Quantitative chemical exchange saturation transfer (qCEST) MRI – omega plot analysis of RF‐spillover‐corrected inverse CEST ratio asymmetry for simultaneous determination of labile proton ratio and exchange rate

Chemical exchange saturation transfer (CEST) MRI is sensitive to labile proton concentration and exchange rate, thus allowing measurement of dilute CEST agent and microenvironmental properties. However, CEST measurement depends not only on the CEST agent properties but also on the experimental conditions. Quantitative CEST (qCEST) analysis has been proposed to address the limitation of the commonly used simplistic CEST‐weighted calculation. Recent research has shown that the concomitant direct RF saturation (spillover) effect can be corrected using an inverse CEST ratio calculation. We postulated that a simplified qCEST analysis is feasible with omega plot analysis of the inverse CEST asymmetry calculation. Specifically, simulations showed that the numerically derived labile proton ratio and exchange rate were in good agreement with input values. In addition, the qCEST analysis was confirmed experimentally in a phantom with concurrent variation in CEST agent concentration and pH. Also, we demonstrated that the derived labile proton ratio increased linearly with creatine concentration (P < 0.01) while the pH‐dependent exchange rate followed a dominantly base‐catalyzed exchange relationship (P < 0.01). In summary, our study verified that a simplified qCEST analysis can simultaneously determine labile proton ratio and exchange rate in a relatively complex in vitro CEST system. Copyright © 2015 John Wiley & Sons, Ltd.     

An update on the origin of SARS‐CoV‐2: Despite closest identity,bat (RaTG13) and pangolin derived coronaviruses varied in the critical binding site and O‐linked glycan residues

The initial cases of severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) occurred in Wuhan, China, in December 2019 and swept the world by 23 June 2020 with 8 993 659 active cases, 469 587 deaths across 216 countries, areas or territories. This strongly implies global transmission occurred before the lockdown of China. However, the initial source's transmission routes of SARS‐CoV‐2 remain obscure and controversial. Research data suggest bat (RaTG13) and pangolin carried CoV were the proximal source of SARS‐CoV‐2. In this study, we used systematic phylogenetic analysis of Coronavirinae subfamily along with wild type human SARS‐CoV, MERS‐CoV, and SARS‐CoV‐2 strains. The key residues of the receptor‐binding domain (RBD) and O‐linked glycan were compared. SARS‐CoV‐2 strains were clustered with RaTG13 (97.41% identity), Pangolin‐CoV (92.22% identity) and Bat‐SL‐CoV (80.36% identity), forms a new clade‐2 in lineage B of beta‐CoV. The alignments of RBD contact residues to ACE2 justified? Those SARS‐CoV‐2 strains sequences were 100% identical by each other, significantly varied in RaTG13 and pangolin‐CoV. SARS‐CoV‐2 has a polybasic cleavage site with an inserted sequence of PRRA compared to RaTG13 and only PRR to pangolin. Only serine (Ser) in pangolin and both threonine (Thr) and serine (Ser) O‐linked glycans were seen in RaTG13, suggesting that a detailed study needed in pangolin (Manis javanica) and bat (Rhinolophus affinis) related CoV.     

Time‐dependent diffusion in skeletal muscle with the random permeable barrier model (RPBM): application to normal controls and chronic exertional compartment syndrome patients

The purpose of this work was to carry out diffusion tensor imaging (DTI) at multiple diffusion times T_d in skeletal muscle in normal subjects and chronic exertional compartment syndrome (CECS) patients and analyze the data with the random permeable barrier model (RPBM) for biophysical specificity. Using an institutional review board approved HIPAA‐compliant protocol, seven patients with clinical suspicion of CECS and eight healthy volunteers underwent DTI of the calf muscle in a Siemens MAGNETOM Verio 3 T scanner at rest and after treadmill exertion at four different T_d values. Radial diffusion values λ_rad were computed for each of seven different muscle compartments and analyzed with RPBM to produce estimates of free diffusivity D₀, fiber diameter a, and permeability κ. Fiber diameter estimates were compared with measurements from literature autopsy reference for several compartments. Response factors (post/pre‐exercise ratios) were computed and compared between normal controls and CECS patients using a mixed‐model two‐way analysis of variance. All subjects and muscle compartments showed nearly time‐independent diffusion along and strongly time‐dependent diffusion transverse to the muscle fibers. RPBM estimates of fiber diameter correlated well with corresponding autopsy reference. D₀ showed significant (p < 0.05) increases with exercise for volunteers, and a increased significantly (p < 0.05) in volunteers. At the group level, response factors of all three parameters showed trends differentiating controls from CECS patients, with patients showing smaller diameter changes (p = 0.07), and larger permeability increases (p = 0.07) than controls. Time‐dependent diffusion measurements combined with appropriate tissue modeling can provide enhanced microstructural specificity for in vivo tissue characterization. In CECS patients, our results suggest that high‐pressure interfiber edema elevates free diffusion and restricts exercise‐induced fiber dilation. Such specificity may be useful in differentiating CECS from other disorders or in predicting its response to either physical therapy or fasciotomy. Copyright © 2014 John Wiley & Sons, Ltd.     

Size and shape changes during late fetal growth (137–157 gestational days) in the pigtailed macaque (Macaca nemestrina) craniofacial complex: An application using three‐dimensional coordinate data and finite element scaling analysis

Form changes within the fetal pigtailed macaque (Macaca nemestrina) craniofacial complex was documented using finite element scaling analysis (FESA) and three‐dimensional (3D) coordinate data for 35 craniofacial landmarks. Coordinate data were digitized from 3D reconstructions of computed tomography (CT) images and 2D axial slices. Twenty‐two fetal pigtailed macaques ranging in age from 137 to 157 gestational days were included (in this species, birth is estimated at 170 gestational days). The null hypothesis that the craniofacial complex grows with isometry during late fetal growth of the craniofacial complex was tested (P < 0.05), and the prediction that morphological change along an anteroposterior axis dominates late fetal growth was also investigated. The null hypothesis was rejected, indicating that allometric growth is present during late fetal growth. Growth along an anteroposterior axis is localized in the palate and mandible. The neurocranium grows along a superoinferior axis, while the neurofacial junction displays growth along both the anteroposterior and superoinferior axes. Mediolateral changes are localized between asterions, the external auditory meati, and maxillary and mandibular alveolar points. Finally, a 3D model of craniofacial growth for this species was created, localizing size and shape changes that occur during late fetal growth for each of the 35 craniofacial landmarks defined in this study. Anat Rec 267:307–320, 2002. © 2002 Wiley‐Liss, Inc.     

Multiple clusters of A(H1N1)pdm09 virus circulating in severe cases of influenza during the 2010–2011 season: A phylogenetic and molecular analysis of the neuraminidase gene

The molecular characterization of circulating influenza A viruses is crucial to detect mutations potentially involved in increased virulence, drug resistance and immune escape. A molecular and phylogenetic analysis of A(H1N1)pdm09 neuraminidase (NA) gene sequences from different patient categories defined according to the severity of influenza infection were analyzed. A total of 126 influenza A(H1N1)pdm09 positive samples from patients with severe infections in comparison with those with moderate and mild infections was performed in Lombardy (Northern Italy, nearly 10 million inhabitants) during the 2010–2011 season. NA sequences included in this study segregated into five distinct clusters. Nineteen amino acid substitutions were detected exclusively in NA sequences of viruses identified in patients with severe or moderate influenza infection. Three of them (F74S, S79P, E287K) were observed in virus strains with the 222G/N hemagglutinin mutation. None of NA sequences under study had mutations related to the resistance to the NA inhibitors. Four out of 126 (3.2%) NA sequences from patients with severe infection lost a N‐linked glycosylation site due to the change from N to K at residue 386. Two additional N‐linked glycosylation sites in the NA stalk region (residues 42 and 44) were found in 12 (9.5%) NA sequences. Sporadic NA mutations were detected in NA viral sequences from critically ill patients, and no variants with reduced sensitivity to NA inhibitors were observed either in treated or untreated patients. J. Med. Virol. 85: 944–952, 2013. © 2013 Wiley Periodicals, Inc.