bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractHuman 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

AbstractHuman 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

AbstractConcordant 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

AbstractPeripheral 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

AbstractDuring 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

AbstractAcute 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

AbstractObjectiveTo 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.MethodsFour 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).ResultsThe different waiting times do not appear to imply significant differences among the corresponding OCT‐images as represented by the intensity profiles.ConclusionWe 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

AbstractA 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

AbstractMultichannel 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

AbstractChemical 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

AbstractParallel 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

AbstractChemical 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

ABSTRACTWe 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

AbstractThe 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.