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The human parainfluenza virus type 4 (HPIV4) can be classified into two distinct subtypes, 4a and 4b. The full lengths of the fusion gene ( F gene) of 48 HPIV4 strains collected during the period of 1966-2022 were analyzed. Based on these gene sequences, the time-scaled evolutionary tree was constructed using Bayesian Markov chain Monte Carlo methods. A phylogenetic tree showed that the first division of the two subtypes occurred around 1823, and the most recent common ancestors of each type, 4a and 4b, existed until about 1940 and 1939, respectively. Although the mean genetic distances of all strains were relatively wide, the distances in each subtype were not wide, indicating that this gene was conserved in each subtype. The evolutionary rates of the genes were relatively low (4.41 × 10 -4 substitutions/site/year). Moreover, conformational B-cell epitopes were predicted in the apex of the trimer fusion protein. These results suggest that HPIV4 subtypes diverged 200 years ago and the progenies further diverged and evolved.

The radioisotope thorium-229 ( 229 Th) is renowned for its extraordinarily low-energy, long-lived nuclear first-excited state. This isomeric state can be excited by vacuum ultraviolet (VUV) lasers and 229 Th has been proposed as a reference transition for ultra-precise nuclear clocks. To assess the feasibility and performance of the nuclear clock concept, time-controlled excitation and depopulation of the 229 Th isomer are imperative. Here we report the population of the 229 Th isomeric state through resonant X-ray pumping and detection of the radiative decay in a VUV transparent 229 Th-doped CaF 2 crystal. The decay half-life is measured to 447(25) s, with a transition wavelength of 148.18(42) nm and a radiative decay fraction consistent with unity. Furthermore, we report a new "X-ray quenching" effect which allows to de-populate the isomer on demand and effectively reduce the half-life. Such controlled quenching can be used to significantly speed up the interrogation cycle in future nuclear clock schemes., (© 2024. The Author(s).)

Extremophile organisms are known that can metabolize at temperatures down to - 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins - rubredoxins - from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of 'corresponding states' posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although 'corresponding states' would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent., (© 2024. The Author(s).)

This study aimed to investigate the optimal conditions for Papanicolaou (Pap) smear to increase the success rate of target cell isolation through manual microdissection (MMD) and prevent cell spread. Pap smears were prepared using an HPV42-positive SurePath™ liquid-based cytology case, and 46 and 50 koilocytes were used in wet and dried Pap smears, respectively, to verify the success rate of target cell isolation using MMD based on the HPV detection rate. During MMD, the microscopic examination of both specimens revealed that cells in dried smears could be easily identified; however, cell debris remained in the surrounding area after MMD. Although it was difficult to observe cells in wet smears, there was no cell debris. When the needle tip was immersed in DNA lysate after cell isolation through MMD, a difference in cell solubility was found between dry and wet smears. HPV42 was detected in 94.7% and 97.4% of dried and wet Pap smears, respectively, via polymerase chain reaction genotyping using lysed cell solution; the detection rates were not significantly different. The isolation of target cells from wet Pap smears using MMD reduced the risk of contamination and increased the success rate of HPV detection. This study might facilitate the identification of new CIN-derived HPV-infected cells using MMD with wet Pap smears.

To better understand the evolution of the SARS-CoV-2 Omicron subvariants, we performed molecular evolutionary analyses of the spike ( S ) protein gene/S protein using advanced bioinformatics technologies. First, time-scaled phylogenetic analysis estimated that a common ancestor of the Wuhan, Alpha, Beta, Delta variants, and Omicron variants/subvariants diverged in May 2020. After that, a common ancestor of the Omicron variant generated various Omicron subvariants over one year. Furthermore, a chimeric virus between the BM.1.1.1 and BJ.1 subvariants, known as XBB, diverged in July 2021, leading to the emergence of the prevalent subvariants XBB.1.5 and XBB.1.16. Next, similarity plot (SimPlot) data estimated that the recombination point (breakpoint) corresponded to nucleotide position 1373. As a result, XBB.1.5 subvariants had the 5' nucleotide side from the breakpoint as a strain with a BJ.1 sequence and the 3' nucleotide side as a strain with a BM.1.1.1 sequence. Genome network data showed that Omicron subvariants were genetically linked with the common ancestors of the Wuhan and Delta variants, resulting in many amino acid mutations. Selective pressure analysis estimated that the prevalent subvariants, XBB.1.5 and XBB.1.16, had specific amino acid mutations, such as V445P, G446S, N460K, and F486P, located in the RBD when compared with the BA.4 and BA.5 subvariants. Moreover, some representative immunogenicity-associated amino acid mutations, including L452R, F486V, R493Q, and V490S, were also found in these subvariants. These substitutions were involved in the conformational epitopes, implying that these mutations affect immunogenicity and vaccine evasion. Furthermore, these mutations were identified as positive selection sites. These results suggest that the S gene/S protein Omicron subvariants rapidly evolved, and mutations observed in the conformational epitopes may reduce the effectiveness of the current vaccine, including bivalent vaccines such as mRNA vaccines containing the BA.4/BA.5 subvariants.

The purpose is to evaluate whether deep learning-based denoising (DLD) algorithm provides sufficient image quality for abdominal computed tomography (CT) with a 30% reduction in radiation dose, compared to standard-dose CT reconstructed with conventional hybrid iterative reconstruction (IR). The subjects consisted of 50 patients who underwent abdominal CT with standard dose and reconstructed with hybrid IR (ASiR-V50%) and another 50 patients who underwent abdominal CT with approximately 30% less dose and reconstructed with ASiR-V50% and DLD at low-, medium- and high-strength (DLD-L, DLD-M and DLD-H, respectively). The standard deviation of attenuation in liver parenchyma was measured as image noise. Contrast-to-noise ratio (CNR) for portal vein on portal venous phase was calculated. Lesion conspicuity in 23 abdominal solid mass on the reduced-dose CT was rated on a 5-point scale: 0 (best) to -4 (markedly inferior). Compared with hybrid IR of standard-dose CT, DLD-H of reduced-dose CT provided significantly lower image noise (portal phase: 9.0 (interquartile range, 8.7-9.4) HU vs 12.0 (11.4-12.7) HU, P < 0.0001) and significantly higher CNR (median, 5.8 (4.4-7.4) vs 4.3 (3.3-5.3), P = 0.0019). As for DLD-M of reduced-dose CT, no significant difference was found in image noise and CNR compared to hybrid IR of standard-dose CT (P > 0.99). Lesion conspicuity scores for DLD-H and DLD-M were significantly better than hybrid IR (P < 0.05). Dynamic contrast-enhanced abdominal CT acquired with approximately 30% lower radiation dose and generated with the DLD algorithm exhibit lower image noise and higher CNR compared to standard-dose CT with hybrid IR., (© 2023. The Author(s) under exclusive licence to Society for Imaging Informatics in Medicine.)

Despite the increasing evidence of the clinical impact of Pseudomonas -derived cephalosporinase (PDC) sequence polymorphisms, the molecular evolution of its encoding gene, bla PDC , remains elusive. To elucidate this, we performed a comprehensive evolutionary analysis of bla PDC . A Bayesian Markov Chain Monte Carlo phylogenetic tree revealed that a common ancestor of bla PDC diverged approximately 4660 years ago, leading to the formation of eight clonal variants (clusters A-H). The phylogenetic distances within clusters A to G were short, whereas those within cluster H were relatively long. Two positive selection sites and many negative selection sites were estimated. Two PDC active sites overlapped with negative selection sites. In docking simulation models based on samples selected from clusters A and H, piperacillin was bound to the serine and the threonine residues of the PDC active sites, with the same binding mode for both models. These results suggest that, in P. aeruginosa , bla PDC is highly conserved, and PDC exhibits similar antibiotic resistance functionality regardless of its genotype.

Molecular interactions between respiratory syncytial virus (RSV) fusion protein (F protein) and the cellular receptor Toll-like receptor 4 (TLR4) and myeloid differentiation factor-2 (MD-2) protein complex are unknown. Thus, to reveal the detailed molecular interactions between them, in silico analyses were performed using various bioinformatics techniques. The present simulation data showed that the neutralizing antibody (NT-Ab) binding sites in both prefusion and postfusion proteins at sites II and IV were involved in the interactions between them and the TLR4 molecule. Moreover, the binding affinity between postfusion proteins and the TLR4/MD-2 complex was higher than that between prefusion proteins and the TLR4/MD-2 complex. This increased binding affinity due to conformational changes in the F protein may be able to form syncytium in RSV-infected cells. These results may contribute to better understand the infectivity and pathogenicity (syncytium formation) of RSV.

DNA gyrase plays important roles in genome replication in various bacteria, including Pseudomonas aeruginosa . The gyrA gene encodes the gyrase subunit A protein (GyrA). Mutations in GyrA are associated with resistance to quinolone-based antibiotics. We performed a detailed molecular evolutionary analyses of the gyrA gene and associated resistance to the quinolone drug, ciprofloxacin, using bioinformatics techniques. We produced an evolutionary phylogenetic tree using the Bayesian Markov Chain Monte Carlo (MCMC) method. This tree indicated that a common ancestor of the gene was present over 760 years ago, and the offspring formed multiple clusters. Quinolone drug-resistance-associated amino-acid substitutions in GyrA, including T83I and D87N, emerged after the drug was used clinically. These substitutions appeared to be positive selection sites. The molecular affinity between ciprofloxacin and the GyrA protein containing T83I and/or D87N decreased significantly compared to that between the drug and GyrA protein, with no substitutions. The rate of evolution of the gene before quinolone drugs were first used in the clinic, in 1962, was significantly lower than that after the drug was used. These results suggest that the gyrA gene evolved to permit the bacterium to overcome quinolone treatment.

Background: Single-center studies indicated a high diagnostic accuracy of dynamic computed tomography perfusion (CTP) imaging in the diagnosis of coronary artery disease (CAD)., Objectives: This prospective multicenter study determined the diagnostic performance of combined coronary computed tomography angiography (CTA) and CTP for detecting hemodynamically significant CAD defined by invasive coronary angiography (ICA) with fractional flow reserve (FFR)., Methods: Seven centers enrolled 174 patients with suspected or known CAD who were clinically referred for ICA. CTA and dynamic CTP were performed using dual-source CT before ICA. FFR was done as part of ICA in the case of 26% to 90% coronary diameter stenosis. Hemodynamically significant stenosis was defined as FFR of <0.8 or >90% stenosis on ICA., Results: The study protocol was completed in 157 participants, and hemodynamically significant stenosis was detected in 76 of 157 patients (48%) and 112 of 442 vessels (25%). According to receiver-operating characteristic curve analysis, adding dynamic CTP to CTA significantly increased the area under the curve from 0.65 (95% CI: 0.57-0.72) to 0.74 (95% CI: 0.66-0.81; P = 0.011) on the patient level, with decreased sensitivity (93% vs 72%; P < 0.001), improved specificity (36% vs 75%; P < 0.001), and improved overall accuracy (64% vs 74%; P < 0.001)., Conclusions: In this prospective multicenter study on dynamic CTP, the combination of anatomic assessment with coronary CTA and functional evaluation with dynamic CTP allowed more accurate identification of hemodynamically significant CAD compared with CTA alone. However, the clinical significance of this approach needs to be further investigated, including its usefulness in improving prognosis. (Assessment of Myocardial Perfusion Linked to Infarction and Fibrosis Explored With Dual-Source CT [AMPLIFiED]; UMIN000016353)., Competing Interests: Funding Support and Author Disclosures Sponsored by Bayer Yakuhin, Ltd. The study sponsor was not involved in any stage of the study design, data acquisition, data analysis, or manuscript preparation. Dr Kitagawa is the Endowed Chair for Department of Advanced Diagnostic Imaging at Mie University Graduate School of Medicine funded by donations from Siemens Healthcare K.K. and FUJIFILM Medical Co, Ltd. All other authors have reported that they have no relationships relevant to the contents of this paper to disclose., (Copyright © 2021 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.)

Objective: Third-generation dual-source computed tomography (3rd-DSCT) allows dynamic myocardial CT perfusion imaging (dynamic CTP) with a 10.5-cm z-axis coverage. Although the increased radiation exposure associated with the 50% wider scan range compared to second-generation DSCT (2nd-DSCT) may be suppressed by using a tube voltage of 70 kV, it remains unclear whether image quality and the ability to quantify myocardial blood flow (MBF) can be maintained under these conditions. This study aimed to compare the image quality, estimated MBF, and radiation dose of dynamic CTP between 2nd-DSCT and 3rd-DSCT and to evaluate whether a 10.5-cm coverage is suitable for dynamic CTP., Materials and Methods: We retrospectively analyzed 107 patients who underwent dynamic CTP using 2nd-DSCT at 80 kV (n = 54) or 3rd-DSCT at 70 kV (n = 53). Image quality, estimated MBF, radiation dose, and coverage of left ventricular (LV) myocardium were compared., Results: No significant differences were observed between 3rd-DSCT and 2nd-DSCT in contrast-to-noise ratio (37.4 ± 11.4 vs. 35.5 ± 11.2, p = 0.396). Effective radiation dose was lower with 3rd-DSCT (3.97 ± 0.92 mSv with a conversion factor of 0.017 mSv/mGy·cm) compared to 2nd-DSCT (5.49 ± 1.36 mSv, p < 0.001). Incomplete coverage was more frequent with 2nd-DSCT than with 3rd-DSCT (1.9% [1/53] vs. 56% [30/54], p < 0.001). In propensity score-matched cohorts, MBF was comparable between 3rd-DSCT and 2nd-DSCT in non-ischemic (146.2 ± 26.5 vs. 157.5 ± 34.9 mL/min/100 g, p = 0.137) as well as ischemic myocardium (92.7 ± 21.1 vs. 90.9 ± 29.7 mL/min/100 g, p = 0.876)., Conclusion: The radiation increase inherent to the widened z-axis coverage in 3rd-DSCT can be balanced by using a tube voltage of 70 kV without compromising image quality or MBF quantification. In dynamic CTP, a z-axis coverage of 10.5 cm is sufficient to achieve complete coverage of the LV myocardium in most patients., Competing Interests: One of the authors (H.S.) received a research grant from DAIICHI SANKYO COMPANY, LIMITED, Fuji Pharma Co., Ltd., FUJIFILM RI Pharma Co., Ltd., Eisai Co., Ltd. All the authors have nothing to disclose., (Copyright © 2020 The Korean Society of Radiology.)

Bone matrix collagen, is one of the major contributors to bone quality. No studies have examined how bone quality affects the results of bone transplantation. Collagen cross-links (CCL) are the key factor in collagen properties. The purpose was to investigate the influences of CCL for both grafted bone and recipient site bone on the success of bone augmentation. Four-week-old male Wister rats ( n = 54) were divided into control and test groups. Control and test groups equally sub-divided into donors and recipients. An additional six rats were used to characterize bone at day zero. Test groups received 0.2% beta-aminoproperionitrile (BAPN) for 4 weeks as CCL inhibitor. Animals were further divided into donor and recipient groups. The transplanted bone chips integrated with host bone by 25% more in CCL-deficient animals compared to control. However, no difference in cortical thickness among all conditions. CCL-deficient transplanted bone did not show any extra signs of osteocyte apoptosis, while sclerostin expression was comparable to that in control. The host periosteum of CCL-deficient animals showed higher cellular activity, as well as higher bone quantity and osteoclast activity. Collagen cross-links deficiency in host bone might accelerate the incorporation of grafted bone. effect. Incorporation of the bone grafts appears to depend mainly on host condition rather than graft condition., Competing Interests: The authors declare no conflict of interest.

Poly(vinyl alcohol) (PVA) is a biocompatible polymer with low toxicity. It is possible to prepare physically cross-linked PVA gels having hydrogen bonds without using a cross-linking agent. The newly reported physically cross-linked PVA cast-drying (CD) on freeze-thawed (FT) hybrid gel has an excellent friction property, which is expected to be applied as a candidate material for artificial cartilage. Gamma ray sterilization for clinical applications usually causes additional chemical cross-linking and changes physical properties of gels. In this study, CD on FT hybrid gels were irradiated using gamma rays at a different dose rate and irradiance. The results showed the optimized irradiation conditions for gamma irradiated gels to retain excellent friction characteristics.

Leaf senescence is an important physiological process involving the degradation of a number of metabolites and their remobilization to new reproductive and storage organs. NAC (NAM, ATAF, and CUC) transcription factors are reported as important regulators of the senescence process. Here, we describe the identification and functional characterization of the NAC transcription factor gene, OsY37 (Oryza sativa Yellow37, ONAC011) obtained from Oryza sativa cv. indica , and japonica . We created transgenic plants expressing the OsY37 gene under the control of a strong and constitutive CaMV35S promoter. The resulting transgenic plants overexpressing OsY37 gene showed early heading and precocious senescence phenotype of flag leaves compared with wild-type plants. By contrast, blocking the function of this gene via RNAi (RNA interference) and CRES-T (Chimeric Repressor Silencing Technology) technology, delayed both heading time and leaf senescence. Furthermore, knockdown of OsY37 expression caused dwarfism and high accumulation of chlorophyll during the vegetative phase. Irrespective of early or delayed senescence, transgenic plants showed reduced grain yields. Our results indicate that OsY37 acts as a positive regulator of heading and senescence during the reproductive phase in rice. In addition, OsY37 may be involved in plant development and grain yield., Competing Interests: The authors declare no conflict of interest.