factors warranting the need for this trial and evaluate the process whereby the United States Food and Drug Administration (FDA) gave approval for a placebo‐controlled design. Although the focus of this trial is GP IIb/IIIa inhibition therapy, the issues pertaining to the trial and how they were resolved are general enough to be applied to the design and conduct of clinical trials across a broad spectrum of illnesses and therapeutic modalities. (J Interven Cardiol 2003;16:97–105)
A New Biological Matrix for Septal Occlusion
Authors: JUX CHRISTIAN , WOHLSEIN PETER , BRUEGMANN MICHAEL , BIRGIT FRANZBACH M. ZUTZ , BERTRAM HARALD
Published: November 2010

The ideal septal occluder scaffold should promote the healthiest and most complete healing response possible while eventually facilitating the full resorption of the material, leaving “native” tissue behind. An excellent biocompatibility of the scaffold tissue is a prerequisite for quick, complete, and firm ingrowth of the device, optimizing outcomes and minimizing the potential for complications. Intestinal collagen layer (ICL) is a highly purified (acellular) bioengineered type‐1 collagen derived from porcine submucosa. It is gradually resorbed by the host organism and subsequently replaced by the host tissue. CardioSEAL® occluders were modified by substituting the conventional polyester fabric for an intestinal collagen layer (ICL). Percutaneous transcatheter closure of interventionally created atrial septal defects was performed in lambs using these modified occluders. A complete pathomorphological investigation including histology was carried out after 2, 4, and 12 weeks follow‐up. Standard CardioSEAL implants served as a control group. After 2 weeks in vivo the devices were already covered completely by neo‐endothelium. Compared with the conventional synthetic scaffold, ICL devices showed a quicker endothelialization, decreased thrombogenicity, and superior biocompatibility with no significant cellular infiltration observed in the histology of explants with ICL fabrics. After 3 months in vivo the collagen layer remained mechanically intact, but began to show the first histological signs of mild disintegration, gradual resorption, and remodeling. In conclusion, short‐term results from preliminary in vivo experiments using a bioengineered collagen matrix as the occluder tissue scaffold showed excellent biocompatibility. This resulted in superior overall results: quicker endothelialization, a decreased thrombogenicity, and decreased immunological host response. (J Interven Cardiol 2003;16:149–152)
Interventional Strategies in the Management of Peripheral Pulmonary Artery Stenosis
Authors: TRIVEDI KALYANI R , BENSON LEE N
Published: November 2010

Peripheral pulmonary artery stenosis challenges therapeutic algorithms for the management of congenital heart malformations. Surgical repair of the proximal pulmonary artery lesion remains with a high recurrence rate while the distal lesions are difficult to access. With the development of transcatheter interventional strategies in the early 1980s, a number of transcatheter treatment options became available. In this review, we summarize the current state of the art for interventional strategies in the management of peripheral pulmonary artery stenosis. (J Interven Cardiol 2003;16:171–188)
Unusual Stents in Infants with Severe Congenital Heart Disease
Authors: VINCENT ROBERT N. , DIEHL HELEN J.
Published: November 2010

Two infants with severe congenital heart disease requiring intervention are described. Although both required conventional surgical therapy, mitigating circumstances led to catheter intervention for short‐term palliation. The feasibility and advisability of such procedures is discussed. (J Interven Cardiol 2003;16:189–191)
Effect of impurity ions on the geodesic acoustic mode
Authors: Guo Wenfeng , Wang Shaojie , Li Jiangang
Published: November 2010

A dispersion relation of the geodesic acoustic mode with the effect of impurity ions is systematically derived. It is found that the frequency of the geodesic acoustic mode for a plasma with impurity ions is lower than that without impurity ions, which are mainly due to the polarization of impurity ions. It is also found that the damping rate of the mode increases with the increase in effective charge in the small effective charge limit due to the polarization currents of impurity ions, and decreases in the large effective charge limit mainly due to the effect of the curvature drift of impurity ions. A maximum damping rate is found in the intermediate effective charge regime.
Flow dynamics past a simplified wing body junction
Authors: Gand Fabien , Deck Sébastien , Brunet Vincent , Sagaut Pierre
Published: November 2010

Junction flows may suffer from secondary flows such as horseshoe vortices and corner separations that can dramatically impair the performances of aircrafts. The present article brings into focus the unsteady aspects of the flow at the intersection of a wing and a flat plate. The simplified junction flow test case is designed according to a literature review to favor the onset of a corner separation. The salient statistical and fluctuating properties of the flow are scrutinized using large eddy simulation and wind tunnel tests, which are carried out at a Reynolds number based on the wing chord c and the free stream velocity U∞ of Rec=2.8×105. As the incoming boundary layer at Reθ=2100 (θ being the boundary layer momentum thickness one-half chord upstream the junction) experiences the adverse pressure gradient created by the wing, a three dimensional separation occurs at the nose of the junction leading to the formation of a horseshoe vortex. The low frequency, large scale bimodal behavior of the horseshoe vortex at the nose of the junction is characterized by multiple frequencies within f.δ/U∞=[0.05−0.1] (where δ is the boundary layer thickness one-half chord upstream the wing). Downstream of the bimodal region, the meandering of the core of the horseshoe vortex legs in the crossflow planes is scrutinized. It is found that the horseshoe vortex oscillates around a mean location over an area covering almost 10% of the wing chord in the tranverse plane at the trailing edge at normalized frequencies around f.δ/U∞=0.2–0.3. This so-called meandering is found to be part of a global dynamics of the horseshoe vortex initiated by the bimodal behavior. Within the corner, no separation is observed and it is shown that a high level of anisotropy (according to Lumley’s formalism) is reached at the intersection of the wing and the flat plate, which makes the investigated test case challenging for numerical methods. The conditions of apparition of a corner separation are eventually discussed and we assume that the vicinity of the horseshoe vortex suction side leg might prevent the corner separation. It is also anticipated that higher Reynolds number junction flows are more likely to suffer from such separations.
Relaxed states in relativistic multifluid plasmas
Authors: Pino Jesse , Li Hui , Mahajan Swadesh
Published: November 2010

The evolution equations for a plasma comprising multiple species of charged fluids with relativistic bulk and thermal motion are derived. It is shown that a minimal fluid coupling model allows a natural casting of the evolution equations in terms of generalized vorticity, which treats the fluid motion and electromagnetic fields equally. Equilibria can be found using a variational principle based on minimizing the total enstrophy subject to energy and helicity constraints. A subset of these equilibria corresponds to minimum energy. The equations for these states are presented with example solutions showing the structure of the relaxed states.
Large anisotropic thermoelectricity in perovskite related layered structure: SrnNbnO3n+2 (n=4,5)
Authors: Sakai Akihiro , Kanno Tsutomu , Takahashi Kouhei , Yamada Yuka , Adachi Hideaki
Published: November 2010

We measured the thermal and charge transport properties of perovskite-related layered structures. Strontium-Niobates, which were expressed as SrnNbnO3n+2 (n=4: Sr1.8La0.2Nb2O7, n=5: Sr5Nb5O17), to explore their thermoelectricities and thermal anisotropies. The behaviors of the thermoelectric parameters (thermal conductivity, Seebeck coefficient, resistivity) were strongly anisotropic in all crystallographic axes (a, b, and c) and large anisotropy exists even in the in-plane direction of the layered structure. Especially, along the a-axis in which corner-sharing NbO6 octahedra aligned straightly, contrastive properties were observed between Sr1.8La0.2Nb2O7 and Sr5Nb5O17. For Sr1.8La0.2Nb2O7, a thermally activated charge conduction is pronounced in the temperature dependence of Seebeck coefficient and resistivity, on the other hand, it was a metallic nature for Sr5Nb5O17. In both compounds, ZT results in anisotropic due to the anisotropic properties of thermoelectric parameters, the best performance is commonly observed in the a-axis. The respective ZT values at room temperature are 3.5×10−2 and 3.6×10−3.
Controllable introduction of twin boundaries into nanowires
Authors: Zhang Yongfeng , Huang Hanchen
Published: November 2010

Crystalline nanowires particularly metallic nanowires with twin boundaries have higher strength than those without. Achieving the higher strength requires controllable introduction of twin boundaries, which is impossible at the present. Turning the impossibility to a possibility, this paper proposes a mechanism of controllably introducing twin boundaries into crystalline nanowires by design; and demonstrates its feasibility using molecular dynamics simulations. This mechanism relies on the combination of mechanical torsion and local melting (and subsequent solidification). Under torsion, a nanowire twists by an angle along its axis. Upon local melting, the torsion concentrates at the molten zone. With proper twist angle for each crystal orientation, a geometrically necessary twin boundary forms controllably during solidification of the molten zone. Repeating this process generates controllable patterns of twin boundaries in nanowires.
Analysis of the slope efficiency for terahertz quantum-cascade lasers
Authors: Schrottke L. , Wienold M. , Giehler M. , Hey R. , Grahn H. T.
Published: November 2010

The slope efficiency is, in addition to the threshold current density and operating voltage, a decisive target value for the operation of quantum-cascade lasers (QCLs) in order to achieve an optimal total efficiency for the conversion of electrical input power into optical output power. We analyze the light-current characteristics for a set of similar, high-power, bound-to-continuum terahertz QCLs. The calculated internal slope efficiency shows a clear dependence on the height and thickness of the barriers. In contrast to the simulations, we found experimentally a significant difference in the threshold current densities and slope efficiencies for QCLs with nominally identical layer structures, which we mainly attribute to different line broadening.
Impact of stress on the recombination at metal precipitates in silicon
Authors: Gundel Paul , Schubert Martin C. , Heinz Friedemann D. , Kwapil Wolfram , Warta Wilhelm , Martinez-Criado Gema , Reiche Manfred , Weber Eicke R.
Published: November 2010

Metals corrupt the performance of silicon solar cells severely. In this paper we investigate the recombination activity of metal precipitates and present a strong positive correlation between their recombination activity and the stress around them, independent of the type of metal forming the precipitate. This fundamental observation suggests that stress, together with the size of the precipitate, has a dominant effect on the recombination activity of metallic precipitates. We explain the recombination enhancing effect of stress near precipitates by the strong piezoresistance of silicon.
Damping of linear waves via ionization and recombination in homogeneous plasmas
Authors: Dodin I. Y. , Fisch N. J.
Published: November 2010

An oscillation-center model is proposed that analytically describes transformation of an arbitrary homogeneous linear wave at gradual ionization and recombination in homogeneous plasma. For the case when either of the processes dominates, general adiabatic invariants are found, from which the wave energy is derived as a function of the frequency.
Amorphous indium-gallium-zinc-oxide visible-light phototransistor with a polymeric light absorption layer
Authors: Zan Hsiao-Wen , Chen Wei-Tsung , Hsueh Hsiu-Wen , Kao Shih-Chin , Ku Ming-Che , Tsai Chuang-Chuang , Meng Hsin-Fei
Published: November 2010

This work demonstrates a real-time visible-light phototransistor comprised of a wide-band-gap amorphous indium-gallium-zinc-oxide (a-IGZO) thin-film transistor (TFT) and a narrow-band-gap polymeric capping layer. The capping layer and the IGZO layer form a p-n junction diode. The p-n junction absorbs visible light and consequently injects electrons into the IGZO layer, which in turn affects the body voltage as well as the threshold voltage of a-IGZO TFT. The hysteresis behavior due to the charges at IGZO back interface is also discussed.
Pulsed laser deposition of graphite counter electrodes for dye-sensitized solar cells
Authors: Acharya Krishna P. , Khatri Himal , Marsillac Sylvain , Ullrich Bruno , Anzenbacher Pavel , Zamkov Mikhail
Published: November 2010

We report on pulsed laser deposition of graphite onto flexible plastic and conductive glass substrates for use as a counter electrode in dye-sensitized solar cells. The efficiency of as-prepared graphite electrodes was tested using CdS-sensitized solar cell architecture resulting in external quantum efficiency comparable to that of conventional platinum counter electrodes. This work highlights the possibility of using pulsed laser deposited graphite as a low-cost alternative to platinum, which could be fabricated both on flexible and rigid substrates.
Density effect on relativistic electron beams in a plasma fiber
Authors: Zhou C. T. , Wang X. G. , Wu S. Z. , Cai H. B. , Wang F. , He X. T.
Published: November 2010

Intense short-petawatt-laser driven relativistic electron beams in a hollow high-Z plasma fiber embedded in low-Z plasmas of different densities are studied. When the plasma is of lower density than the hollow fiber, resistive filamentation of the electron beam is observed. It is found that the electron motion and the magnetic field are highly correlated with tens of terahertz oscillation frequency. Depending on the material property around the hollow fiber and the plasma density, the beam electrons can be focused or defocused as it propagates in the plasma. Relativistic electron transport and target heating are also investigated.
Role of hydrogen in evolution of plasma parameters and dust growth in capacitively coupled dusty plasmas
Authors: Chai K. B. , Choe Wonho , Seon C. R. , Chung C. W.
Published: November 2010

The temporal behavior of naturally produced dust parameters (radius and density) and plasma parameters (electron temperature and ion flux) was investigated in radio frequency SiH4/H2/Ar plasmas. As a result, the electron temperature and ion flux were shown to be strongly correlated with the three-step dust growth pattern. In addition, the generation of dust particles was suppressed by mixing more hydrogen gas due to the plasma chemistry, and consequently, the dust growth rate in the molecular accretion growth, which is known to be proportional to the growth rate of thin film deposition, increased.
Effect of ridge tillage, no-tillage, and conventional tillage on soil temperature, water use, and crop performance in cold and semi-arid areas in Northeast China
Authors: He Jin , Li Hongwen , Kuhn N. J. , Wang Qingjie , Zhang Xuemin
Published: November 2010

In cold and semi-arid Northeast China, insufficient soil accumulative temperature and low water use efficiency (WUE) are the limiting factors for the further development of agriculture. Ridge tillage (RT) has been proposed to improve soil temperature and water conservation. Data from a 3-year field experiment conducted at two locations (Sujiatun and Lanxi) in Northeast China were used to compare RT, no-tillage (NT), and conventional tillage (CT) in a spring maize cropping system. At both sites, RT and NT significantly (P < 0.05) increased mean soil temperature to 0.10 m depth, relative to CT, by 0.7–2.4°C in the cold season during the spring maize growing stage. Mean soil moisture depletion in the RT treatment was greater by 1.2–4.1% (Sujiatun) and 0.6–3.0% (Lanxi) than in NT and CT, respectively. Mean maize yields over 3 years for RT were ~9.9% greater than for CT, whereas the yield advantage in the NT treatment was only slight. In Sujiatun, WUE was 8.0% and 8.6% greater under RT than under NT and CT, respectively, and in Lanxi, WUE was 7.7% and 9.6% greater under RT than NT and CT. Ridge tillage is recommended to the farmers to obtain higher crop yield and WUE in Northeast China.
Formation of organo-mineral complexes as affected by particle size, pH, and dry - wet cycles
Authors: Pan B. , Tao S. , Dawson R. W. , Xing B. S.
Published: November 2010

The formation of organo-mineral complexes is an important process controlling carbon cycling and the properties of soil particles. However, differences between the complexes formed in aqueous systems and those found in terrestrial systems have not been clearly recognised. This study simulated the formation of organo-mineral complexes between dissolved humic acid (DHA) and mineral particles using a solid/aqueous adsorption experiment (aqueous system) and a wet–dry cycling methodology (terrestrial system). The clay fraction of mineral particles contributed greatly (>90%) to overall DHA adsorption on soil particles in adsorption experiments where DHA fractionation was clearly observed. Aromatic content was found to be less favourable for adsorption under all conditions. For particles of different sizes, the significance of fractionation increased with adsorption. High adsorption was observed under acid conditions, although there was less fractionation as a result of the acid-facilitated ligand exchange process. When using a wet–dry cycling methodology, a much higher fOC was observed for the complexes than when using the adsorption experiment, and DHA fractionation was not significant. Further, the distinctly decreased E465/E665 ratio suggests that the DHA washed off from acid complexes was different from the original DHA and most likely the result of DHA precipitation during wet–dry cycles under acid conditions.
Assessing P fertiliser use in vegetable production: agronomic and environmental implications
Authors: Chan K. Y. , Wells T. , Fahey D. , Eldridge S. M. , Dorahy C. G.
Published: November 2010

Vegetable production is often located in the peri-urban areas close to large cities. In Sydney, Australia, excessive levels of phosphorus (P) have been reported in the soils, and vegetable farms have long been regarded as a potential source of the P that enters Sydney’s waterways. We report vegetable production under varying soil P conditions and the consequent changes in soil P, as well as water quality of runoff and leachate after growing 5 crops in a field trial where inputs in the form of garden organic compost were compared to current farmers’ practice. No difference in vegetable yield was observed between 100 and 400 mg/kg of soil Colwell P (0–0.10 m); therefore, our results indicate that the excessive soil P levels in the vegetable farms around Sydney are not important for optimal vegetable production. Results from runoff and leachate studies clearly demonstrate that high concentrations of P in soils used for vegetable production under the current farming practice around Sydney have increased the potential to export P and to negatively affect water quality of receiving environments. The significant increases in soluble P concentrations found in the soil and runoff water from the current farming practice can be attributed to the use of poultry litter. In contrast, using compost in place of poultry litter resulted in significantly reduced soil P accumulation and P concentration in runoff and leachate. Training and education programs for farmers and their advisors are recommended to encourage more sustainable fertiliser management practices and reduce the accumulation of P in the environment.
Forced chemical confinement fusion: μ-catalysed fusion by taking resonance escape probability of tμ(1s) atoms using an alternative kinetic model
Authors: Gheisari R.
Published: November 2010

The emission of tμ atoms in a two-layer arrangement consisting of H/T and D2 is investigated with an alternative kinetic model. The slowing down of tμ(1s) atoms in pure deuterium and their falling down into resonance regions force chemical confinement fusion (μCF). By considering the resonance escape probability of tμ(1s) atoms, point kinematic equations are numerically solved to obtain the muon conversion efficiency and also the cycling coefficient. Under the optimal condition we show that the μ-cycling coefficient and the efficiency equal 104.5 ± 2.5 and ∼0.7%, respectively. Our model is compared with previous suggestions. The muon conversion efficiency is estimated for a possible design and compared with recent experimental results for H/T⊕D/T.
ALOHA: an Advanced LOwer Hybrid Antenna coupling code
Authors: Hillairet J. , Voyer D. , Ekedahl A. , Goniche M. , Kazda M. , Meneghini O. , Milanesio D. , Preynas M.
Published: November 2010

The Advanced LOwer Hybrid Antenna (ALOHA) code, has been developed to improve the modelling of the coupling of lower hybrid (LH) waves from the antenna to a cold inhomogeneous plasma while keeping a fast tool. In contrast to the previous code Slow Wave ANtenna (SWAN) (that only described the interaction of the slow wave between the waveguides and the plasma in a 1D model), the equations are now solved in 2D including the contribution of both the slow and fast waves, with a low computational cost. This approach is completed either by a full-wave computation of the antenna that takes into account its detailed geometry or by a mode-matching code dedicated to multijunctions modelling, which is convenient in preliminary design phases. Moreover, ALOHA can treat more realistic scrape-off layers in front of the antenna, by using a two-layer electron density profile. The ALOHA code has been compared with experimental results from Tore Supra LH antennas of different geometries, as well as benchmarked against other LH coupling codes, with very good results. Once validated, ALOHA has been used as a support for the design of COMPASS and ITER LH antennas and has shown to be a fast and reliable tool for LH antenna design.
Molecular Dynamics Simulations of Silica Nanotube: Structural and Vibrational Properties Under Different Temperatures
Authors: Zhang Sheng-li , Zhang Yong-hong , Huang Shi-ping , Wang Peng , Tian Hui-ping
Published: November 2010

Four-, six-, and eight-membered ring silica nanotubes at temperatures from 300 K to 1600 K are relaxed by classical molecular dynamics simulations with three potential models. The simulation results indicate that the stability of the end rings of the three silica nanotubes gradually decreases with increase in temperature. The validity of the vibrational features of silica nanotubes is shown by the vibrational density of states. Infrared spectra on the silica nanotubes under different temperatures are investigated. A detailed assignment of each spectral peak to the corresponding vibrational mode of the three nanotubes has been addressed. The results are in good agreement with the other theoretical and experimental studies.
Structures and Intermolecular Interactions in Dimethyl Sulfoxide-Water System Studied by All-atom Molecular Simulations
Authors: Zhang Rong , Wu Wen-juan
Published: November 2010

An all-atom dimethyl sulfoxide (DMSO) and water model have been used for molecular dynamics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. And there are traditional strong hydrogen bonds and weak C-H ··· O contacts existing in the mixtures according to the analysis of the radial distribution functions. The insight structures in the DMSO-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Interestingly, the molar fraction of DMSO 0.35 is found to be a special concentration by the network. It is the transitional region which is from the water rich region to the DMSO rich region. The stable aggregates of (DMSO)m·S=O···HW-OW·(H2O)n might play a key role in this region. Moreover, the simulation is compared with the chemical shifts in NMR and wavenumbers in IR with concentration dependence. And the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data in NMR and IR spectra.
Threshold Photoelectron-photoion Coincidence Imaging of Dissociation Dynamic of NO+ atc3Π(v′=0) State
Authors: Sun Jin-da , Shan Xiao-bin , Liu Fu-yi , Sheng Liu-si , Tang Xiao-feng , Niu Ming-li , Song Lei , Zhou Xiao-guo , Liu Shi-lin
Published: November 2010

The photodissociation of NO+ at c3Π(v′ = 0) state is studied by threshold photoelectron-photoion coincidence imaging method. By some assumptions, the relations between velocity in center of mass (CM) coordinates and most probable center of mass (MPCM) coordinates, time of flight and displacement in the velocity map image of fragment ions are derived using vector addition of velocity and displacement on the condition of perpendicular molecular beam. Using these relations the velocity in CM coordinates, the velocity and angular distribution of N+ fragment ions in MPCM coordinates are obtained and discussed, respectively.
Three-dimensional Potential Energy Surface and Bound States of the Ar2-Ne Complex
Authors: Niu Mei , Xu Xiao-tao , Chen Xia , Hu Xiao-long , Feng Er-yin
Published: November 2010

The first three-dimensional interaction potential energy surface (PES) of the Ar2-Ne complex is developed using the single and double excitation coupled cluster theory with noniterative treatment of triple excitations CCSD(T). The aug-cc-pVQZ basis sets are employed for all atoms, including an additional (3s3p2d2f1g) set of midpoint bond functions. The calculated single point energies are fitted to an analytic two-dimensional potential model at each of seven fixed rAr2 values. The seven model potentials are then used to construct the three-dimensional PES by interpolating along (r—re) using a sixth-order polynomial. The PES is used in the following rovibrational energy levels calculations. The comparisons of theoretical transition frequencies and spectroscopic constants with the experimental results are given.
First-principles Study of Single Tin-phthalocyanine Molecule on Ag(111) Surface
Authors: Fan Hui-li , Lei Shu-lai , Huang Jing , Li Qun-xiang
Published: November 2010

Adsorption behavior and electronic structure of tin-phthalocyanine (SnPc) on Ag(111) surface with Sn-up and Sn-down conformations are investigated using first-principles calculations. Two predicted adsorption configurations agree well with the experimentally determined structures. SnPc molecule energetically prefers to adsorb on Ag(111) surface with Sn-down conformation. The energy required to move the central Sn atom through the frame of a phthalocyanine molecule, switching from the Sn-up to Sn-down conformation, is about 1.68 eV. The simulated scanning tunneling microscopy images reproduce the main features of experimental observations. Moreover, the experimentally proposed hole attachment mechanism is verified based on the calculated density of states of SnPc on Ag(111) with three different adsorption configurations.
Quasi-classical Trajectory Study of Ba+HI→BaI+H Reaction
Authors: N. Atasie V.
Published: November 2010

The quasi-classical trajectory calculations based on extended London-Eyring-Polanyi-Sato potential energy surface have been used to study the reaction of Ba+HI→BaI+H system. The rotational, vibrational, translational, and angular distributions of the product BaI have been calculated. The calculated results are in good agreement with the experimental ones.
Characterization of CuInS2 Thin Films with Different Cu/In Ratio
Authors: Kundakçi Mutlu
Published: November 2010

Thin films of CuInS2 were grown on glass substrate by successive ionic layer adsorption and reaction method with different [Cu]/[In] ratios and annealed at 400 °C for 30 min. The crystal structure and grain sizes of the thin films were characterized by X-ray diffraction method. Atomic force microscopy was used to determine surface morphology of the films. Optical and electrical properties of these films were investigated as a function of [Cu]/[In] ratios. The electrical resistivity of CuInS2 of thin films was determined using a direct current-two probe method in the temperature range of 300–470 K. It is observed that, the electrical resistivity values show a big decreasing with increasing [Cu]/[In] ratio. Hence, the [Cu]/[In] ratio in the solution can drastically affect the structural, electrical, and optical properties of thin films of CuInS2.
Synthesis and Microwave Absorption Properties of BaTiO3-polypyrrole Composite
Authors: Li Qiao-ling , Zhang Cun-rui , Li Jian-qiang
Published: November 2010

BaTiO3 powders are prepared by sol-gel method by cotton template. Polypyrrole is prepared by chemical oxidation route in the emulsion polymerization system. Then BaTiO3-polypyrrole composites with different mixture ratios are prepared by as-prepared material. The structure, morphology, and properties of the composites are characterized with Infrared spectrum, X-ray diffraction, scanning electron microscope, and net-wok analyzer. The complex permittivity and reflection loss of the composites are measured at different microwave frequencies in S-band and C-band (0.03–6 GHz) employing vector network analyzer model PNA 3629D vector. The effect of the mass ratio of BaTiO3 to polypyrrole on the microwave loss properties of the composites is investigated. A possible microwave absorbing mechanism of BaTiO3-polypyrrole composite is proposed. The BaTiO3-polypyrrole composite can find applications in suppression of electromagnetic interference and reduction of radar signature.
High-level Stark Effect and Spectrum of Spherical Nanometer System
Authors: Wu Qiang , Long Xiao-xia , Zheng Rui-lun
Published: November 2010

In the electric field and layer-to-layer interaction energy, the law of split-level of high-level Stark effect of spherical nanometer system is explored as well as the frequency of spectrum, intensity and size effect of coefficient of spontaneous radiation. Taking three layers CdS/HgS spherical nanometer system as an example, the influence of the electric field and layer-to-layer interaction energy is explored on Stark effect and spectrum. The results show that in the Stark effect system, the energy level is split based on 1, 3, ···, (2n−1), when it is in the electric field only, similar to the hydrogen atoms; and in the electric field and layer-to-layer interaction, it is split based on 1, 4, ···, n2; with the quantum transition, the frequency of the spectrum decreases with the increasing size of the system; apart from a few spectral lines, the intensity of most spectral lines will decreased as the size increases; while the coefficient of spontaneous radiation will increase with the increasing size; the electric field will cause the changes of spectrum frequency; its spectrum frequency shift is proportional to the square of the electric field intensity; apart from a few spectral lines, the frequency shift of spectral lines that is caused by the electric field and layer-to-layer interaction will decrease as the size increases; the interaction will make the level of electronic energy level lower slightly (the order of magnitude is between 10−7−10−9 eV), the slightly increased spectrum intensity and the slightly increased value of coefficient of spontaneous radiation, but it will not influence the frequency of spectrum, intensity, and the trend that coefficient of spontaneous radiation changes with the size; when the size is smaller, the layer-to-layer interaction effect will be significant.
Comparative Studies on Degradation of Methyl Orange by Nanostructured Zinc and Zinc Oxide Films
Authors: Wu Bing-jun , Hao Chang-shan , Xie Bin , Li Ming
Published: November 2010

Nanostructured zinc and zinc oxide films were prepared by magnetron sputtering processes and succeeded air annealing treatments. Comparison of reductive degradation rate of methyl orange (MO) by zinc films and photocatalytic degradation rate of MO by zinc oxide films was carried out. Both reductive degradation and photocatalytic degradation process of MO by zinc and zinc oxide films can be described by first order kinetic model. It was found that although MO liquid was most quickly decolorized by metallic zinc films, the mineralization of MO was not thorough. Observation of extra ultraviolet absorption peaks indicated the formation of aromatic intermediates. On the other hand, although the photocatalytic degradation rate of MO liquid by ZnO films was only as about 1/4 large as the reductive degradation rate by zinc films, no signs of aromatic intermediates were found. Moreover, it was found that partially oxidized zinc oxide film showed higher photocatalytic efficiency than the totally oxidized ZnO films. Synergy effect between zinc and zinc oxide phase in the partially oxidized films was considered to be responsible for the higher photocatalytic efficiency.
GPU-BLAST: using graphics processors to accelerate protein sequence alignment
Authors: Vouzis Panagiotis D. , Sahinidis Nikolaos V.
Published: November 2010

Motivation: The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 53 000 citations that this software has received in the past two decades, and the use of the word ‘blast’ as a verb referring to biological sequence comparison. Any improvement in the execution speed of BLAST would be of great importance in the practice of bioinformatics, and facilitate coping with ever increasing sizes of biomolecular databases.

Results: Using a general-purpose graphics processing unit (GPU), we have developed GPU-BLAST, an accelerated version of the popular NCBI-BLAST. The implementation is based on the source code of NCBI-BLAST, thus maintaining the same input and output interface while producing identical results. In comparison to the sequential NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly between 3 and 4.

Availability: The source code of GPU-BLAST is freely available at http://archimedes.cheme.cmu.edu/biosoftware.html.

Contact:  sahinidis@cmu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing
Authors: Misra Sanchit , Agrawal Ankit , Liao Wei-keng , Choudhary Alok
Published: November 2010

Motivation: Recently, a number of programs have been proposed for mapping short reads to a reference genome. Many of them are heavily optimized for short-read mapping and hence are very efficient for shorter queries, but that makes them inefficient or not applicable for reads longer than 200 bp. However, many sequencers are already generating longer reads and more are expected to follow. For long read sequence mapping, there are limited options; BLAT, SSAHA2, FANGS and BWA-SW are among the popular ones. However, resequencing and personalized medicine need much faster software to map these long sequencing reads to a reference genome to identify SNPs or rare transcripts.

Results: We present AGILE (AliGnIng Long rEads), a hash table based high-throughput sequence mapping algorithm for longer 454 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process. In our experiments, we observe that AGILE is more accurate than BLAT, and comparable to BWA-SW and SSAHA2. For practical error rates (< 5%) and read lengths (200–1000 bp), AGILE is significantly faster than BLAT, SSAHA2 and BWA-SW. Even for the other cases, AGILE is comparable to BWA-SW and several times faster than BLAT and SSAHA2.

Availability:  http://www.ece.northwestern.edu/~smi539/agile.html.

Contact:  smi539@eecs.northwestern.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.