bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical investigation of slow light in the coupled resonator optical waveguides using the local Fourier modal method
Authors: Park Junghyun , Kim Hwi , Lee Byoungho 
Published: April 2011

AbstractWe present the Bloch modal analysis of photonic crystal coupled resonator optical waveguide (CROW) based on the local Fourier modal method (LFMM). The objective of this analysis is to extract the dispersion relation and analyze optical Bloch eigenmodes of the structure. The evolution of each Bloch eigenmode with varying frequency can be visualized with the proposed LFMM. The recently proposed CROW structure of NTT Basic Research Laboratory group with missing center holes and perturbed lateral shift of holes near the center is taken as the exemplary CROW structure (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Evidence of anti free volume creation during deformation induced nanocrystallization of Nd–Fe–B metallic glass
Authors: Shukla Shashwat , Banas Agnieszka , Ramanujan Raju 
Published: April 2011

AbstractThe Extended X‐ray Absorption Fine‐Structure (EXAFS) technique was used to study the time evolution of the structure of Nd–Fe–B metallic glass undergoing nanocrystallization during mechanical milling. Negative as well as positive fluctuations in atomic density were observed, providing direct evidence of the creation of deformation‐induced pairs of free volume and anti‐free volume defects. These defects migrated during milling, leading to the atomic redistribution and precipitation of nanocrystals. Our results demonstrate that atomic defects caused by deformation of metallic glasses involve more extensive athermal changes in short‐range order than nearest neighbour bond breaking as suggested by the free volume model. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes
Authors: Basiuk Vladimir A. 
Published: April 2011

AbstractTo address the choice of an appropriate value of electron smearing to facilitate self‐consistent field (SCF) convergence, we studied the interaction of doxorubicin with short armchair and zigzag single‐walled carbon nanotube models with closed caps, at the PWC/DNP level of density functional theory. By gradually reducing the electron smearing value from a large and most commonly used one of 0.005 Ha to zero (Fermi occupation), we monitored the changes in close contacts between the interacting species, total energy of the molecular system, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy and isosurfaces, HOMO‐LUMO gap energy, and plots of electrostatic potential. It became evident that the commonly used smearing values of ≥0.001 Ha can alter the results significantly (for example, by one order of magnitude for HOMO–LUMO gap energy). We suggest the setting of electron smearing value at 0.0001 Ha, which does not imply too high computation cost and can guarantee the results close to the ones obtained with Fermi occupation. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Computational study of the catalytic synthesis of 5‐nitro‐1,2,4‐triazol‐3‐one
Authors: Cheng Ken‐Fa , Liu Min‐Hsien , Yang Ping‐Hua 
Published: April 2011

AbstractIn this study, 5‐nitro‐1,2,4‐triazol‐3‐one (NTO) was theoretically synthesized from urea via chlorination followed by amination, formylation, and nitration under aqueous and gaseous environments based on experience of experimental methods, and metal chlorides and metal oxides were used as catalysts to promote reaction. Reaction routes closely related to experimental processes were successfully constructed, and the corresponding energy barriers were estimated for each elementary reaction. Reaction conditions distinct from those reported in the literature (including the adoption of aluminum chloride, ferric chloride, aluminum oxide, ferrous oxide, and chromium oxide catalysts, the use of nitric acid and dinitrogen pentoxide as nitration agents, and adjustment of the reaction temperature) were used in corresponding reaction systems, and the modeling results suggested that ferric chloride is a good catalyst for the chlorination reaction, ferrous oxide is suitable for catalyzing amination, formylation, and nitration, and nitric acid is the better agent for nitration. Estimates of the comparable energy barriers for each reaction stage were considered to imply more feasible pathways for NTO synthesis. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
CCSD(T)‐F12 investigations on HBNH and its isotopologues
Authors: Brites Vincent , Léonard Céline 
Published: April 2011

AbstractCCSD(T)‐F12 ab initio computations are performed to investigate the isomerization path between HBNH and BNH2, and the six‐dimensional potential energy surface of the electronic ground state X̃1Σ+ of the linear isomer. The equilibrium geometries and harmonic wavenumbers obtained at the CCSD(T)‐F12a/aug‐cc‐pVTZ level of theory are nearly those computed with the CCSD(T)/aug‐cc‐pV5Z level, but with a smaller amount of CPU time for the evaluation of the total energy. The analytical representation of the potential energy surface is used in variational calculations of the rovibrational energy levels of H11BNH and isotopologues. The computed rovibrational energy levels are compared with the available experimental data, and a good agreement is generally noticed. We also propose an assignment of the rovibrational energy levels of H11BNH up to 3000 cm−1 above the zero point energy. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Theoretical study of static (Hyper)polarizabilities of twisted intramolecular charge transfer chromophores
Authors: Liu Liuxia , Xue Ying , Wang Xin , Chu Xiang , Yang Mingli 
Published: April 2011

AbstractDensity functional theory calculations are performed to study the (hyper)polarizabilities of a series of planar and twisted intramolecular charge transfer molecules (tictoids) with different electron‐donating and electron‐withdrawing groups. Both similarity and difference between the planar and twisted molecules are noted in their (hyper)polarizability variation with respect to substituent and solvent dielectric constant. When compared with dramatic enhancements resulting from geometry twist and solvent effect, substitution to D/A pairs leads to relatively moderate variation in (hyper) polarizability. In addition, tictoids with different substituents may exhibit different solvent effects in their hyperpolarizability magnitudes. Our calculations suggest that the nonlinear optical response of the tictoids could be tuned by appropriately selecting the donor/acceptor pairs and solvents. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Approximate Hamilton decompositions of random graphs
Authors: Knox Fiachra , Kühn Daniela , Osthus Deryk 
Published: April 2011

AbstractWe show that if pn ≫ log n the binomial random graph Gn,p has an approximate Hamilton decomposition. More precisely, we show that in this range Gn,p contains a set of edge‐disjoint Hamilton cycles covering almost all of its edges. This is best possible in the sense that the condition that pn ≫ log n is necessary. © 2011 Wiley Periodicals, Inc. Random Struct. Alg., 2012
Assessing the sensitivity of [11C]p943, a novel 5‐HTIB radioligand, to endogenous serotonin release
Authors: Cosgrove Kelly P. , Kloczynski Tracy , Nabulsi Nabeel , Weinzimmer David , Lin Shu‐Fei , Staley Julie K. , Bhagwagar Zubin , Carson Richard E. 
Published: April 2011

AbstractThe main objective of the current study was to determine the sensitivity of the positron emission tomography (PET) radioligand [11C]P943 to fenfluramine‐induced changes in endogenous 5‐HT in nonhuman primate brain. Fenfluramine‐induced changes in 5‐HT1B occupancy were compared to those obtained by self‐block with unlabeled P943. Two baboons and 1 rhesus monkey were given preblocking or displacing doses of fenfluramine (1–5 mg/kg) or preblocking doses of unlabeled P943 (0.2 mg/kg) and imaged with [11C]P943 PET. Receptor occupancy by the low dose of fenfluramine (1 mg/kg) in the baboons was 25 and 29% and by the high dose of fenfluramine (5 mg/kg) in the rhesus macaque was 42%. Receptor occupancy by P943 (0.2 mg/kg) was 68 and 86% in the baboons. PET imaging of 5‐HT1B receptors with [11C]P943 may be a useful approach for measuring changes in endogenous 5‐HT in the living human brain. Synapse, 2011. © 2011 Wiley‐Liss, Inc.
Selection of STOP‐free sequences from random mutagenesis for ‘loss of interaction’ two‐hybrid studies
Authors: Lickfeld Manuela , Schmitz Hans‐Peter 
Published: April 2011

AbstractThe investigation of protein–protein interactions is an essential part of biological research. To obtain a deeper insight into regulatory protein networks, the identification of the components, domains and especially single residues that are involved in these interactions is helpful. A widespread and attractive genetic tool for investigation of protein–protein interactions is the yeast two‐hybrid system. This method enables large‐scale screens and its application is cheap and relatively simple. For identification of the amino acids in a protein sequence that are essential for interaction with a specific partner, yeast two‐hybrid assays can be combined with random mutagenesis of the sequence of interest. A common problem with such an experiment is the generation of stop codons within the mutagenized fragments, leading to the isolation of many false positives when screening for loss of interaction using the two‐hybrid method. To overcome this problem, we modified the yeast two‐hybrid system to allow selection for sequences without stop codons. To achieve this, we fused the ScURA3 marker‐gene in frame to the mutagenized fragments. We show here that this marker is fully functional when fused to a two‐hybrid construct with a nuclear localization signal, such as a Gal4 activation domain and a prey protein, thus allowing selection of stop‐free sequences on media without uracil. Using the Rho‐binding domain from a Bni1‐like formin and different Rho‐type GTPases from Ashbya gossypii as examples, we further show that our system can be used to screen large numbers of transformants for loss of protein–protein interactions in combination with random mutagenesis. Copyright © 2011 John Wiley & Sons, Ltd.
Hydrophilic Interaction Liquid Chromatography: ESI–MS/MS of Plasmalogen Phospholipids from Pectinatus Bacterium
Authors: Řezanka Tomáš , Siristova Lucie , Matoulková Dagmar , Sigler Karel 
Published: April 2011

AbstractLiquid chromatography–electrospray tandem mass spectrometry (LC/ESI–MS/MS) was used to analyze phospholipids from three species of the anaerobic beer‐spoilage bacterial genus Pectinatus. Analysis of total lipids by HILIC (Hydrophilic Interaction Liquid Chromatography) column succeeded in separating diacyl‐ and plasmalogen phospholipids. Plasmalogens were then analyzed by means of the ESI–MS/MS and more than 220 molecular species of four classes of plasmalogens (PlsCho (choline plasmalogen), PlsEtn (ethanolamine plasmalogen), PlsGro (glycerol plasmalogen), and PlsSer (serine plasmalogen)) were identified. Major molecular species were c‐p19:0/15:0 PlsEtn and PlsSer, which accounted for more than 4% of the total lipids.
Power laws, memory capacity, and self-tuned critical branching in an LIF model with binary synapses
Authors: Kello Christopher , Kerster Bryan 
Published: April 2011

AbstractBoth fluctuations and distributions of spontaneous neural spiking activity have been observed to closely follow a variety of power laws. Multiple explanations have been offered for each observation, but few lead to mechanisms that encompass their widespread occurrence. A canonical, leaky integrate-and-fire model is presented in which synapses are updated based on the timing of pre- and post-synaptic spikes in order to maintain a state of critical branching. Results showed that 1) the self-tuning algorithm maintained critical branching under a range of parameters; 2) power laws were obtained in spiking activity fluctuations (1/f scaling), size distributions of network bursts (neural avalanches), and temporal correlations in interspike intervals (Allan factor); 3) power laws disappeared once the self-tuning algorithm was disabled; and 4) critical branching was adaptive in that it maximized the network’s memory capacity when assessed as a liquid state machine.
Advancing transcriptome platforms
Authors: Shi Shuobo 
Published: April 2011

AbstractDuring the last decade of years, remarkable technological innovations have emerged that allow the direct or indirect determination of the transcriptome at unprecedented scale and speed. Studies using these methods have already altered our view of the extent and complexity of transcript profiling, which has advanced from one-gene-at-a-time to a holistic view of the genome. Here, we outline the major technical advances in transcriptome characterization, including the most popular used hybridization-based platform, the well accepted tag-based sequencing platform, and the recently developed RNA-Seq (RNA sequencing) based platform. Importantly, these next-generation technologies revolutionize assessing the entire transcriptome via the recent RNA-Seq technology.
Noninvasive Ventilation and Alveolar Recruitment Maneuver Improve Respiratory Function during and after Intubation of Morbidly Obese Patients
Authors: Futier Emmanuel , Constantin Jean-Michel , Pelosi Paolo , Chanques Gerald , Massone Alexandre , Petit Antoine , Kwiatkowski Fabrice , Bazin Jean-Etienne , Jaber Samir 
Published: April 2011

Background
Morbid obesity predisposes patients to lung collapse and hypoxemia during induction of anesthesia. The aim of this prospective study was to determine whether noninvasive positive pressure ventilation (NPPV) improves arterial oxygenation and end-expiratory lung volume (EELV) compared with conventional preoxygenation, and whether NPPV followed by early recruitment maneuver (RM) after endotracheal intubation (ETI) further improves oxygenation and respiratory function compared with NPPV alone.

Methods
Sixty-six consecutive patients (body mass index, 46 ± 6 kg/m²) were randomized to receive 5 min of either conventional preoxygenation with spontaneous breathing of 100% O₂ (CON), NPPV (pressure support and positive end-expiratory pressure), or NPPV followed by RM (NPPV+RM). Gas exchange was measured in awake patients, at the end of preoxygenation, immediately after ETI, and 5 min after the onset of mechanical ventilation. EELV was measured immediately after ETI and 5 min after mechanical ventilation. The primary endpoint was arterial oxygenation 5 min after the onset of mechanical ventilation. Results are presented as mean ± SD.

Results
At the end of preoxygenation, Pao₂ was higher in the NPPV and NPPV+RM groups (382 ± 87 mmHg and 375 ± 82 mmHg, respectively; both P < 0.001) compared with the CON group (306 ± 51 mmHg) and remained higher after ETI (225 ± 104 mmHg and 221 ± 110 mmHg, in the NPPV and NPPV+RM groups, respectively; both P < 0.01 compared with the CON group [150 ± 50 mmHg]). After the onset of mechanical ventilation, Pao₂ was 93 ± 25 mmHg in the CON group, 128 ± 54 mmHg in the NPPV group (P = 0.035 vs. CON group), and 234 ± 73 mmHg in the NPPV+RM group (P < 0.0001 vs. NPPV group). After ETI, EELV was higher in the NPPV group compared with the CON group (P < 0.001). Compared with NPPV alone, RM further improved gas exchange and EELV (all P < 0.05). A significant correlation was found between Pao2 obtained 5 min after mechanical ventilation and EELV (R = 0.41, P < 0.001).

Conclusion
NPPV improves oxygenation and EELV in morbidly obese patients compared with conventional preoxygenation. NPPV combined with early RM is more effective than NPPV alone at improving respiratory function after ETI.
Oral desensitization as a useful treatment in 2‐year‐old children with cow's milk allergy
Authors: Martorell A. , De la Hoz B. , Ibáñez M. D. , Bone J. , Terrados M. S. , Michavila A. , Plaza A. M. , Alonso E. , Garde J. , Nevot S. , Echeverria L. , Santana C. , Cerdá J. C. , Escudero C. , Guallar I. , Piquer M. , Zapatero L. , Ferré L. , Bracamonte T. , Muriel A. , Martínez M. I. , Félix R. 
Published: April 2011

SummaryBackground
Limited published evidence shows oral desensitization to be a potential intervention option for cow's milk protein (CMPs) allergy.Objective
The aim of this study was to evaluate the safety and efficacy of oral desensitization in 2‐year‐old children with cow's milk allergy, as a treatment alternative to elimination diet.Methods
A total of 60 children aged 24–36 months with IgE‐mediated allergy to CMPs were included in this multi‐center study and were randomized into two groups. Thirty children (group A: treatment group) began oral desensitization immediately, whereas the remaining 30 (group B: control group) were kept on a milk‐free diet and followed‐up for 1 year.Results
After 1‐year follow‐up period, 90% of the children in group A had become completely tolerant vs. 23% of the children in group B. In group A, cow's milk skin reactivity and serum‐specific IgE to milk and casein decreased significantly from the initial assessment, whereas group B showed no significant change after 1 year of follow‐up. Twenty‐four patients (80%) developed some reaction during the treatment period: 14 children developed moderate reaction (47%) and 10 mild reaction (33%). The most common manifestations were urticaria‐angioedema, followed by cough.Conclusions and Clinical Relevance
In this study, oral desensitization was found to be effective in a significant percentage of 2‐year‐old children with cow's milk allergy. Oral desensitization appears to be efficacious as an alternative to elimination diet in the treatment of 2‐year‐old children with cow's milk allergy. The side‐effect profile appears acceptable but requires further study. Cite this as: A. Martorell, B. De la Hoz, M. D. Ibáñez, J. Bone, M. S. Terrados, A. Michavila, A. M. Plaza, E. Alonso, J. Garde, S. Nevot, L. Echeverria, C. Santana, J. C. Cerdá, C. Escudero, I. Guallar, M. Piquer, L. Zapatero, L. Ferré, T. Bracamonte, A. Muriel, M. I. Martínez and R. Félix, Clinical & Experimental Allergy, 2011 (41) 1297–1304.
Shifting dynamic forces in fish stock fluctuations triggered by age truncation?
Authors: ROUYER TRISTAN , OTTERSEN GEIR , DURANT JOËL M. , HIDALGO MANUEL , HJERMANN DAG Ø. , PERSSON JONAS , STIGE LEIF CHR. , STENSETH NILS CHR. 
Published: April 2011

AbstractAccumulating evidence shows that environmental fluctuations and exploitation jointly affect marine fish populations, and understanding their interaction is a key issue for fisheries ecology. In particular, it has been proposed that age truncation induced by fisheries exploitation may increase the population's sensitivity to climate. In this study, we use unique long‐term abundance data for the Northeast Arctic stock of cod (Gadus morhua) and the Norwegian Spring‐Spawning stock of herring (Clupea harengus), which we analyze using techniques based on age‐structured population matrices. After identifying time periods with different age distributions in the spawning stock, we use linear models to quantify the relative effect of exploitation and temperature on the population growth rates. For the two populations, age truncation was found to be associated with an increasing importance of temperature and a relatively decreasing importance of exploitation, while the population growth rate became increasingly sensitive to recruitment variations. The results suggested that the removal of older age classes reduced the buffering capacity of the population, thereby making the population growth rate more dependent on recruitment than adult survival and increasing the effect of environmental fluctuations. Age structure appeared as a key characteristic that can affect the response of fish stocks to climate variations and its consequences may be of key importance for conservation and management.
Quantitative assessment of serum‐specific IgE in the diagnosis of human cystic echinococcosis
Authors: MARINOVA I. , NIKOLOV G. , MICHOVA A. , KURDOVA R. , PETRUNOV B. 
Published: April 2011

SummaryAnti‐Echinococcus serum immunoglobulin (Ig)E was assessed by the ImmunoCAP system and compared with anti‐Echinococcus serum IgG assessed by enzyme‐linked immunosorbent assay (ELISA) and Western blot. The ImmunoCAP system revealed very high specificity (one false positive of 110 healthy individuals), low cross‐reactivity (one false positive of 58 patients with other diseases) and decreased sensitivity (73·55%). Receiver operating characteristic analysis displayed a beneficial diagnostic value with high accuracy. Comparison of the ImmunoCAP system with ELISA and Western blot showed significantly higher specificity and significantly lower cross‐reactivity compared with the ELISA. Examination of sera from 155 patients with cystic echinococcosis (CE) showed varying levels of anti‐Echinococcus IgE (range, 0·01–118·33 kUA/L). However, most samples had moderately elevated IgE levels. Analysis of serum‐specific IgE revealed significantly higher sensitivity of the ImmunoCAP system and significantly higher antibody levels in hepatic CE compared with pulmonary CE.
The yam nematode (Scutellonema bradys), a potential threat to potato (Solanum tuberosum) production in West Africa
Authors: Coyne D. L. , Akpheokhai L. I. , Adeniran A. F. 
Published: April 2011

Potato (Solanum tuberosum) production in Africa is rapidly expanding and becoming increasingly important. As its geographical production range broadens, so does its potential to host new pests and diseases. Following the discovery that potato can be affected by Scutellonema bradys, further studies were undertaken to assess its potential pathogenicity on potato under screenhouse and field conditions, and on marketed tubers. Potato plants inoculated with S. bradys produced tubers with substantial cracking and evident tuber rot, compared with tubers from uninoculated plants. Symptoms of nematode infection on tubers included a scaly appearance, surface cracking as well as deeper tissue cracks, distortions, and darkened surface patches. In most cases these patches were related to sub‐surface rot. Nematodes were recovered from the soil, roots and tubers of inoculated plants. Eight weeks after inoculation, the reproduction factor of the nematode was greatest (2·0) at the lowest inoculation rate assessed (1000 nematodes per 2·5‐L pot) and least (0·4) at the highest inoculation rate (5000 nematodes per pot). In the screenhouse, potato tuber weights were low and mostly unaffected by nematode inoculation rate, except at 5000 nematodes per pot. In the field, non‐inoculated plants yielded over nine times more tubers than plants inoculated with 2000 S. bradys. Low densities of S. bradys were also recovered from 10 of 15 (67%) samples collected from market stalls, indicating field infection. This study confirms that potato can host and be damaged by S. bradys, raising its prospect as a likely significant biotic constraint to the crop.