bluuebunny/crossref_metadata_2025 huggingface dataset:
Ischemic extent as a biomarker for characterizing severity of coronary artery stenosis with blood oxygen‐sensitive MRI
Authors: Tsaftaris Sotirios A. , Tang Richard , Zhou Xiangzhi , Li Debiao , Dharmakumar Rohan
Published: January 2012

Purpose:

To investigate whether a statistical analysis of myocardial blood‐oxygen‐level‐dependent (mBOLD) signal intensities can lead to the identification and quantification of the ischemic area supplied by the culprit artery.

Materials and Methods:

Cardiac BOLD images were acquired in a canine model (n = 9) with controllable LCX stenosis at rest and during adenosine infusion on a 1.5T clinical scanner. Statistical distributions of myocardial pixel‐intensities derived from BOLD images were used to compute an area metric (ischemic extent, IE). True myocardial perfusion was estimated from microsphere analysis. IE was compared against a standard metric (segment‐intensity‐response, SIR). Additional animals (n = 3) were used to investigate the feasibility of the approach for identifying ischemic territories due to LAD stenosis from mBOLD images.

Results:

Regression analyses showed that IE and myocardial flow ratio between rest and adenosine infusion (MFR) were exponentially related (R2 > 0.70, P < 0.001, for end‐systole and end‐diastole), while SIR and MFR were linearly related to end‐systole (R2 = 0.51, P < 0.04) and unrelated to end‐diastole (R2 ≈ 0, P = 0.91). Receiver‐operating‐characteristic analysis that IE was superior to SIR for detecting critical stenosis (MFR ≤2) in end‐systole and end‐diastole. Feasibility studies on LAD narrowing demonstrated that the proposed approach could also identify oxygenation changes in the LAD territories.

Conclusion:

The proposed evaluation of cardiac BOLD magnetic resonance imaging (MRI) offers marked improvement in sensitivity and specificity for detecting critical coronary stenosis at 1.5T compared to the mean segmental intensity approach. Patient studies are now warranted to determine its clinical utility. J. Magn. Reson. Imaging 2012;35:1338–1348. © 2012 Wiley Periodicals Inc.
Estimation of intersubject variability of cerebral blood flow measurements using MRI and positron emission tomography
Authors: Henriksen Otto M. , Larsson Henrik B.W. , Hansen Adam E. , Grüner Julie M. , Law Ian , Rostrup Egill
Published: January 2012

Purpose:

To investigate the within and between subject variability of quantitative cerebral blood flow (CBF) measurements in normal subjects using various MRI techniques and positron emission tomography (PET).

Materials and Methods:

Repeated CBF measurements were performed in 17 healthy, young subjects using three different MRI techniques: arterial spin labeling (ASL), dynamic contrast enhanced T1 weighted perfusion MRI (DCE) and phase contrast mapping (PCM). All MRI measurements were performed within the same session. In 10 of the subjects repeated CBF measurements by 15O labeled water PET had recently been performed. A mixed linear model was used to estimate between subject (CVbetw) and within subject (CVwith) coefficients of variation.

Results:

Mean global CBF, CVbetw and CVwith using each of the four methods were for PCM 65.2 mL/100 g/min, 17.4% and 7.4%, for ASL 37.1 mL/100 g/min, 16.2% and 4.8%, for DCE 43.0 mL/100 g/min, 20.0%, 15.1% and for PET 41.9 mL/100 g/min, 16.5% and 11.9%, respectively. Only for DCE and PCM a significant positive correlation between measurements was demonstrated.

Conclusion:

These findings confirm large between subject variability in CBF measurements, but suggest also that in healthy subjects a subject‐method interaction is a possible source of between subject variability and of method differences. J. Magn. Reson. Imaging 2012;35:1290–1299. © 2012 Wiley Periodicals, Inc.
Accuracy of MR elastography and anatomic MR imaging features in the diagnosis of severe hepatic fibrosis and cirrhosis
Authors: Rustogi Rahul , Horowitz Jeanne , Harmath Carla , Wang Yi , Chalian Hamid , Ganger Daniel R. , Chen Zongming E. , Bolster Bradley D. , Shah Saurabh , Miller Frank H.
Published: January 2012

Purpose:

To compare the diagnostic accuracy of magnetic resonance imaging elastography (MRE) and anatomic MRI features in the diagnosis of severe hepatic fibrosis and cirrhosis.

Materials and Methods:

Three readers independently assessed presence of morphological changes associated with hepatic fibrosis in 72 patients with liver biopsy including: caudate to right lobe ratios, nodularity, portal venous hypertension (PVH) stigmata, posterior hepatic notch, expanded gallbladder fossa, and right hepatic vein caliber. Three readers measured shear stiffness values using quantitative shear stiffness maps (elastograms). Sensitivity, specificity, and diagnostic accuracy of stiffness values and each morphological feature were calculated. Interreader agreement was summarized using weighted kappa statistics. Intraclass correlation coefficient was used to assess interreader reproducibility of stiffness measurements. Binary logistic regression was used to assess interreader variability for dichotomized stiffness values and each morphological feature.

Results:

Using 5.9 kPa as a cutoff for differentiating F3‐F4 from F0‐2 stages, overall sensitivity, specificity, and diagnostic accuracy for MRE were 85.4%, 88.4%, and 87%, respectively. Overall interreader agreement for stiffness values was substantial, with an insignificant difference (P = 0.74) in the frequency of differentiating F3‐4 from F0‐2 fibrosis. Only hepatic nodularity and PVH stigmata showed moderately high overall accuracy of 69.4% and 72.2%. Interreader agreement was substantial only for PVH stigmata, moderate for C/R m, deep notch, and expanded gallbladder fossa. Only posterior hepatic notch (P = 0.82) showed no significant difference in reader rating.

Conclusion:

MRE is a noninvasive, accurate, and reproducible technique compared with conventional features of detecting severe hepatic fibrosis. J. Magn. Reson. Imaging 2012;35:1356–1364. © 2012 Wiley Periodicals, Inc.
Improving quality of arterial spin labeling MR imaging at 3 tesla with a 32‐channel coil and parallel imaging
Authors: Ferré Jean‐Christophe , Petr Jan , Bannier Elise , Barillot Christian , Gauvrit Jean‐Yves
Published: January 2012

Purpose:

To compare 12‐channel and 32‐channel phased‐array coils and to determine the optimal parallel imaging (PI) technique and factor for brain perfusion imaging using Pulsed Arterial Spin labeling (PASL) at 3 Tesla (T).

Materials and Methods:

Twenty‐seven healthy volunteers underwent 10 different PASL perfusion PICORE Q2TIPS scans at 3T using 12‐channel and 32‐channel coils without PI and with GRAPPA or mSENSE using factor 2. PI with factor 3 and 4 were used only with the 32‐channel coil. Visual quality was assessed using four parameters. Quantitative analyses were performed using temporal noise, contrast‐to‐noise and signal‐to‐noise ratios (CNR, SNR).

Results:

Compared with 12‐channel acquisition, the scores for 32‐channel acquisition were significantly higher for overall visual quality, lower for noise and higher for SNR and CNR. With the 32‐channel coil, artifact compromise achieved the best score with PI factor 2. Noise increased, SNR and CNR decreased with PI factor. However mSENSE 2 scores were not always significantly different from acquisition without PI.

Conclusion:

For PASL at 3T, the 32‐channel coil at 3T provided better quality than the 12‐channel coil. With the 32‐channel coil, mSENSE 2 seemed to offer the best compromise for decreasing artifacts without significantly reducing SNR, CNR. J. Magn. Reson. Imaging 2012;35:1233‐1239. © 2012 Wiley Periodicals, Inc.
Rubella immune status among immigrant and nonimmigrant women in Spain
Authors: Ramos J.M. , Milla A. , Rodríguez J.C. , Gutiérrez F.
Published: January 2012

A cross‐sectional study of seroprevalence of rubella antibodies was carried out in all immigrant pregnant women (1,627) from February 2006 to June 2010. For each immigrant woman one Spanish pregnant woman was recruited. The seroprevalence of IgG antibodies against rubella in immigrant women was 92% (95% confidence interval [CI]: 90.4–93.3), and in native women was 97.7% (95%CI: 96.7–98.4) (P < 0.001). Immunity against was lowest among women from Latin America (odds ratio [OR]: 0.17), followed by women from Asia (OR: 0.20), Sub‐Saharan Africa (OR: 0.27) and Northern Africa (OR: 0.37). Female immigrants from developing countries should be targeted for immunization to reduce the risk of congenital rubella. J. Med. Virol. 84:548–550, 2012. © 2011 Wiley Periodicals, Inc.
High detection frequency and viral loads of human rhinovirus species A to C in fecal samples; diagnostic and clinical implications
Authors: Harvala H. , McIntyre C.L. , McLeish N.J. , Kondracka J. , Palmer J. , Molyneaux P. , Gunson R. , Bennett S. , Templeton K. , Simmonds P.
Published: January 2012

Human rhinoviruses (HRVs) can be divided into three species; HRV‐A to HRV‐C. Up to 148 different HRV (sero)types have been identified to date. Because of sequence similarity between 5′‐NCR of HRVs and enteroviruses (EVs), it is problematic to design EV‐specific RT‐PCR assays. The aims of this study were to assess the rate of false‐detection of different rhinoviruses by EV RT‐PCR, and to evaluate the diagnostic and clinical significance of such cross‐reactivity. In vitro RNA transcripts of HRV A‐C created from cDNA templates were quantified spectrophotometrically. Six hundred twenty‐one stool samples screened as part of routine diagnostic for EV, 17 EV‐positive stool samples referred for typing, 288 stool samples submitted for gastroenteritis investigations, and 1,500 CSF samples were included in the study. EV‐specific RT‐PCR detected RNA transcripts of HRV‐A1b, HRV‐B14, and HRV‐Crpat18 but with 10–1,000 reduced sensitivity compared to EV transcripts. Screening fecal samples by EV RT‐PCR identified 13 positive samples identified subsequently as rhinoviruses; a further 26 HRV‐positive samples were identified by nested HRV RT‐PCR. All individuals were hospitalized and presented mostly with diarrhea. A total of 26 HRV types were identified (HRV‐A: 46%; HRV‐B: 13%; HRV‐C: 41%). Results confirm that EV‐specific RT‐PCR can detect HRVs, and at a practical level, identify potential problems of interpretation if fecal samples are used for surrogate screening in cases of suspected viral meningitis. High detection frequencies (10%) and viral loads in stool samples provide evidence for enteric replication of HRV, and its association with enteric disease requires further etiological studies. J. Med. Virol. 84:536–542, 2012. © 2011 Wiley Periodicals, Inc.
Confirmation of the low clinical effect of human herpesvirus‐6 and ‐7 infections after renal transplantation
Authors: Caïola Delphine , Karras Alexandre , Flandre Philippe , Boutolleau David , Scieux Catherine , Agut Henri , Legendre Christophe , Gautheret‐Dejean Agnès
Published: January 2012

Human herpesvirus‐6 and ‐7 (HHV‐6 and HHV‐7) may lead to pathological manifestations in renal transplant recipients. The aim of this study was to investigate beta‐herpesvirus infections in 50 adult kidney transplant recipients after transplantation to examine the effect, interactions, and pathogenic consequences of infection and the effect of immunosuppressive regimens and Human cytomegalovirus (HCMV) prophylaxis with VACV. Beta‐herpesviruses loads in the blood of 50 adult kidney transplant recipients over a 6‐month period after transplantation and 198 blood donors were determined using polymerase chain reaction. The rate of HHV‐6 detection in peripheral mononuclear cells (PBMCs) was higher in patients with end‐stage renal disease and during the post‐transplantation follow‐up than in healthy subjects (33% and 68% vs. 12%, respectively). The detection rate of HHV‐7 in PBMCs was similar between patients, both before grafting and during the follow‐up for transplant recipients (69% and 88%, respectively), and healthy subjects (78%), and correlated with the number of lymphocytes. HCMV in plasma was detected only in patients during the post‐transplant period (24%). VACV prophylaxis had no negative effect on the replication of HHV‐6 or HHV‐7, and univariate analyses demonstrated associations between HHV‐6 infection and acute graft rejection [Odds ratio (OR) = 2.94, 95% confidence interval (CI), 1.05–8.2, P = 0.04], and between HHV‐7 infection and cholestasis [OR = 2.61 (95% CI, 1.08–6.3), P = 0.03]. Immunosuppressive regimens had no effect on beta‐herpesviruses infections. This study revealed the differing behavior of HCMV, HHV‐6, and HHV‐7 in kidney transplant recipients, and confirmed the association of HHV‐6 with graft rejection. J. Med. Virol. 84:450–456, 2012. © 2011 Wiley Periodicals, Inc.
Discordance in HIV‐1 Co‐receptor use prediction by different genotypic algorithms and phenotype assay: Intermediate profile in relation to concordant predictions
Authors: Trabaud Mary‐Anne , Icard Vinca , Scholtes Caroline , Perpoint Thomas , Koffi Joseph , Cotte Laurent , Makhloufi Djamila , Tardy Jean Claude , André Patrice
Published: January 2012

Concordant and discordant genotypic predictions of HIV‐1 co‐receptor tropism were analyzed. V3 region was sequenced from plasma samples of patients screened for R5 tropism by the Trofile® assay, before CCR5 antagonist prescription. Ten tools including geno2pheno, PSSM, an “11/25” and “net charge” rule, and other published algorithms were used. Patients were grouped according to concordance or discordance between tools and Trofile® result. Trofile® tropism reports from 50 patient samples were R5 in 38 and Dual/Mixed (DM) in 12. Prediction with the genotypic tools were concordant for 23 R5 samples, and discordant for the 15 other ones. From Trofile® DM strains were concordant in 6 and discordant in 6. V3 sequences were not clearly distinct between R5 and DM strains, except a greater diversity in the later. Discordances were found with any tool or combination of them, so that no one can be proposed as better than the others. Predictive values of each algorithm were similar and rather good (efficacy ranged from 74% to 84%), but the rate of non‐confirmed prediction is greater when compelling the results of all tools with each individual sample. The mean of quantitative values obtained with one tool when another tool give the opposite prediction were different from those obtained when all tools agree with that prediction. The two discordant groups were often not distinguishable from each other. These results suggest that viruses giving discordant prediction with bioinformatic tools could be functionally distinct and/or in a different evolutionary state compared to those with concordant prediction. J. Med. Virol. 84:402–413, 2012. © 2011 Wiley Periodicals, Inc.
Quantitation of hepatitis C virus RNA in peripheral blood mononuclear cells in HCV‐monoinfection and HIV/HCV‐coinfection
Authors: Chary Aarthi , Winters Mark A. , Eisen Robert , Knight Thomas H. , Asmuth David M. , Holodniy Mark
Published: January 2012

Peripheral blood mononuclear cells (PBMCs) represent an extrahepatic hepatitis C virus (HCV) reservoir, the significance of which is unclear due to limited studies and varying test methodologies. In this study, a commercial viral load assay for measuring cell‐associated PBMC HCV RNA was evaluated. HCV RNA was extracted from PBMCs, sorted CD14+, and CD19+ cells and corresponding plasma samples using the Abbott m2000 and Real‐Time HCV assay. Test performance and influence of HIV seropositivity on plasma and PBMC HCV RNA were studied. Among 51 patients, 67 and 62 unique patient samples had detectable plasma and PBMC HCV viral load, respectively. The median PBMC viral load was 535 IU/1 M cells (range 29–5,190). CD19+ cells had significantly higher viral load than CD14+ cells (median log10 HCV viral load 2.63 vs. 1.50 IU/ml; P< 0.001). Stability of PBMC viral load over time was demonstrated in untreated patients; all patients with an undetectable plasma HCV viral load after HCV treatment also demonstrated undetectable PBMC viral load. Repeated testing in nine samples yielded consistent PBMC viral load, differing by only 1.3‐fold (range 1.0–1.7‐fold). Among samples with detectable plasma HCV RNA, the correlation between PBMC and plasma viral load was moderate (r = 0.66) and was greater among HCV mono‐infected compared to HIV/HCV co‐infected subjects (r = 0.80 vs. 0.52). Measurement of cell‐associated PBMC HCV RNA using a commercial assay demonstrated promising test characteristics. Differences in PBMC HCV viral load based on HIV‐coinfection status and the significance of greater copy number in B‐cells requires further study. J. Med. Virol. 84:431–437, 2012. © 2011 Wiley Periodicals, Inc.
Increase of GII.2 norovirus infections during the 2009–2010 season in Osaka City, Japan
Authors: Iritani Nobuhiro , Kaida Atsushi , Abe Niichiro , Sekiguchi Jun‐ichiro , Kubo Hideyuki , Takakura Koh‐Ichi , Goto Kaoru , Ogura Hisashi , Seto Yoshiyuki
Published: January 2012

During the 2009–2010 season, a significant numerical increase of genotype GII.2 norovirus (NoV)‐associated outbreaks was observed in Osaka City, Japan. The most common genotype in that season was GII.2 (44.6%), followed by GII.4 (39.2%). Mostly, GII.2 strains were associated with outbreaks in children and with person‐to‐person contact. The National Infectious Disease Surveillance Center reported that GII.2 NoV infections were widespread in Japan in that season. Comparative phylogenetic analysis of RNA‐dependent RNA polymerase (RdRp) and capsid sequences revealed that this GII.2 epidemic resulted from two genetic strains. The first, GII.2p2 strains, had an identical genotype in the RdRp and capsid genes. GII.2p2 strains in the 2009–2010 season were a different genetic cluster from the strains of spring 2004, the previous epidemic of GII.2 NoV, but showed no unique amino acid change. The second, GII.2 chimera virus (GII.2p16), had GII.16 RdRp and GII.2 capsid genotypes, suggesting prior recombination at the junction of ORF1 and ORF2. GII.2p16 strains had four significant amino acid changes in the P2 subdomain, suggesting antigenic changes. Before the 2009–2010 season, GII.2 chimera viruses had been observed only sporadically. This spreading of GII.2p16 strains in the 2009–2010 season might be the first epidemic of GII.2 chimera virus. This study revealed that the NoV epidemic in the 2009–2010 season differed considerably from the prior season, when GII.4 was predominant. Furthermore, GII.2 strains persisted in human populations by drastic recombination and gradual accumulation of mutations, indicating a prevalent pattern of non‐GII.4 genotypes with genetic evolution. J. Med. Virol. 84:517–525, 2012. © 2011 Wiley Periodicals, Inc.
Transient ischemic attack associated with acute cytomegalovirus infection
Authors: Amit Sharon , Gadoth Avi , Giladi Michael , Justo Dan
Published: January 2012

Acute cytomegalovirus (CMV) infection is associated with thromboembolism. However, cerebrovascular ischemic events have not been reported in relation to acute CMV infection. A patient with a transient ischemic attack and acute CMV infection is described. Transient appearance of anti‐phospholipid antibodies suggests a causal relationship between the two. Physicians should be alert to symptoms and signs of acute CMV infection in patients with idiopathic cerebrovascular ischemic events. J. Med. Virol. 84:487–489, 2012. © 2011 Wiley Periodicals, Inc.
Validation of an ex vivo human cervical tissue model for optical imaging studies
Authors: Gallwas Julia , Mortensen Uwe , Gaschler Rebecca , Ochsenkuehn Robert , Stepp Herbert , Friese Klaus , Dannecker Christian
Published: January 2012

Objective

To establish and validate an ex vivo human cervical tissue model for optical coherence tomography (OCT) studies with special emphasis on investigating time dependent structural changes of the epithelium.

Methods

Four hundred OCT images were taken from 80 unsuspicious and suspicious areas of 18 fresh conisation specimens immediately after resection (0 hour) and 1, 2, 3, and 4 hours, referred to as waiting times in the following, postoperatively and compared to the corresponding histology. For each 2D‐OCT‐image, a 1D‐intensity profile was generated. The profiles were analyzed with respect to systematic differences which may result from different waiting times, employing discriminant analysis (DA).

Results

The different waiting times do not appear to imply significant differences among the corresponding OCT‐images as represented by the intensity profiles.

Conclusion

We conclude that the proposed cervical tissue model appears to be applicable for ex vivo OCT studies. Lasers Surg. Med. 44:245–248, 2012. © 2012 Wiley Periodicals, Inc.
Navigating Drug‐Like Chemical Space of Anticancer Molecules Using Genetic Algorithms and Counterpropagation Artificial Neural Networks
Authors: Jalali‐Heravi Mehdi , Mani‐Varnosfaderani Ahmad
Published: January 2012

A total of 6289 drug‐like anticancer molecules were collected from Binding database and were analyzed by using the classification techniques. The collected molecules were encoded to a diverse set of descriptors, spanning different physical and chemical properties of the molecules. A combination of genetic algorithms and counterpropagation artificial neural networks was used for navigating the generated drug‐like chemical space and selecting the most relevant molecular descriptors. The proposed method was used for the classification of the molecules according to their therapeutic targets and activities. The selected molecular descriptors in this work define discrete areas in chemical space, which are mainly occupied by particular classes of anticancer molecules. The obtained structure‐activity relationship (SAR) patterns and classification rules contain valuable information, which help to screen the large databases of compounds, more precisely. Such rules and patterns can be considered as virtual filters for mining the large databases of compounds and are useful in finding new anticancer candidates.
Parallel excitation for B‐field insensitive fat‐saturation preparation
Authors: Heilman Jeremiah A. , Derakhshan Jamal D. , Riffe Matthew J. , Gudino Natalia , Tkach Jean , Flask Chris A. , Duerk Jeffrey L. , Griswold Mark A.
Published: January 2012

Multichannel transmission has the potential to improve many aspects of MRI through a new paradigm in excitation. In this study, multichannel transmission is used to address the effects that variations in B0 homogeneity have on fat‐saturation preparation through the use of the frequency, phase, and amplitude degrees of freedom afforded by independent transmission channels. B1 homogeneity is intrinsically included via use of coil sensitivities in calculations. A new method, parallel excitation for B‐field insensitive fat‐saturation preparation, can achieve fat saturation in 89% of voxels with Mz ≤ 0.1 in the presence of ±4 ppm B0 variation, where traditional CHESS methods achieve only 40% in the same conditions. While there has been much progress to apply multichannel transmission at high field strengths, particular focus is given here to application of these methods at 1.5 T. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
CEST phase mapping using a length and offset varied saturation (LOVARS) scheme
Authors: Song Xiaolei , Gilad Assaf A. , Joel Suresh , Liu Guanshu , Bar‐Shir Amnon , Liang Yajie , Gorelik Michael , Pekar James J. , van Zijl Peter C. M. , Bulte Jeff W. M. , McMahon Michael T.
Published: January 2012

Chemical exchange saturation transfer MRI is a promising new technique for cellular and molecular imaging. This contrast allows the detection of tumors and ischemia without the use of gadolinium as well as the design of microenvironment‐sensitive probes that can be discriminated based on their exchange contrast properties and saturation frequency. Current acquisition schemes to detect and analyze this contrast suffer from sensitivity to spatial B0 inhomogeneity and low contrast‐to‐noise‐ratio, which is an obstacle to widespread adoption of the technology. A new method to detect chemical exchange saturation transfer contrast is proposed here, termed “length and offset varied saturation” which acquires a set of images with the saturation parameters varied so as to modulate the exchange contrast. Either fast fourier transform or the general linear model can be employed to decompose the modulation patterns into separate sources of water signal loss. After transformation, a length and offset varied saturation phase map is generated, which is insensitive to B0 inhomogeneity. When collected on live mice bearing 9L gliosarcomas, and compared to the conventional asymmetry in the magnetization transfer ratio map using offset increment correction, the results show that length and offset varied saturation phase mapping obtains about three to four times contrast‐to‐noise‐ratio and exhibits less B0 artifacts. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
Reconstruction of MRI data encoded by multiple nonbijective curvilinear magnetic fields
Authors: Lin Fa‐Hsuan , Witzel Thomas , Schultz Gerrit , Gallichan Daniel , Kuo Wen‐Jui , Wang Fu‐Nien , Hennig *Juergen , Zaitsev Maxim , Belliveau John W.
Published: January 2012

Parallel imaging technique using localized gradients (PatLoc) uses the combination of surface gradient coils generating nonbijective curvilinear magnetic fields for spatial encoding. PatLoc imaging using one pair of multipolar spatial encoding magnetic fields (SEMs) has two major caveats: (1) The direct inversion of the encoding matrix requires exact determination of multiple locations which are ambiguously encoded by the SEMs. (2) Reconstructed images have a prominent loss of spatial resolution at the center of field‐of‐view using a symmetric coil array for signal detection. This study shows that a PatLoc system actually has a higher degree of freedom in spatial encoding to mitigate the two challenges mentioned above. Specifically, a PatLoc system can generate not only multipolar but also linear SEMs, which can be used to reduce the loss of spatial resolution at the field‐of‐view center. Here, we present an efficient and generalized image reconstruction method for PatLoc imaging using multiple SEMs without explicitly identifying the locations where SEM encoding is not unique. Reconstructions using simulations and empirical experimental data are compared with those using conventional linear gradients to demonstrate that the general combination of SEMs can improve image reconstructions. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
Chemical shift‐based water/fat separation in the presence of susceptibility‐induced fat resonance shift
Authors: Karampinos Dimitrios C. , Yu Huanzhou , Shimakawa Ann , Link Thomas M. , Majumdar Sharmila
Published: January 2012

Chemical shift‐based water/fat separation methods have been emerging due to the growing clinical need for fat quantification in different body organs. Accurate quantification of proton‐density fat fraction requires the assessment of many confounding factors, including the need of modeling the presence of multiple peaks in the fat spectrum. Most recent quantitative chemical shift‐based water/fat separation approaches rely on a multipeak fat spectrum with precalibrated peak locations and precalibrated or self‐calibrated peak relative amplitudes. However, water/fat susceptibility differences can induce fat spectrum resonance shifts depending on the shape and orientation of the fatty inclusions. The effect is of particular interest in the skeletal muscle due to the anisotropic arrangement of extracellular lipids. In this work, the effect of susceptibility‐induced fat resonance shift on the fat fraction is characterized in a conventional complex‐based chemical shift‐based water/fat separation approach that does not model the susceptibility‐induced fat resonance shift. A novel algorithm is then proposed to quantify the resonance shift in a complex‐based chemical shift‐based water/fat separation approach that considers the fat resonance shift in the signal model, aiming to extract information about the orientation/geometry of lipids. The technique is validated in a phantom and preliminary in vivo results are shown in the calf musculature of healthy and diabetic subjects. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
Sn‐catalyzed silicon nanowire solar cells with 4.9% efficiency grown on glass
Authors: Cho Jinyoun , O'Donnell Benedict , Yu Linwei , Kim Ka‐Hyun , Ngo Irène , Cabarrocas Pere Roca i
Published: January 2012

We present a single pump‐down process to texture hydrogenated amorphous silicon solar cells. Mats of p‐type crystalline silicon nanowires were grown to lengths of 1 µm on glass covered with flat ZnO using a plasma‐assisted Sn‐catalyzed vapor‐liquid‐solid process. The nanowires were covered with conformal layers of intrinsic and n‐type hydrogenated amorphous silicon and a sputtered layer of indium tin oxide. Each cell connects in excess of 107 radial junctions over areas of 0.126 cm². Devices reach open‐circuit voltages of 0.8 V and short‐circuit current densities of 12.4 mA cm−2, matching those of hydrogenated amorphous silicon cells deposited on textured substrates. Copyright © 2012 John Wiley & Sons, Ltd.
Secreted proteins as a fundamental source for biomarker discovery
Authors: Stastna Miroslava , Van Eyk Jennifer E.
Published: January 2012

The proteins secreted by various cells (the secretomes) are a potential rich source of biomarkers as they reflect various states of the cells at real time and at given conditions. To have accessible, sufficient and reliable protein markers is desirable as they mark various stages of disease development and their presence/absence can be used for diagnosis, prognosis, risk stratification and therapeutic monitoring. As direct analysis of blood/plasma, a common and noninvasive patient screening method, can be difficult for candidate protein biomarker identification, the alternative/complementary approaches are required, one of them is the analysis of secretomes in cell conditioned media in vitro. As the proteins secreted by cells as a response to various stimuli are most likely secreted into blood/plasma, the identification and pre‐selection of candidate protein biomarkers from cell secretomes with subsequent validation of their presence at higher levels in serum/plasma is a promising approach. In this review, we discuss the proteins secreted by three progenitor cell types (smooth muscle, endothelial and cardiac progenitor cells) and two adult cell types (neonatal rat ventrical myocytes and smooth muscle cells) which can be relevant to cardiovascular research and which have been recently published in the literature. We found, at least for secretome studies included in this review, that secretomes of progenitor and adult cells overlap by 48% but the secretomes are very distinct among progenitor cell themselves as well as between adult cells. In addition, we compared secreted proteins to protein identifications listed in the Human Plasma PeptideAtlas and in two reports with cardiovascular‐related proteins and we performed the extensive literature search to find if any of these secreted proteins were identified in a biomarker study. As expected, many proteins have been identified as biomarkers in cancer but 18 proteins (out of 62) have been tested as biomarkers in cardiovascular diseases as well.
Unraveling the resistance of microbial biofilms: Has proteomics been helpful?
Authors: Seneviratne C. Jayampath , Wang Yu , Jin Lijian , Wong Sarah S. W. , Herath Thanuja D. K. , Samaranayake Lakshman P.
Published: January 2012

Biofilms are surface‐attached, matrix‐encased, structured microbial communities which display phenotypic features that are dramatically different from those of their free‐floating, or planktonic, counterparts. Biofilms seem to be the preferred mode of growth of microorganisms in nature, and at least 65% of all human infections are associated with biofilms. The most notable and clinically relevant property of biofilms is their greater resistance to antimicrobials compared with their planktonic counterparts. Although both bacterial and fungal biofilms display this phenotypic feature, the exact mechanisms underlying their increased drug resistance are yet to be determined. Advances in proteomics techniques during the past decade have facilitated in‐depth analysis of the possible mechanisms underpinning increased drug resistance in biofilms. These studies have demonstrated the ability of proteomics techniques to unravel new targets for combating microbial biofilms. In this review, we discuss the putative drug resistance mechanisms of microbial biofilms that have been uncovered by proteomics and critically evaluate the possible contribution of the new knowledge to future development in the field. We also summarize strategic uses of novel proteomics technologies in studies related to drug resistance mechanisms of microbial biofilms.
Combinatorial peptide ligand libraries for the analysis of low‐expression proteins: Validation for normal urine and definition of a first protein MAP
Authors: Santucci Laura , Candiano Giovanni , Bruschi Maurizio , D'Ambrosio Chiara , Petretto Andrea , Scaloni Andrea , Urbani Andrea , Righetti Pier G. , Ghiggeri Gian M.
Published: January 2012

In this review, we report the evolution on experimental conditions for the analysis of normal urine based on combinatorial peptide ligand library (CPLL) treatment and successive 2‐DE and 2‐DE/MS analysis. The main topics are (i) definition of the urine sample requirements, (ii) optimization of the urine/ligand ratio, (iii) essay conditions, (iv) en bloc elution. Overall, normal urine protein composition as studied by 2‐DE includes over 2600 spots. Relevant data on inter and intraessay reproducibility obtained by the analysis of different normal urines repeated several times are also here presented. We found a 73% reproducibility upon analysis of the same sample and 68% correspondence of protein composition among different normal urine samples. Based on the above results, we are completing the characterization with LC‐MS of 249 spots. The composition of normal urine proteins after CPLLs is finally shown with the indication of those spots which are currently under identification. This map will be completed in a near future; in the meantime this would represent the basic reference sample for newly developed studies on human diseases.
Probing protein stability and proteolytic resistance by loop scanning: A comprehensive mutational analysis
Authors: Ahmad Shoeb , Kumar Virender , Ramanand K. Bhanu , Rao N. Madhusudhana
Published: January 2012

Improvement in protein thermostability was often found to be associated with increase in its proteolytic resistance as revealed by comparative studies of homologous proteins from extremophiles or mutational studies. Structural elements of protein responsible for this association are not firmly established although loops are implicated indirectly due to their structural role in protein stability. To get a better insight, a detailed study of protein wide mutants and their influence on stability and proteolytic resistance would be helpful. To generate such a data set, a model protein, Bacillus subtilis lipase was subjected to loop scanning site‐saturation mutagenesis on 86 positions spanning all loops including termini. Upon screening of ∼16,000 clones, 17 single mutants with improved thermostability were identified with increment in apparent melting temperature (Tmapp) by 1–6°C resulting in an increase in free energy of unfolding (ΔGunf) by 0.04–1.16 kcal/mol. Proteolytic resistance of all single mutants upon incubation with nonspecific protease, Subtilisin A, was determined. Upon comparison, post‐proteolysis residual activities as well as kinetics of proteolysis of mutants showed excellent correlation with ΔGunf, (r > 0.9), suggesting that proteolysis was strongly correlated with the global stability of this protein. This significant correlation in this set, with least possible sequence changes (single aa substitution), while covering >60% of protein surface strongly argues for the covariance of these two variables. Compared to studies from extremophiles, with large sequence heterogeneity, the observed correlation in such a narrow sequence space (ΔΔGunf = 1.57 kcal−1) justifies the robustness of this relation.
A novel amino acid substitution Ala‐122‐Tyr in ALS confers high‐level and broad resistance across ALS‐inhibiting herbicides
Authors: Han Heping , Yu Qin , Purba Edison , Li Mei , Walsh Michael , Friesen Shane , Powles Stephen B
Published: January 2012

BACKGROUND: Wild radish, a problem weed worldwide, is a severe dicotyledonous weed in crops. In Australia, sustained reliance on ALS‐inhibiting herbicides to control this species has led to the evolution of many resistant populations endowed by any of several ALS mutations. The molecular basis of ALS‐inhibiting herbicide resistance in a novel resistant population was studied.

RESULTS: ALS gene sequencing revealed a previously unreported substitution of Tyr for Ala at amino acid position 122 in resistant individuals of a wild radish population (WARR30). A purified subpopulation individually homozygous for the Ala‐122‐Tyr mutation was generated and characterised in terms of its response to the different chemical classes of ALS‐inhibiting herbicides. Whole‐plant dose‐response studies showed that the purified subpopulation was highly resistant to chlorsulfuron, metosulam and imazamox, with LD50 or GR50 R/S ratio of > 1024, > 512 and > 137 respectively. The resistance to imazypyr was found to be relatively moderate (but still substantial), with LD50 and GR50 R/S ratios of > 16 and > 7.8 respectively. In vitro ALS activity assays showed that Ala‐122‐Tyr ALS was highly resistant to all tested ALS‐inhibiting herbicides.

CONCLUSION: The molecular basis of ALS‐inhibiting herbicide resistance in wild radish population WARR30 was identified to be due to an Ala‐122‐Tyr mutation in the ALS gene. This is the first report of an amino acid substitution at Ala‐122 in the plant ALS that confers high‐level and broad‐spectrum resistance to ALS‐inhibiting herbicides, a remarkable contrast to the known mutation Ala‐122‐Thr endowing resistance to imidazolinone herbicide. Copyright © 2012 Society of Chemical Industry
Determination of dislocation densities in InN
Authors: Ardali Sukru , Tiras Engin , Gunes Mustafa , Balkan Naci , Ajagunna Adebowale Olufunso , Iliopoulos Eleftherios , Georgakilas Alexandros
Published: January 2012

The magneto‐transport measurements, carried out at magnetic fields up to 11 T and in the temperature range between 1.8 K and 300 K, are used to investigate the scattering mechanisms in GaN/InN/AlN double heterojunctions. Theoretical modeling is based on a variational approach to solving Boltzmann transport equation. It is found that dislocation scattering is the dominant scattering mechanisms at low temperatures because of the large lattice mismatch with the substrate and hence the high density of dislocations in these material systems. Nevertheless, InN epilayers are characterized by a high background carrier density, probably associated with unwanted impurities. Therefore, we also included in our calculations the ionized impurity scattering. However, the effect of ionized impurity scattering as well as the acoustic phonon scattering, remote‐ background‐ionized impurity scattering, and interface roughness scattering on electron mobility are much smaller than that of dislocation scattering. The dislocation densities, in samples with InN thicknesses of 0.4, 0.6 and 0.8 µm, are then determined from the best fit to the experimental data for the low‐temperature transport mobility (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigation of the properties of In‐related alloys by AFM
Authors: Minj Albert , Cavalcoli Daniela , Cavallini Anna
Published: January 2012

MOCVD grown Al1‐xInxN/AlN/GaN heterostructures have been characterized by atomic force microscopy(AFM) in semi‐contact and conductive mode. The surface of In‐related alloys consist of grain‐like structures indicating step flow and 3D‐growth with TDs of density equal to ∼108/cm2, the origin of which is mostly attributed to lattice mismatch between GaN and sapphire. These TDs with screw or mixed components terminate at the surface of overgrown layers as V‐defects, which are six‐facetted inverted pyramidal structures. Strain relaxation mechanism, formation of cracks and its propagation to the surface of the samples have been also investigated. With phase‐imaging (in semi‐contact AFM), we have traced sites of indium segregation in the V‐defects, surface‐relaxation and crack propagation in In‐related alloys. These sites in V‐defects and cracks were found to be highly conductive by current‐AFM either due to the presence of In‐segregation or due to lowering of potential barrier as a consequence of strain‐relaxation. They may be the possible dominant cause of leakage current in Schottky diodes. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Inhomogeneous electron distribution in InN nanowires: Influence on the optical properties
Authors: Molina‐Sánchez A. , Segura‐Ruiz J. , Garro N. , García‐Cristóbal A. , Cantarero A. , Iikawa F. , Denker C. , Malindretos J. , Rizzi A.
Published: January 2012

In this work, we study theoretically and experimentally the influence of the surface electron accumulation on the optical properties of InN nanowires. For this purpose, the photoluminescence and photoluminescence excitation spectra have been measured for a set of self‐assembled InN NWs grown under different conditions. The photoluminescence excitation experimental lineshapes have been reproduced by a self‐consistent calculation of the absorption in a cylindrical InN nanowires. With the self‐consistent model we can explore how the optical absorption depends on nanowires radius and doping concentration. Our model solves the Schrödinger equation for a cylindrical nanowire of infinite length, assuming a parabolic conduction band. The columnar geometry introduces effects in both the electron density and in the self‐consistent conduction band profile, with no equivalence in planar layer. On the other hand, the differences in the photoluminescence excitation spectra are related to the inhomogeneous electron distribution inside the nanowires, caused by a bulk donor concentration and a two‐dimensional density of ionized surface states. For nanowire radii larger than 30 nm, such concentrations modify the absorption edge and the lineshape, respectively, and can be determined from the comparison with the experimental data (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carbothermal Reduction of Iron Ore Applying Microwave Energy
Authors: Renato de Castro Edmilson , Breda Mourão Marcelo , Jermolovicius Luiz Alberto , Takano Cyro , Thomaz Senise José
Published: January 2012

This paper presents the results of a study on carbothermal reduction of iron ore made under the microwave field in equipment specially developed for this purpose. The equipment allows the control of radiated and reflected microwave power, and therefore measures the microwave energy actually applied to the load in the reduction process. It also allows performing energy balances and determining the reaction rate with high levels of confidence by simultaneously measuring temperature and mass of the material upon reduction with high reproducibility. We used a microwave generator of 2.45 GHz with variable power up to 3000 W. Self‐reducing pellets under argon atmosphere, containing iron ore and petroleum coke, with 3.5 g of mass and 15 mm of diameter were declined. We obtained the kinetic curves of reduction of iron ore and of energy consumption to the process in the maximum electric field, in the maximum magnetic field and at different values of power/mass. The data allow analyzing how the microwave energy was actually consumed in the reduction of ore.
An Intercomparison Study of Analytical Methods for the Determination of Magnesium in Low Alloy Steel
Authors: Recknagel Sebastian , Richter Silke , Reinholdsson Fredrik , Pettersson Jean , Gustavsson Ingemar
Published: January 2012

In an intercomparison study three low alloy steel materials were analyzed on their content of the trace element Mg, and five different analytical techniques were used, namely spark‐OES, inductively coupled plasma optical emission spectrometry (ICP‐OES), inductively coupled plasma time of flight mass spectrometry (ICP‐TOFMS), inductively coupled plasma quadrupole mass spectrometry (ICP‐QMS), and glow discharge mass spectrometry (GD‐MS). Solid steel discs were used for analysis with spark‐OES and GD‐MS. For the analyses with ICP‐OES, ICP‐TOFMS, and ICP‐QMS steel chips were wet‐digested in aqua regia, and the wet‐digestion was performed either in polypropylene tubes placed in a heating block or in Teflon pressure vessels using a microwave assisted system. The Mg concentrations obtained for the three steel materials were: 2.0, 2.8, and 10.3 µg g−1, respectively, and the spread in results was acceptable, giving RSD values in the range of 20–30%.
Experimental Investigation on Optimal Carbon/Hydrogen Ratio for Developing Iron Bath Reactor with H2–C Mixture Reduction
Authors: Bo Zhang , Jie Guo , Huaiwei Zhang , Jiajun Mao , Qiuju Li , Dongyan Wang , Xin Hong
Published: January 2012

The basic idea of H2–C mixture reduction reflects advantages of hydrogen for fast reaction and low heat absorption in smelting reduction reactor, where hydrogen is used as main reducing agent and carbon as main heat generator on purpose to cut down total energy consumption and CO2 emission. This article aimed at the experimental investigation of optimal carbon/hydrogen ratio, a key parameter of iron oxide reduction with mixture reductive agents of carbon and hydrogen. Experiments were carried out using a pure Al2O3 crucible which was placed in a tubular furnace for high temperature. Two investigation methods were adopted, one was injecting acetylene/hydrogen mixture reducing gas into molten iron oxides and another was blowing hydrogen into iron bath during continuous feeding fine ore mixing solid carbon dust. Parameters such as apparent de‐oxidation rate and utilization ratio of reductive agents were calculated from content analysis of exhaust gas after dust removing and drying. In experiments highest total de‐oxidation rate and satisfied apparent utilization ratio of hydrogen were obtained under conditions with temperatures of 1823 K and carbon/hydrogen ratio in region from 0.5:1 to 2:1.
The Novel Function of OCT4B Isoform-265 in Genotoxic Stress
Authors: Gao Yuan , Wei Jianshu , Han Jin , Wang Xia , Su Guannan , Zhao Yannan , Chen Bing , Xiao Zhifeng , Cao Jiani , Dai Jianwu
Published: January 2012

OCT4 is a key transcription factor in maintaining the pluripotency and self-renewal of embryonic stem cells (ESCs). Human OCT4 gene can generate three mRNA isoforms (OCT4A, OCT4B, and OCT4B1) by alternative splicing and four protein isoforms (OCT4A, OCT4B-265, OCT4B-190, and OCT4B-164) by alternative splicing or alternative translation initiation. OCT4A is a transcription factor responsible for the stemness of ESCs, while the function of OCT4B protein isoforms is still not clear. We have previously reported that OCT4B-190 functioned in cell stress response. Here, we present another product of OCT4 gene, OCT4B-265, which is upregulated under genotoxic stress in stem cells, and it may function in stress response through p53 signaling pathway. This work gives an insight into the novel function of OCT4B protein isoforms and helps us to understand the complex expression patterns and biological functions of OCT4 gene.

Disclosure of potential conflicts of interest is found at the end of this article.