bluuebunny/crossref_metadata_2025 huggingface dataset:
Width adjustment in experimental gravel‐bed channels in response to overbank flows
Authors: Pitlick John , Marr Jeff , Pizzuto Jim
Published: March 2013

We conducted a series of flume experiments to investigate the response of self‐formed gravel‐bed channels to floods of varying magnitude and duration. Floods were generated by increasing the discharge into a channel created in sand‐ and gravel‐sized sediment with a median grain size of 2 mm. Flooding increased the Shields stress along the channel perimeter, causing bank erosion and rapid channel widening. The sediment introduced to the channel by bank erosion was not necessarily deposited on the channel bed, but was rather transported downstream, a process likely facilitated by transient fining of the bed surface. At the end of each experiment, bank sediments were no longer in motion, “partial bed load transport” characterized the flat‐bed portion of the channel, and the Shields stress approached a constant value of 0.056, about 1.2 times the critical Shields stress for incipient motion. Furthermore, the discharge was entirely accommodated by flow within the channel: the creation of a stable channel entirely eliminated overbank flows. We speculate that similar processes may occur in nature, but only where bank sediments are non‐cohesive and where channel‐narrowing processes cannot counteract bank erosion during overbank flows. We also demonstrate that a simple model of lateral bed load transport can reproduce observed channel widening rates, suggesting that simple methods may be appropriate for predicting width increases in channels with non‐cohesive, unvegetated banks, even during overbank flows. Last, we present a model for predicting the equilibrium width and depth of a stable gravel‐bed channel with a known channel‐forming Shields stress.
Clinical symptoms, immune factors, and molecular characteristics of an adult male in Shenzhen, China infected with influenza virus H5N1
Authors: Wu Chunli , Lu Xing , Wang Xin , Jin Tao , Cheng Xiaowen , Fang Shisong , Wang Xiaohui , Ma Hanwu , Zhang Renli , Cheng Jinquan
Published: March 2013

On December 29, 2011, a man infected with a subclade of the H5N1 virus was confirmed in Shenzhen, China. The clinical symptoms and immune factors of the patient were investigated and the phylogenetic and molecular characteristics of the virus were analyzed. High fever, rapid development of serious pneumonia and multi‐organ failure were the main clinical symptoms. Arterial blood gas analysis showed that PaCO2 rose sharply and PO2 decreased. Leukocyte and platelet counts decreased rapidly. Peripheral blood lymphocyte counts indicated lymphopenia and inverted ratios of CD4+ to CD8+ cells. Cytokine analysis showed that the levels of serum IL‐6, IL‐10, and IFN‐r continued to increase, whereas the levels of IL‐12 and TNFs decreased during the clinical course. MCP‐1 and IP‐10 remained at a high level after infection. Phylogenetic analysis confirmed that the virus A/Shenzhen/1/2011 belongs to the new subclade 2.3.2.1. An Arg (R) insertion at P6 and an RP8I substitution in the HA cleavage site motif were detected in the virus. Compared to the vaccine strain, 16 specific substitutions occurred in the HA1 protein. Some of them were located on the receptor‐binding site, glycosylation site and the region of the antigenic determinant. In summary, serious complications and immune system disorders were the main features of the infection with H5N1. Gene variation did not weaken the highly pathogenic features of viruses and the pathogenicity and antigenicity of the new subclade virus were changed. J. Med. Virol. 85:760–768, 2013. © 2013 Wiley Periodicals, Inc.
Hepatitis B virus candidate subgenotype I1 varies in distribution throughout Guangxi, China and may have originated in Long An county, Guangxi
Authors: Li Guo‐Jian , Hue Stéphane , Harrison Tim J. , Yang Jin‐Ye , Chen Qin‐Yan , Wang Xue‐Yan , Fang Zhong‐Liao
Published: March 2013

Sequencing of the complete hepatitis B virus (HBV) genomes from Vietnam, China and Laos led to the identification of a complex recombinant, referred to initially as an aberrant genotype and later proposed to be a new genotype, I. However, epidemiological data regarding this new genotype are lacking. A cross‐sectional study was carried out to investigate the epidemiology of HBV candidate genotype I in Guangxi, China using stratified, random cluster sampling. Four thousand five hundred thirteen subjects were recruited from five counties within Guangxi. Three genotypes, B, C, and I, were identified with a prevalence of 32.6% (114/350), 64% (224/350), and 3.4% (12/350), respectively. All the genotype I isolates belong to candidate subgenotype I1 and were found in Bing Yang (15.3%, 9/59) and Na Po (5.0%, 3/60) counties only. The prevalence of this subgenotype is significantly higher in males (5.1%, 10/195) than in females (1.3%, 2/155; X2 = 3.959, P < 0.05) but does not differ significantly with age. It was found in the Han (4.5%, 9/201) and Zhuang (3.1%, 3/97) ethnic populations only. There is no significant difference from other genotypes in the prevalence of HBV serological markers. Phylogeographic analysis revealed that genotype I1 likely arose in Long An county, then spread later to Bing Yang, Na Po counties and elsewhere in southeast Asia. In conclusion, the distribution of candidate genotype I within Guangxi is not even and it is highly endemic in some counties. Its prevalence is associated with gender and ethnicity. Subgenotype I1 likely originated in Long An county. J. Med. Virol. 85:799–807, 2013. © 2013 Wiley Periodicals, Inc.
Serum immunoglobulin G subclass responses in different phases of hepatitis E virus infection
Authors: Deshmukh Tejaswini M. , Shah Rachita R. , Gurav Yogesh K. , Arankalle Vidya A.
Published: March 2013

To investigate the specific immunoglobulin (Ig) G subclass responses in patients with hepatitis E virus (HEV) infection, an open reading frame 2 (ORF2) protein based enzyme‐linked immunosorbant assay was used to measure antibody levels in sera obtained at different phases of infection. Sera were collected at 2–31 days and at 6 months after the onset of symptoms corresponding to the acute (n = 48, 100% IgM‐positive) and convalescent (n = 17/48, 53% IgM‐positive) phases of infection, respectively. IgM‐negative sera from 61 individuals infected at least ≥6 months ago (prior exposure) were also tested. IgG1, IgG2, IgG3, and IgG4 antibodies were detected in 100%, 6%, 56%, and 4% of acute phase sera, respectively, and in 100%, 0%, 0%, and 65% of convalescent phase sera, respectively. IgG1 antibody levels were significantly higher than those of the other detectable subclasses of IgG in the acute and convalescent sera (P < 0.05). The IgG3 antibodies in six acute phase patients were replaced by IgG4 antibodies in the convalescent phase of infection. Patients with prior exposure to HEV had low total IgG antibody titers and decreased IgG1 seropositivity compared with those in the acute and convalescent phases. IgG1 was the only major subclass of antibody to be detected in all the three phases of infection. Other than IgG1 antibodies, the subclass antibody response was restricted to IgG3 and IgG4 antibodies in the acute and convalescent phases of infection, respectively. J. Med. Virol. 85:828–832, 2013. © 2013 Wiley Periodicals, Inc.
Use of the human colorectal adenocarcinoma (Caco‐2) cell line for isolating respiratory viruses from nasopharyngeal aspirates
Authors: Chan K.H. , Yan M.K. , To K.K.W. , Lau S.K. , Woo P.C. , Cheng V.C.C. , Li W.S. , Chan J.F.W. , Tse H. , Yuen K.Y.
Published: March 2013

The human colorectal adenocarcinoma‐derived Caco‐2 cell line was evaluated as a means isolating common respiratory viruses from nasopharyngeal aspirates for the diagnosis of respiratory diseases. One hundred eighty‐nine direct immunofluorescence positive nasopharyngeal aspirates obtained from patients with various viral respiratory diseases were cultured in the presence of Caco‐2 cells or the following conventional cell lines: LLC‐MK2, MDCK, HEp‐2, and A549. Caco‐2 cell cultures effectively propagated the majority (84%) of the viruses present in nasopharyngeal aspirate samples compared with any positive cultures obtained using the panel cells (78%) or individual cell line MDCK (38%), HEp‐2 (21%), LLC‐MK2 (27%), or A549 (37%) cell lines. The differences against individual cell line were statistically significant (P = < 0.000001). Culture in Caco‐2 cells resulted in the isolation of 85% (36/42) of viruses which were not cultivated in conventional cell lines. By contrast, 80% (24/30) of viruses not cultivated in Caco‐2 cells were isolated using the conventional panel. The findings indicated that Caco‐2 cells were sensitive to a wide range of viruses and can be used to culture a broad range of respiratory viruses. J. Med. Virol. 85:874–879, 2013. © 2013 Wiley Periodicals, Inc.
Hepatitis C virus subtyping based on sequencing of the C/E1 and NS5B genomic regions in comparison to a commercially available line probe assay
Authors: Avó Ana Patrícia , Água‐Doce Ivone , Andrade Ana , Pádua Elizabeth
Published: March 2013

Hepatitis C virus (HCV) genotype determination is required in clinical practice to establish the dose and duration of antiviral treatment. Although subtype identification does not impact on current therapy this is changing with new specific inhibitors of HCV enzymes and functions which are becoming available worldwide. These new drugs may yield different antiviral responses and resistance profiles. Accurate classification of HCV genotype and subtype is therefore crucial. An “in‐house” method was developed for improving HCV subtyping and the results were compared with a second‐generation line probe assay (LiPA) used extensively in Portugal. Phylogenetic analysis was undertaken of the C/E1 and NS5B genomic regions of HCV isolated from 72 prisoners with chronic HCV infection and from reference samples. Although LiPA is considered to be a good method for genotyping, HCV was subtyped in only 47.2% of cases compared with 95.8% of cases by the “in‐house” method. Molecular data for both C/E1 and NS5B regions were obtained in 88.9% of the samples. Two out of 23 cases of subtype 1a were misclassified as subtype 1b by LiPA. A putative recombinant like RF1_2k/1b, two potential inter‐genotypic recombinants 1b/4a and 3a/4a, and also a potential intra‐genotypic recombinant 2q/2k in C/E1 and 2k/2a in NS5B were also identified. The “in‐house” method enabled HCV to be subtyped accurately with the detection, in some cases, of recombinant viruses or dual HCV infections. Near full‐length genomic analysis to characterize these potential recombinant viruses is planned. J. Med. Virol. 85:815–822, 2013. © 2013 Wiley Periodicals, Inc.
Association of polymorphism in MicroRNA 219‐1 with clearance of hepatitis B virus infection
Authors: Cheong Jae Youn , Shin Hyoung Doo , Kim Yoon Jun , Cho Sung Won
Published: March 2013

Polymorphisms in the primary microRNA region may be associated with natural course of hepatitis B virus (HBV) infection. This study evaluated if the mircoRNA 219‐1 (miR‐219‐1) polymorphism can influence the susceptibility towards persistence of HBV infection and the progression to hepatocellular carcinoma (HCC) in patients with chronic HBV infection. A total of 1,439 individuals having either past or present evidence of HBV infection were enrolled for the study. The subjects were divided into four groups; (1) spontaneous recovery (n = 404), (2) chronic HBV carrier (n = 313), (3) chronic HBV carrier with cirrhosis (n = 305), and (4) hepatocellular carcinoma (n = 417). Genotyping was performed at three polymorphic variants (rs421446, rs107822, and rs213210) in the pri‐miRNA region of miR‐219‐1. The rs421446 T allele was found to be strongly associated with HBV clearance (OR = 0.73, P = 0.0005 in a codominant model and OR = 0.67, P = 0.0009 in a dominant model, OR = 0.69, P = 0.04 in a recessive model, respectively). The rs107822 G allele was also found to be associated with HBV clearance (OR = 0.79, P = 0.008 in a codominant model and OR = 0.72, P = 0.01 in a dominant model, respectively). In haplotype analysis, ht2 (T‐G‐T) and ht1 (C‐A‐C) were found to be in significant association with the clearance of HBV. However, no significant association was observed between miR‐219‐1 polymorphism and the risk of HCC occurrence. This result suggests that polymorphisms in the pri‐miRNA region of miR‐219‐1 might be a genetic factor for HBV clearance after infection. J. Med. Virol. 85:808–814, 2013. © 2013 Wiley Periodicals, Inc.
Repeatability of gait analysis for measuring knee osteoarthritis pain in patients with severe chronic pain
Authors: Asay Jessica L. , Boyer Katherine A. , Andriacchi Thomas P.
Published: March 2013

Gait measures are receiving increased attention in the evaluation of patients with knee osteoarthritis (OA). Yet, there remains a need to assess variability of gait analysis in patients with knee osteoarthritis over time and how pain affects variation in these gait parameters. The purpose of this study was to determine if important gait parameters, such as the knee adduction moment, knee flexion moment, peak vertical ground reaction force, and speed, were repeatable in patients with mild‐to‐moderate knee OA over a trial period of 12 weeks. Six patients were enrolled in this cross‐over study design after meeting strict inclusion criteria. Gait tests were conducted three times at 4 week intervals and once after the placebo arm of a randomized treatment sequence; each gait test followed a 2‐week period of receiving a placebo for a pain modifying drug. Repeatability for each gait variable was found using intraclass correlation coefficients (ICC) with a two‐way random model. This study found that the knee adduction moment was repeatable throughout the four gait tests. However, normalized peak vertical ground reaction force and knee flexion moment were not as repeatable, varying with pain. This suggests that these gait outcomes could offer a more objective way to measure a patient's level of pain. © 2012 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 31:1007–1012, 2013
Serial coupling of reversed‐phase and zwitterionic hydrophilic interaction LC/MS for the analysis of polar and nonpolar phenols in wine
Authors: Greco Giorgia , Grosse Sylvia , Letzel Thomas
Published: March 2013

In the present study, an easy and efficient method based on the serial coupling of analytical reversed‐phase and zwitterionic hydrophilic interaction liquid chromatography was developed for the simultaneous separation of polar and nonpolar phenols occurring in wine. The zwitterionic hydrophilic column was connected in series to the reversed‐phase one via a T‐piece, with which the ACN content in eluent of the second dimension was increased, in order to cope the solvent strength incompatibility between the two columns. The final mobile phase at low‐flow rate (≤0.5 mL/min), high‐ACN content (90%), and low‐salt concentration was directed to an ESI‐TOF‐MS , for high accurate mass detections. The developed method was applied for the identification of target phenols in several wines. Retention time and peak width intra‐ and interday repeatability studies proved the reliability of the method for the simultaneous analysis of all the polar and nonpolar analytes in wine. The serial reversed‐phase/zwitterionic hydrophilic interaction liquid chromatography coupling offered the possibility to enlarge the number of identified compounds and it represents a valid approach for nontarget analysis of complex samples by a single injection.
Reversal of elution order of N‐(2,4‐dinitrophenyl)‐proline and N‐(2,4‐dinitrophenyl)‐serine in HPLC by BSA chiral stationary phase
Authors: Wang Qiuyun , Xiong Yajin , Lu Baozhu , Fan Jun , Zhang Sheng , Zheng Shengrun , Zhang Weiguang
Published: March 2013

N‐(2,4‐dinitrophenyl)‐proline and N‐(2,4‐dinitrophenyl)‐serine were enantiomerically resolved on the BSA chiral stationary phase by HPLC in reversed‐phase mode. Effects of chromatographic conditions on enantioseparation and elution order have been investigated in detail. For these two samples, reversal of enantiomer elution order was observed by changing buffer pH, the content of acetonitrile, or alcohol modifiers in mobile phase, which is firstly reported in the BSA chiral stationary phase studies. More interestingly, combined effect between buffer pH and the content of acetonitrile was also observed. In addition, coelution range of enantiomers varied along with the content of acetonitrile in mobile phase.
Use of chiral derivatization for the determination of dichlorprop in tea samples by ultra performance LC with fluorescence detection
Authors: Inoue Koichi , Prayoonhan Nuntawat , Tsutsui Haruhito , Sakamoto Tasuku , Nishimura Maiko , Toyo'oka Toshimasa
Published: March 2013

Dichlorprop is available for agricultural use as a chiral pesticide. In this study, the stereoselective determination of dichlorprop enantiomers in tea samples such as green, black, jasmine, and oolong was developed by ultra performance LC with fluorescence spectrometry after covalent chiral derivatization. The separation was achieved on an Acquity BEH C18 column with the mobile phase consisting of 0.1% formic acid in acetonitrile/water at a flow rate of 0.4 mL/min. In the covalent chiral derivatization using (S)‐(+)‐4‐(N,N‐dimethylaminosulfonyl)‐7‐(3‐aminopyrrolidin‐1‐yl)‐2,1,3‐benzoxadiazole, the peak resolution between the S and R‐dichlorprop enantiomers was 2.6. LODs and LOQs values were 10 and 50 ng/mL standard solution. The linearity of the calibration curves yielded the coefficients (r2 > 0.99, ranging from 0.05 to 5 μg/mL) of determination of each of the dichlorprop enantiomers. SPE extraction was used for the sample preparation of dichlorprop in various tea samples. Recoveries were in the range of 82.4–97.6% with associated precision values (within‐day: 82.4–95.8%, n = 6, and between‐day: 83.7–97.6% for 3 days) for repeatability and reproducibility. Based on this result, our method has been proven to be highly efficient and suitable for the routine assay of dichlorprop enantiomers in various tea samples. We propose that the ultra performance LC assay after covalent chiral derivatization would be the renewed tools in the era of chiral stationary platform for chiral pesticide residues in foods.
Photodynamic inactivation of chlorin e6‐loaded CTAB‐liposomes against Candida albicans
Authors: Yang Yu‐Tsai , Chien Hsiung‐Fei , Chang Po‐Han , Chen Yee‐Chun , Jay Michael , Tsai Tsuimin , Chen Chin‐Tin
Published: March 2013

Background and Objectives

Antimicrobial photodynamic inactivation (PDI) is a promising therapeutic modality for the treatment of local infections. To increase the efficacy of PDI, chlorine e6 (Ce6) was encapsulated in cationic CTAB‐liposomes composed of various ratios of dimyristoyl‐sn‐glycero‐phosphatidylcholine (DMPC) and the cationic surfactant, cetyltrimethyl ammonium bromide (CTAB). The PDI efficacy of the liposomal‐Ce6 was assessed in vitro against susceptible and drug‐resistant clinical isolates of Candida albicans (C. albicans) as well as in infected burn wounds.

Study Design/Materials and Methods

Ce6 was encapsulated in CTAB‐liposomes by the film hydration method. Particle size distribution and zeta potential of the cationic liposomes were measured using a Zetasizer Nano‐ZS. UV‐visible spectra were used to measure lipid/Ce6 (L/C) ratio and drug entrapment efficiency while differential scanning calorimetry (DSC) was used to study the thermotropic behavior of DMPC liposomes upon CTAB addition. In vivo PDI efficacy was carried out in an infected burn wound using a rat model.

Results

The increase in zeta potential and a shift in the phase transition temperature (Tm) upon CTAB addition confirmed its entrapment within the lipid bilayers of the liposome. Meanwhile, the CTAB addition did not affect the Ce6 entrapment efficiency and physical attributes of the liposomes. In vitro studies showed that the PDI effect of the Ce6‐loaded CTAB‐liposomes was dependent on the lipid to Ce6 molar ratio (L/C), particle size and the concentration of CTAB in the liposomes. The lower L/C ratio and smaller liposomes exerted significantly higher PDI effects. In addition, an increase in the CTAB to lipid ratio led to a significant increase in the PDI effect of Ce6 against susceptible and drug‐resistant clinical isolates of C. albicans after light illumination.

Conclusions

Our results indicate that a low L/C ratio, high positive charge, and small particle size of CTAB‐liposomes significantly enhances their PDI efficacy against C. albicans. Lasers Surg. Med. 45: 175–185, 2013. © 2013 Wiley Periodicals, Inc.
Non‐Natural Amino Acids for Protein Engineering and New Protein Chemistries
Authors: Kwon Inchan , Lim Sung In
Published: March 2013

Non‐natural amino acids can be used to expand the protein sequence space significantly beyond the limits set by nature. Expanding the protein sequence space opens a new door to engineering and chemically modifying proteins. Reassigning codons to non‐natural amino acids as well as engineering protein translational machinery is required to incorporate non‐natural amino acids into a single or multiple sites of a target protein in cells. Non‐natural amino acid incorporation holds a great promise in substantially improving protein intrinsic properties and providing new orthogonal chemistries to proteins for bioconjugation.

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High‐Efficiency Preparation of Macrocyclic Polymers via a Circulatory Extraction–Cyclization Strategy
Authors: Zhu Xing , Zhou Nianchen , Zhu Jian , Zhang Zhengbiao , Zhang Wei , Cheng Zhenping , Tu Yingfeng , Zhu Xiulin
Published: March 2013

Typically, intramolecular cyclization reactions need to be conducted at high dilution to avoid interchain coupling, which leads to the production of cyclic polymer at an extremely low output. Herein, a high‐efficiency Cu‐catalyzed azide/alkyne cycloaddition “click” synthesis of cyclic polystyrene (PS) and cyclic poly (methyl methacrylate) (PMMA) is reported via a circulatory technique of evaporation–condensation–extraction–inflow strategy by the utilization of elaborately designed equipment. High‐output cyclic PS (one batch, 0.71 g cyclic polymer from 1.0 g linear polymer loading) and cyclic PMMA (one batch, 0.62 g cyclic PMMA from 1.0 g linear polymer loading) are achieved. This promising preparation should be beneficial to the large‐scale application and research of cyclic polymers.

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Hetero Diels–Alder Chemistry for the Functionalization of Single‐Walled Carbon Nanotubes with Cyclopentadienyl End‐Capped Polymer Strands
Authors: Zydziak Nicolas , Preuss Corinna M. , Winkler Volker , Bruns Michael , Hübner Christof , Barner‐Kowollik Christopher
Published: March 2013

Single‐walled carbon nanotubes (SWCNTs) are pre‐functionalized with a pyridinyl‐based dithioester to undergo a hetero Diels–Alder (HDA) reaction with cyclopentadienyl end‐capped poly(methyl)methacrylate (Mn = 2700 g mol−1, PDI = 1.14). Fourier transform infrared spectroscopy, thermogravimetric analysis, elemental analysis (EA), and X‐ray photoelectron spectroscopy (XPS) evidence the success of the grafting process. The estimated resulting grafting density (from XPS and EA) via the HDA reaction increases by a factor of more than two (0.0774 chains·nm−2 via XPS) compared with typical values obtained via a direct cyclopentadiene driven Diels–Alder conjugation onto non‐functional SWCNTs under similar conditions.

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Expression of Fap amyloids in Pseudomonas aeruginosa,P. fluorescens, and P. putida results in aggregation and increased biofilm formation
Authors: Dueholm Morten S. , Søndergaard Mads T. , Nilsson Martin , Christiansen Gunna , Stensballe Allan , Overgaard Michael T. , Givskov Michael , Tolker‐Nielsen Tim , Otzen Daniel E. , Nielsen Per H.
Published: March 2013

The fap operon, encoding functional amyloids in Pseudomonas (Fap), is present in most pseudomonads, but so far the expression and importance for biofilm formation has only been investigated for P. fluorescens strain UK4. In this study, we demonstrate the capacity of P. aeruginosa PAO1, P. fluorescens Pf‐5, and P. putida F1 to express Fap fibrils, and investigated the effect of Fap expression on aggregation and biofilm formation. The fap operon in all three Pseudomonas species conferred the ability to express Fap fibrils as shown using a recombinant approach. This Fap overexpression consistently resulted in highly aggregative phenotypes and in increased biofilm formation. Detailed biophysical investigations of purified fibrils confirmed FapC as the main fibril monomer and supported the role of FapB as a minor, nucleating constituent as also indicated by bioinformatic analysis. Bioinformatics analysis suggested FapF and FapD as a potential β‐barrel membrane pore and protease, respectively. Manipulation of the fap operon showed that FapA affects monomer composition of the final amyloid fibril, and that FapB is an amyloid protein, probably a nucleator for FapC polymerization. Our study highlights the fap operon as a molecular machine for functional amyloid formation.
Sparse BLIP: BLind Iterative Parallel imaging reconstruction using compressed sensing
Authors: She Huajun , Chen Rong‐Rong , Liang Dong , DiBella Edward V. R. , Ying Leslie
Published: March 2013

Purpose

To develop a sensitivity‐based parallel imaging reconstruction method to reconstruct iteratively both the coil sensitivities and MR image simultaneously based on their prior information.

Methods

Parallel magnetic resonance imaging reconstruction problem can be formulated as a multichannel sampling problem where solutions are sought analytically. However, the channel functions given by the coil sensitivities in parallel imaging are not known exactly and the estimation error usually leads to artifacts. In this study, we propose a new reconstruction algorithm, termed Sparse BLind Iterative Parallel, for blind iterative parallel imaging reconstruction using compressed sensing. The proposed algorithm reconstructs both the sensitivity functions and the image simultaneously from undersampled data. It enforces the sparseness constraint in the image as done in compressed sensing, but is different from compressed sensing in that the sensing matrix is unknown and additional constraint is enforced on the sensitivities as well. Both phantom and in vivo imaging experiments were carried out with retrospective undersampling to evaluate the performance of the proposed method.

Results

Experiments show improvement in Sparse BLind Iterative Parallel reconstruction when compared with Sparse SENSE, JSENSE, IRGN‐TV, and L1‐SPIRiT reconstructions with the same number of measurements.

Conclusion

The proposed Sparse BLind Iterative Parallel algorithm reduces the reconstruction errors when compared to the state‐of‐the‐art parallel imaging methods. Magn Reson Med 71:645–660, 2014. © 2013 Wiley Periodicals, Inc.
In vitro mapping of 1H ultrashort T2* and T2 of porcine menisci
Authors: Kirsch S. , Kreinest M. , Reisig G. , Schwarz M. L. R. , Ströbel P. , Schad L. R.
Published: March 2013

In this study, mapping of ultrashort T2 and T2* of acutely isolated porcine menisci at B0 = 9.4 T was investigated. Maps of T2 were measured from a slice through the pars intermedia with a spin echo‐prepared two‐dimensional ultrashort‐TE T2 mapping technique published previously. T2* mapping was performed by two‐dimensional ultrashort‐TE MRI with variable acquisition delay. The measured signal decays were fitted by monoexponential, biexponential and Gaussian‐exponential fitting functions. The occurrence of Gaussian‐like signal decays is outlined theoretically. The quality of the curve fits was visualized by mapping the value δ = abs(1 – χ2red). For T2* mapping, the Gaussian‐exponential fit showed the best performance, whereas the monoexponential and biexponential fits showed regionally high values of δ (δ > 20). Interpretation of the Gaussian‐exponential parameter maps was found to be difficult, because a Gaussian signal component can be related to mesoscopic (collagen texture) or macroscopic (slice profile, shim, sample geometry) magnetic field inhomogeneities and/or residual 1H dipole–dipole couplings. It seems likely that an interplay of these effects yielded the observed signal decays. Modulation of the T2* signal decay caused by chemical shift was observed and addressed to fat protons by means of histology. In the T2 measurements, no modulation of the signal decay was observed and the biexponential and Gaussian‐exponential fits showed the best performance with comparable values of δ. Our results suggest that T2 mapping provides the more robust method for the characterization of meniscal tissue by means of MRI relaxometry. However, mapping of ultrashort T2, as performed in this study, is time consuming and provides less signal‐to‐noise ratio per time than the mapping of T2*. If T2* mapping is used, pixel‐wise monitoring of the fitting quality based on reduced χ2 should be employed and great care should be taken when interpreting the parameter maps of the fits. Copyright © 2013 John Wiley & Sons, Ltd.
Two‐stepping to increase peptide spectra matches in large databases
Authors: Molloy Mark P.
Published: March 2013

Metaproteomics and proteogenomic studies face unique challenges in peptide spectra identification due to the very large number of sequences in search databases. Conventional, stringent filtering needed to avoid false positives limits results in these studies due to increasing false negatives, that is, poor sensitivity. Jagtap et al. (Proteomics 2013, 13, 1352–1357) find a solution to this issue by employing a facile two‐step search strategy.
Protein misfolding in the late‐onset neurodegenerative diseases: Common themes and the unique case of amyotrophic lateral sclerosis
Authors: Mulligan Vikram Khipple , Chakrabartty Avijit
Published: March 2013

Enormous strides have been made in the last 100 years to extend human life expectancy and to combat the major infectious diseases. Today, the major challenges for medical science are age‐related diseases, including cancer, heart disease, lung disease, renal disease, and late‐onset neurodegenerative disease. Of these, only the neurodegenerative diseases represent a class of disease so poorly understood that no general strategies for prevention or treatment exist. These diseases, which include Alzheimer's disease, Parkinson's disease, Huntington's disease, the transmissible spongiform encephalopathies, and amyotrophic lateral sclerosis (ALS), are generally fatal and incurable. The first section of this review summarizes the diversity and common features of the late‐onset neurodegenerative diseases, with a particular focus on protein misfolding and aggregation—a recurring theme in the molecular pathology. The second section focuses on the particular case of ALS, a late‐onset neurodegenerative disease characterized by the death of central nervous system motor neurons, leading to paralysis and patient death. Of the 10% of ALS cases that show familial inheritance (familial ALS), the largest subset is caused by mutations in the SOD1 gene, encoding the Cu, Zn superoxide dismutase (SOD1). The unusual kinetic stability of SOD1 has provided a unique opportunity for detailed structural characterization of conformational states potentially involved in SOD1‐associated ALS. This review discusses past studies exploring the stability, folding, and misfolding behavior of SOD1, as well as the therapeutic possibilities of using detailed knowledge of misfolding pathways to target the molecular mechanisms underlying ALS and other neurodegenerative diseases. Proteins 2013; 81:1285–1303. © 2013 Wiley Periodicals, Inc.
Structural and functional analyses of catalytic domain of GH10 xylanase from Thermoanaerobacterium saccharolyticum JW/SL‐YS485
Authors: Han Xu , Gao Jian , Shang Na , Huang Chun‐Hsiang , Ko Tzu‐Ping , Chen Chun‐Chi , Chan Hsiu‐Chien , Cheng Ya‐Shan , Zhu Zhen , Wiegel Juergen , Luo Wenhua , Guo Rey‐Ting , Ma Yanhe
Published: March 2013

Xylanases are capable of decomposing xylans, the major components in plant cell wall, and releasing the constituent sugars for further applications. Because xylanase is widely used in various manufacturing processes, high specific activity, and thermostability are desirable. Here, the wild‐type and mutant (E146A and E251A) catalytic domain of xylanase from Thermoanaerobacterium saccharolyticum JW/SL‐YS485 (TsXylA) were expressed in Escherichia coli and purified subsequently. The recombinant protein showed optimal temperature and pH of 75°C and 6.5, respectively, and it remained fully active even after heat treatment at 75°C for 1 h. Furthermore, the crystal structures of apo‐form wild‐type TsXylA and the xylobiose‐, xylotriose‐, and xylotetraose‐bound E146A and E251A mutants were solved by X‐ray diffraction to high resolution (1.32–1.66 Å). The protein forms a classic (β/α)8 folding of typical GH10 xylanases. The ligands in substrate‐binding groove as well as the interactions between sugars and active‐site residues were clearly elucidated by analyzing the complex structures. According to the structural analyses, TsXylA utilizes a double displacement catalytic machinery to carry out the enzymatic reactions. In conclusion, TsXylA is effective under industrially favored conditions, and our findings provide fundamental knowledge which may contribute to further enhancement of the enzyme performance through molecular engineering. Proteins 2013; 81:1256–1265. © 2013 Wiley Periodicals, Inc.
Routine fabrication of reduced graphene oxide microarray devices via all solution processing
Authors: Lanche Ruben , Delle Lotta E. , Weil Maryam , Vu Xuan Thang , Pachauri Vivek , Munief Walid M. , Wagner Patrick , Ingebrandt Sven
Published: March 2013

A method for the routine fabrication of graphene (reduced graphene oxide (r‐GO)) based devices is reported. We describe a solution‐based technique for the fabrication of the devices on alternative substrates and subsequent on‐substrate processing of graphene oxide into reduced graphene oxide. As sensor platform we mainly used interdigitated gold electrodes forming microarray structures on glass substrates. Graphene oxide was site‐specifically deposited onto microelectrode arrays by dielectrophoresis followed by a solution‐based reduction of graphene oxide with L‐ascorbic acid. In order to test the r‐GO sensor stability and performance, impedance spectroscopy was used. The optimized all solution processed fabrication provides an attractive fabrication route for robust r‐GO microarray devices in a flexible, scalable and cost‐effective approach.

Schematics for a microarray chip based on reduced graphene oxide.
Spectroscopic studies of Tm‐doped zirconia nanoparticles
Authors: Soares M. R. N. , Rino L. , Costa F. M. , Monteiro T.
Published: March 2013

Intra‐4f12 transitions of Tm3+ ions in zirconia powders processed by solution combustion synthesis (CS) were studied by optical techniques. The results were compared with the ones obtained in reference samples of yttria stabilized zirconia fibers grown by laser floating zone. The spectroscopic features observed for the tetragonal fibre were compared with the Stark lines detected in the polyphasic (monoclinic and tetragonal) powder suggesting additional Tm3+ sites/environments due to the ions in the monoclinic host. The stability of the blue 1D2 → 3F4 and red 1G4 → 3H6 transitions was found to be strongly dependent on temperature. For the fibres, the blue luminescence increases by a factor of two between 15 K and the room temperature when pumping the sample in the 1D2 level. When the excitation is performed in the 1G4 state a higher stability of the red luminescence was found to occur in fibres than in the polyphasic powder. Constant 1G4 → 3H6 integrated intensity was observed in the fibres, while a decrease of the red luminescence efficiency occurs with temperature for the polyphasic powder. The suppression of the nonradiative paths which compete with the radiative transition could be attained by using thulium doped yttria stabilized CS powders.
Modelling escape and capture processes in GaInNAs quantum well solar cells
Authors: Kengradomying O. , Jiang S. , Wang Q. , Vogiatzis N. , Rorison J. M.
Published: March 2013

Carrier escape and capture processes in a GaInA/GaAs quantum well (QW) and a GaInNAs/GaAs QW are compared through modelling using a rate equation approach. QW compositions corresponding to bandgaps of 0.983 eV, 1.000 eV and 1.100 eV are considered for applications in solar cells. For GaInAs a standard alloy model is used, including strain effects, while for GaInNAs the Band Anticrossing (BAC) model is used. The roles of 1. the conduction band QW barrier height and 2. the corresponding effective mass in affecting the electron escape and capture in the QW are considered in detail. The contribution of photogenerated currents from the barrier and QW are considered. The effect of QW depth is found to be larger than changes in the electron effective mass. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nitrogen incorporation into GaAsN and InGaAsN layers grown by liquid‐phase epitaxy
Authors: Milanova Malina , Vitanov Petko , Terziyska Penka , Koleva Greta , Popov Georgy
Published: March 2013

This paper presents the comparison of nitrogen incorporation in GaAsN and InGaAsN layers grown on GaAs substrate from Ga‐ and In‐rich solution, respectively, by liquid‐phase epitaxy. Polycrystalline GaN has been used as a source of nitrogen in two cases. The initial epitaxy temperature has been varied in the temperature range 600‐550 °C. Nitrogen content in Ga1‐xAsNx grown layers has been determined to be in the range 0.1‐0.5%. Higher nitrogen incorporation efficiency has been found for quaternary InGaAsN layers grown under carefully chosen lattice matched conditions. The incorporation of nitrogen into GaAsN and InGaAsN layers has been study by vibrational mode absorption spectroscopy. Nitrogen‐induced vibration mode near 472 cm‐1 has been registered in GaAsN samples. Preferential In‐N bonds and the formation of N‐centred In3Ga1 clusters have been identified for lattice matched to GaAs epitaxial InGaAsN layers. Electrical properties of the samples have been characterized by temperature‐dependent Hall effect measurements. Nominally undoped GaAsN and InGaAsN grown layers are n‐type with Hall concentration about one order of magnitude higher in comparison to layers not containing nitrogen. Thermally activated increase in the free carrier concentration at temperatures higher than 150 K is observed which indicates the presence of N‐related deep donor levels below dilute nitride conduction band edge. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Improved control of the phosphorous surface concentration during in‐line diffusion of c‐Si solar cells by APCVD
Authors: Davis Kristopher O. , Jiang Kaiyun , Demberger Carsten , Zunft Heiko , Haverkamp Helge , Habermann Dirk , Schoenfeld Winston V.
Published: March 2013

Emitter formation for industrial crystalline silicon (c‐Si) solar cells is demonstrated by the deposition of phosphorous‐doped silicate glasses (PSG) on p‐type monocrystalline silicon wafers via in‐line atmospheric pressure chemical vapor deposition (APCVD) and subsequent thermal diffusion. Processed wafers with and without the PSG layers have been analysed by SIMS measurements to investigate the depth profiles of the resultant phosphorous emitters. Subsequently, complete solar cells were fabricated using the phosphorous emitters formed by doped silicate glasses to determine the impact of this high‐throughput doping method on cell performance. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Field and laboratory experiments on aerosol‐induced cooling in the nocturnal boundary layer
Authors: Mukund V. , Singh D. K. , Ponnulakshmi V. K. , Subramanian G. , Sreenivas K. R.
Published: March 2013

Heat transfer processes in the nocturnal boundary layer (NBL) influence the surface energy budget and play an important role in many micrometeorological processes, including the formation of inversion layers, radiation‐fog and in the control of air‐quality near the ground. Under calm and clear‐sky conditions, radiation plays an important role in determining the characteristics of the NBL. In this article, we report observations, close to ground, of hypercooling that has a radiative origin, and which leads to anomalous vertical temperature profiles with elevated minima. In addition, a laboratory experimental set‐up is developed that is capable of capturing the thermal structure of the NBL, close to ground, under various conditions. Results from the laboratory experiments indicate that the high cooling rates near the ground, observed in the field experiments, arise from a near‐surface heterogeneity in the (aerosol‐laden) NBL; a feature ignored in radiation models used for atmospheric simulations. Many of these models nevertheless predict preferential near‐ground cooling in apparent agreement with our field observations. However, the cooling is spurious, and arises from the use of an incorrect frequency‐averaged transmittance in the radiation model. Based on our observations, a non‐dimensional number is proposed that characterizes the evolution in the lowest metres of the NBL; in particular, the effect of radiation on the NBL thermal structure. Our results should help in parametrizing NBL transport process, and highlight the need to account for both the effects of aerosols close to the ground and a varying ground emissivity, via appropriate boundary conditions in general circulation and climate models.
Quantifying flood risk of extreme events using density forecasts based on a new digital archive and weather ensemble predictions
Authors: McSharry Patrick E. , Little Max A. , Rodda Harvey J. E. , Rodda John
Published: March 2013

Non‐coastal flood events in the UK are usually associated with extreme rainfall and can last from minutes to weeks. Efficient management and mitigation of flood risk requires accurate and reliable precipitation forecasts as inputs to flood risk models. We constructed an archive of British Rainfall data from 1866 to the present day to improve our understanding of historical extreme rainfall events. The relationship between record rainfall and flooding is nonlinear and uncertain, implying that probabilistic forecasts of rainfall are required. We developed an objective classification scheme of extreme rainfall events consisting of eight types, analysed extreme rainfall events and produced probabilistic forecasts by combining statistical techniques with the outputs of ensemble predictions from a numerical weather predictions model. Copyright © 2010 Royal Meteorological Society
For most graphsH, mostH‐free graphs have a linear homogeneous set
Authors: Kang Ross J. , McDiarmid Colin , Reed Bruce , Scott Alex
Published: March 2013

Erdős and Hajnal conjectured that for every graphHthere is a constantsuch that every graphGthat does not haveHas an induced subgraph contains a clique or a stable set of order.

The conjecture would be false if we set; however, in an asymptotic setting, we obtain this strengthened form of Erdős and Hajnal's conjecture for almost every graphH, and in particular for a large class of graphsHdefined by variants of the colouring number. © 2013 Wiley Periodicals, Inc. Random Struct. Alg., 45, 343–361, 2014
Cooperative strategies in satellite assisted emergency services
Authors: Morosi Simone , Jayousi Sara , Falletti Emanuela , Araniti Giuseppe
Published: March 2013

This paper deals with the cooperative strategies, which can be adopted in emergency scenarios by integrating space and terrestrial segments, and communication and localization services. First, the cooperative solutions for integrated Navigation and Communication systems are reviewed and an effective software‐defined radio implementation is described. Then, cooperative systems for broadcast and multicast communications in Incident Area Network are proposed and evaluated: in the broadcast scenario, low‐complexity relaying techniques are adopted to overcome the propagation impairments and the performance degradation; in the multicast system, radio resources management techniques for group communications are designed to allow the efficient use of scarce resources and improve connectivity and reliability of the overall system. The technical solutions have been studied and tested in the framework of the Italian National Research Project SAtellite‐assisted LocalIzation and Communication system for Emergency services [1]. Copyright © 2013 John Wiley & Sons, Ltd.
Parallel Gaussian elimination for XL family over GF(2)
Authors: Huang Heliang , Bao Wansu , Liu Shukai
Published: March 2013

The security of many cryptographic systems is based on the difficulty of solving systems of quadratic multivariate polynomial equations. XL family (which stands for eXtended Linearization) is a traditional type of algorithm for solving systems of multivariate polynomial equations over finite fields. The main idea of these algorithms is to extend the initial system by monomials multiplications and use linear algebra techniques to solve the system. The overall complexity of XL family is essentially determined by the workload of Gaussian elimination step. In this paper, we use the structured Gaussian elimination and parallel fast Gaussian elimination to reduce the complexity of XL family over GF(2). Because of the sparsity of the extended system, structured Gaussian elimination is applied to reduce the dimensions of the extended system. Thus, a great reduction of the storage can be obtained. By slightly modifying the logic of ordinarily Gaussian elimination, we parallelly compute the reduced system. Theory analysis indicates that the complexity of our improved XL, XL_SP, is (λT)2, which is far lower than (7/64)T2.8, the complexity of XL, where T is the number of monomials and λ is the ratio of the dimensions of the reduced system to the extended system. Further experiments to Hidden Field Equation cryptosystems show that about 90% reduction of the extended system is achieved by using structured Gaussian elimination, which means λ is about 1/10 in our experiments. Copyright © 2013 John Wiley & Sons, Ltd.
Tribological behaviors of a novel trilayer nanofilm: the influence of outer chain length and interlayer thickness
Authors: Ou Junfei , Wang Ying , Li Changquan , Wang Fajun , Xue Mingshan , Wang Jinqing
Published: March 2013

Polydopamine (coded as PDA) is reported to be very adhesive and reactive due to the attached functional groups, such as amine and hydroxyl groups. In this work, taking advantage of the condensation between Si–OH of the hydroxylated alkyltrichlorosilane (ATS) and C–OH on PDA surface, ATS molecules with different chain carbon number of 10, 14 and 18 were grafted onto the 3‐aminopropyl triethoxysilane (APTES)‐PDA dual‐layer film, which was composed of PDA outerlayer and APTES underlayer, on Si substrate. Thus, hydrophobic trilayer films coded as APTES‐PDA‐ATS were prepared successfully. In order to reveal the dependence of the tribological behaviors upon the microstructures of the film, tribological experiments were conducted on an atomic force microscope and a ball‐on‐plate tribometer. Experimental results showed that the (micro‐) friction reducing (characterized by a parameter of relative friction coefficient or friction coefficient, RFC or FC) and macro‐wear resisting (characterized by anti‐wear life) behaviors were related with the chain length of outerlayer and the PDA thickness. Specifically, on one hand, as the chain length increases, RFC/FC decreased and macro anti‐wear life lengthened; on the other hand, as PDA gets thicker, RFC increased and the anti‐wear life enhanced. Copyright © 2013 John Wiley & Sons, Ltd.